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Genome-wide association and validation of key loci for yield-related traits in wheat founder parent Xiaoyan 6

Ma, Feifei, Xu, Yunfeng, Ma, Zhengqiang, Li, Lihui, An, Diaoguo
Molecular breeding 2018 v.38 no.7 pp. 91
Triticum aestivum, agronomic traits, alleles, breeding programs, genetic markers, genome-wide association study, genotyping, grain yield, growing season, inbred lines, loci, marker-assisted selection, microsatellite repeats, parents, phenotypic variation, plant height, polymerase chain reaction, quantitative trait loci, seeds, spikelets, wheat, China
Xiaoyan 6, one of the most important founder parents in wheat, possesses many superior agronomic traits and has played a crucial role in Chinese wheat breeding programs. In this study, a panel of 66 elite wheat accessions derived from Xiaoyan 6 was planted in four growing seasons; genome-wide association study (GWAS) was performed for six yield-related traits using the wheat 90K genotyping assay. A total of 803 significant marker-trait associations (MTAs) that explained up to 35.0% of the phenotypic variation were detected. Of these, the locus QTkw-5B which contains 19 MTAs for thousand kernel weight (TKW) was consistently detected in three growing seasons and confirmed in a recombinant inbred line (RIL) population by developing simple sequence repeats (SSR) and kompetitive allele-specific PCR (KASP) markers. The locus QPh-3A containing eight repetitive MTAs for plant height (PH) was consistently identified in all the four growing seasons and validated in a RIL population by developing SSR markers. The transmission of Xiaoyan 6 allele indicated that the favorite allele of QPh-3A was strongly selected in breeding programs. Comparing with previous studies, QTkw-5B and QPh-3A should be novel QTL. The locus QFss-2D for fertile spikelet number per spike (FSS) was identified and then validated in three bi-parental populations. This locus controlled various spike-related traits and may be a key spike polymorphic locus. This study could provide insight into dissecting yield-related traits in the breeding population and reliable molecular markers that might be valuable for marker-assisted selection in wheat high-yield breeding programs.