Identification of Major Quantitative Trait Loci for Seed Oil Content in Soybeans by Combining Linkage and Genome-Wide Association Mapping

Abstract

Soybean oil is the most widely produced vegetable oil in the world and its content in soybean seed is an important quality trait in breeding programs. More than 100 quantitative trait loci (QTLs) for soybean oil content have been identified. However, most of them are genotype specific and/or environment sensitive. Here, we used both a linkage and association mapping methodology to dissect the genetic basis of seed oil content of Chinese soybean cultivars in various environments in the Jiang-Huai River Valley. One recombinant inbred line (RIL) population (NJMN-RIL), with 104 lines developed from a cross between M8108 and NN1138-2, was planted in five environments to investigate phenotypic data, and a new genetic map with 2,062 specific-locus amplified fragment markers was constructed to map oil content QTLs. A derived F₂ population between MN-5 (a line of NJMN-RIL) and NN1138-2 was also developed to confirm one major QTL. A soybean breeding germplasm population (279 lines) was established to perform a genome-wide association study (GWAS) using 59,845 high-quality single nucleotide polymorphism markers. In the NJMN-RIL population, 8 QTLs were found that explained a range of phenotypic variance from 6.3 to 26.3% in certain planting environments. Among them, qOil-5-1, qOil-10-1, and qOil-14-1 were detected in different environments, and qOil-5-1 was further confirmed using the secondary F₂ population. Three loci located on chromosomes 5 and 20 were detected in a 2-year long GWAS, and one locus that overlapped with qOil-5-1 was found repeatedly and treated as the same locus. qOil-5-1 was further localized to a linkage disequilibrium block region of approximately 440 kb. These results will not only increase our understanding of the genetic control of seed oil content in soybean, but will also be helpful in marker-assisted selection for breeding high seed oil content soybean and gene cloning to elucidate the mechanisms of seed oil content.

Keywords: genome-wide association study (GWAS); linkage mapping; quantitative trait locus (QTL); seed oil content; single nucleotide polymorphism (SNP) markers; soybean.

FIGURE 1

Distribution of markers in 20 linkage groups (LGs) in the NJMN-RIL population. The black bars in each LG represent mapped SLAF-seq markers. Detailed information is presented in Supplementary Table S2.

FIGURE 2

Detection and confirmation of qOil-5-1 using NJMN-RIL and secondary F₂ populations by linkage mapping. (A) qOil-5-1 was detected in the NJMN-RIL population in five environments. The physical location of the confidence interval of qOil-5-1 was approximately 2.5 Mb, from 38.04 to 40.51 Mb on chromosome 05. (B) Physical location of the 1- logarithm of odds (LOD) confidence interval of qOil-5-1 on chromosome 05. (C) qOil-5-1 was confirmed in the secondary F2 population. The peak marker was InDel-5-7. The 1- logarithm of odds (LOD) confidence interval of the QTL spanned approximately 1 Mb.

FIGURE 3

Genome-wide association study (GWAS) results for seed oil content in the germplasm population. (A) Manhattan plot of the seed oil content in two different environments. The dashed horizontal line depicts a significant threshold level [–log₁₀ (1/59845)]. (B) GWAS results of the 36–42 Mb genomic region of chromosome 05. (C) The distribution of linkage disequilibrium (LD) blocks of the major locus on chromosome 05. All the single nucleotide polymorphisms (SNPs) that had a significant association with seed oil content in the 2 years investigated were located in one LD block from 38.13 to 38.57 Mb.