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

Abstract

Reniform nematode (Rotylenchulus reniformis, Linford and Oliveira) is a sedentary, semi-endoparasite that infects a wide range of plant hosts and is one of the top three nematode pathogens affecting 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 distinguish reniform nematode-resistant soybean based on genotype. A collection of 44 soybean plant introductions with resistant phenotype to reniform nematode and 40 susceptible soybean lines were genotyped at the two target loci to validate the KASP assay design. Of the 44 observed resistant lines, two carried the susceptible genotype; PI 438489B at the locus on chromosome 18 and PI 495017C on chromosome 11. Of the 40 observed susceptible soybean lines, only 25 had the expected susceptible genotype at the loci on chromosome 18 and 13 on chromosome 11. Our KASP assay was 68% accurate in predicting the phenotype of 84 soybean accessions based on their genotype at the SNP marker on chromosome 18 and 83% accurate at chromosome 11. These results indicate a moderate correlation of soybean SNP markers GlyREN18_46 and GlyREN11_190 with reniform nematode resistance. Further research is required to improve the accuracy of KASP assays to predict soybean response to reniform nematode, particularly host susceptibility.