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Title: High-throughput genotyping with the GoldenGate assay in the highly complex genome of soybean

Author
item Hyten, David
item SONG, QIJIAN - UNIVERSITY OF MARYLAND
item CHOI, IK-YOUNG - KOREA
item YOON, MUN-SUP - KOREA
item SPECHT, JAMES - UNIVERSITY OF NEBRASKA
item MATUKUMALLI, LAKSHMI - GEORGE MASON UNIVERSITY
item Shoemaker, Randy
item YOUNG, NEVIN - UNIVERSITY OF MINNESOTA
item Cregan, Perry

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/16/2008
Publication Date: 2/16/2008
Citation: Hyten, D.L., Song, Q., Choi, I., Yoon, M., Specht, J.E., Matukumalli, L.K., Shoemaker, R.C., Young, N.D., Cregan, P.B. 2008. High-throughput genotyping with the GoldenGate assay in the highly complex genome of soybean. Theoretical and Applied Genetics. 116:945-952.

Interpretive Summary: Molecular markers have become extremely important in helping to improve crops such as soybean because they can be used to determine the position of genes that lead to genetic improvements and they can subsequently be used to identify breeding lines that carry those genes. However, methods for testing large numbers of molecular markers such as single nucleotide polymorphisms (SNPs) simultaneously in soybean have remained untested. A new method called the GoldenGate assay which is capable of testing up to 1536 SNPs simultaneously in soybean was tested to determine how successful this method could be in helping to accelerate molecular marker analysis in soybean. Successful assays were obtained for 90% of the SNPs tested in soybean genetic mapping populations. The high success rate of the GoldenGate assay indicates that it is a useful technique for quickly assaying large numbers of SNPs in soybean. This information will be used by crop researchers, crop breeders and seed companies to increase the efficiency of SNP analysis for gene discovery and soybean improvement.

Technical Abstract: Large numbers of single nucleotide polymorphism (SNP) markers are becoming available for crops such as soybean. However, the high-throughput methods for multiplexing SNP assays developed are untested in complex genomes such as soybean which has a high percentage of paralogous genes. The Illumina GoldenGate assay is capable of multiplexing from 96 to 1,536 SNPs in a single reaction over a three day period. We tested the GoldenGate assay in soybean to determine the success rate of converting verified SNPs into working assays. A 384 SNP GoldenGate assay was designed such that each SNP was polymorphic in at least one of three recombinant inbred line mapping populations. Successful assays were obtained for 90% of the SNPs tested in the mapping populations indicating that the complex nature of the soybean genome did not impact assay function. In addition, 80% of the SNPs that were mapped had a minor allele frequency >10% in a diverse sample of Asian landrace germplasm accessions. The high success rate of the GoldenGate assay makes this a useful technique for quickly creating high density genetic maps in species where SNP markers are becoming available.