CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world
Breeding programs in developing countries still cannot afford the new genotyping technologies, hindering their research. We aimed to assemble an Association Mapping panel to serve as CGIAR Barley Breeding Toolbox (CBBT), especially for the Developing World. The germplasm had to be representative of...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/126718 |
| _version_ | 1855520437912469504 |
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| author | Bouhlal, Outmane Visioni, Andrea Verma, Ramesh Pal Singh Kandil, Mostafa Gyawali, Sanjaya Capettini, Flavio Sanchez-Garcia, Miguel |
| author_browse | Bouhlal, Outmane Capettini, Flavio Gyawali, Sanjaya Kandil, Mostafa Sanchez-Garcia, Miguel Verma, Ramesh Pal Singh Visioni, Andrea |
| author_facet | Bouhlal, Outmane Visioni, Andrea Verma, Ramesh Pal Singh Kandil, Mostafa Gyawali, Sanjaya Capettini, Flavio Sanchez-Garcia, Miguel |
| author_sort | Bouhlal, Outmane |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Breeding programs in developing countries still cannot afford the new genotyping technologies, hindering their research. We aimed to assemble an Association Mapping panel to serve as CGIAR Barley Breeding Toolbox (CBBT), especially for the Developing World. The germplasm had to be representative of the one grown in the Developing World; with high genetic variability and be of public domain. For it, we genotyped with the Infinium iSelect 50K chip, a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environments. 40,342 markers were polymorphic with an average polymorphism information content of 0.35 and 66% of them exceeding 0.25. The analysis of the population structure identified 8 subpopulations mostly linked to geographical origin, four of them with significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines. ICARDA material showed the widest diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and the fact that ICARDA lines were present in all 8 subpopulations and carried all 16 allelic combinations. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, ICARDA-derived lines and cultivated landraces were pre-selected to form the CBBT. Using the Mean of Transformed Kinships method, we assembled a panel capturing most of the allelic diversity in the GBP. The CBBT (N=250) preserves good balance between row-types and good representation of both phenology allelic combinations and subpopulations of the GBP. The CBBT and its genotypic data is available to researchers worldwide as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation. |
| format | Journal Article |
| id | CGSpace126718 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1267182026-01-15T02:05:18Z CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world Bouhlal, Outmane Visioni, Andrea Verma, Ramesh Pal Singh Kandil, Mostafa Gyawali, Sanjaya Capettini, Flavio Sanchez-Garcia, Miguel barley biodiversity food security health nutrition phenology population structure goal 1 no poverty environmental health goal 2 zero hunger goal 3 good health and well-being goal 13 climate action goal 17 partnerships for the goals barley genetic diversity climate adaptation and mitigation poverty reduction, livelihoods and jobs global barley panel barley breeding toolbox association mapping (am) Breeding programs in developing countries still cannot afford the new genotyping technologies, hindering their research. We aimed to assemble an Association Mapping panel to serve as CGIAR Barley Breeding Toolbox (CBBT), especially for the Developing World. The germplasm had to be representative of the one grown in the Developing World; with high genetic variability and be of public domain. For it, we genotyped with the Infinium iSelect 50K chip, a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environments. 40,342 markers were polymorphic with an average polymorphism information content of 0.35 and 66% of them exceeding 0.25. The analysis of the population structure identified 8 subpopulations mostly linked to geographical origin, four of them with significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines. ICARDA material showed the widest diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and the fact that ICARDA lines were present in all 8 subpopulations and carried all 16 allelic combinations. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, ICARDA-derived lines and cultivated landraces were pre-selected to form the CBBT. Using the Mean of Transformed Kinships method, we assembled a panel capturing most of the allelic diversity in the GBP. The CBBT (N=250) preserves good balance between row-types and good representation of both phenology allelic combinations and subpopulations of the GBP. The CBBT and its genotypic data is available to researchers worldwide as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation. 2023-01-09T21:36:03Z 2023-01-09T21:36:03Z Journal Article https://hdl.handle.net/10568/126718 en Open Access application/pdf Frontiers Media Outmane Bouhlal, Andrea Visioni, Ramesh Pal Singh Verma, Mostafa Kandil, Sanjaya Gyawali, Flavio Capettini, Miguel Sanchez-Garcia. (14/11/2022). CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world. Frontiers in Plant Science, 13. |
| spellingShingle | barley biodiversity food security health nutrition phenology population structure goal 1 no poverty environmental health goal 2 zero hunger goal 3 good health and well-being goal 13 climate action goal 17 partnerships for the goals barley genetic diversity climate adaptation and mitigation poverty reduction, livelihoods and jobs global barley panel barley breeding toolbox association mapping (am) Bouhlal, Outmane Visioni, Andrea Verma, Ramesh Pal Singh Kandil, Mostafa Gyawali, Sanjaya Capettini, Flavio Sanchez-Garcia, Miguel CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world |
| title | CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world |
| title_full | CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world |
| title_fullStr | CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world |
| title_full_unstemmed | CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world |
| title_short | CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world |
| title_sort | cgiar barley breeding toolbox a diversity panel to facilitate breeding and genomic research in the developing world |
| topic | barley biodiversity food security health nutrition phenology population structure goal 1 no poverty environmental health goal 2 zero hunger goal 3 good health and well-being goal 13 climate action goal 17 partnerships for the goals barley genetic diversity climate adaptation and mitigation poverty reduction, livelihoods and jobs global barley panel barley breeding toolbox association mapping (am) |
| url | https://hdl.handle.net/10568/126718 |
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