ARS | Publication request: Development and Implementation of High-Throughput SNP Genotyping in Barley

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 11, 2009
Publication Date: December 1, 2009
Repository URL: http://parking.nal.usda.gov/shortterm/20142___242873.pdf
Citation: Close, T.J., Bhat, P., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J., Wanamaker, S., Bozdag, S., Roose, M., Moscou, M., Chao, S., Varshney, R., Szucs, P., Sato, K., Hayes, P., Matthews, D.E., Kleinhofs, A., Muehlbauer, G., Deyoung, J., Marshall, D.F., Madishetty, K., Fenton, R.D., Condamine, P., Graner, A., Waugh, R. 2009. Development and Implementation of High-Throughput SNP Genotyping in Barley. Biomed Central (BMC) Genomics. 10:582.

Interpretive Summary: Single nucleotide polymorphism (SNP) is a DNA marker system that can differentiate individuals based on variations detected at the level of a single nucleotide base in the genome. Such variations are present in high abundance in the genomes of higher organisms including plants. In barley, approximately 22,000 SNPs were identified from gene-derived regions of the barley genome, 4,596 of them were tested for large-scale high throughput genotyping performance using the genotyping assays developed by Illumina in three pilot phase. During the pilot phase of the studies, a consensus genetic map was developed by positioning these SNPs on seven barley chromosomes by using and merging data obtained from three genetic mapping populations. In addition, the genetic diversity detected by these SNPs was assessed among 200 barley germplasm, principally European and U.S. breeding materials. We selected 3,072 of these tested SNPs based on their technical performance, map location, level of genetic diversity, and biological interest to fill two 1536-SNP “production” genotyping assays named barleyOPA1 and barleyOPA2, or BOPA1 and BOPA2, respectively. They were then made generally available to the worldwide barley genetics community. Data generated using one of the production assays were added from a fourth mapping population, culminating in a consensus map containing 2943 SNP positions. The unprecedented density of genic markers and map stability enabled a high resolution comparison of the genomes of barley and rice, which reflected the evolutionary changes on the distributions of genes on chromosomes. The results showed that the regions with high gene density varied on different chromosomes in barley. Examination of U.S. breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of genetic diversity among genetically narrow materials.

Technical Abstract: Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Pilot phase data from three barley doubled haploid mapping populations supported the production of an initial consensus map, and over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP “production” BeadArray assays (BOPA1 and BOPA2), which were then made generally available to the worldwide barley genetics community. Data generated using one of the production assays were added from a fourth mapping population, culminating in a consensus map containing 2943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. The unprecedented density of genic markers, marker bins, and map stability enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is clearly reflected by bins containing many more than the average number of markers, suggesting that a large number of genes are recombinationally locked into the genetic centromeres of several barley chromosomes. Examination of U.S. breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.