Genome‐wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus

Abstract

SummaryBrassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twentyfour genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.

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

“…Other studies also pointed out the importance of GST in potato, rice, and tobacco to Phytophthora infestans , Magnaporthe oryzae , and two Colletotrichum species, respectively (Dean, Goodwin, & Hsiang, ; Leonards‐Schippers et al., ; Wisser, Sun, Hukbert, Kresovich, & Nelson, ). 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., ).…”

“…Other than GST, redox‐related genes were up‐regulated after S. sclerotiorum inoculation and were significantly enriched in cluster IV, and redox‐related enzymes such as an oxidoreductase and a cytochrome b‐561 were found in GWAS for lesion or nodal resistance, respectively. Although the molecular function of cytochrome b‐561 in plant resistance is not clear, it has been also discovered for S. sclerotiorum resistance in B. napus using GWAS and RNA‐Seq (Wei et al., ). Surprisingly, our combined RNA‐Seq and GWAS strategy to search for S. sclerotiorum resistance in pea ended up with results similar to the study of B. napus , where β‐glucosidase, TPR‐containing protein, ARM repeat superfamily protein, cytochrome b‐561, LRR‐containing proteins, and the GST were also found for B. napus (Supporting Information Tables and ; Wei et al., ).…”

“…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.…”

“…RNA‐Seq and GWAS both have their advantages, and combining them provides a powerful tool to discover not only active genes that express in response to treatments, but also genetic diversity and SNPs associated with the treatment. This combined strategy has been applied to understand white mold resistance and yields in B. napus (Lu et al., ; Wei et al., ) and soybean (Wen et al., ), but not in pea. Because genes that can be found by both GWAS and RNA‐Seq will have higher potential in contributing to white mold resistance, this study aimed to understand and compare the genetics of lesion and nodal resistance by applying both GWAS and RNA‐Seq approaches in the pea‐ S. sclerotiorum pathosystem.…”

A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus

“…Based on integrative analyses of RNA-seq and GWAS in B. napus , 8 and 24 candidate genes putatively associated with drought tolerance and stem resistance to Sclerotinia sclerotiorum , respectively, were identified3840. More recently, QTL fine mapping, digital gene expression (DGE) profiling, and whole-genome re-sequencing (WGS) were combined to identify a NODULIN 26-LIKE INTRINSIC PROTEIN gene involved in regulating boron uptake efficiency in B. napus 39.…”