Genome-wide association study reveals marker-trait associations with resistance to Pythium irregulare from soybean germplasm

Authors: Detranaltes, Christopher; MA, JIANXIN - Purdue University; Cai, Guohong

Submitted to: Journal of Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/12/2024
Publication Date: 8/15/2024
Citation: Detranaltes, C.E., Ma, J., Cai, G. 2024. Genome-wide association study reveals marker-trait associations with resistance to Pythium irregulare from soybean germplasm. Journal of Plant Biology. https://doi.org/10.3390/ijpb15030056.
DOI: https://doi.org/10.3390/ijpb15030056

Interpretive Summary: Seedling diseases are a broad diagnosis encompassing the symptoms of pre-emergence seed rots and post-emergence seedling decay caused by biotic pathogens. For the past two decades, soybean yield loss due to seedling diseases have consistently ranked as the second highest behind only those caused by soybean cyst nematode. Pythium irregulare is one of the major pathogens causing seedling disease in soybean. In this study, we screened a set of 208 soybean accessions in maturity groups 0-IV with diverse genetic background for resistance to two isolates of this pathogen from Indiana and Ohio. Ten accession were found to be significantly more resistant than the population mean to one or both of two isolates. Genome-wide association study led to the discovery of two significant marker-trait associations (MTAs) located on chromosomes 10 and 15. The resistant germplasm and MTAs uncovered through this study provide additional resources and tools for the genetic improvement of soybean resistance to seedling disease caused by P. irregulare.

Technical Abstract: Soybean (Glycine max (L.) Merr.) ranks as the second-largest crop by total production in the United States, despite production experiencing significant constraints from diseases, including seedling diseases. Pythium irregulare Buisman stands out as a predominant driver of yield loss associated with the seedling disease complex. There is currently a lack of public or commercial varieties available to growers with adequate genetic resistance to manage this pathogen. To address the pressing need for germplasm resources and molecular markers associated with P. irregulare resistance, we conducted a screening of 208 genetically diverse soybean accessions from the United States Department of Agriculture Soybean Germplasm Collection (USDA-SGC) against two geographically and temporally distinct isolates under controlled greenhouse conditions. Disease severity was assessed through comparisons of the root weight and stand count ratios of inoculated plants to mock-inoculated controls. Employing linear mixed modelling, we identified ten accessions (PI 548520, PI 548360, PI 548362, PI 490766, PI 547459, PI 591511, PI 547460, PI 84946 -2, PI 578503, FC 29333) with significantly higher resistance than the population mean to one or both of two isolates originating from Ohio or Indiana. Previously curated genotyping data, publicly available through the SoyBase database, was then used to conduct a genome-wide association study. This analysis led to the discovery of two significant marker-trait associations (MTAs) located on chromosomes 10 and 15 accounting for 9.3% and 17.2% of the phenotypic variance, respectively. The resistant germplasm and MTAs uncovered through this study provide additional resources and tools for the genetic improvement of soybean resistance to seedling disease caused by P. irregulare.