Genome-Wide Association Study and Genomic Prediction for Soybean Cyst Nematode Resistance in USDA Common Bean (Phaseolus vulgaris) Core Collection

Ainong Shi; Paul Gepts; Qijian Song; Haizheng Xiong; Thomas E Michaels; Senyu Chen

doi:10.3389/fpls.2021.624156

Genome-Wide Association Study and Genomic Prediction for Soybean Cyst Nematode Resistance in USDA Common Bean (Phaseolus vulgaris) Core Collection

Front Plant Sci. 2021 Jun 7:12:624156. doi: 10.3389/fpls.2021.624156. eCollection 2021.

Authors

Ainong Shi¹, Paul Gepts², Qijian Song³, Haizheng Xiong¹, Thomas E Michaels⁴, Senyu Chen⁵

Affiliations

¹ Department of Horticulture, PTSC316, University of Arkansas, Fayetteville, AR, United States.
² Department of Plant Sciences, University of California, Davis, Davis, CA, United States.
³ United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States.
⁴ Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States.
⁵ Southern Research and Outreach Center, University of Minnesota, Waseca, MN, United States.

Abstract

Soybean cyst nematode (SCN, Heterodera glycines) has become the major yield-limiting biological factor in soybean production. Common bean is also a good host of SCN, and its production is challenged by this emerging pest in many regions such as the upper Midwest USA. The use of host genetic resistance has been the most effective and environmentally friendly method to manage SCN. The objectives of this study were to evaluate the SCN resistance in the USDA common bean core collection and conduct a genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN HG Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips, consisting of 4,654 SNPs. Results showed that 15 accessions were resistant to SCN with a Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. The association study showed that 11 SNP markers, located on chromosomes Pv04, 07, 09, and 11, were strongly associated with resistance to HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type 1.2.3.5.6.7 based on the public dataset (N = 276), consisting of a diverse set of common bean accessions genotyped with the BARCBean6K_3 chip. Six SNPs associated with HG Type 2.5.7 resistance on Pv 01, 02, 03, and 07, and 12 SNPs with HG Type 1.2.3.5.6.7 resistance on Pv 01, 03, 06, 07, 09, 10, and 11 were detected. The accuracy of genomic prediction (GP) was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that genomic selection (GS) of SCN resistance is feasible. This study provides basic information for developing SCN-resistant common bean cultivars, using the USDA core germ plasm accessions. The SNP markers can be used in molecular breeding in common beans through marker-assisted selection (MAS) and GS.

Keywords: Heterodera glycines; Phaseolus vulgaris; common bean; genome wide association study; genomic prediction; genomic selection; single nucleotide polymorphism; soybean cyst nematode.

Associated data

Dryad/10.25338/B8KP45