95% of researchers rate our articles as excellent or good
Learn more about the work of our research integrity team to safeguard the quality of each article we publish.
Find out more
ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1520999
Identification and Genetic Analysis of Candidate Genes for Resistance against Phytophthora sojae in Soybean using a Genome-wide Association Study
Provisionally accepted
Hye Rang Park 1
Su Vin Heo 1* Beom Kyu Kang 1 Hyoseob Seo 1
Eunsoo Lee 1
Jihee Park 1 Yun Woo Jang 2
Jeong Hyun Seo 1
Girim Park 1 Jun Hoi Kim 1 Yeong Hoon Lee 1 Won Young Han 1 Myung Chul Seo 1 Ji-Ung Jeung 1- 1 Division of Upland Crop Breeding Research, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
- 2 Division of Crop Production Technology Research, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
Phytophthora root and stem rot (PRSR), an infection caused by Phytophthora sojae in soybean [Glycine max (L.) Merr.], is an important threat to soybean production in South Korea; however, the precise genetic mechanisms related to PRSR resistance remain largely unclear, limiting the development of resistant cultivars. This study aimed to identify candidate resistance (R) genes related to PRSR resistance in soybeans through a genomewide association study (GWAS). We evaluated 205 soybean accessions inoculated with P. sojae isolates GJ3053 or AD3617 using the hypocotyl inoculation method and genotyped them using a 180K Axiom SoyaSNP chip. We identified 19 significant single-nucleotide polymorphisms (SNPs) related to resistance against one or both of the two isolates: GJ3053 resistance was associated with SNPs on chromosomes 2, 3, 9, 10, 14, and 16, whereas AD3617 resistance was related to SNPs on chromosomes 3, 13, and 16. The SNP AX-90410433 (3,628,549 bp) on chromosome 3 was significantly linked to resistance against both isolates, based on the linkage disequilibrium (480 kb) and -log10(p) values (6.62). This region harbors key resistance gene analogs (RGAs), including nucleotide-binding site leucine-rich repeat and serine-threonine protein kinases. Among the 34 identified RGAs in the 2.9-4.4 Mbp region, Glyma.03g036500, which encodes a protein with serine kinase activity, emerged as a strong candidate. Haplotype analysis revealed that this gene exhibited genotypic patterns consistent with the resistance phenotypes of the selected accessions. Validation through gene expression and kompetitive allele-specific PCR marker analysis supported the role of Glyma.03g036500 in PRSR resistance. These findings underscore the significance of identifying and utilizing PRSR resistance genes, such as Glyma.03g036500, to enhance pathogen resistance in soybean breeding programs. Our results can inform the development of cultivars with improved resistance to P. sojae, thus potentially mitigating the effect of pathogenic stress on crop productivity and quality, and contributing to sustainable agriculture.
Keywords: Soybean, Phytophthora sojae, Genome-Wide Association Study, Phytophthora root and stem rot, nucleotide-binding site leucine-rich repeat, and serine-threonine protein kinases
Received: 01 Nov 2024; Accepted: 01 Apr 2025.
Copyright: © 2025 Park, Heo, Kang, Seo, Lee, Park, Jang, Seo, Park, Kim, Lee, Han, Seo and Jeung. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Su Vin Heo, Division of Upland Crop Breeding Research, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.