QTL/Segment Mapping and Candidate Gene Analysis for Oil Content Using a Wild Soybean Chromosome Segment Substitution Line Population

TL;DR

This study identifies genetic regions and candidate genes affecting oil content in soybeans using wild and cultivated soybean lines.

Contribution

The study discovers a novel candidate gene for oil content and validates a known gene using a chromosome substitution population.

Findings

Two major QTL/segments (qOC14 and qOC20) explain 39.46% of oil content variation in soybeans.

A novel candidate gene, Glyma.14G179800, and a known gene, Glyma.20G085100 (POWR1), are linked to oil content regulation.

Wild alleles at these QTLs reduce oil content, consistent with wild soybeans having lower oil.

Abstract

Annual wild soybean, the ancestor of cultivated soybean, underwent a significant increase in seed oil content during domestication. To elucidate the genetic basis of this change, a chromosome segment substitution line population (177 lines) constructed with cultivated soybean NN1138-2 as recipient and wild soybean N24852 as donor was used in this study. Phenotypic evaluation across three distinct environments led to the identification of two major QTL/segments, qOC14 on chromosome 14 and qOC20 on chromosome 20, which collectively explained 39.46% of the phenotypic variation, with individual contributions of 17.87% and 21.59%, respectively. Both wild alleles exhibited negative additive effects, with values of −0.35% and −0.42%, respectively, consistent with the inherently low oil content of wild soybeans. Leveraging transcriptome and genome data from the two parents, two candidate genes were predicted. Notably, Glyma.14G179800 is a novel candidate gene encoding a PHD-type zinc finger domain-containing protein, and the hap-A haplotype exhibits a positive effect on oil content. In contrast, Glyma.20G085100 is a reported POWR1 gene, known to regulate protein and oil content. Our findings not only validate the role of known gene but, more importantly, unveil a new candidate gene, offering valuable genetic resources and theoretical targets for molecular breeding of high-oil soybean.

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