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Article|01 Jan 2019|OPEN
Genome-wide association and genomic prediction identifies soybean cyst nematode resistance in common bean including a syntenic region to soybean Rhg1 locus
Liwei Wen1,2 , Hao-Xun Chang1,3 and Patrick J. Brown1,4 , Leslie L. Domier1,5 , Glen L. Hartman,1,5 ,
1Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
2Present address: Monsanto, St. Louis, MO 63167, USA
3Present address: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
4Present address: Department of Plant Sciences, University of California, Davis, CA 95616, USA
5United States Department of Agriculture—Agricultural Research Service, Urbana, IL, USA
*Corresponding author. E-mail: glen.hartman@ars.usda.gov; ghartman@illinois.edu

Horticulture Research 6,
Article number: 9 (2019)
doi: https://doi.org/10.1038/s41438-018-0085-3
Views: 1098

Received: 19 Apr 2018
Revised: 18 Jul 2018
Accepted: 13 Aug 2018
Published online: 01 Jan 2019

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.