Identification of candidate genes for a major quantitative disease resistance locus from soybean PI 427105B for resistance to phytophthora sojae

Authors: KARHOFF, STEPHANIE - The Ohio State University; VARGAS GARCIA, CHRISTIAN - The Ohio State University; LEE, SUNGWOO - Chungnam National University; Mian, Rouf; Graham, Michelle; DORRANCE, ANNE - The Ohio State University; MCHALE, LEAH - The Ohio State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/2/2022
Publication Date: 6/14/2022
Citation: Karhoff, S., Vargas-Garcia, C., Lee, S., Mian, R.M., Graham, M.A., Dorrance, A., McHale, L. 2022. Identification of candidate genes for a major quantitative disease resistance locus from soybean PI 427105B for resistance to phytophthora sojae. Frontiers in Plant Science. 13. Article 893652.
DOI: https://doi.org/10.3389/fpls.2022.893652

Interpretive Summary: Phytophthora root and stem rot causes the second most yield loss of soybean in the U.S., after soybean cyst nematode. It is particularly severe in the North Central Region of the country, where 80% of U.S. soybeans are grown. Phytophthora root and stem rot (PRR) is caused by the soil-borne oomycete Phytophthora sojae. Breeders have historically relied on single, dominant Rps genes, to control this disease. However, the widespread use of Rps genes in soybean cultivar development combined with the rapid pace of P. sojae evolution has caused a shift in pathogen virulence. Moreover, P. sojae populations have continued to adapt to the previously deployed Rps genes making them ineffective to control this disease. The second type of host resistance, referred to as partial resistance, is quantitatively inherited and considered race non-specific. Partial resistance to P. sojae has also been utilized in soybean cultivar development and is conferred by multiple quantitative disease resistance loci. Although multiple quantitative disease resistance loci (QDRL) have been identified, most explain less than 10% of the phenotypic variation (PV) in resistance. A major QDRL explaining up to 45% of the PV was previously identified on soybean chromosome 18 and represents a valuable source of durable resistance for soybean breeding programs. Resistance alleles from Plant introductions 427105B significantly increase yield in disease-prone fields and result in no significant yield difference in fields with little to no disease pressure. In this study, high resolution mapping pinpointed a single gene of interest which was downregulated in inoculated lines carrying the resistant allele (gene) compared to inoculated with the susceptible allele at all time points. This gene of interest putatively encodes a serine threonine kinase (STK) related to the AtCR4 family, and may be acting as a susceptibility factor, based on the specific increase of jasmonic acid. This is a valuable step forward towards cloning the allele for PRR resistance at this locus.

Technical Abstract: Phytophthora root and stem rot is a yield-limiting soybean disease caused by the soil-borne oomycete Phytophthora sojae. Although multiple quantitative disease resistance loci (QDRL) have been identified, most explain less than 10% of the phenotypic variation (PV). A major QDRL explaining up to 45% of the PV was previously identified on chromosome 18 and represents a valuable source of resistance for soybean breeding programs. Resistance alleles from Plant introductions 427105B and 427106 significantly increase yield in disease-prone fields and result in no significant yield difference in fields with little to no disease pressure. In this study, high resolution mapping reduced the QDRL interval to 3.1 cM, and RNA-seq analysis of near-isogenic lines (NILs) varying at QDRL-18 pinpointed a single gene of interest which was downregulated in inoculated NILs carrying the resistant allele compared to inoculated NILs with the susceptible allele at all time points. This gene of interest putatively encodes a serine threonine kinase (STK) related to the AtCR4 family, and may be acting as a susceptibility factor, based on the specific increase of jasmonic acid in inoculated NILs. concentration analysis. This work facilitates further functional analyses and marker-assisted breeding efforts by prioritizing candidate genes and narrowing the targeted region for introgression.