Genome-Wide Detection of Major and Epistatic Effect QTLs for Seed Protein and Oil Content in Soybean Under Multiple Environments Using High-Density Bin Map.

Benjamin Karikari,Yongce Cao,Junyi Gai,Jiejie Kong,Javaid Bhat,Tuanjie Zhao,Shuguang Li,Jiayin Yang

doi:10.3390/ijms20040979

Abstract

Seed protein and oil content are the two important traits determining the quality and value of soybean. Development of improved cultivars requires detailed understanding of the genetic basis underlying the trait of interest. However, it is prerequisite to have a high-density linkage map for precisely mapping genomic regions, and therefore the present study used high-density genetic map containing 2267 recombination bin markers distributed on 20 chromosomes and spanned 2453.79 cM with an average distance of 1.08 cM between markers using restriction-site-associated DNA sequencing (RAD-seq) approach. A recombinant inbred line (RIL) population of 104 lines derived from a cross between Linhefenqingdou and Meng 8206 cultivars was evaluated in six different environments to identify main- and epistatic-effect quantitative trait loci (QTLs)as well as their interaction with environments. A total of 44 main-effect QTLs for protein and oil content were found to be distributed on 17 chromosomes, and 15 novel QTL were identified for the first time. Out of these QTLs, four were major and stable QTLs, viz., qPro-7-1, qOil-8-3, qOil-10-2 and qOil-10-4, detected in at least two environments plus combined environment with R2 values >10%. Within the physical intervals of these four QTLs, 111 candidate genes were screened for their direct or indirect involvement in seed protein and oil biosynthesis/metabolism processes based on gene ontology and annotation information. Based on RNA sequencing (RNA-seq) data analysis, 15 of the 111 genes were highly expressed during seed development stage and root nodules that might be considered as the potential candidate genes. Seven QTLs associated with protein and oil content exhibited significant additive and additive × environment interaction effects, and environment-independent QTLs revealed higher additive effects. Moreover, three digenic epistatic QTLs pairs were identified, and no main-effect QTLs showed epistasis. In conclusion, the use of a high-density map identified closely linked flanking markers, provided better understanding of genetic architecture and candidate gene information, and revealed the scope available for improvement of soybean quality through marker assisted selection (MAS).

Highlights

The high nutritional importance of soybean is due to higher levels of protein and oil in its seed [1], which makes the cultivation of soybean central to agriculture in China and other parts of the world [2]
analysis of variance (ANOVA) results showed that the differences among recombinant inbred line (RIL) of mapping population were highly significant for both traits (p < 0.01, Table S3)
All main-effect QTLs identified in the present study had no epistatic interaction, which increases the heritability of the trait and makes selection easier

Summary

Introduction

The high nutritional importance of soybean is due to higher levels of protein (average 40%) and oil (average 20%) in its seed [1], which makes the cultivation of soybean central to agriculture in China and other parts of the world [2]. By comparing the modern soybean cultivars with the landraces, it is evident that traditional breeding methods have developed soybean lines with high oil content but at the cost of decreasing seed protein content or vice versa [6]. The improvement of both traits simultaneously in the same cultivar is a challenging task through conventional breeding, as protein and oil content are negatively correlated [7]. Confirmation and integration of protein and oil QTLs in soybean breeding leading cultivars with high protein and oil could increase the economic value of the crop, thereby enriching the entire value chain from farmers to processors and to the end-users [8]

Methods

Results

Discussion

Conclusion