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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 #369614

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

Location: Genetics and Animal Breeding

Title: Assessing the potential of low-pass sequencing and imputation to genotype sequence variants in beef cattle

item Snelling, Warren
item Kuehn, Larry
item LI, JEREMIAH - Gencove, Inc
item HOFF, JESSE - Gencove, Inc
item PICKRELL, JOSEPH - Gencove, Inc

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 1/2/2020
Publication Date: 1/11/2020
Citation: Snelling, W.M., Kuehn, L.A., Li, J.H., Hoff, J.L., Pickrell, J.K. 2020. Assessing the potential of low-pass sequencing and imputation to genotype sequence variants in beef cattle [abstract]. In: Plant and Animal Genome Conference Proceedings, January 11-15, 2020, San Diego, California. Paper No. PE0330.

Interpretive Summary:

Technical Abstract: Low-coverage whole-genome sequence (WGS) can be obtained at a cost similar to the low cost, low density cattle genotyping arrays. While few genotypes can be called directly from the <1X coverage that might be acquired, sequence variant genotypes have been imputed with high accuracy from <1X coverage of human samples. For an initial assessment of low-coverage sequencing and imputation in beef cattle, reads were sampled from bulls with >4X WGS to mimic low-pass sequencing. Each bull was downsampled to five coverage levels: 0.4X, 0.6X, 0.8X, 1X and 2X. The downsampled fastq files were submitted to the Gencove pipeline for imputation to a broad reference of Bos taurus, Bos indicus and indicus-influenced composites. Imputed genotypes were compared to genotypes from the BovineHD (HD) and GGP-F250 (F250) assays, as well as to genotypes called directly from deeper sequence on these bulls. Sequence reads were from eleven bulls, one representing each of the seven most predominant Bos taurus breeds in the U.S., a Brahman, and one representing each of three indicus-influenced composite breeds. Genotypes were imputed for 59M variants that included 588K expected to alter coded proteins. For all bulls, agreement between imputed and assayed genotypes increased slightly with coverage. Bos taurus bulls consistently had concordance >0.99 between imputed and assayed genotypes. Concordance for the indicus x taurus composite bulls was between 0.96 and 0.97, and the Brahman was intermediate between the taurus and composite bulls. These results encourage use of low-pass sequencing and imputation as a viable alternative to genotyping assays.