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Su K, Ao W, Sun Z, Li J, Gao Y, Gan D, Yang J. Resequencing and Transcriptome Analyses Reveal Variations and Expression Patterns of the RR Gene Family in Cucumber. Genes (Basel) 2025; 16:409. [PMID: 40282369 PMCID: PMC12027353 DOI: 10.3390/genes16040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2025] [Revised: 03/27/2025] [Accepted: 03/28/2025] [Indexed: 04/29/2025] Open
Abstract
BACKGROUND Cucumber (Cucumis sativus L.) is an important economic crop worldwide. Response regulators (RRs) play crucial roles in plant growth, development, and responses to both biotic and abiotic stresses. METHODS Combined analysis of 182 re-sequencing and transcriptome datasets was conducted to investigate CsRR variations, with subsequent RT-qPCR experiments confirming its functional significance. RESULTS In this study, 18 CsRR genes were identified and classified into three groups according to their protein structures: A-ARRs (3), B-ARRs (8), and PRRs (7). Resequencing uncovered critical mutations (non-synonymous SNPs, frameshift, and stop-gain variants) in CsRR genes. Transcriptome data revealed that five genes responded to abiotic stress and four responded to biotic stress. CsPRR1 was upregulated in both resistant and susceptible lines at five dpi, downregulated in resistant plants at nine dpi, and showed no significant difference at 11 dpi. CsPRR2 was consistently upregulated in both lines at 5, 9, and 11 dpi. CsPRR3 was upregulated in resistant lines at nine dpi but downregulated at 11 dpi. CsARR8 was significantly downregulated in both lines at 9 and 11 dpi. Notably, CsPRR2 demonstrated dual functionality related to (i) the regulation of immature fruit skin color via a stop-gain InDel and (ii) resistance to Foc, as the gene was upregulated in both resistant and susceptible lines after inoculation with the pathogen. CONCLUSIONS This study integrated resequencing and transcriptomic data to comprehensively characterize CsRR genes, establishing a foundation for further exploration of their functional mechanisms in cucumber.
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Affiliation(s)
- Ke Su
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China; (K.S.); (Z.S.); (J.L.)
- Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (W.A.); (Y.G.)
| | - Wenhong Ao
- Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (W.A.); (Y.G.)
| | - Zhaolong Sun
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China; (K.S.); (Z.S.); (J.L.)
- Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (W.A.); (Y.G.)
| | - Jing Li
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China; (K.S.); (Z.S.); (J.L.)
- Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (W.A.); (Y.G.)
| | - Yu Gao
- Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (W.A.); (Y.G.)
| | - Defang Gan
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China; (K.S.); (Z.S.); (J.L.)
| | - Jingjing Yang
- Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (W.A.); (Y.G.)
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Münte E, Viebahn G, Khurana A, Fujiki J, Nakamura T, Lang S, Demir M, Schnabl B, Hartmann P. Faecalibacterium prausnitzii Is Associated with Disease Severity in MASLD but Its Supplementation Does Not Improve Diet-Induced Steatohepatitis in Mice. Microorganisms 2025; 13:675. [PMID: 40142567 PMCID: PMC11944644 DOI: 10.3390/microorganisms13030675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 03/13/2025] [Accepted: 03/14/2025] [Indexed: 03/28/2025] Open
Abstract
The gut microbiota plays an important role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). In this study, we aimed to evaluate the role of the butyrate-producing bacterium Faecalibacterium prausnitzii in MASLD and whether supplementation with butyrate-producing bacteria, in particular Faecalibacterium prausnitzii, can ameliorate diet-induced steatohepatitis in mice. The relative abundance of the genus Faecalibacterium and its most abundant strain Faecalibacterium prausnitzii was determined by 16S rRNA sequencing and quantitative polymerase chain reaction (qPCR), respectively, in 95 participants with MASLD and 19 healthy control subjects. Butyrate and butyrate-producing bacteria (Faecalibacterium prausnitzii and Coprococcus comes) were gavaged to C57BL/6 mice fed a steatohepatitis-inducing diet. The fecal relative abundance of Faecalibacterium and Faecalibacterium prausnitzii was decreased in subjects with MASLD versus healthy controls and lower in individuals with MASLD and stage 3-4 fibrosis versus those with stage 0-2 fibrosis. Sodium-butyrate supplementation improved hepatic steatosis in mice on high-fat diet (HFD). Gavage of various butyrate-producing bacteria including Faecalibacterium prausnitzii and Coprococcus comes isolated from humans did not improve HFD-induced liver disease in mice. Although the abundance of Faecalibacterium prausnitzii is associated with MASLD severity in humans, its gavage to mice does not improve experimental diet-induced liver disease.
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Affiliation(s)
- Eliane Münte
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Greta Viebahn
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA (J.F.)
| | - Amit Khurana
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Jumpei Fujiki
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA (J.F.)
- Department of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Hokkaido, Japan
| | - Tomohiro Nakamura
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA (J.F.)
| | - Sonja Lang
- Department of Gastroenterology and Hepatology, University Hospital Cologne, 50937 Cologne, Germany
- Faculty of Medicine, University of Cologne, 50931 Cologne, Germany
| | - Münevver Demir
- Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, 13353 Berlin, Germany
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA (J.F.)
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Phillipp Hartmann
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Division of Gastroenterology, Hepatology & Nutrition, Rady Children’s Hospital San Diego, San Diego, CA 92123, USA
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Nowrouzian FL, Lumingkit K, Gio-Batta M, Jaén-Luchoro D, Thordarson T, Elfvin A, Wold AE, Adlerberth I. Tracing Staphylococcus capitis and Staphylococcus epidermidis strains causing septicemia in extremely preterm infants to the skin, mouth, and gut microbiota. Appl Environ Microbiol 2025; 91:e0098024. [PMID: 39692500 PMCID: PMC11784025 DOI: 10.1128/aem.00980-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 11/25/2024] [Indexed: 12/19/2024] Open
Abstract
Coagulase-negative staphylococci (CoNS) comprise about 50 species, some of which cause septicemia in preterm neonates. CoNS establish early on the skin and in the oral and gut microbiota, from where they may spread to the bloodstream. The colonization pattern preceding septicemia is not well-defined. Forty-two extremely preterm neonates (≤28 + 0 gestational weeks) were followed from birth to 2 months with regular sampling and culturing of the skin and oral and gut microbiota. Blood samples were drawn upon clinical suspicion of septicemia and cultured. CoNS species were identified using matrix-assisted laser-desorption ionization time of flight mass spectrometry (MALDI-TOF). Random amplified polymorphic DNA was used for strain typing, and strains were characterized regarding biofilm production and virulence gene carriage. CoNS blood isolates underwent whole genome sequencing. Staphylococcus epidermidis represented 72% of the CoNS isolates on skin or mucous membranes, followed by Staphylococcus capitis (13%) and Staphylococcus haemolyticus (7%). CoNS septicemia was diagnosed in nine infants, yielding 11 septicemia isolates: seven S. capitis and four S. epidermidis, of which nine were further analyzed. The S. capitis septicemia isolates belonged to the NRCS-A clone. Two-thirds of the septicemia strains were traced back to the commensal microbiota. Colonization of the oral cavity by S. capitis was significantly associated with CoNS septicemia development, although the blood-borne S. capitis strains were more commonly found on the skin than in the mouth prior to invasion. Biofilm production was not associated with septicemia. Our results implicate CoNS colonization as a step that precedes septicemia in preterm neonates. Early colonization of the oral cavity by S. capitis may represent a particular risk. IMPORTANCE Septicemia is a major cause of morbidity in preterm infants. Coagulase-negative staphylococci (CoNS) can colonize skin, oral cavity, and intestines and are a common cause of septicemia in this group. The relation between CoNS colonization pattern at the species and strain level and septicemia has scarcely been studied. We mapped colonization of the skin, oral cavity, and intestines by CoNS species in extremely preterm infants and speciated and strain-typed the skin, mucosal, and blood isolates. Two-thirds of the CoNS septicemia blood strains, including a majority of S. capitis strains belonging to the NRCS-A clone, were tracked to the commensal microbiota. We demonstrated that CoNS species differ in their colonization patterns, whereby S. capitis was primarily a skin colonizer. However, its colonization of the oral cavity was enhanced among infants developing septicemia. Our study provides a starting point for further explorations of the relationship between CoNS colonization and septicemia in preterm infants.
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Affiliation(s)
- Forough L. Nowrouzian
- Institute of Biomedicine, Department of Infectious Diseases,The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kirth Lumingkit
- Institute of Biomedicine, Department of Infectious Diseases,The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Monica Gio-Batta
- Institute of Biomedicine, Department of Infectious Diseases,The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Jaén-Luchoro
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Thordur Thordarson
- Institute of Clinical Science, Department of Pediatrics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Pediatrics, Sahlgrenska University Hospital, The Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Anders Elfvin
- Institute of Clinical Science, Department of Pediatrics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Pediatrics, Sahlgrenska University Hospital, The Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Agnes E. Wold
- Institute of Biomedicine, Department of Infectious Diseases,The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ingegerd Adlerberth
- Institute of Biomedicine, Department of Infectious Diseases,The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Li S, Guo C, Feng X, Wang J, Pan W, Xu C, Wei S, Han X, Yang M, Chen Q, Wang J, Hu L, Qi Z. Development and Validation of Kompetitive Allele-Specific Polymerase Chain Reaction Markers for Seed Protein Content in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:3485. [PMID: 39771183 PMCID: PMC11728539 DOI: 10.3390/plants13243485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 12/07/2024] [Accepted: 12/09/2024] [Indexed: 01/16/2025]
Abstract
Seed protein content is a critical trait in soybean breeding, as it provides a primary source of high-quality protein for both human consumption and animal feed. This study aimed to enhance molecular marker-assisted selection for high-protein soybean varieties by developing Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) markers targeted at loci associated with seed protein content. Nineteen markers with high genotyping efficacy were identified through screening. Utilizing SN76 (a high-protein line) as the male parent and SN49 and DS1 (both low-protein lines) as female parents, 484 F6 generation individuals from these hybrid combinations were selected to validate the predictive accuracy of the 19 KASP markers. Notably, KASP-Pro-1, KASP-Pro-2, and KASP-Pro-3 effectively distinguished genotypes associated with high and low protein content, with prediction accuracies of 68.4%, 75.0%, and 83.3%, respectively. These results underscore the reliability and practical utility of the selected molecular markers, which are located within the genes Glyma.03G219900, Glyma.14G119000, and Glyma.17G074400, respectively. Haplotype analysis and gene pyramiding indicate that these three genes may influence seed protein content. Consequently, these KASP markers can be effectively integrated into genetic and genomic research on soybean seed protein content as well as into marker-assisted breeding.
