Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics
ABSTRACT Breeding programs are often constrained by the genetic diversity of the parental lines, even though these lines can be a rare source of unique alleles not found elsewhere. Therefore, identifying these rare alleles is crucial for keeping them in the breeding programs while introducing new ge...
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| Format: | Article |
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Wiley
2024-12-01
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| Series: | Legume Science |
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| Online Access: | https://doi.org/10.1002/leg3.70019 |
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| author | Ivana Kaňovská Jana Biová Jana Slivková Kristin Bilyeu Mária Škrabišová |
| author_facet | Ivana Kaňovská Jana Biová Jana Slivková Kristin Bilyeu Mária Škrabišová |
| author_sort | Ivana Kaňovská |
| collection | DOAJ |
| description | ABSTRACT Breeding programs are often constrained by the genetic diversity of the parental lines, even though these lines can be a rare source of unique alleles not found elsewhere. Therefore, identifying these rare alleles is crucial for keeping them in the breeding programs while introducing new genetic resources. The growing amount of whole genome sequenced data has made Genome‐wide Association Study (GWAS) dominant in investigations to find causal genes for all crops, including legumes. However, GWAS often fails to predict more than one causative mutation (CM) in multiple alleles of a single causal gene. Consequently, multiple alleles complicate breeding when not recognized by a single associated marker, which typically identifies only the most frequent CM and discriminates against the others. In this work, we focus on adopting recent applied genomics methods to identify multiple independent alleles and rare alleles in soybean as a model for other legumes. We predicted, identified, and confirmed a new and extremely rare CM for the loss of black pigmentation in the soybean seed coat and hilum color R gene, the Q25fs. The deletion of eight bases leads to a frameshift, a premature stop codon, and a truncated, nonfunctional protein. Our results also suggest a possibly new gene or an allele of the seed coat color inhibitor I gene. Using a soybean model, we demonstrate how applied genomics methods can accelerate pre‐breeding, and additionally, we discuss the potential for adopting these methods for application to other legumes. |
| format | Article |
| id | doaj-art-c694817e8ffd4bc79e7dabdd278fe97b |
| institution | OA Journals |
| issn | 2639-6181 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wiley |
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| series | Legume Science |
| spelling | doaj-art-c694817e8ffd4bc79e7dabdd278fe97b2025-08-20T02:32:05ZengWileyLegume Science2639-61812024-12-0164n/an/a10.1002/leg3.70019Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied GenomicsIvana Kaňovská0Jana Biová1Jana Slivková2Kristin Bilyeu3Mária Škrabišová4Department of Biochemistry, Faculty of Science Palacký University in Olomouc Olomouc CzechiaDepartment of Biochemistry, Faculty of Science Palacký University in Olomouc Olomouc CzechiaDepartment of Biochemistry, Faculty of Science Palacký University in Olomouc Olomouc CzechiaUnited States Department of Agriculture‐Agricultural Research Service Plant Genetics Research Unit Columbia Missouri USADepartment of Biochemistry, Faculty of Science Palacký University in Olomouc Olomouc CzechiaABSTRACT Breeding programs are often constrained by the genetic diversity of the parental lines, even though these lines can be a rare source of unique alleles not found elsewhere. Therefore, identifying these rare alleles is crucial for keeping them in the breeding programs while introducing new genetic resources. The growing amount of whole genome sequenced data has made Genome‐wide Association Study (GWAS) dominant in investigations to find causal genes for all crops, including legumes. However, GWAS often fails to predict more than one causative mutation (CM) in multiple alleles of a single causal gene. Consequently, multiple alleles complicate breeding when not recognized by a single associated marker, which typically identifies only the most frequent CM and discriminates against the others. In this work, we focus on adopting recent applied genomics methods to identify multiple independent alleles and rare alleles in soybean as a model for other legumes. We predicted, identified, and confirmed a new and extremely rare CM for the loss of black pigmentation in the soybean seed coat and hilum color R gene, the Q25fs. The deletion of eight bases leads to a frameshift, a premature stop codon, and a truncated, nonfunctional protein. Our results also suggest a possibly new gene or an allele of the seed coat color inhibitor I gene. Using a soybean model, we demonstrate how applied genomics methods can accelerate pre‐breeding, and additionally, we discuss the potential for adopting these methods for application to other legumes.https://doi.org/10.1002/leg3.70019genetic diversitygenome‐wide association studieslegume genomicssoybean |
| spellingShingle | Ivana Kaňovská Jana Biová Jana Slivková Kristin Bilyeu Mária Škrabišová Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics Legume Science genetic diversity genome‐wide association studies legume genomics soybean |
| title | Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics |
| title_full | Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics |
| title_fullStr | Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics |
| title_full_unstemmed | Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics |
| title_short | Identifying Rare Alleles Affecting Seed Coat and Hilum Color in Soybean (Glycine max) Using Applied Genomics |
| title_sort | identifying rare alleles affecting seed coat and hilum color in soybean glycine max using applied genomics |
| topic | genetic diversity genome‐wide association studies legume genomics soybean |
| url | https://doi.org/10.1002/leg3.70019 |
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