Association Mapping and Genomic Selection for Soybean Cyst Nematode Resistance

Soybean cyst nematode (SCN) resistance is an important quantitative trait that has yet to be investigated through association mapping (AM) or genomic selection (GS). We genotyped 282 representative accessions from the University of Minnesota soybean breeding program using a genome-wide panel of 1,536 single nucleotide polymorphism (SNP) markers and evaluated plant responses to SCN HG type 0. After adjusting for population structure, AM detected significant signals at two loci corresponding to rhg1 and FGAM1 plus a third locus located at the opposite end of chromosome 18. Our analysis also identified a discontinuous long-range haplotype of over 600 kb around rhg1 locus associated with resistance to SCN HG type 0. The same phenotypic and genotypic datasets were then used to access GS accuracy for SCN resistance in the presence of major genes through a 6-fold cross-validation study. GS using full marker set produced prediction accuracy ranging from 0.59 to 0.71 for SCN resistance. GS was significantly more accurate than conventional marker-assisted selection (MAS) based on the frequently employed strategy of using two rhg1-associated DNA makers. Reducing the number of markers to 288 SNPs in the GS training population had little effect on genomic prediction accuracy. This study demonstrates that AM can be an effective genomic tool for identifying genes of interest in diverse germplasm. The results also indicate that improved MAS and GS can enhance breeding efficiency for SCN resistance in existing soybean improvement programs.