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Affiliation(s)
- Shuangzhe Li
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Chenyijun Guo
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Xuezhen Feng
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Jing Wang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Wenjing Pan
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (W.P.); (J.W.)
| | - Chang Xu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Siming Wei
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Xue Han
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Mingliang Yang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Qingshan Chen
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Jinxing Wang
- Suihua Branch of Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (W.P.); (J.W.)
| | - Limin Hu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
| | - Zhaoming Qi
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.L.); (C.G.); (X.F.); (J.W.); (C.X.); (S.W.); (X.H.); (M.Y.); (Q.C.)
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Petolescu C, Sarac I, Popescu S, Tenche-Constantinescu AM, Petrescu I, Camen D, Turc A, Fora GC, Turcus V, Horablaga NM, Gorinoiu G, Mariana G, Onisan E. Assessment of Genetic Diversity in Alfalfa Using DNA Polymorphism Analysis and Statistical Tools. PLANTS (BASEL, SWITZERLAND) 2024; 13:2853. [PMID: 39458800 PMCID: PMC11511019 DOI: 10.3390/plants13202853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Revised: 10/07/2024] [Accepted: 10/09/2024] [Indexed: 10/28/2024]
Abstract
The cultivation of alfalfa is crucial for farmers as it is an excellent forage crop with a high nitrogen-fixing capacity, making it indispensable in crop rotations. Breeding programs face challenges in advancing more rapidly in genetic diversity to achieve a higher heterosis effect and, consequently, greater yield. In this study, we used 30 alfalfa varieties, which were used for molecular analyses by 5 ISSR primers and 13 RAPD primers. The results obtained highlighted the greater efficiency of ISSR primers in identifying genetic diversity. On the other hand, the simultaneous use of ISSR + RAPD allowed for clearer clustering of varieties that enabled more efficiently distinguishing the genetic diversity. The most efficient ISSR primer, A17, generated 31 polymorphic bands, while the most efficient RAPD primer, L-07, generated only 21 bands. Varieties such as "Pastoral" and "F1413-02" exhibited low similarity coefficients (0.39), suggesting their potential for enhancing genetic variability through crossbreeding, thereby increasing the potential of achieving a greater heterosis effect. Conversely, varieties with high similarity coefficients, such as "Cristal" and "Viking" (0.81) are less suited for this purpose. The correlation between specific markers highlights that using both ISSR and RAPD markers together offers a clear understanding of genetic diversity in alfalfa, aiding in more effective selection for crossbreeding in breeding programs.
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Affiliation(s)
- Cerasela Petolescu
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Mihai I” from Timisoara, 119 Calea Aradului Street, 300645 Timisoara, Romania; (C.P.); (I.S.); (S.P.); (A.-M.T.-C.); (I.P.); (D.C.); (A.T.); (G.C.F.)
| | - Ioan Sarac
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Mihai I” from Timisoara, 119 Calea Aradului Street, 300645 Timisoara, Romania; (C.P.); (I.S.); (S.P.); (A.-M.T.-C.); (I.P.); (D.C.); (A.T.); (G.C.F.)
| | - Sorina Popescu
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Mihai I” from Timisoara, 119 Calea Aradului Street, 300645 Timisoara, Romania; (C.P.); (I.S.); (S.P.); (A.-M.T.-C.); (I.P.); (D.C.); (A.T.); (G.C.F.)
| | - Alina-Maria Tenche-Constantinescu
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Mihai I” from Timisoara, 119 Calea Aradului Street, 300645 Timisoara, Romania; (C.P.); (I.S.); (S.P.); (A.-M.T.-C.); (I.P.); (D.C.); (A.T.); (G.C.F.)
| | - Irina Petrescu
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Mihai I” from Timisoara, 119 Calea Aradului Street, 300645 Timisoara, Romania; (C.P.); (I.S.); (S.P.); (A.-M.T.-C.); (I.P.); (D.C.); (A.T.); (G.C.F.)
| | - Dorin Camen
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Mihai I” from Timisoara, 119 Calea Aradului Street, 300645 Timisoara, Romania; (C.P.); (I.S.); (S.P.); (A.-M.T.-C.); (I.P.); (D.C.); (A.T.); (G.C.F.)
| | - Alina Turc
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Mihai I” from Timisoara, 119 Calea Aradului Street, 300645 Timisoara, Romania; (C.P.); (I.S.); (S.P.); (A.-M.T.-C.); (I.P.); (D.C.); (A.T.); (G.C.F.)
| | - George Ciprian Fora
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Mihai I” from Timisoara, 119 Calea Aradului Street, 300645 Timisoara, Romania; (C.P.); (I.S.); (S.P.); (A.-M.T.-C.); (I.P.); (D.C.); (A.T.); (G.C.F.)
| | - Violeta Turcus
- Faculty of Medicine, “Vasile Goldis” Western University of Arad, 310045 Arad, Romania;
| | - Nicolae Marinel Horablaga
- Faculty of Agriculture, University of Life Sciences “King Mihai I” from Timisoara, 300645 Timisoara, Romania;
- Agricultural Research and Development Station Lovrin, 307260 Lovrin, Romania;
| | - Gabriela Gorinoiu
- Agricultural Research and Development Station Lovrin, 307260 Lovrin, Romania;
| | - Ganea Mariana
- Faculty of Medicine and Pharmacy, University of Oradea, 10 P-ta 1 December Street, 410073 Oradea, Romania;
| | - Emilian Onisan
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Mihai I” from Timisoara, 119 Calea Aradului Street, 300645 Timisoara, Romania; (C.P.); (I.S.); (S.P.); (A.-M.T.-C.); (I.P.); (D.C.); (A.T.); (G.C.F.)
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Abd-Elrahman SM, Abdel-Rahman SM, Bakir HY, Othman RA, Khedr AA, Khalifa MM, Abdel-Hakeem SS. Genetic relatedness and diversity of Capillaria species infecting bayad (Bagrus bajad) in upper Egypt. BMC Vet Res 2024; 20:235. [PMID: 38822316 PMCID: PMC11141003 DOI: 10.1186/s12917-024-04076-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND This study investigates the genetic characteristics of Capillaria isolates from the infected fish, Bagrus bajad, and their relation to human Capillaria philippinensis using Random Amplified Polymorphic DNA (RAPD-PCR) analysis. Fifteen fish Capillaria were isolated and compared to identified human C. philippinensis using six primers: M-are, M-1, G-7, G-11, G-15, and G-18. RESULTS All six primers successfully amplified DNA, highlighting their efficacy in distinguishing between human and fish Capillaria isolates. The analysis revealed distinctive banding patterns between fish and human isolates, with variations in size and number of DNA fragments. Additionally, genetic similarity analysis showed intriguing patterns of relatedness, with certain pairs exhibiting high similarity percentages. Comparative assessment of RAPD polymorphism demonstrated consistent findings of 100% polymorphism across all primers. The Unweighted Pair Group Method with Arithmetic Mean Algorithm (UPGMA) evaluated the closest relationship between human and fish isolates. These results underscore the utility of RAPD analysis in delineating the genetic diversity among Capillaria isolates from different hosts. CONCLUSION Overall, this study contributes to our understanding of the genetic variability and relatedness among Capillaria isolates, shedding light on their evolutionary dynamics and zoonotic potential.
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Affiliation(s)
| | - Salma M Abdel-Rahman
- Department of Medical Parasitology Faculty of Medicine, Assiut University, Asyut, 71515, Egypt
| | - Hanaa Y Bakir
- Department of Medical Parasitology Faculty of Medicine, Assiut University, Asyut, 71515, Egypt
| | - Ragaa A Othman
- Department of Medical Parasitology Faculty of Medicine, Assiut University, Asyut, 71515, Egypt
| | - Abeer A Khedr
- Department of Parasitology, Faculty of Veterinary Medicine, New Valley University, New Valley, El-Khargah, 72511, Egypt
| | - Mervat M Khalifa
- Department of Medical Parasitology Faculty of Medicine, Assiut University, Asyut, 71515, Egypt
| | - Sara S Abdel-Hakeem
- Parasitology Laboratory, Zoology and Entomology Department, Faculty of Science, Assiut University, Assiut, 71526, Egypt.
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Tanjila N, Islam S, Akhter MS, Hossain MM, Alam MS, Begum F. Characterization of Sclerotium rolfsii causing foot rot: a severe threat of betel vine cultivation in Bangladesh. 3 Biotech 2024; 14:58. [PMID: 38298554 PMCID: PMC10825092 DOI: 10.1007/s13205-023-03890-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 12/16/2023] [Indexed: 02/02/2024] Open
Abstract
The development of the foot rot disease caused by the fungus Sclerotium rolfsii is one of the primary variables endangering betel vine production in Bangladesh. Consequently, with the ultimate objective of finding efficient preventive and control strategies for this infamous phytopathogen, the current study was undertaken for comprehensive population structure analysis, exploration of physiological features and incidence patterns of pathogenic S. rolfsii isolates. We discovered 22 S. rolfsii isolates from nine northern districts of Bangladesh. Mohanpur (51.90%), Bagmara (54.09%), and Durgapur (49.45%) upazilas in the Rajshahi district had the more severe occurrences of foot rot disease, while Chapainawabganj (18.89%) had the least number of cases. The isolates differed substantially in terms of morphology and growth rate. By employing the UPGMA algorithm to analyze the combined morphological data from 22 S. rolfsii isolates, these isolates were divided into six different groups with a 62% similarity level. Somatic incompatibility was also found in some isolates. The RAPD-4 primer confirmed 100% polymorphism among these isolates, and these genetic variations were further validated by molecular analysis. The results of the morphological and molecular analysis revealed that there was significant variation among the S. rolfsii isolates. Finally, a comprehensive characterization of S. rolfsii would allow for a suitable management strategy for betel vine's deadly foot rot disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03890-8.
