Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean
Faba bean (Vicia faba L.) is an important pulse crop with a wide range of agroecological adaptations. The development of genomic tools and a comprehensive catalog of extant genetic diversity are crucial for developing improved faba bean cultivars. The lack of a cost-effective genotyping platform lim...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Wiley Open Access
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/162736 |
| _version_ | 1855526653275406336 |
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| author | Zhang, Hailin Fechete, Lavinia Himmelbach, Axel Poehlein, Anja Lohwasser, Ulrike Börner, Andreas Maalouf, Fouad Agrawal, Shiv Kumar Khazaei, Hamid Stein, Nils Jayakodi, Murukarthick |
| author_browse | Agrawal, Shiv Kumar Börner, Andreas Fechete, Lavinia Himmelbach, Axel Jayakodi, Murukarthick Khazaei, Hamid Lohwasser, Ulrike Maalouf, Fouad Poehlein, Anja Stein, Nils Zhang, Hailin |
| author_facet | Zhang, Hailin Fechete, Lavinia Himmelbach, Axel Poehlein, Anja Lohwasser, Ulrike Börner, Andreas Maalouf, Fouad Agrawal, Shiv Kumar Khazaei, Hamid Stein, Nils Jayakodi, Murukarthick |
| author_sort | Zhang, Hailin |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Faba bean (Vicia faba L.) is an important pulse crop with a wide range of agroecological adaptations. The development of genomic tools and a comprehensive catalog of extant genetic diversity are crucial for developing improved faba bean cultivars. The lack of a cost-effective genotyping platform limits the characterization of large germplasm collections, understanding of genetic diversity across populations, and implementing breeder's tools like genomic selection. Genotyping-by-sequencing (GBS) offers high-resolution genotyping for both model and crop plant species, even without a reference genome sequence. The genome fragments targeted by GBS depend substantially on the restriction enzyme (RE) used for the complexity reduction step. Species with complex genomic architecture require optimization of GBS with proper RE to realize the full potential of GBS. Here, we evaluated various REs in the GBS method and identified that the combination of ApeKI/MseI proved to be the most appropriate for faba bean based on the best library quality, a high number of genomic loci spread across chromosomes, and high enrichment loci associated with the gene space. With the new optimized protocol, we constructed a genetic map using a recombinant inbred line (RIL) population and identified a QTL for seed hilum color on Chromosome 1. In addition, we also genotyped a diversity panel and performed a genome-wide association studies (GWAS) for important agronomic traits, including plant height (PH), flowering time (FT), and number of pods per plant (PPP). We identified six SNP markers significantly associated with these traits and listed potential candidate genes. The optimized faba bean-specific GBS procedure will facilitate access to the untapped genetic diversity for genetic research and breeding and may facilitate functional genomics. |
| format | Journal Article |
| id | CGSpace162736 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Wiley Open Access |
| publisherStr | Wiley Open Access |
| record_format | dspace |
| spelling | CGSpace1627362026-01-26T21:41:01Z Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean Zhang, Hailin Fechete, Lavinia Himmelbach, Axel Poehlein, Anja Lohwasser, Ulrike Börner, Andreas Maalouf, Fouad Agrawal, Shiv Kumar Khazaei, Hamid Stein, Nils Jayakodi, Murukarthick gwas genotyping vicia faba genetic diversity Faba bean (Vicia faba L.) is an important pulse crop with a wide range of agroecological adaptations. The development of genomic tools and a comprehensive catalog of extant genetic diversity are crucial for developing improved faba bean cultivars. The lack of a cost-effective genotyping platform limits the characterization of large germplasm collections, understanding of genetic diversity across populations, and implementing breeder's tools like genomic selection. Genotyping-by-sequencing (GBS) offers high-resolution genotyping for both model and crop plant species, even without a reference genome sequence. The genome fragments targeted by GBS depend substantially on the restriction enzyme (RE) used for the complexity reduction step. Species with complex genomic architecture require optimization of GBS with proper RE to realize the full potential of GBS. Here, we evaluated various REs in the GBS method and identified that the combination of ApeKI/MseI proved to be the most appropriate for faba bean based on the best library quality, a high number of genomic loci spread across chromosomes, and high enrichment loci associated with the gene space. With the new optimized protocol, we constructed a genetic map using a recombinant inbred line (RIL) population and identified a QTL for seed hilum color on Chromosome 1. In addition, we also genotyped a diversity panel and performed a genome-wide association studies (GWAS) for important agronomic traits, including plant height (PH), flowering time (FT), and number of pods per plant (PPP). We identified six SNP markers significantly associated with these traits and listed potential candidate genes. The optimized faba bean-specific GBS procedure will facilitate access to the untapped genetic diversity for genetic research and breeding and may facilitate functional genomics. 2024-09-01 2024-11-25T19:19:55Z 2024-11-25T19:19:55Z Journal Article https://hdl.handle.net/10568/162736 en https://www.ebi.ac.uk/ena/browser/view/PRJEB75354 Open Access application/pdf Wiley Open Access Hailin Zhang, Lavinia Fechete, Axel Himmelbach, Anja Poehlein, Ulrike Lohwasser, Andreas Börner, Fouad Maalouf, Shiv Kumar Agrawal, Hamid Khazaei, Nils Stein, Murukarthick Jayakodi. (1/9/2024). Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean. Legume Science, 6 (3). |
| spellingShingle | gwas genotyping vicia faba genetic diversity Zhang, Hailin Fechete, Lavinia Himmelbach, Axel Poehlein, Anja Lohwasser, Ulrike Börner, Andreas Maalouf, Fouad Agrawal, Shiv Kumar Khazaei, Hamid Stein, Nils Jayakodi, Murukarthick Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean |
| title | Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean |
| title_full | Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean |
| title_fullStr | Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean |
| title_full_unstemmed | Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean |
| title_short | Optimization of Genotyping-by-Sequencing (GBS) forGermplasm Fingerprinting and Trait Mapping in Faba Bean |
| title_sort | optimization of genotyping by sequencing gbs forgermplasm fingerprinting and trait mapping in faba bean |
| topic | gwas genotyping vicia faba genetic diversity |
| url | https://hdl.handle.net/10568/162736 |
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