Genetic Dissection of Grain Yield, Agronomic Traits and End-Use Quality in Texas Wheat Using Linkage and Association Study

Quantitative trait loci (QTL) study opens the door to marker-assisted selection by dissecting loci into individual component loci, their genetic effects and interactions. The objectives of this study were to find stable marker-trait association and to map QTL associated with grain yield, agronomic traits and end-use quality traits. An association mapping panel consisting of 298 synthetic derived lines from nine environments were phenotyped for end-use quality traits and genotyped with 76K genotype-by-sequencing (GBS) to find marker-trait association. Another population of 124 Fv5:7 recombinant inbred lines were phenotyped for end-use quality in seven environments and for grain yield and agronomic traits in 28 environments. With the use of 90K single nucleotide polymorphism (SNP) and GBS, QTLs for grain yield, agronomic traits and end-use quality traits were determined. Association analysis revealed two sub-population structures originating from maternal parents of the backcross and slight relatedness among lines. Loci on the short arm of chromosome 1B (17.2-30.4 Mb) were significantly associated with mixograph parameters explaining up to 13.0% of the R^2. Hardness loci on the short arm of chromosome 5D (0.3-9.3 Mb) also affected hardness index and flour yield, explaining up to 27% and 33%, respectively. Glu-D1 loci had strong influence on dough rheology of bi-parental population explaining up to 54.6% of the variation in midline peak time, with favorable allele coming from TAM 112. From multi-trait QTL analysis, homologue group 1 QTLs were strongly linked to mixograph traits from linkage analysis as well. Phenological development gene dependent QTLs were identified on chromosome 1A, 3B for grain yield, and 2B, 4B and 5B for test weight. Phonological development gene independent QTLs were also identified on chromosome 6D, 7D for grain yield, and on 4D, 6B for test weight. We found five genomic regions on chromosome 1D, 4B, 4D and 7D that are related to more than a single trait analyzed. This study unveiled previously identified loci linked to major genes as well as some newly identified QTLs. It will be necessary to validate these QTLs in different wheat backgrounds evaluated under similar growth conditions before developing markers for marker-assisted selection