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

Abstract

The first genetic transcript map of the soybean genome was created by mapping one SNP in each of 1141 genes in one or more of three recombinant inbred line mapping populations, thus providing a picture of the distribution of genic sequences across the mapped portion of the genome. Singlenucleotide polymorphisms (SNPs) were discovered via the resequencing of sequence-tagged sites (STSs) developed from expressed sequence tag (EST) sequence. From an initial set of 9459 polymerase chain reaction primer sets designed to a diverse set of genes, 4240 STSs were amplified and sequenced in each of six diverse soybean genotypes. In the resulting 2.44 Mbp of aligned sequence, a total of 5551 SNPs were discovered, including 4712 single-base changes and 839 indels for an average nucleotide diversity of u ¼ 0.000997. The analysis of the observed genetic distances between adjacent genes vs. the theoretical distribution based upon the assumption of a random distribution of genes across the 20 soybean linkage groups clearly indicated that genes were clustered. Of the 1141 genes, 291 mapped to 72 of the 112 gaps of 5-10 cM in the preexisting simple sequence repeat (SSR)-based map, while 111 genes mapped in 19 of the 26 gaps .10 cM. The addition of 1141 sequence-based genic markers to the soybean genome map will provide an important resource to soybean geneticists for quantitative trait locus discovery and map-based cloning, as well as to soybean breeders who increasingly depend upon marker-assisted selection in cultivar improvement.

Whole-genome sequencing and intensive analysis of the undomesticated soybean ( Glycine soja Sieb. and Zucc.) genome

“…These findings indicated that 35.6% (16,519 out of 46,430) of the high-confidence gene set are affected by nonsynonymous SNPs in the G. soja genome. The frequency of SNPs in both wild and cultivated soybeans was 2.67 SNPs per 1 kb, consistent with previous studies of G. max varieties (24)(25)(26). The G. soja genome contained 196,356 indels (−35 to +14 bp) compared with Glyma1.01, and 78.54% (154,211) of the indels were located in nongenic regions (Table 1).…”

Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean

“…All of the scaffolds were mapped in silico onto the Soybean Consensus Map 3.0 (http://soybase. org) by BLAST searches against a database comprising sequences of simple sequence repeat (SSR)-containing clones (Song et al, 2004) and SNP-containing ESTs (Choi et al, 2007). Only the best hits among the scaffolds were selected to avoid mispositioning due to duplicated sequence.…”

A Fluorescence in Situ Hybridization System for Karyotyping Soybean

“…More recently, a bacterial artificial chromosome (BAC)-based physical map was generated for soybean, which then was linked via a number of markers to the MLGs (Shoemaker et al 2008). The dense soybean genetic map (Song et al 2004;Choi et al 2007), as well as the physical map, were significant aids during the assembly of the soybean genome sequence (Schmutz et al 2010).…”