Genetic analysis of soft white wheat end-use quality traits in a club by common wheat cross

Improved understanding of the genetic architecture of end-use quality traits and identification of associated quantitative trait loci (QTL) allow breeders to target loci and clarify the complex relationships among these traits. A set of 207 recombinant inbred lines from a 'Coda' by 'Brundage' soft wheat mapping population was grown in five environments over four years at Aberdeen, ID, Moscow, ID, and Pullman, WA, USA. The population was evaluated for grain, milling, and baking end-use quality traits using AACCI methods. A linkage map consisting of 570 single nucleotide polymorphisms and 136 simple sequence repeat markers was developed using JMP Genomics. This linkage map covered 20 of the 21 wheat chromosomes. Multiple interval mapping with the R/qtl package yielded 71 significant QTL associated with 14 end-use quality traits. QTL on chromosomes 2B, 2D, 4B and 6B were consistently associated with multiple end-use quality traits across multiple environments. Depending on the trait, both Coda and Brundage contributed favorable alleles for end-use quality. For some QTL, both Coda and Brundage contributed favorable alleles, but for different end-use quality traits, indicating these alleles may be linked in repulsion. Combining favorable alleles from each parent into a single line can improve the end-use quality. The identified QTL not only provide breeders with potentially useful markers for selection, but also improve understanding of genetic factors related to soft wheat end-use quality traits.