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Affiliation(s)
- Nargis Tanjila
- Microbiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Shaikhul Islam
- Plant Pathology Division, Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur, 5200 Bangladesh
| | - Md. Shamim Akhter
- Plant Pathology Division, Agricultural Research Institute (BARI), Joydebpur, Gazipur, 1701 Bangladesh
| | - Md. Monzur Hossain
- Plant Breeding and Gene Engineering Laboratory, Department of Botany, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Mohammad Shahidul Alam
- Mycology and Plant Pathology Laboratory, Department of Botany, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Ferdousi Begum
- Microbiology Laboratory, Department of Botany, University of Rajshahi, Rajshahi, 6205 Bangladesh
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Freitas FTDM, da Costa MSC, da Costa KHR, Alves EG. Antimicrobial resistance and epidemic clustering of late-onset neonatal infections in a Brazilian intensive care unit. J Trop Pediatr 2023; 70:fmad045. [PMID: 38085999 DOI: 10.1093/tropej/fmad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Nosocomial infections in the neonatal intensive care unit (NICU) tend to cluster and multidrug-resistant (MDR) pathogens are rising in developing countries. We did a retrospective cohort study of neonates admitted to a NICU in Brazil with late-onset neonatal sepsis (LOS) confirmed by blood culture from October 2012 to December 2016 and from July 2018 to December 2021. We defined a cluster of infection when at least two cases of LOS occurred within two different time intervals: 15 and 30 days with the same pathogen in different patients. A random amplified polymorphic DNA (RAPD) was performed from samples from one of these clusters. A logistic regression model was applied having death as the outcome and the infection with an MDR pathogen as the exposure of interest. There were 987 blood cultures from 754 neonates, 621 (63%) were gram-positive cocci, 264 (30%) were gram-negative rods and 72 (7%) fungi. A third of Enterobacterales were resistant to cefepime and a third of non-fermenting glucose rods were resistant to carbapenems. There were 100 or 104 clusters of infection in the 15- or 30-day interval, respectively. A RAPD analysis from an outbreak of MDR Acinetobacter baumannii showed that all five samples belonged to a single clone. An infection with an MDR pathogen was associated with death (OR 1.82, 95% CI 1.03-3.21). In conclusion, clusters of infections in a Brazilian NICU are a frequent phenomenon as seen elsewhere. They suggest cross-transmission of pathogens with increasing antimicrobial resistance and should prompt intensified surveillance and infection control measures.
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Affiliation(s)
- Felipe Teixeira de Mello Freitas
- Hospital Materno Infantil de Brasilia, Brasilia 70203-900, Brazil
- Escola Superior de Ciências da Saúde, Fundação de Ensino e Pesquisa, Brasilia 70710-907, Brazil
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9
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Hopper KR. Reduced-representation libraries in insect genetics. CURRENT OPINION IN INSECT SCIENCE 2023; 59:101084. [PMID: 37442341 DOI: 10.1016/j.cois.2023.101084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 05/04/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023]
Abstract
Genotyping-by-sequencing of reduced-representation libraries has ushered in an era where genome-wide data can be gotten for any species. Here, I review research on this topic during the last two years, report meta-analysis of the results, and discuss analysis methods and issues. Scanning the literature from 2021 to 2022 identified 21 papers, the majority of which were on population differences, including local adaptation and migration, but several papers were on genetic maps and their use in assembly scaffolding or analysis of quantitative trait loci, on the origin of incursions of pest insects, or on infection rates of a pathogen in a disease vector. The research reviewed includes 33 species from 25 families and 11 orders. Meta-analysis showed that less than 16%, and most often, less than 1% of the genome was implicated in local adaptation and that the number of adaptive loci correlated with genetic divergence among populations.
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Affiliation(s)
- Keith R Hopper
- Beneficial Insect Introductions Research Unit, ARS, USDA, Newark, DE, United States.
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10
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Singh P, Ansari N, Rai SP, Agrawal M, Agrawal SB. Effect of elevated ozone on the antioxidant response, genomic stability, DNA methylation pattern and yield in three species of Abelmoschus having different ploidy levels. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:59401-59423. [PMID: 37004611 DOI: 10.1007/s11356-023-26538-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 03/14/2023] [Indexed: 05/10/2023]
Abstract
The majority of polyploids can withstand many stresses better than their monoploid counterparts; however, there is no proven mechanism that can fully explain the level of tolerance at the biochemical and molecular levels. Here, we make an effort to provide an explanation for this intriguing but perplexing issue using the antioxidant responses, genomic stability, DNA methylation pattern and yield in relation to ploidy level under the elevated level of ozone in Abelmoschus cytotypes. The outcome of this study inferred that the elevated ozone causes an increase in reactive oxygen species leading to enhanced lipid peroxidation, DNA damage and DNA de-methylation in all the Abelmoschus cytotypes. The monoploid cytotype of Abelmoschus, that is Abelmoschus moschatus L., experienced the highest oxidative stress under elevated O3, resulting in maximum DNA damage and DNA de-methylation leading to the maximum reduction in yield. While the diploid (Abelmoschus esculentus L.) and triploid (Abelmoschus caillei A. Chev.) cytotypes of Abelmoschus with lower oxidative stress result in lesser DNA damage and DNA de-methylation which ultimately leads to lower yield reduction. The result of this experiment explicitly revealed that polyploidy confers better adaptability in the case of Abelmoschus cytotypes under ozone stress. This study can further be used as a base to understand the mechanism behind the ploidy-induced stress tolerance in other plants mediated by gene dosage effect.
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Affiliation(s)
- Priyanka Singh
- Laboratory of Air Pollution and Climate Change, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Naushad Ansari
- Laboratory of Air Pollution and Climate Change, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Shashi Pandey Rai
- Laboratory of Morphogenesis, Centre of Advance Study in Botany, Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Madhoolika Agrawal
- Laboratory of Air Pollution and Climate Change, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Shashi Bhushan Agrawal
- Laboratory of Air Pollution and Climate Change, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India.
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11
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Wojciechowska-Koszko I, Mnichowska-Polanowska M, Roszkowska P, Sławiński M, Giedrys-Kalemba S, Dołęgowska B, Sienkiewicz M, Hukowska-Szematowicz B, Kwiatkowski P. Improved RAPD Method for Candida parapsilosis Fingerprinting. Genes (Basel) 2023; 14:genes14040868. [PMID: 37107626 PMCID: PMC10137414 DOI: 10.3390/genes14040868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/26/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Recently, methods based on the analysis of arbitrarily amplified target sites of genome microorganisms have been extensively applied in microbiological studies, and especially in epidemiological studies. The range of their application is limited by problems with discrimination and reproducibility resulting from a lack of standardized and reliable methods of optimization. The aim of this study was to obtain optimal parameters of the Random Amplified Polymorphic DNA (RAPD) reaction by using an orthogonal array as per the Taguchi and Wu protocol, modified by Cobb and Clark for Candida parapsilosis isolates. High Simpson’s index values and low Dice coefficients obtained in this study indicated a high level of interspecies DNA polymorphism between C. parapsilosis strains, and the optimized RAPD method proved useful in the microbiological and epidemiological study.
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Affiliation(s)
| | | | - Paulina Roszkowska
- Department of Diagnostic Immunology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland
| | - Michał Sławiński
- Department of Laboratory Diagnostics, Public Clinical Hospital No. 2 in Szczecin, 70-111 Szczecin, Poland
| | - Stefania Giedrys-Kalemba
- Department of Medical Microbiology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland
| | - Barbara Dołęgowska
- Department of Laboratory Medicine, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland
| | - Monika Sienkiewicz
- Department of Pharmaceutical Microbiology and Microbiological Diagnostic, Medical University of Lodz, 90-151 Lodz, Poland
| | - Beata Hukowska-Szematowicz
- Institute of Biology, University of Szczecin, 71-412 Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, 71-412 Szczecin, Poland
| | - Paweł Kwiatkowski
- Department of Diagnostic Immunology, Pomeranian Medical University in Szczecin, 70-111 Szczecin, Poland
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12
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Nie H, Park H, Kim S, Kim D, Kim S, Kwon SY, Kim SH. Genetic diversity assessment and genome-wide association study reveal candidate genes associated with component traits in sweet potato (Ipomoea batatas (L.) Lam). Mol Genet Genomics 2023; 298:653-667. [PMID: 36943475 DOI: 10.1007/s00438-023-02007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/11/2023] [Indexed: 03/23/2023]
Abstract
The Korean sweet potatoes were bred by various cultivars introduced from Japanese, American, Porto Rico, China, and Burundi. This issue enriched their genetic diversity but also resulted in a mixture of cultivars. For genotyping, we collected and sequenced 66 sweet potato germplasms from different localities around Korea, including 36 modern cultivars, 5 local cultivars, and 25 foreign cultivars. This identified 447.6 million trimmed reads and 324.8 million mapping reads and provided 39,424 single nucleotide polymorphisms (SNPs) markers. Phylogenetic clustering and population structure analysis distinctly classified these germplasms into 5 genetic groups, group 1, group 2, group 3, group 4, and group 5, containing 20, 15, 10, 7, and 14 accessions, respectively. Sixty-three significant SNPs were selected by genome-wide association for sugar composition-related traits (fructose, glucose, and total sugars), total starch, amylose content, and total carotenoid of the storage root. A total of 37 candidate genes encompassing these significant SNPs were identified, among which, 7 genes were annotated to involve in sugar and starch metabolism, including galactose metabolism (itf04g30630), starch and sucrose metabolism (itf03g13270, itf15g09320), carbohydrate metabolism (itf14g10250), carbohydrate and amino acid metabolism (itf12g19270), and amino sugar and nucleotide sugar metabolism (itf03g21950, itf15g04880). This results indicated that sugar and starch are important characteristics to determine the genetic diversity of sweet potatoes. These findings not only illustrate the importance of component traits to genotyping sweet potatoes but also explain an important reason resulting in genetic diversity of sweet potato.
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Affiliation(s)
- Hualin Nie
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Hyungjun Park
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Sujung Kim
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, 58545, Republic of Korea
| | - Doyeon Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Sun-Hyung Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, South Korea.
