Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS
Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Vara...
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1036064/full |
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| author | Sahadev Singh Shailendra Singh Gaurav Neeraj Kumar Vasistha Uttam Kumar Arun Kumar Joshi Vinod Kumar Mishra Ramesh Chand Pushpendra Kumar Gupta Pushpendra Kumar Gupta Pushpendra Kumar Gupta |
| author_facet | Sahadev Singh Shailendra Singh Gaurav Neeraj Kumar Vasistha Uttam Kumar Arun Kumar Joshi Vinod Kumar Mishra Ramesh Chand Pushpendra Kumar Gupta Pushpendra Kumar Gupta Pushpendra Kumar Gupta |
| author_sort | Sahadev Singh |
| collection | DOAJ |
| description | Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation. |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-04-10T22:18:22Z |
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| spelling | doaj.art-342306dc5c63436bbb27a5fc5cd684972023-01-18T06:16:16ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-01-011310.3389/fpls.2022.10360641036064Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWASSahadev Singh0Shailendra Singh Gaurav1Neeraj Kumar Vasistha2Uttam Kumar3Arun Kumar Joshi4Vinod Kumar Mishra5Ramesh Chand6Pushpendra Kumar Gupta7Pushpendra Kumar Gupta8Pushpendra Kumar Gupta9Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, IndiaMolecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, IndiaDepartment of Genetics-Plant Breeding and Biotechnology, Dr Khem Singh Gill, Akal College of Agriculture, Eternal University, Sirmaur, IndiaBorlaug Institute for South Asia (BISA), Ludhiana, IndiaThe International Maize and Wheat Improvement Center (CIMMYT), Borlaug Institute for South Asia (BISA), G-2, B-Block, NASC Complex, DPS Marg, New Delhi, IndiaDepartment of Genetics and Plant Breeding, Indian Institute of Agricultural Science, Banaras Hindu University, Varanasi, IndiaDepartment of Mycology and Plant Pathology, Indian Institute of Agricultural Science Banaras Hindu University, Varanasi, IndiaMolecular Biology Laboratory, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, IndiaBorlaug Institute for South Asia (BISA), Ludhiana, IndiaMurdoch’s Centre for Crop & Food Innovation, Murdoch University, Murdoch, WA, AustraliaGenetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.https://www.frontiersin.org/articles/10.3389/fpls.2022.1036064/fullTriticum aestivum LGWASMTAepistasiscandidate genes |
| spellingShingle | Sahadev Singh Shailendra Singh Gaurav Neeraj Kumar Vasistha Uttam Kumar Arun Kumar Joshi Vinod Kumar Mishra Ramesh Chand Pushpendra Kumar Gupta Pushpendra Kumar Gupta Pushpendra Kumar Gupta Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS Frontiers in Plant Science Triticum aestivum L GWAS MTA epistasis candidate genes |
| title | Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS |
| title_full | Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS |
| title_fullStr | Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS |
| title_full_unstemmed | Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS |
| title_short | Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS |
| title_sort | genetics of spot blotch resistance in bread wheat triticum aestivum l using five models for gwas |
| topic | Triticum aestivum L GWAS MTA epistasis candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1036064/full |
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