The genetics and genomics of linear type traits in Irish beef cattle

Irish beef genetic evaluations are currently undertaken using a multi-breed population; thus estimated breeding values for all beef animals are comparable regardless of breed. The two indexes published on Irish beef cattle, the Replacement index and Terminal index, both include carcass traits. These traits, however, are only measured after the animal is slaughtered. Linear type traits are measured on young live animals and are strongly correlated with carcass merit. The value in linear type traits is the ability to select for more morphologically superior carcasses, even for the same carcass weight. The objectives of this thesis were to: 1) determine if the genetic architecture of 5 muscular and 5 skeletal linear type traits differ by breed and/or sex with the aim of improving the accuracy of multi-breed beef genetic evaluations, using linear type traits as an example, and 2) to detect quantitative trait loci (QTL) associated with the linear type traits. Of particular interest was if detected QTLs overlapped both among traits and among breeds. Data used consisted of phenotypic data on 198,351 animals and imputed whole genome sequence data on 23,943 animals from 5 beef breeds and the Holstein-Friesian dairy breed. The heritability estimates and pairwise genetic correlations among the linear traits estimated within breed were similar to the respective statistics across the 3 continental breeds with the same phenomenon observed when comparing the two British breeds (i.e. Angus and Hereford). The majority of the QTL identified as being associated with the linear type traits were both trait- and breed-specific, with only some overlap in the QTLs occurring between the Charolais and Limousin for the muscular traits, while for the skeletal traits there was commonalities between the Angus and Limousin as well as between the Angus and Holstein-Friesian. While sexual dimorphism was evident at a genome level, only 1% of SNPs tested exhibited it; this was consistent with the near unity genetic correlations between the same linear type trait in both sexes estimated using mixed models. In summary, considering the continental beef breeds separately to the British beef breeds in genetic evaluations may improve the accuracy of these evaluations; however, it is unlikely that the consideration of each sex separately will impact the accuracy of selection. Furthermore, including the linear type traits in multi-trait genetic evaluations alongside (more granular) carcass traits may enable the breeding of morphologically different animals in the future with a more valuable carcass, even for the same carcass weight