ARS | Publication request: Development of low-cost, high-throughput genotyping to complement SNP discovery by individual animal whole-genome sequencing

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 30, 2012
Publication Date: January 1, 2013
Citation: Thallman, R.M., Snelling, W.M., Curry, J.D., Smith, T.P., Kalbfleisch, T.S., Kuehn, L.A., McDaneld, T.G., Bennett, G.L., Lindholm-Perry, A.K., Fofanov, V.Y., Koshinsky, H., Pollak, E.J. 2013. Development of low-cost, high-throughput genotyping to complement SNP discovery by individual animal whole-genome sequencing [abstract]. Plant and Animal Genome XXI Conference. Workshop Abstract No. W146.

Technical Abstract: Development of marker systems with reliable predictive merit for genome-enabled selection requires that candidate markers be efficiently identified and then genotyped in very large numbers of animals. Low cost sequencing of individual animals is becoming a cost-effective approach to marker identification, which was applied on 96 influential sires of the USMARC cattle population to identify over 10,000,000 segregating polymorphisms, with over 30,000 predicted to affect function of annotated genes. Approaches to screening these candidate markers using phenotypes in the USMARC herd are being tested. In order to identify which candidate markers would be most useful in developing genomic predictions in other populations, assays for those markers need to be developed and genotyped in very large numbers of additional phenotyped animals. Unfortunately, most current genotyping systems are too expensive to achieve these ends. Therefore, a low-cost genotyping method was developed in which barcodes identifying individuals are economically added to DNA fragments programmed by specific loci. Next generation sequencing of pools of these DNA fragments from more than 1,000 animals yields enough sequence reads to reliably determine genotypes. The method is highly versatile, permitting switching in and out of particular markers at will. Using this technology, low cost genotyping assays are being developed and tested in the USMARC herd, and validated in other populations. In the first iteration of this strategy, assays for 66 markers, including SNPs, INDELS, and short tandem repeats were successfully designed and used to genotype 2858 animals.