Utilising Next Generation Sequencing Data to Fine-Map Milk Production QTL on Bos taurus Autosome 29

Genome wide association studies (GWAS) have identified numerous quantitative trait loci (QTL) across the bovine genome that are associated with milk production traits in dairy cattle breeds. However, many of the causal mutations underlying these QTL have not been identified. The emergence of Next Generation Sequencing (NGS) technology should aid the identification of causal mutations and candidate genes underlying quantitative traits as whole genome re-sequencing can be utilised for variant discovery. Re-sequencing should allow identification of all genetic variants, including the causal variant(s), within the relevant QTL regions and study population(s).

This study aimed to identify causal mutations underlying milk production QTL across Bos taurus autosome 29 (BTA29) in Australian Holstein and Jersey cattle. Genetic variants on BTA29 were identified using NGS data from 429 animals, representing 14 breeds of cattle, that were re-sequenced for the 1000 Bull Genomes Project. After filtering, 670,773 variants, comprising 635,009 single nucleotide polymorphisms (SNP) and 35,764 INDELs, were identified on BTA29. Of the variants identified on BTA29, over 460,000 SNP and over 28,000 INDELs were polymorphic in either Holstein, Jerseys or both breeds. Genotypes for the genetic variants were imputed into 12,023 Holstein animals and 4,888 Jersey animals. A single SNP regression was then performed on BTA29 using imputed genotypes for the polymorphic SNP markers in the Holstein and Jersey data. Results will be presented for milk yield, protein yield, fat yield, protein percentage and fat percentage.