Genome-wide association study of powdery mildew resistance in cultivated soybean from Northeast China

Yongsheng Sang; Hongkun Zhao; Xiaodong Liu; Cuiping Yuan; Guangxun Qi; Yuqiu Li; Lingchao Dong; Yingnan Wang; Dechun Wang; Yumin Wang; Yingshan Dong

doi:10.3389/fpls.2023.1268706

Genome-wide association study of powdery mildew resistance in cultivated soybean from Northeast China

Front Plant Sci. 2023 Nov 2:14:1268706. doi: 10.3389/fpls.2023.1268706. eCollection 2023.

Authors

Yongsheng Sang^{1

2}, Hongkun Zhao², Xiaodong Liu³, Cuiping Yuan², Guangxun Qi², Yuqiu Li², Lingchao Dong², Yingnan Wang², Dechun Wang⁴, Yumin Wang², Yingshan Dong^{1

2}

Affiliations

¹ College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China.
² Soybean Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China.
³ Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, Jilin, China.
⁴ Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States.

Abstract

Powdery mildew (PMD), caused by the pathogen Microsphaera diffusa, leads to substantial yield decreases in susceptible soybean under favorable environmental conditions. Effective prevention of soybean PMD damage can be achieved by identifying resistance genes and developing resistant cultivars. In this study, we genotyped 331 soybean germplasm accessions, primarily from Northeast China, using the SoySNP50K BeadChip, and evaluated their resistance to PMD in a greenhouse setting. To identify marker-trait associations while effectively controlling for population structure, we conducted genome-wide association studies utilizing factored spectrally transformed linear mixed models, mixed linear models, efficient mixed-model association eXpedited, and compressed mixed linear models. The results revealed seven single nucleotide polymorphism (SNP) loci strongly associated with PMD resistance in soybean. Among these, one SNP was localized on chromosome (Chr) 14, and six SNPs with low linkage disequilibrium were localized near or in the region of previously mapped genes on Chr 16. In the reference genome of Williams82, we discovered 96 genes within the candidate region, including 17 resistance (R)-like genes, which were identified as potential candidate genes for PMD resistance. In addition, we performed quantitative real-time reverse transcription polymerase chain reaction analysis to evaluate the gene expression levels in highly resistant and susceptible genotypes, focusing on leaf tissues collected at different times after M. diffusa inoculation. Among the examined genes, three R-like genes, including Glyma.16G210800, Glyma.16G212300, and Glyma.16G213900, were identified as strong candidates associated with PMD resistance. This discovery can significantly enhance our understanding of soybean resistance to PMD. Furthermore, the significant SNPs strongly associated with resistance can serve as valuable markers for genetic improvement in breeding M. diffusa-resistant soybean cultivars.

Keywords: GWAS; candidate genes; powdery mildew; single nucleotide polymorphism; soybean.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was funded by the National key R & D Program of China (2021YFD1201604-04). The funder took part in the design of the study; collection, analysis and interpretation of the data; and writing of the manuscript.