BREEDING FOR WELFARE: ENHANCING CLIMATIC RESILIENCE AND LONGEVITY IN SWINE AND CATTLE

Improving animal health, production, and reproductive performance is of great relevance in breeding programs. The integration of pedigree, large-scale phenotypic data, and genomic information for breeding purposes can lead to a more sustainable livestock industry. In this context, the main objectives of this dissertation were to develop background knowledge for improving livestock welfare and understand the genetic and genomic background of welfare indicators in livestock using quantitative genomic strategies.

This dissertation includes five original studies. The first study objective aimed to estimate genetic parameters of vaginal temperature (T_V) across time and environments in lactating sows under hot conditions and identify genomic regions associated with T_V variability. We evaluated multiple random regression models. The random regression model fitting fourth order Legendre orthogonal polynomials had the lowest BIC (best model) and required relatively lower computational time. The heritability estimates for T_V ranged from 0.09 to 0.20 across time and environments. Two important genomic regions located on chromosomes 10 (59.370–59.998 Mb) and 16 (21.548–21.966 Mb) were identified.

The second study objective proposed 15 novel climatic resilience indicators based on variability in automatically recorded T_V and investigated their genomic background. Our findings showed that most of these novel indicators are heritable and could be used for selecting pigs with improved climatic resilience during lactation. We also found that individuals with a higher climatic resilience are more likely to exhibit better physiological responses, have higher body condition score, and enhanced reproductive performance under hot conditions.

The third study aimed to identify genomic regions and biological mechanisms underlying climatic resilience indicators in lactating sows under heat stress conditions. The genomic regions identified were located at SSC6:16,449,770 bp and SSC7:39,254,889 bp. Many heat tolerance or heat stress related genes were identified, including HSP90AB1, DMGDH, and HOMER1.

The fourth study aimed to systematically investigate population structure and genetic diversity of worldwide Duroc subpopulations and other selected pig breeds based on genomic information. Significant differences were found in the genetic diversity levels, population structure, and ancestry within Duroc subpopulations and between Duroc and other selected pig breeds. High linkage disequilibrium levels were observed in Durocs. The objective of the fifth study was to investigate the genetic relationship between longitudinal trait functional longevity and other economically important traits, including growth, carcass, management and teat health-related traits, in American angus cattle using bivariate random regression model. The genetic correlations between functional longevity and other traits were mostly different in primiparous and multiparous cattle, which indicates parity has important impact on functional longevity. Also, Older animals with longer functional longevity tend to have lower growth performance, more ideal foot health, better temperament, bigger ultrasound fat thickness and ultrasound ribeye area, smaller teat size, and tighter udder suspension would have longer functional longevity.

This dissertation focuses on improving livestock welfare and sustainability by integrating genomic, phenotypic, and pedigree information in breeding programs. Key findings include the heritability of traits like climatic resilience, vaginal temperature, and functional longevity in pigs and cattle, as well as identifying genomic regions and diversity patterns critical for breeding decisions. These insights contribute to developing more resilient, productive, and welfare-oriented livestock populations.