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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #289119
Title: Development and applications of low-cost, high-throughput genotyping

Author
item Thallman, Richard - Mark
item Lindholm-Perry, Amanda
item CURRY, JOHN - Eureka Genomics Corporation
item FOFANOV, VIACHESLAV - Eureka Genomics Corporation
item KOSHINSKY, HEATHER - Eureka Genomics Corporation

Submitted to: Midwestern Section of the American Society of Animal Science
Publication Type: Abstract Only
Publication Acceptance Date: 1/22/2013
Publication Date: 3/1/2013
Citation: Thallman, R.M., Lindholm-Perry, A.K., Curry, J.D., Fofanov, V.Y., Koshinsky, H. 2013. Development and applications of low-cost, high-throughput genotyping [abstract]. Journal of Animal Science. 91(Supplement 2):20. Abstract No. O063.

Interpretive Summary:

Technical Abstract: Most current genotyping systems are too expensive to justify routine genotyping of all animals in livestock breeding and/or production. Therefore, a low-cost genotyping method was developed in which barcodes identifying individuals are 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, referred to as Next Generation Genotyping (NGG), is an economical and highly versatile method that permits switching in and out of particular markers at will. Validation of the NGG method was performed using 95 B. taurus markers (commonly used for parentage testing) on 1080 cattle samples. Concordance with genotypes determined using a commercial genome typing panel was 99.1% with a call rate of 96.1%. Potential applications of NGG in seedstock breeding include parentage testing, genetic defects, single gene traits (color, polledness, etc.), and prediction of economically relevant traits from small panels of SNP. Potential applications in livestock production include precision management of diets, growth promotants, marketing targets, and time-on-feed in fed cattle or assignment of specific carcasses to different marketing channels. Current efforts include development of a panel of 1,000 to 3,000 highly informative markers that is sufficiently inexpensive to make it practical to genotype all individuals in pedigreed beef cattle populations. Such a panel, with sufficient marker density to track inheritance throughout a completely genotyped population, and used in conjunction with higher density SNP chips on sires and genomic sequence on very influential ancestors, might be used to impute reasonably complete sequence to entire populations of seedstock.