Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

Henry T Nguyen,Fang Lu,Gunvant Patil,Rupesh Deshmukh,Babu Valliyodan,Siva Kumpatla,Xiaolei Wu,Sandip Kale,J Grover Shannon,Chengsong Zhu,Dennis Yungbluth,Rajeev K Varshney,Yonghe Bai,Tri D Vuong

doi:10.1111/pbi.12929

Abstract

SummaryThe cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil, and high sucrose. In this study, an interspecific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3× depth. Based on 91 342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high‐resolution bin map was developed (4070 bins). In addition to bin mapping, quantitative trait loci (QTL) analysis for protein, oil, and sucrose was performed using 3343 polymorphic SNPs (3K‐SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared, and a significant concordance was observed between bin and 3K‐SNP markers. Importantly, the bin map derived from next‐generation sequencing technology enhanced mapping resolution (from 1325 to 50 Kb). A total of five, nine, and four QTLs were identified for protein, oil, and sucrose content, respectively, and some of the QTLs coincided with soybean domestication‐related genomic loci. The major QTL for protein and oil were mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL were identified on Chr. 8 (qSuc_08) and harbours putative genes involved in sugar transport. In addition, genome‐wide association using 91 342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL‐based haplotype using whole‐genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean.

Highlights

A major part of human, poultry, and livestock diets is derived from cereals and legumes (Mandal and Mandal, 2000)
The recombinant inbred line (RIL) showed a transgressive segregation where several RILs have exceeded in protein and sucrose content as compared to the parents, PI 483460B and Williams 82, respectively
It is well studied that seed protein content is negatively correlated to seed oil and sucrose content in soybean (Nichols et al, 2006; Patil et al, 2017b; Sonah et al, 2015) Based on the phenotypic correlation among traits estimated for protein, oil, and sucrose across four environments, a similar trend was observed in this population (Figure 1)

Summary

Introduction

A major part of human, poultry, and livestock diets is derived from cereals and legumes (Mandal and Mandal, 2000). Cultivated soybean [Glycine max (L.) Merr.] is a unique legume species that has 38%–42% protein, 18%–22% oil, and 4%–6% sucrose in seed and is commonly adapted to and grown in many areas in the world for human consumption, animal feed, and biodiesel production. Wild soybean species (Glycine soja Siebold & Zucc.), contains lower oil (8%–10%, nearly half of cultivated soybean), and lower sucrose (3%–4%), and relatively high protein content (46%–48%). Protein and oil contents in soybean seed are more important because approximately 60% of the value of soybeans comes from its protein meal, and the remaining 40% comes from its oil. In the United States, a minimum of 47.5% protein in soybean meal is demanded by the marketplace; the meal protein value of most commodity soybean cultivars is below this minimum threshold level (http://unitedsoy bean.org/)

Objectives

Methods

Results

Conclusion