Application of large-scale sequence datasets for the discovery of genomic variations of economic importance in dairy cattle

Abstract Text: Livestock Improvement Corporation has undertaken whole-genome sequencing of 500 Holstein-Friesian, Jersey and crossbred dairy animals with the objective of increasing the rate of genetic improvement through increasing accuracy of genomic prediction.  An output of the whole-genome sequence is a pool of variants to which the 100,000 genotyped animals can be imputed.  The imputed genotypes can be then used in genome wide association mapping to identify causal variants or markers in strong linkage disequilibrium with them.  These markers can be used to increase the accuracy of genomic prediction. In addition, RNA-sequencing of mammary tissue for 188 lactating cows has been undertaken to augment identification of causal variants.  This is demonstrated with identification of variants affecting the expression of AGPAT6 and differential milk fat synthesis. The whole-genome sequence has also been used to identify two deleterious recessive variants in the New Zealand dairy population.

Keywords:

dairy cattle

genome sequence

breeding