Association mapping of wheat distinctness, uniformity, and stability traits identifies evidence of TaDof-B copy number variation associated with stem pith thickness

For new varieties to be sold, they must first pass assessment using a set of phenotypic criteria that test for distinctness, uniformity, and stability (DUS) and which serve as the basis for the awarding of plant breeders’ rights. The objective of this study was to use historical DUS phenotypic data to investigate the genetic architecture of DUS characteristics in wheat ( Triticum aestivum L.). Using a panel of 334 varieties, genome-wide association studies (GWAS) identified significant marker–trait associations for 18 of the 33 wheat DUS characteristics investigated. The most significant was the genetic locus P22_3B_821 for stem pith thickness, located between 818 and 830 Mb on chromosome 3B. Haplotype analysis informed conversion of three genetic markers selected from the genotyping array to the KASP genotyping platform, allowing alleles associated with low–medium versus thick pith thickness to be easily tracked. Subsequent genomic and molecular analysis found evidence that TaDof-B copy number variation (CNV) may underlie control of pith thickness in wheat, whereby CNV ≥3 was associated with the solid stem phenotype, analogous to that previously observed for TdDof-B in durum wheat ( T. turgidum subsp. durum ) and lower CNV with hollow stems. Finally, correlations between DUS characteristics with yield, grain quality traits, and year of release indicated that reduced ear density is under breeder selection and that this has a beneficial effect on the quality traits ‘grain test weight’ and ‘Hagberg falling number’. Collectively, these findings and molecular tools will help inform commercial, DUS regulatory and scientific advances in future wheat research and development programmes.