Genetics. Published Articles Ahead of Print: March 4, 2007, Copyright © 2007
doi:10.1534/genetics.107.070821


A more recent version of this article appeared on May 1, 2007.

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A Soybean Transcript Map: Gene Distribution, Haplotype and SNP Analysis

Ik-Young Choi 1, David L. Hyten 2, Lakshmi K. Matukumalli 2, Qijian Song 2, Julian M. Chaky 3, Charles V. Quigley 2, Kevin Chase 4, Karl G. Lark 4, Robert S. Reiter 5, Mun-Sup Yoon 6, Eun-Young Hwang 2, Seung-In Yi 7, Nevin D. Young 8, Randy C. Shoemaker 2, Curtis P. van Tassell 2, James E. Specht 3 and Perry B. Cregan 2*

1 Seoul National University
2 USDA, ARS
3 University of Nebraska, Lincoln
4 University of Utah
5 Monsanto Company
6 Rural Development Administration, Suwon, Republic of Korea
7 National Seed Management Office, Suwon, Republic of Korea
8 University of Minnesota

* To whom correspondence should be addressed. E-mail: creganp{at}ba.ars.usda.gov.

Submitted on January 12, 2007
Revised on February 7, 2007
Accepted on 16 February 2007


Abstract

The first genetic transcript map of the soybean genome was created by mapping one SNP in each of 1,141 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. Single nucleotide polymorphisms (SNPs) were discovered via the re-sequencing of sequence tagged sites (STS) developed from EST sequence. From an initial set of 9,459 polymerase chain reaction primer sets designed to a diverse set of genes, 4,240 STS were amplified and sequenced in each of six diverse soybean genotypes. In the resulting 2.44 mbp of aligned sequence, a total of 5,551 SNPs were discovered, including 4,712 single base changes and 839 indels for an average nucleotide diversity of {vartheta}=0.000997. The analysis of the observed genetic distances between adjacent genes versus 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 1,141 genes, 291 mapped to 72 of the 112 gaps of 5 to 10 cM in the pre-existing SSR-based map, while 111 genes mapped in 19 of the 26 gaps larger than 10 cM. The addition of 1,141 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.

Key Words: EST, SNP discovery, paralog, single nucleotide polymorphism, unigene




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