Project : USDA ARS

ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Research Project #433992

Research Project: Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production

Location: Genetics and Animal Breeding

2020 Annual Report

Accomplishments
1. Application of pooling individual whole blood samples prior to DNA extraction. Genotyping pooled samples from multiple animals can substantially reduce genotyping costs. However, these methods need to accurately generate equal representation of individuals within pools. ARS researchers at Clay Center, Nebraska, in collaboration with researchers at South Dakota State University, evaluated methods of pooling to determine accuracy of pool construction based on white blood cell counts compared to two common DNA quantification methods. The researchers constructed pools of 50 animals with the target of equal representation of each animal based on number of white blood cells, spectrophotometric readings of DNA, spectrofluorometric readings of DNA, and whole blood volume. The method of pooling whole blood samples based on white blood cell count was more predictive of sample representation compared to pooling based on DNA concentration. Therefore, constructing pools using white blood cell counts prior to DNA extraction may reduce cost associated with genotyping and improve representation of individuals in a pool.

2. Tracking down sources of error when using DNA pooling in genetic evaluation. Pooling DNA from multiple animals can be used to reduce the cost of genetic evaluation and generate expected progeny differences (EPD) that producers use for selection. Relationships between the animals in the pools and candidates for selection are established through allele frequency estimates from genotypes of the pools. The accuracy of these EPD are affected by various errors in the pooling process. ARS researchers at Clay Center, Nebraska, performed experiments to optimize pooling strategies, and demonstrated that pooling equal weight of liver before DNA extraction, or pooling based on extracted DNA estimated concentration, were both effective in estimating allele frequency of the pool as long as at least 10 animals were contained in the pool. These results suggest that pools containing more than 10 animals are robust and can be used to economically decrease genotyping costs in livestock genetic evaluation programs.

3. Verified efficacy of a reference-panel based imputation algorithm. Genomic sequence from influential individuals in a crossbred population representing the eighteen most predominant beef breeds in the United States was combined with publicly available sequence representing beef and dairy breeds. ARS researchers at Clay Center, Nebraska, identified individuals for sequencing with a novel algorithm based on haplotypes inferred from high-density single nucleotide polymorphism (SNP) genotypes. In collaboration with Gencove, Inc., relevant public sequence was also identified and incorporated into a phased haplotype reference panel allowing imputation from low-cost, low-coverage genomic sequence. Sequence variant genotypes imputed with this approach are more accurate than those imputed from SNP assay genotypes (SNP chips). Low-coverage sequence with imputation will enable more comprehensive genotyping at a lower cost than currently available SNP arrays. Producers will be able to genotype a larger portion of animals for genetic evaluation programs, which will improve selection accuracy and increase the genetic gain to improve beef efficiency for the industry at a faster rate.

U.S. DEPARTMENT OF AGRICULTURE

Genetics and Animal Breeding: Clay Center, NE