Genetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat
Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat...
| Main Authors: | , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Frontiers Media
2022
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/128240 |
| _version_ | 1855539430502170624 |
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| author | Ali, Mohsin Shan, Danting Jiankang Wang Sadiq, Hafsa Rasheed, Awais He Zhonghu Huihui Li |
| author_browse | Ali, Mohsin He Zhonghu Huihui Li Jiankang Wang Rasheed, Awais Sadiq, Hafsa Shan, Danting |
| author_facet | Ali, Mohsin Shan, Danting Jiankang Wang Sadiq, Hafsa Rasheed, Awais He Zhonghu Huihui Li |
| author_sort | Ali, Mohsin |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan. |
| format | Journal Article |
| id | CGSpace128240 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1282402025-12-08T10:29:22Z Genetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat Ali, Mohsin Shan, Danting Jiankang Wang Sadiq, Hafsa Rasheed, Awais He Zhonghu Huihui Li genotyping genetic diversity selection signatures wheat Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan. 2022-07-12 2023-01-25T20:07:04Z 2023-01-25T20:07:04Z Journal Article https://hdl.handle.net/10568/128240 en Open Access application/pdf Frontiers Media Ali, M., Danting, S., Wang, J., Sadiq, H., Rasheed, A., He, Z., & Li, H. (2022). Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat. Frontiers in Plant Science, 13. https://doi.org/10.3389/fpls.2022.877496 |
| spellingShingle | genotyping genetic diversity selection signatures wheat Ali, Mohsin Shan, Danting Jiankang Wang Sadiq, Hafsa Rasheed, Awais He Zhonghu Huihui Li Genetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat |
| title | Genetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat |
| title_full | Genetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat |
| title_fullStr | Genetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat |
| title_full_unstemmed | Genetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat |
| title_short | Genetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat |
| title_sort | genetic diversity and selection signatures in synthetic derived wheats and modern spring wheat |
| topic | genotyping genetic diversity selection signatures wheat |
| url | https://hdl.handle.net/10568/128240 |
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