Deciphering the Underlying Genetics of Agronomic Traits Comparing Various Association Mapping Models in a Diversified Flax Collection

ABSTRACT The improvement of agronomic traits requires exploring their underlying genetic background. In this study, we investigated marker‐trait associations and identified putative candidate genes related to seed yield and nine yield‐contributing traits in a collection of 337 flax ( Linum usitatissimum L.) germplasm phenotyped across five environments, using 26,171 Single Nucleotide Polymorphism (SNP) markers. Five single‐locus, three multi‐locus and haplotype‐based association mapping models were employed in the analysis. The traits and genotype collection exhibited continuous variation and considerable genetic diversity, respectively. No single model was ideal for all traits in every environment; rather specific models best fitted specific trait‐environment combinations. The analysis identified a total of 104 Quantitative Trait Loci (QTLs) significantly associated with the traits, most of which are novel, as they did not align with previously reported genomic regions. These QTLs encompassed 1195 annotated genes related to various traits. Among these genes, several were designated as putative candidates based on functional annotations and previous evidence linking them to respective traits, although further validation is needed. This research will facilitate marker‐assisted selection in flax breeding programs.