Leveraging RNA-Seq to Characterize Resistance to Brown Stem Rot and the Rbs3 Locus in Soybean

Abstract

Brown stem rot, caused by the fungus Phialophora gregata, reduces soybean yield by up to 38%. Although three dominant resistance loci have been identified (Rbs1 to Rbs3), the gene networks responsible for pathogen recognition and defense remain unknown. Further, identification and characterization of resistant and susceptible germplasm remains difficult. We conducted RNA-Seq of infected and mock-infected leaf, stem, and root tissues of a resistant (PI 437970, Rbs3) and susceptible (Corsoy 79) genotype. Combining historical mapping data with genotype expression differences allowed us to identify a cluster of receptor-like proteins that are candidates for the Rbs3 resistance gene. Reads mapping to the Rbs3 locus were used to identify potential novel single-nucleotide polymorphisms within candidate genes that could improve phenotyping and breeding efficiency. Comparing responses to infection revealed little overlap in differential gene expression between genotypes or tissues. Gene networks associated with defense, DNA replication, and iron homeostasis are hallmarks of resistance to P. gregata. This novel research demonstrates the utility of combining contrasting genotypes, gene expression, and classical genetic studies to characterize complex disease resistance loci.

New tools for characterizing early brown stem rot disease resistance signaling in soybean

“…A previous BSR expression study (McCabe et al., 2018) identified genes responding to P. gregata 1 WAI. In that study, a large response was observed in leaf tissue of the resistant genotype 7 DAI (2,492 total DEGs); however, little differential gene expression was observed in roots (16 total DEGs) and stems (530 DEGs).…”

“…Therefore, we are using high-throughput, whole-genome expression analyses to characterize responses to P. gregata. Our previous study examined transcriptional changes in leaves, stems, and roots 7 d after infection (DAI) with P. gregata in a resistant and susceptible genotype (McCabe, Cianzio, O'Rourke, & Graham, 2018). While that analysis identi-…”

“…Therefore, we are using high‐throughput, whole‐genome expression analyses to characterize responses to P. gregata . Our previous study examined transcriptional changes in leaves, stems, and roots 7 d after infection (DAI) with P. gregata in a resistant and susceptible genotype (McCabe, Cianzio, O'Rourke, & Graham, 2018). While that analysis identified thousands of genes differentially expressed (DE) in response to P. gregata infection, the largest response was observed in leaf tissue of the resistant genotype with fewer genes DE in stems and roots.…”

“…Therefore, the objectives of this study were to use RNA‐seq to characterize the genes and gene networks responding to P. gregata infection in the same resistant soybean genotype 12, 24, and 36 HAI. These time points were selected based on previous reports on the fungal biology, our previous study (McCabe et al., 2018), and a careful review of the soybean disease resistance literature. Allington and Chamberlain (1948) reported germination of conidia 24 h after treatment in distilled water or soybean‐stem juice.…”

Association mapping of a locus that confers Southern stem canker resistance in soybean

“…It was observed in Glycine soja that the overexpression of GsLRPK gene contribute to an increase of tolerance to cold [47]. Finally, a RNA-seq study of the Rbs3 locus aid to identify some candidate genes associated with the resistance against brown stem root, which included some LRR-RPK genes [48]. Besides LRR-RPK genes, allelic variations were also observed in PRSTK (Glyma.14G026700).…”