A Combined Linkage and GWAS Analysis Identifies QTLs Linked to Soybean Seed Protein and Oil Content.

Tengfei Zhang,Caixin Zhen,Cunxiang Wu,Bingjun Jiang,Wensheng Hou,Tingting Wu,Tianfu Han,Liwei Wang,Shi Sun,Shan Yuan

doi:10.3390/ijms20235915

Abstract

Soybean is an excellent source of vegetable protein and edible oil. Understanding the genetic basis of protein and oil content will improve the breeding programs for soybean. Linkage analysis and genome-wide association study (GWAS) tools were combined to detect quantitative trait loci (QTL) that are associated with protein and oil content in soybean. Three hundred and eight recombinant inbred lines (RILs) containing 3454 single nucleotide polymorphism (SNP) markers and 200 soybean accessions, including 94,462 SNPs and indels, were applied to identify QTL intervals and significant SNP loci. Intervals on chromosomes 1, 15, and 20 were correlated with both traits, and QTL qPro15-1, qPro20-1, and qOil5-1 reproducibly correlated with large phenotypic variations. SNP loci on chromosome 20 that overlapped with qPro20-1 were reproducibly connected to both traits by GWAS (p < 10−4). Twenty-five candidate genes with putative roles in protein and/or oil metabolisms within two regions (qPro15-1, qPro20-1) were identified, and eight of these genes showed differential expressions in parent lines during late reproductive growth stages, consistent with a role in controlling protein and oil content. The new well-defined QTL should significantly improve molecular breeding programs, and the identified candidate genes may help elucidate the mechanisms of protein and oil biosynthesis.

Highlights

With an average composition of approximately 40% protein and 20% oil, soybean (Glycine max (L.) Merr.) is the most important source of vegetable protein and edible oil, accounting for 68% of total global protein consumption [1] and more than half of global oilseed production [2]
The protein and oil content of ZGDD/HH27 were different when grown in three different locations, especially in XT (Table 1); the comprehensive climate factors in XT must have led to the significant change in protein and oil content of HH27, producing a wide phenotypic variation in the recombinant inbred lines (RILs) used for quantitative trait loci (QTL) analysis
Comparing the results identified as QTL intervals and single nucleotide polymorphism (SNP) loci, we decided the co-detected SNP loci region 34.60~35.40 Mb extended by approximately 200 kb on Chr. 20, and the qPro15-1/qOil15-1 interval 2.60~3.50 Mb on Chr. 5, an extra region, were the best novel regions for candidate genes, rather novel QTL intervals, that might control protein and/or oil metabolism

Summary

Introduction

With an average composition of approximately 40% protein and 20% oil, soybean (Glycine max (L.) Merr.) is the most important source of vegetable protein and edible oil, accounting for 68% of total global protein consumption [1] and more than half of global oilseed production [2]. To find genetic markers that are near genes controlling traits of interest, linkage analysis can be performed using biparental segregating populations [8]. Since Diers et al [3] first used linkage analysis to discover a major QTL connected to soybean protein and oil content on chromosome (Chr.) 20, studies have been conducted to detect QTL near various types of markers, including amplified fragment length polymorphism (AFLP) markers, restriction fragment length polymorphism (RFLP) markers, and simple sequence repeat (SSR) markers in biparental populations [7,9,10,11,12,13]. Patil et al used a high-resolution bin map (3343 SNP markers) to detect 18 QTL connected to soybean seed protein, oil, and sucrose content QTL that were confirmed by a genome-wide association study (GWAS) [5]

Methods

Results

Discussion

Conclusion