Consensus linkage map construction and QTL mapping for eight yield-related traits in wheat using the BAAFS Wheat 90K SNP array

Abstract

Identifying stable quantitative trait loci (QTLs) for yield-related traits across populations and environments is crucial for wheat breeding and genetic studies. Consensus maps also play important roles in wheat genetic and genomic research. In the present study, a wheat consensus map was constructed using a doubled haploid (DH) population derived from Jinghua 1×Xiaobaidongmai (JX), an F2 population derived from L43×Shanxibaimai (LS) and the BAAFS Wheat 90K SNP array single nucleotide polymorphism (SNP) array. A total of 44,503 SNP markers were mapped on the constructed consensus map, and they covered 5,437.92 cM across 21 chromosomes. The consensus map showed high collinearity with the individual maps and the wheat reference genome IWGSC RefSeq v2.1. Phenotypic data on eight yield-related traits were collected in the JX population, as well as the F2:3 and F2:4 populations of LS, in six, two and two environments, respectively, and those data were used for QTL analysis. Inclusive composite interval mapping (ICIM) identified 32 environmentally stable QTLs for the eight yield-related traits. Among them, four QTLs (QPH.baafs-4B, QKNS.baafs-4B, QTGW.baafs-4B, and QSL.baafs-5A.3) were detected across mapping populations and environments, and nine stable QTLs (qKL.baafs-1D, QPH.baafs-2B, QKNS.baafs-3D, QSL.baafs-3D, QKW.baafs-4B, QPH.baafs-5D, QPH.baafs-6A.1, QSL.baafs-6A, and QSL.baafs-6D) are likely to be new. The physical region of 17.25–44.91 Mb on chromosome 4B was associated with six yield-related traits, so it is an important region for wheat yield. The physical region around the dwarfing gene Rht24 contained QTLs for kernel length (KL), kernel width (KW), spike length (SL), and thousand-grain weight (TGW), which are either from a pleiotropic effect of Rht24 or closely linked loci. For the stable QTLs, 254 promising candidate genes were identified. Among them, TraesCS5A03G1264300, TraesCS1B03G0624000 and TraesCS6A03G0697000 are particularly noteworthy since their homologous genes have similar functions for the corresponding traits. The constructed consensus map and the identified QTLs along with their candidate genes will facilitate the genetic dissection of wheat yield-related traits and accelerate the development of wheat cultivars with desirable plant morphology and high yield.