Genome-wide association study of partial resistance to sclerotinia stem rot of cultivated soybean based on the detached leaf method.

Mingming Sun,Xue Zhao,Yingpeng Han,Weili Teng,Wenbin Li,Lijuan Qiu,Yan Jing,Hongkun Zheng,Istvan Rajcan

doi:10.1371/journal.pone.0233366

Abstract

Sclerotinia stem rot (SSR) is a devastating fungal disease that causes severe yield losses of soybean worldwide. In the present study, a representative population of 185 soybean accessions was selected and utilized to identify the quantitative trait nucleotide (QTN) of partial resistance to soybean SSR via a genome-wide association study (GWAS). A total of 22,048 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) > 5% and missing data < 3% were used to assess linkage disequilibrium (LD) levels. Association signals associated with SSR partial resistance were identified by two models, including compressed mixed linear model (CMLM) and multi-locus random-SNP-effect mixed linear model (mrMLM). Finally, seven QTNs with major effects (a known locus and six novel loci) via CMLM and nine novel QTNs with minor effects via mrMLM were detected in relation to partial resistance to SSR, respectively. One of all the novel loci (Gm05:14834789 on Chr.05), which was co-located by these two methods, might be a stable one that showed high significance in SSR partial resistance. Additionally, a total of 71 major and 85 minor candidate genes located in the 200-kb genomic region of each peak SNP detected by CMLM and mrMLM were found, respectively. By using a gene-based association, a total of six SNPs from three major effects genes and eight SNPs from four minor effects genes were identified. Of them, Glyma.18G012200 has been characterized as a significant element in controlling fungal disease in plants.

Highlights

As one of the most devastating and economically important fungal phytopathogens in soybean [Glycine max (L.) Merr.], sclerotinia stem rot (SSR) is caused by Sclerotinia sclerotiorum (Lib.) de Bary, and humidity and temperature have a profound impact on the prevalence, incidence, development and severity of this disease [1]
The results showed that the first three Principal component (PC) accounted for 13.18% of the overall genetic variations, and the inflection point occurred at PC3, which indicated that the first three PCs could dominate the population structure for the association mapping (Fig 3B and 3C)
As a heritable complex quantitative trait, SSR is controlled by multiple genes with major or minor effects [6] and is affected by environment and genotype through environment interactions [5]

Summary

Introduction

As one of the most devastating and economically important fungal phytopathogens in soybean [Glycine max (L.) Merr.], sclerotinia stem rot (SSR) is caused by Sclerotinia sclerotiorum (Lib.) de Bary, and humidity and temperature have a profound impact on the prevalence, incidence, development and severity of this disease [1]. GWAS for partial resistance to SSR of soybean to publish, or preparation of the manuscript. The specific role of this author is articulated in the ‘author contributions’ section

Objectives

Methods

Results

Conclusion