Quantitative trait loci associated with agronomic traits and stripe rust in winter wheat mapping population using single nucleotide polymorphic markers

Heavy rain during the wheat seedling stage, drought in the flowering stage, and high temperatures with high humidity prior to harvest all contribute to substantial reductions in overall wheat yields in the Chinese province of Sichuan. In this study, we explored the effects of Rht-B1 and Yr18 in Chuannong16 (CN16) and a population derived from breeding line 30481. The population of 188 recombinant inbred lines was genotyped using an iSelect 90,000 single nucleotide polymorphism array and two functional markers for Rht-B1 and Yr18, and was phenotyped over 2 years in replicated trials. Grain yield was highly correlated with leaf color, plant height, and thousand kernel weights, and was negatively correlated with sedimentation. Plant height was positively correlated with grain yield and leaf color and negatively correlated with the number of tillers, thousand kernel weight, and sedimentation volume. In addition, sedimentation was negatively correlated with all five of the other traits (plant height, leaf color, tillers per square meter, grain yield, and thousand kernel weight) using both genetic and phenotypic correlation. The semi-dwarf allele Rht-B1b reduced plant height, grain yield, and thousand kernel weight. Yr18 did not affect stripe rust or other agronomic traits in the population examined. A total of 15 quantitative trait locii (QTLs) were identified for seven traits over 2 years, except for grain yield. One pleiotropic QTL on chromosome 4B was significantly associated with leaf color, thousand kernel weight, and plant height, but it was in different scaffolds with Rht-B1 on the physical map. We found a co-segregation SNP marker with Yr18 in our population; they were not in the same region on the physical map. This may be due to the relatively small population size and limited recombinant events in the population.