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Molecular Approaches for Detection of Trichoderma Green Mold Disease in Edible Mushroom Production. BIOLOGY 2023; 12:biology12020299. [PMID: 36829575 PMCID: PMC9953464 DOI: 10.3390/biology12020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
Due to the evident aggressive nature of green mold and the consequently huge economic damage it causes for producers of edible mushrooms, there is an urgent need for prevention and infection control measures, which should be based on the early detection of various Trichoderma spp. as green mold causative agents. The most promising current diagnostic tools are based on molecular methods, although additional optimization for real-time, in-field detection is still required. In the first part of this review, we briefly discuss cultivation-based methods and continue with the secondary metabolite-based methods. Furthermore, we present an overview of the commonly used molecular methods for Trichoderma species/strain detection. Additionally, we also comment on the potential of genomic approaches for green mold detection. In the last part, we discuss fast screening molecular methods for the early detection of Trichoderma infestation with the potential for in-field, point-of-need (PON) application, focusing on isothermal amplification methods. Finally, current challenges and future perspectives in Trichoderma diagnostics are summarized in the conclusions.
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14
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Alavilli H, Poli Y, Verma KS, Kumar V, Gupta S, Chaudhary V, Jyoti A, Sahi SV, Kothari SL, Jain A. Miracle Tree Moringa oleifera: Status of the Genetic Diversity, Breeding, In Vitro Propagation, and a Cogent Source of Commercial Functional Food and Non-Food Products. PLANTS (BASEL, SWITZERLAND) 2022; 11:3132. [PMID: 36432862 PMCID: PMC9694164 DOI: 10.3390/plants11223132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Moringa oleifera Lam. (MO) is a fast-growing drought-resistant tree belonging to the family Moringaceae and native to the Indian subcontinent and cultivated and/or naturalized worldwide with a semi-arid climate. MO is also popularly known as a miracle tree for its repertoire of nutraceutical, pharmacological, and phytochemical properties. The MO germplasm is collected, conserved, and maintained by various institutions across the globe. Various morphological, biochemical, and molecular markers are used for determining the genetic diversity in MO accessions. A higher yield of leaves and pods is often desirable for making various products with commercial viability and amenable for trade in the international market. Therefore, breeding elite varieties adapted to local agroclimatic conditions and in vitro propagation are viable and sustainable approaches. Here, we provide a comprehensive overview of MO germplasm conservation and various markers that are employed for assessing the genetic diversity among them. Further, breeding and in vitro propagation of MO for various desirable agronomic traits are discussed. Finally, trade and commerce of various functional and biofortified foods and non-food products are enumerated albeit with a need for a rigorous and stringent toxicity evaluation.
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Affiliation(s)
- Hemasundar Alavilli
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Yugandhar Poli
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India
| | - Kumar Sambhav Verma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Vikram Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Swati Gupta
- Department of Biosciences, Manipal University Jaipur, Jaipur 303007, India
| | - Vigi Chaudhary
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Anupam Jyoti
- Biotechnology Department, Chandigarh University, National Highway-95, Ludhiana-Chandigarh State Highway, Chandigarh 160055, India
| | - Shivendra V. Sahi
- Department of Biology, Saint Joseph’s University (University City Campus), 600 South 43rd Street, Philadelphia, PA 19104, USA
| | - Shanker Lal Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
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15
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Naqvi RZ, Siddiqui HA, Mahmood MA, Najeebullah S, Ehsan A, Azhar M, Farooq M, Amin I, Asad S, Mukhtar Z, Mansoor S, Asif M. Smart breeding approaches in post-genomics era for developing climate-resilient food crops. FRONTIERS IN PLANT SCIENCE 2022; 13:972164. [PMID: 36186056 PMCID: PMC9523482 DOI: 10.3389/fpls.2022.972164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.
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16
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Molecular Evaluation of the Impact of Nd:YAG Laser and Static Magnetic Field on Genomic DNA of Some Bacterial Isolates using RAPD-PCR. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.3.62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial therapy is frequently associated with the emergence of resistant bacteria with a high rate of morbidity and mortality worldwide. The present study was aimed at investigating the impact of a neodymium-doped yttrium aluminum (Nd:YAG) laser, and a static magnetic field (SMF) on cellular growth and DNA alteration in some clinical bacterial isolates. Samples from cutaneous wounds were collected by sterile cotton swabs from three elderly women admitted to Tikrit Teaching Hospital, Tikrit City, Iraq. Isolation and identification of Streptococcus agalactiae, Staphylococcus aureus, and Pseudomonas aeruginosa were carried out using cultural characteristics, microscopy, and biochemical tests. Three broth cultures were prepared for each of the test isolates. The first broth culture served as untreated control, the second was exposed to an Nd:YAG laser and the third was exposed to SMF. Colony counting was done on all the samples. DNA was extracted from the test bacteria and used to perform the RAPD-PCR assay. In contrast to the untreated control, the results showed that Nd:YAG laser radiation was more effective than SMF at inhibiting the cellular growth of the test isolates. Also, the radiation caused DNA alteration, which was established by decreased microbial growth, as well as the development of new bands and the loss of original bands. According to the findings of this study, the Nd:YAG laser is a promising technique for influencing the healing of infected cutaneous wounds. RAPD-PCR is also a useful biomarker assay for assessing the biological impact of laser radiation and SMF on bacteria.
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17
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Turtles in Malaysia: A Review of Conservation Status and a Call for Research. Animals (Basel) 2022; 12:ani12172184. [PMID: 36077905 PMCID: PMC9454601 DOI: 10.3390/ani12172184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Turtles are threatened all over the world. Malaysia has 24 species of turtles. This review focuses on current conservation status and some requirements for sustainability. We propose integrating concepts of ecology and molecular biology to provide almost comprehensive turtle reviews in Malaysia. Abstract Approximately 356 species of turtles inhabit saltwater and freshwater habitats globally, except in Antarctica. Twenty-four species of turtles have been reported in Malaysia, four of which are sea turtles. The state of Terengganu harbored the highest number of turtles, with 17 different reported species. Based on the IUCN Red List, 29% of turtle species in Malaysia are critically endangered. In comparison, another 25% are classified as endangered. Likewise, CITES reported that 67% of Malaysia’s turtles are threatened, while 25% are classified as critically endangered. This review discusses the checklists, molecular genetics work, conservation status, recent trends, and recommendations for future research. Factors contributing to their population declines and current endangered status are also discussed.
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18
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Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years. J Fungi (Basel) 2022; 8:jof8080803. [PMID: 36012792 PMCID: PMC9410331 DOI: 10.3390/jof8080803] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Fungi are amongst the most abundant and diverse organisms. Despite being widely known for their adverse role in food spoilage or as pathogens for humans, animals, or plants, they also present several beneficial effects. Fungi contribute to human well-being due to their role as decomposers, degrading decay matter into smaller molecules which can be easily used by other ecosystem members. These organisms can produce medicinal compounds or modulate protective immune responses in human intestine. Fungi intervene in diverse food processes or act as a food supply. Due to fungal diversity, the unequivocal identification of these organisms is crucial to increasing their practical applications and decreasing their adverse effects. The process of identification could be achieved through the integral sequencing of fungi genomes. However, this procedure would be time-consuming and rather cost-inefficient. Therefore, several molecular markers have been developed to overcome these limitations. The chronology of DNA-based molecular markers development can be divided into three main steps: (1) prior to the development of the PCR technique (RFLP); (2) after the development of the PCR technique (RAPD, AFLP, ISSR, VNTR, SNP, InDels, and DNA barcoding); (3) after the development of the massive parallel sequencing technique (Metabarcoding and WGS). Therefore, the present review covers an overview of the most recently developed molecular markers used for fungal detection and identification.
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19
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Noviana E, Indrayanto G, Rohman A. Advances in Fingerprint Analysis for Standardization and Quality Control of Herbal Medicines. Front Pharmacol 2022; 13:853023. [PMID: 35721184 PMCID: PMC9201489 DOI: 10.3389/fphar.2022.853023] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/26/2022] [Indexed: 01/01/2023] Open
Abstract
Herbal drugs or herbal medicines (HMs) have a long-standing history as natural remedies for preventing and curing diseases. HMs have garnered greater interest during the past decades due to their broad, synergistic actions on the physiological systems and relatively lower incidence of adverse events, compared to synthetic drugs. However, assuring reproducible quality, efficacy, and safety from herbal drugs remains a challenging task. HMs typically consist of many constituents whose presence and quantity may vary among different sources of materials. Fingerprint analysis has emerged as a very useful technique to assess the quality of herbal drug materials and formulations for establishing standardized herbal products. Rather than using a single or two marker(s), fingerprinting techniques take great consideration of the complexity of herbal drugs by evaluating the whole chemical profile and extracting a common pattern to be set as a criterion for assessing the individual material or formulation. In this review, we described and assessed various fingerprinting techniques reported to date, which are applicable to the standardization and quality control of HMs. We also evaluated the application of multivariate data analysis or chemometrics in assisting the analysis of the complex datasets from the determination of HMs. To ensure that these methods yield reliable results, we reviewed the validation status of the methods and provided perspectives on those. Finally, we concluded by highlighting major accomplishments and presenting a gap analysis between the existing techniques and what is needed to continue moving forward.
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Affiliation(s)
- Eka Noviana
- Departement of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Abdul Rohman
- Departement of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Center of Excellence, Institute for Halal Industry and Systems, Universitas Gadjah Mada, Yogyakarta, Indonesia
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20
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El-Sitiny MF, M. Omar H, El-Shehawi AM, Elseehy MM, El-Tahan AM, El-Saadony MT, Selem GS. Biochemical and molecular diagnosis of different tomato cultivars susceptible and resistant to Tuta absoluta (Meyrick) infestation. Saudi J Biol Sci 2022; 29:2904-2910. [PMID: 35531183 PMCID: PMC9073022 DOI: 10.1016/j.sjbs.2022.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/29/2021] [Accepted: 01/10/2022] [Indexed: 11/03/2022] Open
Abstract
Resistant plant cultivars which used in breeding programs are considered one of the modern integrated management programs to reduce the usage of synthetic insecticides and environmental contamination the present study aimed to characterize the resistant and susceptible tomato cultivars to Tuta absoluta based on biochemical and molecular levels, in Egypt. The biochemical characters of the tested tomato cultivars (tomato- 86, tomato- Alissa, tomato- Fayarouz, tomato- Omniya, tomato- 036, tomato- GS) were determined colorimetrically and characterized by using native- polyacrylamide gel electrophoresis (PAGE) and agarose gel. Our results showed that there were variations highly significant in all biochemical constituents of the resistant tomato cultivar (tomato- 86) compared with the susceptible one (tomato- GS). Also, native-(PAGE) for peroxidase (POD) isoenzymes techniques of the tested tomato cultivars showed variations in protein band numbers and densities in tomato-86 resistant compared with tomato-GS susceptible to Tuta absoluta infestation. The correlation coefficient between total phenols and peroxidases in infested tomato leaves and percentages of damaged leaves with the tested insect pest was negative and highly significant, while in case of total proteins and reducing sugars in infested tomato leaves as well as lycopene contents in infested tomato fruits was positive, highly significant and significant, respectively. The correlation coefficient between tomato yield means and the infested fruit percentage with T. absoluta larvae was negative and highly significant. Respecting molecular diagnosis random amplified polymorphism DNA- polymerase chain reaction (RAPD- PCR), the results demonstrated that the presence of polymorphism in the resistant tomato cultivar (tomato- 86) compared with (tomato- GS), the most susceptible to the tested insect pest infestation.
