A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis

• DOI: 10.1534/genetics.107.070821
• Publication Date: 2007-03-06T01:01:49Z
• Authors: Ik-Young Choi; David L Hyten; Lakshmi K Matukum...; Qijian Song; Julian M Chaky; Charles V Quigley; Kevin Chase; K Gordon Lark; Robert S Reiter; Mun-Sup Yoon; Eun-Young Hwang; Seung-In Yi; Nevin D Young; Randy C Shoemaker; Curtis P van Tassell; James E Specht; Perry B Cregan
• Keywords: Indel; Sequence-tagged site; Nucleotide diversity

Abstract The first genetic transcript map of the soybean genome was created by mapping one SNP in each 1141 genes or more three recombinant inbred line populations, thus providing a picture distribution genic sequences across mapped portion genome. Single-nucleotide polymorphisms (SNPs) were discovered via resequencing sequence-tagged sites (STSs) developed from expressed sequence tag (EST) sequence. From an initial set 9459 polymerase chain reaction primer sets designed to diverse genes, 4240 STSs amplified and sequenced six genotypes. In resulting 2.44 Mbp aligned sequence, total 5551 SNPs discovered, including 4712 single-base changes 839 indels for average nucleotide diversity θ = 0.000997. analysis observed distances between adjacent vs. theoretical based upon assumption random 20 linkage groups clearly indicated that clustered. Of 291 72 112 gaps 5–10 cM preexisting simple repeat (SSR)-based map, while 111 19 26 >10 cM. addition sequence-based markers will provide important resource geneticists quantitative trait locus discovery map-based cloning, as well breeders who increasingly depend marker-assisted selection cultivar improvement.