Development of SNP assays associated with oleic acid QTLs in N00-3350 soybean

Increasing the amount of oleic acid in soybean oil would reduce the need for hydrogenation, a process that creates unhealthy trans fatty acids. A previous study mapped six oleic acid quantitative trait loci (QTLs) from N00-3350 (similar to 550 g kg(-1) oleic acid) on soybean chromosomes (Gm) 5, 17, 18, and 19, which corresponds to linkage groups (LG) A1, D2, G, and L, respectively. The objectives of this study were to develop high throughput assays to detect single nucleotide polymorphism (SNP) markers associated with these oleic acid QTLs. Several candidate genes that are putatively responsible for the oleic acid phenotype in N00-3350 were identified by BLAST searches against the soybean genomic assembly using the sequences of fatty acid synthesis genes from soybean and Arabidopsis. Putative accC-2 and KAS I genes were located in the region of the cqOle-001 on Gm05 (LG-A1). A putative KAS I gene was located in the region of the cqOle-003 on Gm18 (LG-G) and a putative accB-1 gene was located in the region of the cqOle-004 on Gm18 (LG-G). These fatty acid candidate genes and sequence-tagged sites were used to identify SNPs between N00-3350 and 'Boggs'. Based on these SNPs, seven SimpleProbe probes for melting curve analysis were developed to rapidly identify the alleles from the mid-oleic acid soybean line N00-3350 at the desired loci. These assays provide a high-throughput and rapid SNP genotyping method which can be used to accelerate the development of mid-oleic acid content soybean cultivars.