Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditions
BackgroundWheat landraces represent a reservoir of genetic diversity that can support wheat improvement through breeding. A core panel of 300 Watkins wheat landraces, as well as 16 non-Watkins landraces and elite wheat cultivars, was grown during the 2020–2021 and 2021–2022 seasons at four Agricultu...
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Frontiers Media S.A.
2024-12-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2024.1384220/full |
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| author | Ahmed Fawzy Elkot Ahmed E. Nassar Ahmed E. Nassar Elsayed L. Elmassry Macarena Forner-Martínez Rajani Awal Luzie U. Wingen Simon Griffiths Alsamman M. Alsamman Alsamman M. Alsamman Zakaria Kehel |
| author_facet | Ahmed Fawzy Elkot Ahmed E. Nassar Ahmed E. Nassar Elsayed L. Elmassry Macarena Forner-Martínez Rajani Awal Luzie U. Wingen Simon Griffiths Alsamman M. Alsamman Alsamman M. Alsamman Zakaria Kehel |
| author_sort | Ahmed Fawzy Elkot |
| collection | DOAJ |
| description | BackgroundWheat landraces represent a reservoir of genetic diversity that can support wheat improvement through breeding. A core panel of 300 Watkins wheat landraces, as well as 16 non-Watkins landraces and elite wheat cultivars, was grown during the 2020–2021 and 2021–2022 seasons at four Agricultural Research Stations in Egypt, Gemmiza, Nubaria, Sakha, and Sids, to evaluate the core panel for agromorphological and yield-related traits. The genetic population structure within these genotypes were assessed using 35,143 single nucleotide polymorphisms (SNPs).ResultsCluster analyses using Discriminant Analysis of Principal Components (DAPC) and k-means revealed three clusters with moderate genetic differentiation and population structure, possibly due to wheat breeding systems and geographical isolation. The best ancestry was k = 4, but k = 2 and k = 3 were also significant. A genome-wide association study (GWAS) identified clustered marker trait associations (MTAs) linked to thousand kernel weight on chromosome 5A, plant height on chromosomes 3B and 1D, days to heading on chromosomes 2A, 4B, 5B and 1D, and plant maturity on chromosomes 3A, 2B, and 6B. In the future, these MTAs can be used to accelerate the incorporation of beneficial alleles into locally adapted germplasm through marker-assisted selection. Gene enrichment analysis identified key genes within these loci, including Reduced height-1 (Rht-A1) and stress-related genes.ConclusionThese findings underscore significant genetic connections and the involvement of crucial biological pathways. |
| format | Article |
| id | doaj-art-2f2ff5b916554ec189ec00b32c48ccf8 |
| institution | OA Journals |
| issn | 1664-8021 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj-art-2f2ff5b916554ec189ec00b32c48ccf82025-08-20T02:36:06ZengFrontiers Media S.A.Frontiers in Genetics1664-80212024-12-011510.3389/fgene.2024.13842201384220Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditionsAhmed Fawzy Elkot0Ahmed E. Nassar1Ahmed E. Nassar2Elsayed L. Elmassry3Macarena Forner-Martínez4Rajani Awal5Luzie U. Wingen6Simon Griffiths7Alsamman M. Alsamman8Alsamman M. Alsamman9Zakaria Kehel10Wheat Research Department, Field Crops Research Institute, Agricultural Research Center, Giza, EgyptAgricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, EgyptInternational Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, MoroccoWheat Research Department, Field Crops Research Institute, Agricultural Research Center, Giza, EgyptJohn Innes Centre, Norwich Research Park, Norwich, United KingdomJohn Innes Centre, Norwich Research Park, Norwich, United KingdomJohn Innes Centre, Norwich Research Park, Norwich, United KingdomJohn Innes Centre, Norwich Research Park, Norwich, United KingdomAgricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, EgyptInternational Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, MoroccoInternational Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, MoroccoBackgroundWheat landraces represent a reservoir of genetic diversity that can support wheat improvement through breeding. A core panel of 300 Watkins wheat landraces, as well as 16 non-Watkins landraces and elite wheat cultivars, was grown during the 2020–2021 and 2021–2022 seasons at four Agricultural Research Stations in Egypt, Gemmiza, Nubaria, Sakha, and Sids, to evaluate the core panel for agromorphological and yield-related traits. The genetic population structure within these genotypes were assessed using 35,143 single nucleotide polymorphisms (SNPs).ResultsCluster analyses using Discriminant Analysis of Principal Components (DAPC) and k-means revealed three clusters with moderate genetic differentiation and population structure, possibly due to wheat breeding systems and geographical isolation. The best ancestry was k = 4, but k = 2 and k = 3 were also significant. A genome-wide association study (GWAS) identified clustered marker trait associations (MTAs) linked to thousand kernel weight on chromosome 5A, plant height on chromosomes 3B and 1D, days to heading on chromosomes 2A, 4B, 5B and 1D, and plant maturity on chromosomes 3A, 2B, and 6B. In the future, these MTAs can be used to accelerate the incorporation of beneficial alleles into locally adapted germplasm through marker-assisted selection. Gene enrichment analysis identified key genes within these loci, including Reduced height-1 (Rht-A1) and stress-related genes.ConclusionThese findings underscore significant genetic connections and the involvement of crucial biological pathways.https://www.frontiersin.org/articles/10.3389/fgene.2024.1384220/fullwheatgenome-wide association study (GWAS)Watkinsmarker trait associationspopulation structureagromorphological traits |
| spellingShingle | Ahmed Fawzy Elkot Ahmed E. Nassar Ahmed E. Nassar Elsayed L. Elmassry Macarena Forner-Martínez Rajani Awal Luzie U. Wingen Simon Griffiths Alsamman M. Alsamman Alsamman M. Alsamman Zakaria Kehel Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditions Frontiers in Genetics wheat genome-wide association study (GWAS) Watkins marker trait associations population structure agromorphological traits |
| title | Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditions |
| title_full | Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditions |
| title_fullStr | Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditions |
| title_full_unstemmed | Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditions |
| title_short | Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditions |
| title_sort | assessment of genetic structure and trait associations of watkins wheat landraces under egyptian field conditions |
| topic | wheat genome-wide association study (GWAS) Watkins marker trait associations population structure agromorphological traits |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2024.1384220/full |
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