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ARS Home » Southeast Area » Raleigh, North Carolina » Soybean and Nitrogen Fixation Research » Research » Publications at this Location » Publication #379624
Research Project: Exploiting Genetic Diversity through Genomics, Plant Physiology, and Plant Breeding to Increase Competitiveness of U.S. Soybeans in Global Markets

Location: Soybean and Nitrogen Fixation Research

Title: Development of SNP molecular markers associated with resistance to reniform nematode in soybean using KASP genotyping

Author
item WILKES, JULIET - CLEMSON UNIVERSITY
item Fallen, Benjamin
item SASKI, CHRIS - CLEMSON UNIVERSITY
item AGUDELO, PAULA - CLEMSON UNIVERSITY

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2022
Publication Date: 1/22/2023
Citation: Wilkes, J., Fallen, B.D., Saski, C., Agudelo, P. 2023. Development of SNP molecular markers associated with resistance to reniform nematode in soybean using KASP genotyping. Euphytica. https://doi.org/10.1007/s10681-022-03144-3.
DOI: https://doi.org/10.1007/s10681-022-03144-3

Interpretive Summary: The Germplasm Resource Network (GRIN) lists 44 reniform nematode resistant soybean genotypes. In our study all 44 lines had reduced reniform nematode reproduction compared to a susceptible control, as expected. However, six of the 44 screened soybean germplasm had consistently higher reproductive index (RI) compared to the other 38 germplasm. Interestingly, three (PI 467312, PI 458520, PI 416762) of those six were reported susceptible to reniform nematode in a previous study in 2015. Conversely, PI 437725 had low RI, consistent with the highly resistant germplasm but was classified as susceptible in that same study. In our current study the KASP assay results indicated that two of the genotyped resistant soybean lines carried the susceptible genotype; PI 438489 B at GlyREN18_46 and PI 495017 C at GlyREN11_190. These two soybean germplasm are also of the six germplasm with slightly higher RI than the other 38 RN-resistant germplasm. It is likely that both of these germplasm may carry novel mechanisms of resistance to reniform nematode. The KASP assay designed to target GlyREN18_46 gave clear distinct clusters between all three genotypes. Although the KASP assay for GlyREN11_190 did not yield the expected three genotype clusters, some conclusions can be made based on the sample clustering with the standard controls. The prediction accuracy rate for the phenotypically resistant soybean germplasm was higher than when testing the susceptible germplasm. It is possible that susceptible germplasm has greater genetic diversity in comparison with the resistant germplasm. If there are not many sources of resistance, the genotypes of the resistant germplasm may be more similar than the susceptible germplasm. Additionally, being a quantitative trait, there are multiple loci that are involved in the resistance phenotype. Therefore, presence of one or two known resistance loci may not be sufficient to predict the phenotype.

Technical Abstract: Reniform nematode (Rotylenchulus reniformis, Linford and Oliveira) is a sedentary, semi-endoparasite that can infect a wide range of plant hosts in tropical and subtropical climates and is one of the top three nematode pathogens on soybean in the southeastern United States. Previous studies have linked resistance to reniform nematode in soybean to two quantitative trait loci on Chromosomes 11 and 18. A Kompetitive Allele-Specific PCR (KASP) assay was designed using SNP markers within these two regions to identify reniform nematode resistant soybean germplasm based on genotype. A collection of 44 soybean Plant Introductions (PIs) resistant to reniform nematode and 40 susceptible soybean lines were genotyped at the two target loci to validate the KASP assay design. Of the 44 tested resistant lines, two had the susceptible allele; PI 438489B at the loci on chromosome 18 and PI 495017C on chromosome 11. In contrast, 25 and 13 of the 40 susceptible soybean lines carried the expected susceptible allele at the loci on chromosomes 18 and 11, respectively. These results indicate that the developed KASP assay is not fully accurate in determining the susceptibility of reniform nematode. Based on our sample collection, the KASP assay accurately correlated with the expected genotype 68% and 83% of the time at loci on chr. 18 and 11, respectively. Further testing is required to refine these markers to fully capture all possible genetic sources of reniform nematode resistance for reliable phenotypic prediction.