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

Liwei Wen; Hao-Xun Chang; Patrick J Brown; Leslie L Domier; Glen L Hartman

doi:10.1038/s41438-018-0085-3

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

Hortic Res. 2019 Jan 1:6:9. doi: 10.1038/s41438-018-0085-3. eCollection 2019.

Authors

Liwei Wen^{1

2}, Hao-Xun Chang^{1

3}, Patrick J Brown^{1

4}, Leslie L Domier^{1

5}, Glen L Hartman^{1

5}

Affiliations

¹ 1Department of Crop Sciences, University of Illinois, Urbana, IL 61801 USA.
² 3Present Address: Monsanto, St. Louis, MO 63167 USA.
³ 4Present Address: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA.
⁴ 5Present Address: Department of Plant Sciences, University of California, Davis, CA 95616 USA.
⁵ 2United States Department of Agriculture-Agricultural Research Service, Urbana, IL USA.

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 orthologous 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) for 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.