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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #380352

Research Project: Characterization of Genetic Diversity in Soybean and Common Bean, and Its Application toward Improving Crop Traits and Sustainable Production

Location: Soybean Genomics & Improvement Laboratory

Title: Genome-wide association study and genomic prediction for soybean cyst nematode resistance in USDA common bean (Phaseolus vulgaris) core collection

item SHI, AILONG - University Of Arkansas
item GEPTS, PAUL - University Of California
item Song, Qijian
item XIONG, HAIZHENG - University Of Arkansas
item MICHAELS, THOMAS - University Of Minnesota

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2021
Publication Date: 6/7/2021
Citation: Shi, A., Gepts, P., Song, Q., Xiong, H., Michaels, T.E. 2021. Genome-wide association study and genomic prediction for soybean cyst nematode resistance in USDA common bean (Phaseolus vulgaris) core collection. Frontiers in Plant Science. 12:624156.

Interpretive Summary: The production of dry beans in the U.S. will be challenged by an existing invasive pest – the soybean cyst nematode (SCN). The SCN is the most serious pathogen of soybean in the U.S. and is widespread in North Dakota, Michigan, Nebraska, and Minnesota which also produce approximately 75% of the common beans in the U.S. As SCN becomes a more serious threat to common bean production, resistant common bean varieties will become more important. Currently, no commercial SCN-resistant cultivar is available for dry bean production due to a limited number of genetic studies of SCN resistance in common bean. In this study, we evaluated SCN resistance in a diverse set of 315 common beans from 11 countries including Mexico, Colombia, Guatemala, Peru, Costa Rica, Ecuador, El Salvador, Nicaragua, Honduras, Bolivia, and the U.S., and we mapped genes associated with the SCN resistance. We identified 15 beans highly resistant to SCN race 6 and found candidate genes on different chromosomes that contributed to the resistance to race 6 and other races. We also validated the use of DNA markers to evaluate other common beans for genes with SCN resistance. The common beans identified in this study will be valuable for combating SCN threating U.S. common bean production. Scientists and breeders in the government, at universities, and in private institutions will be able to use this information to select breeding lines with improved SCN resistance in common bean.

Technical 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. 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 USDA common bean core collection, conduct genome-wide association study (GWAS) of SNP markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips consisting of 4,790 single nucleotide polymorphisms (SNPs). Results showed that 15 accessions were resistant to SCN with Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. Association study showed that 11 SNP markers, located on chromosomes 4, 7, 9, and 11 were strongly associated with the resistance to SCN HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type based on the public dataset 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 chromosomes 1, 2, 3, and 7 and 12 SNPs with HG Type resistance on chromosomes 1, 3, 6, 7, 9, 10, and 11 were detected. The accuracy of genomic predictions was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that the genomic selection of SCN resistance is feasible. This study provided basic information for developing SCN-resistant common bean cultivars using the USDA core germplasm accessions. The SNP markers can be used in molecular breeding in common bean through marker-assisted selection and genomic selection.