Development of SNP assays for marker-assisted selection of two southern root-knot nematode resistance QTL in soybean

The identification of single nucleotide polymorphism (SNP) markers tightly linked to soybean [Glycine max (L.) Merr.] quantitative trait loci (QTL) conditioning resistance to southern root-knot nematode (Meloidogyne incognita) (Mi) would enhance the efficiency and cost effectiveness of marker-assisted selection (MAS) for this trait. Bacterial artificial chromosome (BAC) ends and simple sequence repeat (SSR)-containing genomic DNA clones were used to develop SNP markers linked to two soybean Mi resistance QTL on Linkage Group 0 (LG-O) and LG-G. A total of 14 BAC-end sequences and seven SSR flanking regions were used to design primers to amplify genomic frogments of PI 96354 (Mi resistant) and 'Bossier' (Mi susceptible). We discovered three SNPs in Satt358 source-sequences located near a major Mi-resistant QTL on LG-O and three SNPs in Sott199 source-sequences located near a minor Mi-resistant QTL on LG-G. Using a direct hybridization SNP assay detected on a Luminex 100 flow cytometer, the SNP358 genotypes of 94 [F.sub.2:3] lines from a cross of PI 96354 x Bossier were congruent with the genotypes of the SSR marker Sart358. The genotypes of SNP199 marker which targets a SNP in Satt199 source-sequence also showed 100% congruence with the genotypes of the SSR marker Satt199. SNP genotyping of 24 known Mi-resistant or Mi-susceptible cultivars showed that SNP358 and SNP199 markers should be highly effective in MAS for the Mi-resistance QTL on LG-O and LG-G.