Single nucleotide polymorphism discovery and linkage mapping of lipoxygenase-2 gene (Lx 2) in soybean

Lipoxygenase-2 (Lx ₂) in soybean seed is mainly responsible for generation of grassy-beany and bitter flavors. Genetic elimination of this flavor can be accelerated by the development of single nucleotide polymorphism (SNP) markers linked to Lx ₂. A frame map based on simple sequence repeat (SSR) markers was constructed first using a recombinant inbred line (RIL) population of Pureunkong × Jinpumkong 2. Sixty-five SSR markers were incorporated into 13 linkage groups (LGs) spanning a total of 737 cM. Among five primer pairs designed from the Lx ₂ gene sequence, one produced an amplicon with sequence variations between Pureunkong and Jinpumkong 2. Three SNPs, T/C, G/A and C/A, were identified at 251,367 and 420 bp, respectively, in the intron region of the 804 bp amplified product. Using single base chain extension based on the capture probe sequence in the 5' region of the T/C SNP, the 90 RILs were genotyped for each allele of Lx ₂. The allelic segregation for the SNP linked toLx ₂ was in accordance with the expected ratio of 1:1 in the RIL population. Based on the results of linkage analysis between Lx ₂ and the SSR markers, Lx ₂ was found to be positioned on one end of LG F in the frame map, flanked by the SSR markers Satt522 and Sat074. This study demonstrates that SNP markers closely linked to Lx ₂can be developed to facilitate marker-assisted selection and fine mapping of the region around this locus. This revised version was published online in July 2006 with corrections to the Cover Date.