SNP discovery, linkage analysis and microsynteny in tentative consensus sequences derived from roots cDNA in a supernodulating soybean mutant

Abstract

A soybean transcript map with genes mainly expressed in roots of a supernodulating mutant was constructed by mapping of single nucleotide polymorphism (SNP) markers into pre-existing SSR-based map, using a recombinant inbred line (RIL) population from Pureunkong and Jinpumkong 2. For SNP discovery, primer pairs were designed from 793 tentative consensus sequences (TCs) derived from the roots of a supernodulating soybean mutant. Among 520 loci showing high-quality sequence, more than 300 SNPs were identified in 116 loci between the parental genotypes. Average SNP frequency between the parental genotypes was one SNP per 1,010 bp. A total of 325 markers, including 98 SNPs, 208 SSRs, 15 AFLPs and four classical markers, were used to construct a genetic linkage map with 20 linkage groups (LGs) and a total length of 2,379 cM. Ten nonsynonymous changes were detected out of these SNP markers, indicating the possible usage of these markers as functional markers. With 40 of the SNP markers, putative synteny between soybean and Medicago truncatula (Mt) was revealed by identification of 19 short colinear blocks between the two genomes. This genetic map will provide the basis for the identification of gene in relation to nodulation and nitrogen fixation in partially sequenced genome like soybean by comparisons of the model genome (Mt). And, the integration of SNP markers and expression data with available genetic and phenotypic information would be helpful for clarifying function of cloned genes.