Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil

Abstract

BackgroundSclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work together to provide partial resistance. In this study, a genome-wide association study (GWAS) was performed to dissect the complex genetic architecture of soybean quantitative resistance to SSR and to provide effective molecular markers that could be used in breeding programs. A collection of 420 soybean genotypes were selected based on either reports of resistance, or from one of three different breeding programs in Brazil, two commercial, one public. Plant genotype sensitivity to SSR was evaluated by the cut stem inoculation method, and lesion lengths were measured at 4 days post inoculation.ResultsGenotyping-by-sequencing was conducted to genotype the 420 soybean lines. The TASSEL 5 GBSv2 pipeline was used to call SNPs under optimized parameters, and with the extra step of trimming adapter sequences. After filtering missing data, heterozygosity, and minor allele frequency, a total of 11,811 SNPs and 275 soybean genotypes were obtained for association analyses. Using a threshold of FDR-adjusted p-values <0.1, the Compressed Mixed Linear Model (CMLM) with Genome Association and Prediction Integrated Tool (GAPIT), and the Fixed and Random Model Circulating Probability Unification (FarmCPU) methods, both approaches identified SNPs with significant association to disease response on chromosomes 1, 11, and 18. The CMLM also found significance on chromosome 19, whereas FarmCPU also identified significance on chromosomes 4, 9, and 16.ConclusionsThese similar and yet different results show that the computational methods used can impact SNP associations in soybean, a plant with a high degree of linkage disequilibrium, and in SSR resistance, a trait that has a complex genetic basis. A total of 125 genes were located within linkage disequilibrium of the three loci shared between the two models. Their annotations and gene expressions in previous studies of soybean infected with S. sclerotiorum were examined to narrow down the candidates.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4160-1) contains supplementary material, which is available to authorized users.

Exploring the genetics of lesion and nodal resistance in pea (Pisum sativum L.) to Sclerotinia sclerotiorum using genome‐wide association studies and RNA‐Seq

“…Moreover, most studies focusing on B. napus resistance to S. sclerotiorum also identified GST regardless of the methodologies, GWAS or RNA‐Seq (Girard et al., ; Wei et al., ; Wu, Zhao, Liu, et al., ). A recent GWAS for soybean resistance to S. sclerotiorum also identified soybean GST (Wei et al., ) which was also noted to have high expression in a transcriptomic study (Calla et al., ). Consistently, our results also pointed out GST of pea may play a fundamental role in lesion and nodal resistance to S. sclerotiorum .…”

“…While most of these studies focused on the expression comparisons between a resistant and a susceptible variety, the genetic diversity of white mold resistance in B. napus might be underestimated using only this approach. Genome‐wide association study (GWAS) is a robust approach to map white mold resistance and to capture the resistance diversity in a germplasm collection (Moellers et al., ; Wei et al., , ). The GWAS approach has been demonstrated in soybean ( Glycine max Merr.…”

Resistance against Sclerotinia sclerotiorum in soybean involves a reprogramming of the phenylpropanoid pathway and up‐regulation of antifungal activity targeting ergosterol biosynthesis

“…In soybean, bi-parental linkage mapping led to the discovery of many quantitative trait loci (QTL) for resistance to this pathogen. Remarkably, a total of 103 QTL on 18 of the 20 soybean chromosomes have been recorded in SoyBase (Grant et al, 2009) with minimal overlap between QTL reported by different studies (Arahana et al, 2001;Huynh et al, 2010;Kim and Diers, 2000;McCaghey et al, 2017;Moellers et al, 2017;Wei et al, 2017). Despite these efforts, gene level and mechanistic details of soybean resistance mechanisms against S. sclerotiorum remain unknown.…”

Integrated soybean transcriptomics, metabolomics, and chemical genomics reveal the importance of the phenylpropanoid pathway and antifungal activity in resistance to the broad host range pathogenSclerotinia sclerotiorum

“…In soybean, Bi-parental linkage mapping led to the discovery of many quantitative trait loci (QTL) for resistance to this pathogen. Remarkably, a total of 103 QTL on 18 of the 20 soybean chromosomes have been recorded in SoyBase (21) with minimal overlap between QTL reported by different studies (9,22–26). Despite these efforts, gene level and mechanistic details of soybean resistance mechanisms against S .…”