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Affiliation(s)
- Mona F.A. El-Sitiny
- Plant Protection Department, Agricultural Faculty, Zagazig University, Egypt
| | - Habeba M. Omar
- Plant Protection Department, Agricultural Faculty, Zagazig University, Egypt
| | - Ahmed M. El-Shehawi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Mona M. Elseehy
- Department of Genetics, Faculty of Agriculture, University of Alexandria, Alexandria 21545, Egypt
| | - Amira M. El-Tahan
- Plant Production Department, Arid Lands Cultivation Research Institute, The City of Scientific Research and Technological Applications, SRTA-City. Borg El Arab, Alexandria, Egypt
| | - Mohamed T. El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Gamila Sh. Selem
- Plant Protection Department, Agricultural Faculty, Zagazig University, Egypt
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21
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Species-Specific Gene, spt5, in the Qualitative and Quantitative Detection of Boletus reticulatus. J FOOD QUALITY 2022. [DOI: 10.1155/2022/5526810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Boletus reticulatus is a wild edible fungus with high nutritional value in Yunnan Province. In this study, B. reticulatus was used as the research object to diagnose the species characteristics. A commercial kit was used to extract the DNA of various fungi, and the quality of DNA was determined by using universal fungus primers. Through sequence alignment, the spt5 gene was selected as the species-specific gene of B. reticulatus. This gene was then qualitatively and quantitatively analyzed by PCR. In the qualitative detection, the spt5 amplification products were only found in B. reticulatus which proved its good specificity. Meanwhile, SYBR Green I based quantitative PCR results were highly sensitive, and the limit of detection was 0.04 ng of genomic DNA. These experiments illustrated that spt5 is an ideal species-specific gene for the quantitative and qualitative detection of B. reticulatus. This method is also suitable for the analysis of the processed samples of B. reticulatus and the determination of the adulteration of edible wild mushrooms.
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Chen Z, He Y, Iqbal Y, Shi Y, Huang H, Yi Z. Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq. BMC Genomics 2022; 23:43. [PMID: 35012465 PMCID: PMC8751252 DOI: 10.1186/s12864-021-08277-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 12/22/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. RESULTS We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264-364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. CONCLUSIONS As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.
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Affiliation(s)
- Zhiyong Chen
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Yancen He
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Yasir Iqbal
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Yanlan Shi
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Hongmei Huang
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Zili Yi
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
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Kalendar R. A Guide to Using FASTPCR Software for PCR, In Silico PCR, and Oligonucleotide Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2392:223-243. [PMID: 34773626 DOI: 10.1007/978-1-0716-1799-1_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The FastPCR software is an integrated tool environment for PCR primer and probe design and for prediction of oligonucleotide properties. The software provides comprehensive tools for designing primers for most PCR and perspective applications, including standard, multiplex, long-distance, inverse, real-time with TaqMan probe, Xtreme Chain Reaction (XCR), group-specific, overlap extension PCR for multifragment assembling cloning, and isothermal amplification (Loop-mediated Isothermal Amplification). A program is available to design specific oligonucleotide sets for long sequence assembly by ligase chain reaction and to design multiplexed of overlapping and nonoverlapping DNA amplicons that tile across a region(s) of interest for targeted next-generation sequencing, competitive allele-specific PCR (KASP)-based genotyping assay for single-nucleotide polymorphisms and insertions and deletions at specific loci, among other features. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. FastPCR includes various bioinformatics tools for analysis and searching of sequences, restriction I-II-III-type enzyme endonuclease analysis, and pattern searching. The program also supports the assembly of a set of contiguous sequences, consensus sequence generation, and sequence similarity and conservancy analysis. FastPCR performs efficient and complete detection of various repeat types with visual display. FastPCR allows for sequence file batch processing that is essential for automation. The software is available for download at https://primerdigital.com/fastpcr.html and online version at https://primerdigital.com/tools/pcr.html .
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Affiliation(s)
- Ruslan Kalendar
- PrimerDigital Ltd, Biocentre 3, Helsinki, Finland. .,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
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Drought Tolerance and Application of Marker-Assisted Selection in Sorghum. BIOLOGY 2021; 10:biology10121249. [PMID: 34943164 PMCID: PMC8699005 DOI: 10.3390/biology10121249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 12/30/2022]
Abstract
Simple Summary Sorghum is a climate-resilient crop grown in limited rainfall areas globally. However, climate change has increased temperature and shortened rainfall durations, which has constrained crop yield. We reviewed mechanisms of drought tolerance and application of marker-assisted selection in sorghum. Marker-assisted selection uses DNA molecular markers to map quantitative trait loci (QTL) associated with stay-green. Stg1, Stg2, Stg3, Stg4, Stg3A, and Stg3B QTLs associated with stay-green and high yield, have been mapped in sorghum. These QTLs are used for introgression into the senescent sorghum varieties through marker-assisted backcrossing. Abstract Sorghum is an important staple food crop in drought prone areas of Sub-Saharan Africa, which is characterized by erratic rainfall with poor distribution. Sorghum is a drought-tolerant crop by nature with reasonable yield compared to other cereal crops, but such abiotic stress adversely affects the productivity. Some sorghum varieties maintain green functional leaves under post-anthesis drought stress referred to as stay-green, which makes it an important crop for food and nutritional security. Notwithstanding, it is difficult to maintain consistency of tolerance over time due to climate change, which is caused by human activities. Drought in sorghum is addressed by several approaches, for instance, breeding drought-tolerant sorghum using conventional and molecular technologies. The challenge with conventional methods is that they depend on phenotyping stay-green, which is complex in sorghum, as it is constituted by multiple genes and environmental effects. Marker assisted selection, which involves the use of DNA molecular markers to map QTL associated with stay-green, has been useful to supplement stay-green improvement in sorghum. It involves QTL mapping associated with the stay-green trait for introgression into the senescent sorghum varieties through marker-assisted backcrossing by comparing with phenotypic field data. Therefore, this review discusses mechanisms of drought tolerance in sorghum focusing on physiological, morphological, and biochemical traits. In addition, the review discusses the application of marker-assisted selection techniques, including marker-assisted backcrossing, QTL mapping, and QTL pyramiding for addressing post-flowering drought in sorghum.
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Development of Molecular Markers Associated with Resistance to Gray Mold Disease in Onion (Allium cepa L.) through RAPD-PCR and Transcriptome Analysis. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7110436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Onions (Allium cepa L.) are one of the most consumed vegetable crops worldwide and are damaged by several fungal diseases in the field or during storage. Gray mold disease caused by the necrotrophic pathogens Botrytis cinerea and Botrytis squamosa is a disease that reduces the productivity and storage life in onions. However, it is difficult to control gray mold disease in onions by using physical and chemical methods. Breeding resistant onions against gray mold disease can reduce the damage caused by pathogens, reduce the labor required for control, and reduce environmental pollution caused by fungicides. However, onions have a large genome size (16Gb), making them difficult to analyze, and have a biennial cycle, resulting in a very long breeding period. Therefore, in this study, markers were developed to shorten the onion breeding period. First, random amplified polymorphic DNA (RAPD) was performed to confirm the genetic relationship between the gray mold disease-resistant and -susceptible lines through a dendrogram. In addition, the sequence characterized amplified region (SCAR)-OPAN1 marker to select resistant lines was developed using a polymorphic RAPD fragment. Second, the RNA-seq of the gray mold-resistant and -susceptible onion lines were analyzed using NGS technology. Using the RNA-seq results and DEG and GO analyses were performed, and the variants, such as SNPs and indels, were analyzed to develop a selectable marker for the resistant line. This study developed the SNP-3 HRM marker for selecting gray mold disease-resistant lines by using the SNPs present in the aldo-keto reductase (AKR) gene with high expression levels in these lines. The SCAR-OPAN1 and SNP-3 HRM markers developed in this study could be used to select gray mold disease-resistant onions in breeding programs to reduce the damage caused by gray mold disease.
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Azizi MMF, Lau HY, Abu-Bakar N. Integration of advanced technologies for plant variety and cultivar identification. J Biosci 2021. [DOI: 10.1007/s12038-021-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Mathur J, Khare PB, Panwar A, Ranade SA. Analysis of Genetic Variability Amongst Polyploid Genotypes of Pteris vittata L. From Various Geographic Locales of India. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.613847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pteris vittata L. is very common and a widely distributed species belongs to the family Pteridaceae. Various cytotypes from diploid to octaploid is available in this fern species. The present work has been carried out for genetic diversity in this fern both within and between the cytotypes. The molecular analysis at inter- as well as intra-species has been carried out with 57 accessions of P. vittata as well as of other species of Pteris with Microsorium punctatum considered as an out group taxon. For the present study 48 P. vittata (36 tetraploid and 12 pentaploid) and five of other species (four P. cretica, one P. pellucida, one P. tremula, one P. quadriaurita, and two P. ensiformis) accessions were used. The UPGMA (unweighted pair group method with arithmetic mean) dendrograms were generated for each method separately, as well as for all methods cumulatively, after a 1000 replicate bootstrap analysis. In order to determine the utility of each of the method, a comparative statistical assessment was done and marker index (MI), expected average heterozygosity, fraction of polymorphic loci and effective multiplex ratio (EMR) were calculated in case of each of the methods used in the present study. At the level of individual methods highest MI was obtained for directed amplification of minisatellites DNA (DAMD) method. Our findings of the present study concluded that out of the three methods Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR), and Directed Amplification of Minisatellite DNA (DAMD), DAMD was the best in term of polymorphism and heterozygosity as scores exhibited highest MI. The different accessions of P. vittata collected from different phytogeographical regions falls into six groups. Out of six clusters, one cluster is of pentaploid cytotype, four clusters are of tetraploid cytotype and one for outgroup taxon (M. punctatum). The result thus showed that within tetraploid, heterozygosity with variable genomic structure exists.
