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United States Department of Agriculture

Agricultural Research Service

Research Project: DEFINING THE GENETIC DIVERSITY AND STRUCTURE OF THE SOYBEAN GENOME AND APPLICATIONS TO GENE DISCOVERY IN SOYBEAN AND WHEAT GERMPLASM

Location: Soybean Genomics and Improvement

Title: A high density integrated genetic linkage map of soybean and the development of a 1,536 Universal Soy Linkage Panel for QTL mapping

Authors
item Hyten, David
item Choi, Ik-Young -
item Song, Qijian -
item Specht, James -
item Carter, Thomas
item Shoemaker, Randy
item Hwang, Eun-Young -
item Matukumalli, Lakshmi -
item Cregan, Perry

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 15, 2009
Publication Date: December 31, 2001
Citation: Hyten, D.L., Choi, I., Song, Q., Specht, J.E., Carter Jr, T.E., Shoemaker, R.C., Hwang, E., Matukumalli, L.K., Cregan, P.B. 2001. A high density integrated genetic linkage map of soybean and the development of a 1,536 Universal Soy Linkage Panel for QTL mapping. Crop Science. 50:960-968.

Interpretive Summary: Molecular markers have become extremely important in helping to improve crops such as soybean through gene discovery and marker assisted selection. However, the number of single nucleotide polymorphisms (SNPs) positioned in the soybean genome needs to be increased and tested with high-throughput methods to help map genes that contribute to agronomically important traits quickly and cost effectively. The GoldenGate assay is a new method which is capable of testing up to 1,536 SNPs simultaneously and has been used to position an additional 2,500 SNP markers on the soybean genome map. From a total set of 3,000 SNPs which have now been tested with the GoldenGate assay, an optimal set of 1,536 SNPs were selected which are a sufficient number of markers for most applications without the need to test all 3,000 SNP markers. The large number of new markers mapped and the optimal set of 1,536 SNP markers will be used by crop researchers, crop breeders and seed companies to increase the efficiency of molecular marker application in soybean for gene discovery and genetic improvement.

Technical Abstract: Single nucleotide polymorphisms (SNPs) are the marker of choice for many researchers due to their abundance and the high-throughput methods available for their multiplex analysis. Only recently have SNP markers been available to researchers in soybean [Glycine max (L.) Merr.] with the release of the third version of the consensus genetic linkage map that added 1,141 SNP markers to the map. Our objectives were to add 2,500 additional SNP markers to the soybean integrated map and select a set of 1,536 SNPs to create a universal linkage panel for high-throughput soybean QTL mapping. The GoldenGate assay is one high-throughput analysis method capable of genotyping 1,536 SNPs in 192 DNA samples over a three day period. We designed GoldenGate assays for 3,456 SNPs (2,956 new plus 500 previously mapped) which were used to screen three recombinant inbred line populations, a set of 96 diverse landrace accessions, and 96 modern elite cultivars. A total of 3,000 workable assays were obtained (89% success rate) which added about 2,500 new SNP markers to create a fourth version of the soybean integrated linkage map. To create a “Universal Soy Linkage Panel” (USLP 1.0) of 1,536 SNP loci, SNPs were selected based upon equidistant map position within each of the 20 consensus linkage groups and a broad range of allele frequencies in diverse germplasm. The 1,536 USLP 1.0 will be able to quickly create a comprehensive genetic map in most QTL mapping populations and thus will serve as a useful tool for high-throughput QTL mapping.

Last Modified: 4/19/2014
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