Molecular breeding for grain yield in barley: An evaluation of QTL effects in a spring barley cross

We report results from a breeding strategy designed to accumulate favorable QTL alleles for grain yield identified in the Steptoe x 'Morex' (SM) barley germplasm. Two map lines (SM73 and SM 145) from the original mapping population were selected based on their marker genotype and QTL structure. When crossed, these lines would be expected to produce progeny with most favorable QTL alleles. One hundred doubled haploid (DH) lines from the F₁ hybrid of this cross were genotyped with ten RFLP markers and one morphological marker defining grain yield to monitor QTL segregation. A subset of 24 lines representing various combinations of putatively favorable and unfavorable QTL alleles, together with Steptoe, 'Morex', SM73, and SM145, were phenotyped for grain yield in five environments. Multiple regression procedures were used to explore phenotype and genotype relationships. Most target QTLs showed significant effects. However, significance and magnitude of QTL effects and favorable QTL allele phase varied across environments. All target QTLs showed significant QTL-by-environment interaction (QTL x E), and the QTL on chromosome 2 expressed alternative favorable QTL alleles in different environments. Digenic epistatic effects were also detected between some QTL loci. For traits such as grain yield, marker-assisted selection efforts may be better targeted at determining optimum combinations of QTL alleles rather than pyramiding alleles detected in a reference mapping population.