Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions
Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlle...
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Frontiers Media S.A.
2021-08-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.711654/full |
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| author | Ana Borrego-Benjumea Adam Carter Min Zhu James R. Tucker Meixue Zhou Ana Badea |
| author_facet | Ana Borrego-Benjumea Adam Carter Min Zhu James R. Tucker Meixue Zhou Ana Badea |
| author_sort | Ana Borrego-Benjumea |
| collection | DOAJ |
| description | Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8–11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding. |
| first_indexed | 2024-12-22T10:25:10Z |
| format | Article |
| id | doaj.art-dc32d592078e44ed8216f812fdb03ac6 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-22T10:25:10Z |
| publishDate | 2021-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-dc32d592078e44ed8216f812fdb03ac62022-12-21T18:29:30ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-08-011210.3389/fpls.2021.711654711654Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field ConditionsAna Borrego-Benjumea0Adam Carter1Min Zhu2James R. Tucker3Meixue Zhou4Ana Badea5Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, CanadaBrandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, CanadaCollege of Agriculture, Yangzhou University, Yangzhou, ChinaBrandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, CanadaTasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, AustraliaBrandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, CanadaWaterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8–11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.https://www.frontiersin.org/articles/10.3389/fpls.2021.711654/fullbarleywaterlogging tolerancegenome-wide associated studymarker-trait associationquantitative trait locicandidate genes |
| spellingShingle | Ana Borrego-Benjumea Adam Carter Min Zhu James R. Tucker Meixue Zhou Ana Badea Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions Frontiers in Plant Science barley waterlogging tolerance genome-wide associated study marker-trait association quantitative trait loci candidate genes |
| title | Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions |
| title_full | Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions |
| title_fullStr | Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions |
| title_full_unstemmed | Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions |
| title_short | Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions |
| title_sort | genome wide association study of waterlogging tolerance in barley hordeum vulgare l under controlled field conditions |
| topic | barley waterlogging tolerance genome-wide associated study marker-trait association quantitative trait loci candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.711654/full |
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