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Hong N, Chen M, Xu J. Molecular Markers Reveal Epidemiological Patterns and Evolutionary Histories of the Human Pathogenic Cryptococcus. Front Cell Infect Microbiol 2021; 11:683670. [PMID: 34026667 PMCID: PMC8134695 DOI: 10.3389/fcimb.2021.683670] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 04/22/2021] [Indexed: 01/02/2023] Open
Abstract
The human pathogenic Cryptococcus species are the main agents of fungal meningitis in humans and the causes of other diseases collectively called cryptococcosis. There are at least eight evolutionary divergent lineages among these agents, with different lineages showing different geographic and/or ecological distributions. In this review, we describe the main strain typing methods that have been used to analyze the human pathogenic Cryptococcus and discuss how molecular markers derived from the various strain typing methods have impacted our understanding of not only cryptococcal epidemiology but also its evolutionary histories. These methods include serotyping, multilocus enzyme electrophoresis, electrophoretic karyotyping, random amplified polymorphic DNA, restriction fragment length polymorphism, PCR-fingerprinting, amplified fragment length polymorphism, multilocus microsatellite typing, single locus and multilocus sequence typing, matrix-assisted laser desorption/ionization time of flight mass spectrometry, and whole genome sequencing. The major findings and the advantages and disadvantages of each method are discussed. Together, while controversies remain, these strain typing methods have helped reveal (i) the broad phylogenetic pattern among these agents, (ii) the centers of origins for several lineages and their dispersal patterns, (iii) the distributions of genetic variation among geographic regions and ecological niches, (iv) recent hybridization among several lineages, and (v) specific mutations during infections within individual patients. However, significant challenges remain. Multilocus sequence typing and whole genome sequencing are emerging as the gold standards for continued strain typing and epidemiological investigations of cryptococcosis.
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Affiliation(s)
- Nan Hong
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China.,Department of Burn and Plastic Surgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Min Chen
- Department of Dermatology, Shanghai Key Laboratory of Medical Mycology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Molecular and phytochemical variability among genus Albizia: a phylogenetic prospect for future breeding. Mol Biol Rep 2021; 48:2619-2628. [PMID: 33792827 DOI: 10.1007/s11033-021-06316-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Abstract
Fabaceae, the third-largest Angiosperm family, exhibits great morphological diversity with significantly high species diversification rate. Albizia, one of the largest genera of the legume family, possesses high ecological, economical and medicinal application prospects and displays a global distribution. The taxonomic classification among Albizia remains, however, unclear and has been subjected to changes. The resolution of phylogenetic relationships among members of genus Albizia is a priority. Nine Albizia species cultivated in Egypt; Albizia lebbeck, A. julibrissin, A. odoratissima, A. procera, A. anthelmintica, A. guachapele, A. myriophylla, A. richardiana and A. lucida were subjected to molecular classification via DNA fingerprinting techniques viz. Inter Simple Sequence Repeat (ISSR) and Start Codon Targeted polymorphism (SCoT) using ten primers, five for each technique. The total number of bands produced by ISSR and SCoT primers was 28 and 40, respectively. The percentage of polymorphism varied from 64.28% in ISSR to 67.50% in SCoT analysis. Additionally, chemotaxonomic analysis was implemented based on UV spectroscopic profiling and total phenolic content coupled to unsupervised chemometric tools; Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA). Interspecific relationships were confirmed via molecular and phytochemical analyses between A. procera and A. guachapele; A. lebbeck and A. odoratissima; and A. julibrissin and A. lucida. The study reveals that chemotaxonomic data can reflect phylogenetic relationships among examined Albizia species and provides insights to the significance of utilizing the strengths of both molecular taxonomy and chemotaxonomy to resolve phylogenetic relationship among this genus which offers baseline for breeding programs. Future strategies to enrich taxonomic classification among Albizia includes extensive morphological characterization, DNA barcoding techniques and metabolomic profiling.
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Gemmill CEC, Grierson ERP. Inter-Simple Sequence Repeats (ISSR), Microsatellite-Primed Genomic Profiling Using Universal Primers. Methods Mol Biol 2021; 2222:249-262. [PMID: 33301098 DOI: 10.1007/978-1-0716-0997-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inter-simple sequence repeat (ISSR) markers are highly polymorphic, relatively easy to develop, and inexpensive compared to other methods and have numerous applications. Importantly, the same ISSR primers can potentially be used universally across plant phylogenetic diversity. The basic technique of ISSRs is flexible and can be modified with options for implementation for a broad range of projects and budgets. Ranked in increasing order of technical demand and costs, these are manual agarose and manual polyacrylamide with silver staining and automated using fluorescently labeled primers and capillary electrophoresis. Overall manual agarose-based ISSRs are a sound, safe, easy, and low-cost method for reliably inferring plant genetic diversity. Here, we provide detailed protocols to undertake this fingerprinting method and provide guidance to the literature for the many options available for this technique.
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Abdel-Rhman SH, Rizk DE. Comparative Assessment of Different PCR-Based Typing Methods of Pseudomonas aeruginosa Isolates. Infect Drug Resist 2021; 14:1019-1035. [PMID: 33762830 PMCID: PMC7982794 DOI: 10.2147/idr.s298838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/20/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction Pseudomonas aeruginosa is one of the important causes of nosocomial infections. Analyzing the diversity of these isolates is important to control the diseases caused by them. Studies of molecular epidemiology depend on the application of typing methods. Purpose This study aims to assess the performance of PCR- based typing techniques (RAPD, ribotyping, tDNA, and ERIC) in determining the genetic diversity of 44 P. aeruginosa urinary isolates. Methods Performance parameters were analyzed for each of the tested methods. The banding pattern was assessed by calculating polymorphism, genotypic gene diversity and the effective multiplex ratio. Moreover, strain diversity, typeability, and discriminatory power were used to measure the efficiency of typing methods. The congruence among typing methods was calculated by Rand’s and Wallace coefficients. Results P-640 among RAPD primers and Ribo-2 among ribotyping primers were more informative as they gave high strain diversity, the highest number of clusters, and highest discriminatory power (ISD=70.45%, 29 clusters at 70% cutoff, DI=0.97 and ISD=75%, 25 clusters at 70% cutoff DI=0.969, respectively). Comparison of typing methods showed that RAPD-PCR gave the highest mean percent polymorphism per assay (76.85%) followed by ERIC-PCR. ERIC-PCR outperformed in most marker parameters; highest mean number of alleles, number of monomorphic bands per assay unit, mean genotypic gene diversity, effective multiplex ratio, and assay efficiency index. Calculated congruence revealed that individual methods demonstrate moderate to poor predictive power. Interestingly, this power increased by combining data obtained from another method. Conclusion RAPD primer (P-640) had more discrimination power followed by ribo-2 and ERIC. The performance and predictive power of typing methods can be improved by combining data obtained from different methods as ERIC+OPA-02 and ERIC+P-640 combinations gave complete typeability and discrimination of isolates. ERIC, ERIC+OPA-02, and ERIC+P-640 combinations can provide finer discrimination and classification of P. aeruginosa strains than the other tested methods.
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Affiliation(s)
- Shaymaa H Abdel-Rhman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.,Department of Pharmaceutics and Pharmaceutical Biotechnology, Faculty of Pharmacy, Taibah University, AlMadinah Al Munawwarah, Saudi Arabia
| | - Dina E Rizk
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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Hussain S, Alex R, Alyethodi RR, Sharma S, Verma N, Sirohi AS, Singh U, Kumar S, Chand N, Sengar GS, Sharma A, Tyagi R, Arya S, Tyagi S. Development of a RAPD marker-based classification criterion for quality semen production in Holstein crossbred bulls. Reprod Domest Anim 2021; 56:736-743. [PMID: 33559234 DOI: 10.1111/rda.13912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/19/2020] [Accepted: 02/04/2021] [Indexed: 11/30/2022]
Abstract
In cattle production systems, an intense selection pressure for production traits has resulted in the decline of fertility traits. To optimize an efficient reproduction system, the inclusion of both male and female fertility traits in the selection process is very much essential. RAPD (Random Amplified Polymorphic DNA) was developed as a molecular biology tool and has been extensively used, to study intra- and interspecific genetic diversity. The present study was undertaken to utilize RAPD primers to investigate the association between DNA markers and semen quality traits viz. Sperm concentration, total sperm count ejaculate and initial sperm motility and thereby to identify good/poor semen producers. DNA isolated from the blood samples of healthy bulls was subjected to RAPD-PCR. The multiple regression analysis followed by independent t test was carried out to identify suitable markers. Based on the results, only 12 bands were identified as marker suitable for any of the quality trait. This includes, OPA2 ~ 760, OPA2 ~ 700, OPA6 ~ 1,200, OPA9 ~ 400, OPA9 ~ 380, OPA12 ~ 970, OPA14 ~ 715, OPA14 ~ 605, OPA16 ~ 485, OPA17 ~ 860 and OPA18 ~ 480. Multiple regression analysis selected, OPA2 ~ 760 and OPA2 ~ 1,750 for sperm concentration and OPA2 ~ 760, OPA2 ~ 700, OPA9 ~ 620, OPA4 ~ 670 and OPA18 ~ 1,015 for total sperm count/ejaculate. But the t test revealed a significant association between OPA2 ~ 760 and total sperm count. Further, discriminant function analysis also identified this marker in the first step itself. The results of the present study can be exploited as a low-cost alternative strategy for identification of good /poor semen producers in crossbred bulls at an early age.
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Affiliation(s)
- Shaziya Hussain
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Rani Alex
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - Shalini Sharma
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Nitika Verma
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | | | - Umesh Singh
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Sushil Kumar
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Naimi Chand
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | | | - Ankur Sharma
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Rachna Tyagi
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Sarmesh Arya
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Srikant Tyagi
- ICAR-Central Institute for Research on Cattle, Meerut, India
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Cryptic Clitellata: Molecular Species Delimitation of Clitellate Worms (Annelida): An Overview. DIVERSITY-BASEL 2021. [DOI: 10.3390/d13020036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods for species delimitation using molecular data have developed greatly and have become a staple in systematic studies of clitellate worms. Here we give a historical overview of the data and methods used to delimit clitellates from the mid-1970s to today. We also discuss the taxonomical treatment of the cryptic species, including the recommendation that cryptic species, as far as possible, should be described and named. Finally, we discuss the prospects and further development of the field.
