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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Publications at this Location » Publication #364825
Research Project: Integrated Management of Soybean Pathogens and Pests

Location: Soybean/maize Germplasm, Pathology, and Genetics Research

Title: Genome-wide association and genomic prediction identifies soybean cyst nematode resistance in common bean including a syntenic region to soybean Rhg1 locus

Author
item WEN, LIWEI - University Of Illinois
item CHANG, HAO-XUN - University Of Illinois
item BROWN, PATRICK - University Of Illinois
item Domier, Leslie
item Hartman, Glen

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/13/2018
Publication Date: 1/9/2019
Citation: Wen, L., Chang, H., Brown, P.J., Domier, L.L., Hartman, G.L. 2019. Genome-wide association and genomic prediction identifies soybean cyst nematode resistance in common bean including a syntenic region to soybean Rhg1 locus. Horticulture Research. 6:9. https://doi.org/10.1038/s41438-018-0085-3.
DOI: https://doi.org/10.1038/s41438-018-0085-3

Interpretive Summary: Soybean cyst nematode is one of the most important root pathogens of soybean and has recently been identified as a potential problem on common bean. This study found a significant association between molecular markers in the common bean genome to soybean cysts counts on 363 common bean accessions. The identification of molecular markers in common bean associated with soybean cyst nematode resistance will help to understand the genetic architecture in common bean, but also facilitates the genetic improvement of cultivars and the identification of resistance. This information will be used by plant breeders, geneticists, and others interested in host plant resistance.

Technical Abstract: A genome-wide association study (GWAS) was applied to detect single nucleotide polymorphisms (SNPs) significantly associated with resistance to Heterodera glycines (HG) also known as the soybean cyst nematode (SCN) in the core collection of common bean, Phaseolus vulgaris. There were 84,416 SNPs identified in 363 common bean accessions. GWAS identified SNPs on chromosome (Chr) 1 that were significantly associated with resistance to HG type 2.5.7. These SNPs were in linkage disequilibrium with a gene cluster homologous to the three genes at the Rhg1 locus in soybean. A novel signal on Chr 7 was detected and associated with resistance to HG type 1.2.3.5.6.7. Genomic predictions (GPs) of resistance to these two SCN HG types in common bean achieved prediction accuracy of 0.52 and 0.41, respectively. Our study generated a high-quality SNP panel for 363 common bean accessions and demonstrated that both GWAS and GP were effective strategies to understand the genetic architecture of SCN resistance in common bean.