A Soybean Transcript Map: Discovery and Mapping of Single Nucleotide Polymorphisms in Soybean Genes

Authors: CHOI, IK-YOUNG - KOREA; Hyten, David; MATUKUMALLI, LAKSHMI - GEORGE MASON UNIVERSITY; SONG, QIJIAN - UNIVERSITY OF MARYLAND; CHAKY, JULIAN - UNIVERSITY OF NEBRASKA; Quigley, Charles - Chuck; CHASE, KEVIN - UNIVERSITY OF UTAH; LARK, K - UNIVERSITY OF UTAH; REITER, ROBERT - MONSANTO CO.; YOON, MUN-SUP - KOREA; HWANG, EUN-YOUNG - UNIVERSITY OF MARYLAND; YI, SEUNG-IN - KOREA; YOUNG, NEVIN - UNIVERSITY OF MINNESOTA; Shoemaker, Randy; Van Tassell, Curtis - Curt; SPECHT, JAMES - UNIVERSITY OF NEBRASKA; Cregan, Perry

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/16/2007
Publication Date: 5/16/2007
Citation: Choi, I., Hyten, D.L., Matukumalli, L.K., Song, Q., Chaky, J.M., Quigley, C.V., Chase, K., Lark, K.G., Reiter, R.S., Yoon, M., Hwang, E., Yi, S., Young, N.D., Shoemaker, R.C., Van Tassell, C.P., Specht, J.E., Cregan, P.B. 2007. A soybean transcript map: discovery and mapping of single nucleotide polymorphisms in soybean genes. Genetics. 176:685-696.

Interpretive Summary: DNA markers serve as genetic landmarks and are interspersed among the 50,000 or more genes throughout the genome of the soybean. If a marker is located near a gene of interest, the marker can be used to select for the desired form of the gene. For example, the soybean breeder can use a DNA marker to identify plants that carry the form of the gene that gives resistance to a disease rather than the form that leads to susceptibility. The closer the DNA marker is to a gene of interest, the more efficient is this process which is referred to as "DNA marker assisted selection". One type of DNA marker that is now being widely used by human geneticists is referred to as a single nucleotide polymorphism (SNP). This report represents the first description of several thousand newly discovered SNP DNA markers for soybean. The new SNP markers were "mapped" onto the 20 chromosomes of the soybean along with more that 1600 previously mapped DNA markers of other types. Because the new SNP DNA markers were each associated with a different soybean gene, the positions of the SNP markers provide an estimate of the positions of genes on the soybean genetic map. The new SNP markers provide a resource for soybean geneticists and breeders that can be used to locate the position of genes that control important plant traits. These markers can also be used by soybean breeders for DNA marker assisted selection to identify breeding lines that carry desired traits.

Technical Abstract: 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 primers 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 5,535 SNPs were discovered, including 4,708 single base changes and 827 indels for an average nucleotide diversity of theta=0.000995. The first genetic transcript map of the soybean genome was created by mapping one SNP in each of 1,158 genes in one or more of three recombinant inbred line mapping populations. 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 1,158 genes, 127 mapped to 29 of the 41 gaps of 5 to 10 cM in the pre-existing SSR/RFLP-based map, while 19 genes mapped in 5 of the 7 gaps larger than 10 cM. The addition of more than 1,100 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.