AUTHOR=McCabe Chantal E. , Lincoln Lori M. , O’Rourke Jamie A. , Graham Michelle A. 

TITLE=Virus induced gene silencing confirms oligogenic inheritance of brown stem rot resistance in soybean

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1292605

DOI=10.3389/fpls.2023.1292605

ISSN=1664-462X

ABSTRACT=<p>Brown Stem Rot (BSR), caused by the soil borne fungal pathogen <italic>Phialophora gregata</italic>, can reduce soybean yields by as much as 38%. Previous allelism studies identified three Resistant to brown stem Rot genes (<italic>Rbs1, Rbs2</italic>, and <italic>Rbs3</italic>), all mapping to large, overlapping regions on soybean chromosome 16. However, recent fine-mapping and genome wide association studies (GWAS) suggest <italic>Rbs1, Rbs2</italic>, and <italic>Rbs3</italic> are alleles of a single <italic>Rbs</italic> locus. To address this conflict, we characterized the <italic>Rbs</italic> locus using the Williams82 reference genome (Wm82.a4.v1). We identified 120 Receptor-Like Proteins (RLPs), with hallmarks of disease resistance receptor-like proteins (RLPs), which formed five distinct clusters. We developed virus induced gene silencing (VIGS) constructs to target each of the clusters, hypothesizing that silencing the correct RLP cluster would result in a loss of resistance phenotype. The VIGS constructs were tested against <italic>P. gregata</italic> resistant genotypes L78-4094 (<italic>Rbs1</italic>), PI 437833 (<italic>Rbs2</italic>), or PI 437970 (<italic>Rbs3)</italic>, infected with <italic>P. gregata</italic> or mock infected. No loss of resistance phenotype was observed. We then developed VIGS constructs targeting two RLP clusters with a single construct. Construct B1a/B2 silenced <italic>P. gregata</italic> resistance in L78-4094, confirming at least two genes confer <italic>Rbs1</italic>-mediated resistance to <italic>P. gregata</italic>. Failure of B1a/B2 to silence resistance in PI 437833 and PI 437970 suggests additional genes confer BSR resistance in these lines. To identify differentially expressed genes (DEGs) responding to silencing, we conducted RNA-seq of leaf, stem and root samples from B1a/B2 and empty vector control plants infected with <italic>P. gregata</italic> or mock infected. B1a/B2 silencing induced DEGs associated with cell wall biogenesis, lipid oxidation, the unfolded protein response and iron homeostasis and repressed numerous DEGs involved in defense and defense signaling. These findings will improve integration of <italic>Rbs</italic> resistance into elite germplasm and provide novel insights into fungal disease resistance.</p>