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Wang H, Li X, Wang D, Li C, Wang Y, Diao Y, Tang Y. Isolation, identification and genotyping of Candida albicans from Landes geese. Transbound Emerg Dis 2021; 69:349-359. [PMID: 33417748 DOI: 10.1111/tbed.13985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 11/29/2022]
Abstract
In May 2018, Landes geese raised in Weifang, Shandong Province, China, developed a disease characterized by thickened oesophageal mucosa and white, round ulcers. Based on pathogen isolation and identification, differential culture and morphological observations, Candida albicans (C. albicans) was identified as the causative pathogen from the oesophagus of infected geese, and artificial infection experiments were then performed using the isolated strains. In experimental reproduction, the symptoms of infected geese were consistent with those of natural infection, and gosling morbidity and mortality were 75% and 60%, respectively. Re-isolation of the strain from the dead goslings confirmed C. albicans as the causative pathogen of oesophageal ulcers. We further performed internal transcribed space rDNA sequence analysis, ABC genotyping and multi-locus sequence typing analysis. We observed 100% sequence similarity between the two strains, designated as WFCL and WFLQ, which were isolated from different regions, with 100% homology between the strains isolated in the present study and the human-origin C. albicans strains isolated previously from China. The goose-origin strains isolated in this study and the human-origin C. albicans isolates were included in the same branch in phylogenetic trees analysis, indicating that the strain responsible for oesophageal ulcer in geese is closely related to human-origin C. albicans. In addition, based on eBURST analysis of sequence types, goose-origin C. albicans strains were relatively independent in terms of population evolution. To the best of our knowledge, this is the first detailed report on goose oesophageal ulceration caused by C. albicans infection in geese. Considering that C. albicans is an important zoonotic pathogen, this study provides a reference for further studies on avian C. albicans infections and is important for ensuring public health and safety.
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Affiliation(s)
- Hongzhi Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, China
| | - Xudong Li
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, China
| | - Dongxue Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, China
| | - Chong Li
- Hebei Provincial Center of Animal Disease Control and Prevention, Shijiazhuang, China
| | - Yuanyuan Wang
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, China
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Tuvesson SD, Larsson CT, Ordon F. Use of Molecular Markers for Doubled Haploid Technology: From Academia to Plant Breeding Companies. Methods Mol Biol 2021; 2288:49-72. [PMID: 34270004 DOI: 10.1007/978-1-0716-1335-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Molecular markers are employed for doubled haploid (DH) technology by researchers and applied plant breeders in many crops. In the 1990s, isozymes and RFLPs were commonly used marker technologies to characterize DHs and were later replaced by PCR- based markers (e.g., RAPDs, AFLPs, ISSRs, SSRs) and today by SNPs. Markers are used for multiple purposes in DH production, that is, for the study of genes underlying haploid induction and confirming homozygous plants of gametophytic origin. Furthermore, they are tools for investigating segregation in DH populations and for mapping simple and complex traits using DHs. The deployment of DHs and markers for developing trait-linked markers are demonstrated with examples from rapeseed, wheat, and barley. Marker development for resistance to viruses derived from genetic resources and their use in, for example, pyramiding of resistance genes, are given as an example for the combination of DH-technology and marker development in research. Today, marker systems amenable to automation are frequently used in applied plant breeding. Practical examples are given from Lantmännen (LM) ( https://Lantmannen.com ) using large-scale genotyping for variety development based on SSRs and SNPs.
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Affiliation(s)
| | | | - Frank Ordon
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
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Abstract
Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selection of core collections, determination of genetic distances, genome analysis, development of molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest, is cost-effective, and can be performed in a moderate laboratory for most of its applications. In addition, RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like arbitrarily primed polymerase chain reaction (AP-PCR), sequence characterized amplified region (SCAR), DNA amplification fingerprinting (DAF), sequence-related amplified polymorphism (SRAP), cleaved amplified polymorphic sequences (CAPS), random amplified microsatellite polymorphism (RAMPO), and random amplified hybridization microsatellites (RAHM) can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented along with the applications of RAPD in genetic diversity analysis, mapping, varietal identification, genetic fidelity testing, etc.
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Kalendar R, Boronnikova S, Seppänen M. Isolation and Purification of DNA from Complicated Biological Samples. Methods Mol Biol 2021; 2222:57-67. [PMID: 33301087 DOI: 10.1007/978-1-0716-0997-2_3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The isolation of nucleic acids from a biological sample is an important step for many molecular biology applications and medical diagnostic assays. This chapter describes an efficient protocol using established acidic CTAB (with a pH value of 5.0 to 6.8) based extraction method for isolation and/or purification of high molecular weight genomic DNA from a range of fresh and difficult sources from plant, animal, fungi, and soil material. This protocol is suitable for many sequencing and genotyping applications, including large-scale sample screening.
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Affiliation(s)
- Ruslan Kalendar
- Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, Helsinki, Finland. .,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
| | - Svetlana Boronnikova
- Department of Botany and Genetics of Plants, Faculty of Biology, Perm State University, Perm, Russia
| | - Mervi Seppänen
- Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, Helsinki, Finland
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Hassan EM, Örmeci B, DeRosa MC, Dixon BR, Sattar SA, Iqbal A. A review of Cryptosporidium spp. and their detection in water. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 83:1-25. [PMID: 33460403 DOI: 10.2166/wst.2020.515] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cryptosporidium spp. are one of the most important waterborne pathogens worldwide and a leading cause of mortality from waterborne gastrointestinal diseases. Detection of Cryptosporidium spp. in water can be very challenging due to their low numbers and the complexity of the water matrix. This review describes the biology of Cryptosporidium spp. and current methods used in their detection with a focus on C. parvum and C. hominis. Among the methods discussed and compared are microscopy, immunology-based methods using monoclonal antibodies, molecular methods including PCR (polymerase chain reaction)-based assays, and emerging aptamer-based methods. These methods have different capabilities and limitations, but one common challenge is the need for better sensitivity and specificity, particularly in the presence of contaminants. The application of DNA aptamers in the detection of Cryptosporidium spp. oocysts shows promise in overcoming these challenges, and there will likely be significant developments in aptamer-based sensors in the near future.
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Affiliation(s)
- Eman M Hassan
- Department of Civil and Environmental Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada E-mail:
| | - Banu Örmeci
- Department of Civil and Environmental Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada E-mail:
| | - Maria C DeRosa
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Canada, K1S 5B6
| | - Brent R Dixon
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, Canada, K1A 0K9
| | - Syed A Sattar
- Department of Civil and Environmental Engineering, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada E-mail: ; C.R.E.M. Co Labs, Units 1-2, 3403 American Drive, Mississauga, ON, Canada, L4V 1T4
| | - Asma Iqbal
- C.R.E.M. Co Labs, Units 1-2, 3403 American Drive, Mississauga, ON, Canada, L4V 1T4
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Current Scenario and Integrated Approaches for Management of Finger Millet Blast (Magnaporthe grisea). Fungal Biol 2021. [DOI: 10.1007/978-3-030-60585-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions. Microbiol Mol Biol Rev 2020; 85:85/1/e00110-20. [PMID: 33361270 DOI: 10.1128/mmbr.00110-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Duplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative structures, as was shown for many repeated sequences in vitro However, evidence for the formation of noncanonical structures in living cells is difficult to gather. It mainly relies on genetic assays demonstrating their function in vivo or through genetic instability reflecting particular properties of such structures. Efforts were made to reveal their existence directly in a living cell, mainly by generating antibodies specific to secondary structures or using chemical ligands selected for their affinity to these structures. Among secondary structure-forming DNAs are G-quadruplexes, human fragile sites containing minisatellites, AT-rich regions, inverted repeats able to form cruciform structures, hairpin-forming CAG/CTG triplet repeats, and triple helices formed by homopurine-homopyrimidine GAA/TTC trinucleotide repeats. Many of these alternative structures are involved in human pathologies, such as neurological or developmental disorders, as in the case of trinucleotide repeats, or cancers triggered by translocations linked to fragile sites. This review will discuss and highlight evidence supporting the formation of alternative DNA structures in vivo and will emphasize the role of the mismatch repair machinery in binding mispaired DNA duplexes, triggering genetic instability.
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Wanjari RA, Shanware AS, Dhoble SJ. Influence of ultraviolet and gamma ray irradiation on luminescent bacteria and exploring their efficacy as biosensors. LUMINESCENCE 2020; 36:525-530. [PMID: 33119968 DOI: 10.1002/bio.3972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/07/2020] [Accepted: 10/20/2020] [Indexed: 11/07/2022]
Abstract
Toxicity monitoring of harmful radiation is an indispensable issue in modern radioecology. As bioluminescent bacteria have the simplest structure to epitomize the biosphere, their bioluminescence can also act as an indicator of the conditions, therefore assay systems based on luminous bacteria can be used to monitor environmental radiotoxicity. The present investigation explored the measurement of bacterial luminescence, which can be easily computed. Bioluminescent bacterial strains were used to evaluate the effect of ultraviolet (UV) and gamma irradiation. A random amplified polymorphic DNA (RAPD) assay was carried out to observe alterations under exposure. Using a phylogenetic tree, a comparative study of the effect of UV and gamma rays was carried out. The isolated strains showed marked sensitivity towards radiation exposure present in the environment and therefore they could be used as potential biosensing elements for developing an on-site pollution monitoring biosensor.
