Single nucleotide polymorphism discovery and linkage mapping of lipoxygenase-2 gene (Lx₂) in soybean.

Moon Young Kim; Bo-Keun Ha; Tae-Hwan Jun; Eun-Young Hwang; Kyujung Van; Yong In Kuk; Suk-Ha Lee

Lipoxygenase-2 (Lx2) 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 Lx2. 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 Lx2 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 Lx2. The allelic segregation for the SNP linked to Lx2 was in accordance with the expected ratio of 1:1 in the RIL population. Based on the results of linkage analysis between Lx2 and the SSR markers, Lx2 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 Lx2 can be developed to facilitate marker-assisted selection and fine mapping of the region around this locus.

OILSEED plants; GENES; MOLECULAR genetics; DNA; ACTIN; PROTEIN genetics; SOYBEAN; LIPOXYGENASES

Euphytica, 2004, Vol 135, Issue 2, p169

0014-2336

Academic Journal

10.1023/B:EUPH.0000014909.40136.20