Genome-wide association study for resistance to the southern root-knot nematode ( Meloidogyne incognita ) in soybean

Soybean [ Glycine max (L.) Merrill] is one of the most important traded commodities for the world’s economy. However, soybean cultivation is often affected by biotic and abiotic factors that prevent the crop from attaining its full yield potential. With the advent of new tools for next-generation sequencing, the genomic knowledge gained from the study of this major oilseed crop has increased considerably in recent years. In this study, we performed a genotypic characterization of 188 plant introductions (PIs) and five cultivars using a genotyping-by-sequencing (GBS) approach and a phenotypic characterization for resistance/tolerance to the southern root-knot nematode, Meloidogyne incognita . We then performed a genome-wide association study (GWAS) for this important trait. From 46,196 SNP markers identified and validated on this set of genotypes, three were significantly associated with nematode resistance. Remarkably, all of these were in a single, very small (3.4 kb) region of chromosome 10. Most lines (48 out of 57) with the highest level of resistance shared the haplotype composed of the alleles associated with resistance at these three SNP loci. Interestingly, nine of the lines exhibiting a high level of resistance did not exhibit the “resistant haplotype” on Gm10. This suggests either that recombination has broken the association between the SNPs and the resistance locus or that resistance is conferred by a different locus altogether. In the latter case, these lines represent a putative alternative source of resistance, an important information for breeding programs.