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

Abstract

Identification of stable quantitative trait loci (QTL) 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 researches. In the present study, a wheat consensus map was constructed using a doubled haploid (DH) population derived from Jinghua 1×Xiaobaidongmai (JX) and an F2 population derived from L43×Shanxibaimai (LS) using BAAFS AFFY wheat 90K single nucleotide polymorphism (SNP) array. A total of 44503 SNP markers were mapped on the constructed consensus map, covering 5437.92 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 and F2:3 and F2:4 populations of LS in six, two and two environments, respectively, and used for QTL analysis. Inclusive composite interval mapping (ICIM) identified 32 environmentally stable QTL for eight yield-related traits. Among them, four QTL, i.e., QPH.baafs-4B, QKNS.baafs-4B, QTGW.baafs-4B and QSL.baafs-5A.3, were detected across mapping populations and environments, and seven stable QTL i.e., QPH.baafs-2B, QKNS.baafs-3D, QSL.baafs-3D, QKW.baafs-4B, QPH.baafs-5D, QPH.baafs-6A.1 and QSL.baafs-6A, are likely to be new. The physical region of 17.25-44.91 Mb on chromosome 4B was associated with six yield-related traits, which is an important region for wheat yield. The physical region around the dwarfing gene Rht24 contained QTL for KL, KW, SL and TGW, which are either from a pleiotropic effect of Rht24 or closely linked loci. Two hundred and fifty-four promising candidate genes were identified for the stable QTL. Among them, TraesCS5A03G1264300, TraesCS1B03G0624000 and TraesCS6A03G0697000 were particularly noteworthy due to their homologous genes have similar functions for the corresponding traits. The constructed consensus map and the identified QTL 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.