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 identiWed 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 identiWcation of 19 short colinear blocks between the two genomes. This genetic map will provide the basis for the identiWcation of gene in relation to nodulation and nitrogen Wxation 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.

Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean

“…Soybean ESTs from the homologous Rxp region reported by Van et al (2008; M. truncatula chromosome 3: 21,036-21,254 kb) and areas near this region (M. truncatula chromosome 3: 21,254-21,534 kb) were investigated. Developed SNP markers were mapped onto our previous RIL mapping population (Cai et al, 2008a) produced by a recent duplication event. Although small insertions/deletions and inversions were observed between GmB and GmB#, most of the duplicated region was conserved.…”

“…These ESTs were amplified and sequenced as described by Van et al (2004). After SNPs were identified between the two soybean parents of Pureunkong and Jinpumkong 2 (our previous RIL mapping population ;Cai et al, 2008a), SNP genotyping using primer single-base extension was performed on a Victor3 microplate reader (Perkin-Elmer Life Science) as described by Cai et al (2005).…”

Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping

“…Direct sequencing has been a standard method to develop SNP markers, although its efficiency is low, especially in plants with complex genomes [ 8 , 9 ]. Another alternative is to take advantage of the large amount of sequence data available in public databases to develop SNP and InDel markers using bioinformatics [ 10 ].…”