High-resolution mapping through whole-genome resequencing identifies two novel QTLs controlling oil content in peanut

Abstract

Increasing oil content is a key objective in peanut breeding programs. Accurate identification of quantitative trait loci (QTLs) with linked markers for oil content can greatly aid in marker-assisted selection for high-oil breeding. In this study, a high-density bin map was constructed by resequencing a recombinant inbred line (RIL) population (ZH16×J11) consisting of 295 lines. The bin map contained 4,212 loci and had a total length of 1,162.3 cM. Ten QTLs for oil content were identified in six linkage groups. Notably, two of these QTLs, qOCB03.1 and qOCB06.1, were consistently detected in a minimum of three environments and explained up to 13.62% of phenotypic variation. They have not been reported in previous studies and thus are novel QTLs. The combination of favorable alleles from the qOCB03.1 and qOCB06 in the RIL population could increase oil content across multiple environments from 1.50 to 2.46%. Two InDel markers linked to qOCB03.1 and qOCB06.1 were developed and validated to be associated with oil content in another RIL population (ZH10×ICG12625) with diverse phenotypes. Additionally, the high-resolution map allowed for the precise positioning of qOCB03.1 and qOCB06.1 within a 1.77 Mb-interval on chromosome B03 and a 1.51 Mb- interval on chromosome B06, respectively. Annotation of genomic variants, analysis of transcriptome sequencing, and evaluation of the allelic effects in 292 peanut varieties revealed two candidate genes associated with oil content for each of the two QTLs. The identification of candidate genes in this study can enable the map-based cloning of key genes controlling oil content in peanut. Furthermore, these novel and stable QTLs and their tightly linked markers are valuable for marker-assisted breeding for increased oil content in peanut.