Characterization of oat chromosome rearrangements in advanced breeding lines and implications for genetic improvement
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Le résumé fourni par la source
Large-scale chromosomal rearrangements or structural variants (SVs) have shaped the evolution of Avena species, driving domestication and adaptation in oats (Avena sativa L.). The legacy of these reorganizations, including translocations and inversions, remains evident, yet their frequency and impact on phenotypic and genotypic variability in oat breeding populations remain unclear. The objective of this study was to characterize chromosome rearrangements in 1230 oat breeding lines using genotyping-by-sequencing and to utilize this information in genomic loci discovery and prediction. Principal component analysis (PCA) based on single-nucleotide polymorphisms (SNPs) identified distinct clusters at the known locations of 1A/1C translocation, 3C inversion, 4C inversion, and 7D inversion. The distribution of the clusters of the four rearrangements in the genome-wide diversity space of our panel confirmed the role of SVs in population structure, with 1A/1C showing the most significant divergence. Suppression of recombination due to SVs was shown by higher linkage disequilibrium (LD) observed in all samples compared to lines within individual SV clusters. Genome-wide association studies (GWAS) identified markers for grain yield and agronomic traits, with some differences among cluster-based populations. Genomic prediction accuracies improved when cross-validation was performed within SV clusters rather than across the entire dataset. However, using SV clusters as covariates did not improve GWAS and prediction accuracies. These results suggest that SVs cause population stratification, reduce recombination rates, hinder gene discovery, and affect genomic prediction accuracy. Characterizing oat germplasm for SVs can improve breeding decisions, from optimizing parental selection to enhancing genomic predictions, accelerating genetic gains for key traits.
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Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- Characterization of oat chromosome rearrangements in advanced breeding lines and implications for genetic improvement
- Date Crossref
- 01/08/2026
- Éditeur
- Springer Science and Business Media LLC
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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South Dakota State University Department of Agronomy pays non établi dans la noticeUniversité ou école supérieure
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Agriculture and Agri-Food Canada pays non établi dans la noticeOrganisme public
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Ottawa Research and Development Centre pays non établi dans la noticeStructure de recherche
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Edward T. Schafer Agricultural Research Center pays non établi dans la noticeStructure de recherche
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Robert W. Holley Center for Agriculture & Health pays non établi dans la noticeStructure de recherche
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USDA-ARS Cereal Crops Improvement Research Unit pays non établi dans la noticeStructure de recherche
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R.W. Holley Center for Agriculture and Health pays non établi dans la noticeInstitution
Department of Agronomy — South Dakota State University, Agriculture and Agri-Food Canada et Ottawa Research and Development Centre, avec 4 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.