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Affiliation(s)
- Rashmi A Wanjari
- Rajiv Gandhi Biotechnology Center, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, India
| | - Arti S Shanware
- Rajiv Gandhi Biotechnology Center, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, India
| | - Sanjay J Dhoble
- Department of Physics Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, India
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Bonny SQ, Hossain MAM, Uddin SMK, Pulingam T, Sagadevan S, Johan MR. Current trends in polymerase chain reaction based detection of three major human pathogenic vibrios. Crit Rev Food Sci Nutr 2020; 62:1317-1335. [DOI: 10.1080/10408398.2020.1841728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sharmin Quazi Bonny
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - M. A. Motalib Hossain
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Syed Muhammad Kamal Uddin
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Thiruchelvi Pulingam
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Suresh Sagadevan
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Rafie Johan
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
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Özkul C, Hazırolan G. Oxacillinase Gene Distribution, Antibiotic Resistance, and Their Correlation with Biofilm Formation in Acinetobacter baumannii Bloodstream Isolates. Microb Drug Resist 2020; 27:637-646. [PMID: 32991256 DOI: 10.1089/mdr.2020.0130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Objectives: The limitations of treatment options in bloodstream infections caused by multidrug-resistant Acinetobacter baumannii (MDRAB) have been related to high morbidity and mortality. The aim of our present study was to determine antimicrobial susceptibility profiles, molecular resistance patterns, and biofilm properties of A. baumannii isolated from bloodstream infections. Materials and Methods: In the present study, a total of 44 A. baumannii bloodstream isolates were included. Antimicrobial susceptibility profiles and biofilm formation ability were assessed. The distribution of class D carbapenemases, ISAba1, ISAba1/blaOXA-23, blaNDM-1, mcr-1, and ompA was investigated by polymerase chain reaction (PCR). Arbitrarily primed-PCR (AP-PCR) was performed to evaluate clonal relationships. Results: A total of 32 isolates were MDRAB, whereas 6 isolates were also resistant to colistin without mcr-1 positivity. All isolates were harboring blaOXA-51 gene, whereas blaOXA-23 positivity was 63.6%. Fifty percent of the isolates had ISAba1. ISAba1 upstream of blaOXA-23 was determined in 18 isolates. None of the isolates were positive for blaNDM-1 gene. Majority of the strains were strong biofilm producers (86.8%). A total of 56.8% of the isolates were positive for ompA gene with no direct association with strong biofilm formation. However, blaOXA-51 + 23 genotype and trimethoprim-sulfamethoxazole resistance showed a significant relationship with biofilm formation. AP-PCR analysis revealed six distinct clusters of A. baumannii. Conclusions: Herein, majority of the A. baumannii blood isolates were characterized as blaOXA-51+OXA-23 carbapenemase genotype and were strong biofilm formers. None of the isolates were positive for blaNDM-1, which was promising. Resistant isolates were tended to form strong biofilms. Our results highlight the emergence of oxacillinase-producing MDRAB isolated from bloodstream with high biofilm formation ability.
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Affiliation(s)
- Ceren Özkul
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy and Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Gülşen Hazırolan
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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Dissanayake DSB, Holleley CE, Hill LK, O'Meally D, Deakin JE, Georges A. Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction. BMC Genomics 2020; 21:667. [PMID: 32993477 PMCID: PMC7526180 DOI: 10.1186/s12864-020-07071-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females. Conclusions The sex of B. duperreyi can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of B. duperreyi. Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.
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Affiliation(s)
- Duminda Sampath Bandara Dissanayake
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Clare Ellen Holleley
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia
| | - Laura Kate Hill
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Denis O'Meally
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Present Address: Centre for Gene Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Janine Eileen Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
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46
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Wu Y, Li M, He Z, Dreisigacker S, Wen W, Jin H, Zhai S, Li F, Gao F, Liu J, Wang R, Zhang P, Wan Y, Cao S, Xia X. Development and validation of high-throughput and low-cost STARP assays for genes underpinning economically important traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2431-2450. [PMID: 32451598 DOI: 10.1007/s00122-020-03609-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/13/2020] [Indexed: 05/12/2023]
Abstract
We developed and validated 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for 46 genes of important wheat quality, biotic and abiotic stress resistance, grain yield, and adaptation-related traits for marker-assisted selection in wheat breeding. Development of high-throughput, low-cost, gene-specific molecular markers is important for marker-assisted selection in wheat breeding. In this study, we developed 56 gene-specific semi-thermal asymmetric reverse PCR (STARP) markers for wheat quality, tolerance to biotic and abiotic stresses, grain yield, and adaptation-related traits. The STARP assays were validated by (1) comparison of the assays with corresponding diagnostic STS/CAPS markers on 40 diverse wheat cultivars and (2) characterization of allelic effects based on the phenotypic and genotypic data of three segregating populations and 305 diverse wheat accessions from China and 13 other countries. The STARP assays showed the advantages of high-throughput, accuracy, flexibility, simple assay design, low operational costs, and platform compatibility. The state-of-the-art assays of this study provide a robust and reliable molecular marker toolkit for wheat breeding programs.
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Affiliation(s)
- Yuying Wu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Ming Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Susanne Dreisigacker
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Weie Wen
- Department of Cell Biology, Zunyi Medical University, 201 Dalian Road, Zunyi, 563099, Guizhou, China
| | - Hui Jin
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Street, Harbin, 150086, Heilongjiang, China
| | - Shengnan Zhai
- Crop Research Institute, National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Faji Li
- Crop Research Institute, National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Fengmei Gao
- Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Street, Harbin, 150086, Heilongjiang, China
| | - Jindong Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Shenzhen, 518120, Guangdong, China
| | - Rongge Wang
- Farm of Seed Production of Gaoyi County, Gaoyi, 051330, Hebei, China
| | - Pingzhi Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, 230001, Anhui, China
| | - Yingxiu Wan
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, 230001, Anhui, China
| | - Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Salgotra RK, Stewart CN. Functional Markers for Precision Plant Breeding. Int J Mol Sci 2020; 21:E4792. [PMID: 32640763 PMCID: PMC7370099 DOI: 10.3390/ijms21134792] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 01/24/2023] Open
Abstract
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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Damnjanovic D, Vázquez-Campos X, Winter DL, Harvey M, Bridge WJ. Bacteriophage genotyping using BOXA repetitive-PCR. BMC Microbiol 2020; 20:154. [PMID: 32527227 PMCID: PMC7291552 DOI: 10.1186/s12866-020-01770-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/29/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Repetitive-PCR (rep-PCR) using BOXA1R and BOXA2R as single primers was investigated for its potential to genotype bacteriophage. Previously, this technique has been primarily used for the discrimination of bacterial strains. Reproducible DNA fingerprint patterns for various phage types were generated using either of the two primers. RESULTS The similarity index of replicates ranged from 89.4-100% for BOXA2R-PCR, and from 90 to 100% for BOXA1R-PCR. The method of DNA isolation (p = 0.08) and the phage propagation conditions at two different temperatures (p = 0.527) had no significant influence on generated patterns. Rep-PCR amplification products were generated from different templates including purified phage DNA, phage lysates and phage plaques. The use of this method enabled comparisons of phage genetic profiles to establish their similarity to related or unrelated phages and their bacterial hosts. CONCLUSION The findings suggest that repetitive-PCR could be used as a rapid and inexpensive method to preliminary screen phage isolates prior to their selection for more comprehensive studies. The adoption of this rapid, simple and reproducible technique could facilitate preliminary characterisation of a large number of phage isolates and the investigation of genetic relationship between phage genotypes.
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Affiliation(s)
- Dragica Damnjanovic
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, Australia
| | - Daniel L. Winter
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, Australia
| | - Melissa Harvey
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, Australia
| | - Wallace J. Bridge
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Kensington, Australia
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Dheer P, Rautela I, Sharma V, Dhiman M, Sharma A, Sharma N, Sharma MD. Evolution in crop improvement approaches and future prospects of molecular markers to CRISPR/Cas9 system. Gene 2020; 753:144795. [PMID: 32450202 DOI: 10.1016/j.gene.2020.144795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 01/03/2023]
Abstract
The advent of genetic selection and genome modification method assure about a real novel reformation in biotechnology and genetic engineering. With the extensive capabilities of molecular markers of them being stable, cost-effective and easy to use, they ultimately become a potent tool for variety of applications such a gene targeting, selection, editing, functional genomics; mainly for the improvisation of commercially important crops. Three main benefits of molecular marker in the field of agriculture and crop improvement programmes first, reduction of the duration of breeding programmes, second, they allow creation of new genetic variation and genetic diversity of plants and third most promising benefit is help in production of engineered plant for disease resistance, or resistance from pathogen and herbicides. This review is anticipated to present an outline how the techniques have been evolved from the simple conventional applications of DNA based molecular markers to highly throughput CRISPR technology and geared the crop yield. Techniques like using Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) systems have revolutionised in the field of genome editing. These have been promptly accepted in both the research and commercial industry. On the whole, the widespread use of molecular markers with their types, their appliance in plant breeding along with the advances in genetic selection and genome editing together being a novel strategy to boost crop yield has been reviewed.
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Affiliation(s)
- Pallavi Dheer
- Department of Life Sciences, Shri Guru Ram Rai Institute of Technology & Science, Patel Nagar, Dehradun, Uttarakhand, India
| | - Indra Rautela
- Department of Biotechnology, SALS, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Vandana Sharma
- Department of Botany, K.L.DAV (PG) College, Roorkee,Uttarakhand, India
| | - Manjul Dhiman
- Department of Botany, K.L.DAV (PG) College, Roorkee,Uttarakhand, India
| | - Aditi Sharma
- Department of Biotechnology, Graphic Era University, Dehradun, Uttarakhand, India
| | - Nishesh Sharma
- Department of Biotechnology, SALS, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Manish Dev Sharma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand, India.
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An J, Jiang Y, Shi B, Wu D, Wu W. Low-Cost Battery-Powered and User-Friendly Real-Time Quantitative PCR System for the Detection of Multigene. MICROMACHINES 2020; 11:mi11040435. [PMID: 32326194 PMCID: PMC7231343 DOI: 10.3390/mi11040435] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/25/2022]
Abstract
Real-time polymerase chain reaction (PCR) is the standard for nucleic acid detection and plays an important role in many fields. A new chip design is proposed in this study to avoid the use of expensive instruments for hydrophobic treatment of the surface, and a new injection method solves the issue of bubbles formed during the temperature cycle. We built a battery-powered real-time PCR device to follow polymerase chain reaction using fluorescence detection and developed an independently designed electromechanical control system and a fluorescence analysis software to control the temperature cycle, the photoelectric detection coupling, and the automatic analysis of the experimental data. The microchips and the temperature cycling system cost USD 100. All the elements of the device are available through open access, and there are no technical barriers. The simple structure and manipulation allows beginners to build instruments and perform PCR tests after only a short tutorial. The device is used for analysis of the amplification curve and the melting curve of multiple target genes to demonstrate that our instrument has the same accuracy and stability as a commercial instrument.
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Affiliation(s)
- Junru An
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Yangyang Jiang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
| | - Bing Shi
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Di Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Wenming Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China; (J.A.); (Y.J.); (B.S.); (D.W.)
- University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
- Correspondence: ; Tel.: +86-431-8670-8159
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