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.

Combined linkage and association mapping of putative QTLs controlling black tea quality and drought tolerance traits

“…Linkage mapping method has a relatively low genome resolution while AM method is affected by population structure and individual relationships. The integration of linkage mapping and AM has successfully been applied to many plant studies (Fan and Xiong 2003; Jung et al 2005; Lu et al 2010; Lou et al 2015; Cao et al 2017).…”

Quantitative trait loci analysis of seed oil content and composition of wild and cultivated soybean

“…With the completion of the genome sequencing of soybean cv. Williams 82 [29] and the rapid development of next-generation sequencing (NGS) technology, singlenucleotide polymorphism (SNP) markers have been used to construct high-density linkage maps to identify QTL intervals [25,30]. Based on a high-density genetic map consisting of 2062 SNP markers, Cao et al (2017) identified one QTL, qOil-5, for seed oil, which was mapped to Chr.…”

GENETIC SOURCES REQUIRED FOR SOYBEAN BREEDING IN THE CONTEXT OF NEW BIOTECHNOLOGies (review)

“…Since the seeds protein and oil level is resultant of interaction of multiple genes and loci, influenced by the environment, traditional selection for this trait in a number of world breeding centers is accompanied by an analysis of linkage groups to identify QTLs that determine oil and proteins in different genotypes and under different environmental conditions [29][30][31]. Several QTLs affecting seed protein content have been detected.…”