Quantitative genetics and genomics of production and disease in beef cattle

Abstract

Cattle grazing in extensive open pasture of tropical areas are subjected to several environmental stressors such as heat and humidity, high incidence of disease, cattle ticks and worm infestations. These stressors have major impacts on productivity and animal welfare. The overall focus of this PhD thesis was to conduct classical genetic and modern quantitative genomics analyses for growth and carcass related traits, and disease and parasite tolerance/resistance traits in beef cattle. The specific objectives were: (1) to estimate genetic parameters for growth, carcass related traits, and tropical environment stressors, e.g., infectious bovine keratoconjunctivitis or “pinkeye”, cattle tick counts, and helminth or worm egg counts in Australian tropical adapted beef cattle; (2) to identify genetic markers or gene(s) linked to growth and ultrasound measures of carcass related traits in tropical Australian cattle, and bovine tuberculosis (BTB) traits in African zebu cattle using a genome-wide scan methodology; and (3) to evaluate the feasibility of genome-wide epistasis association for growth and carcass related traits using a two-step two-locus model for Australian tropical beef cattle. Field test data obtained from different sources were used in this thesis. Genetic parameter estimates were computed using mixed models by fitting an additive polygenic animal term as a random effect, whereas in genome association analyses, the genetic markers were fitted as fixed effect and significance of marker effects on the traits were evaluated for association. The heritabilities of tropical stressors traits ranged from low to moderate, suggesting genetic selection is feasible, though the selection response will be slow in this resource population. There was no evidence of unfavourable genetic correlations between environment stressors and growth traits; hence selection against environmental stressors would not have a detrimental effect on production performance. A genome-wide scan identified seven SNP markers on chromosome 14 associated with serum concentration of insulin-like growth factor-1, subcutaneous fat depth, and body condition score measured in Australian Brahman cattle. The rs29020688 marker located in the intronic region of Bos taurus XK, Kell blood group complex subunit-related family, member 4 (XKR4) gene was strongly associated with increased blood levels of insulin-like growth factor-1 (IGF-1), and rs29010471 marker located in the intronic of Bos taurus protein kinase, DNA-activated, catalytic polypeptide (PRKDC) gene was strongly associated with subcutaneous fat deposits. These positional genes could be candidate genes influencing IGF-1 and subcutaneous fat depth, and can potentially be used as biomarkers for these traits. Similarly, this thesis investigated associations between SLC11A1 candidate gene and a panel of microsatellite markers and several diagnostic tests of bovine tuberculosis (BTB) phenotypes. Polymorphisms at SLC11A1 alleles 211, 215 and 217 and alleles in ILSTS006 (Alleles: 286, 288, 290, and 292) and BM2113 (Alleles: 133 and 141) were significantly associated with decreased BTB disease incidence in African zebu cattle; hence these could be considered in a marker assisted selection for screening BTB tolerant animals. This study was able to successfully model epistasis interactions between two-SNP loci using two-step approach. Using experimental field data, it was demonstrated and validated that two-step two-locus epistatic interactions are computationally feasible at a genome-wide scale. If automated recording technology for extensive gazing beef cattle becomes available in the future, this will enable the collection of high dimensional data on animals. In addition large number of animals are expected to be genotyped and imputed up to very high marker densities using imputation techniques. These resources will enable the estimation of genetic parameters more accurately and will allow biomarkers and genes underlying many complex traits in animals in extensive grazing system to be identified.