Genomic Evaluations Aimed at Increasing Beef Cattle Sustainability and Resilience

Beef cattle production plays a central role in sustainable food systems, yet it faces growing challenges from climate change, resource limitations, and societal expectations for welfare-oriented and environmentally responsible farming. Enhancing the genetic resilience, efficiency, and longevity of beef cattle is therefore essential to sustain productivity and animal welfare under increasingly variable conditions. This thesis developed quantitative and genomic approaches to improve the sustainability and resilience of Italian beef cattle, focusing on functional longevity, fertility, growth, and their interaction with environmental stressors. The research integrated linear and threshold single-step genomic best linear unbiased prediction models, genomic inbreeding analyses, multiple-trait models for genotype-by-environment interaction, and single-step genome-wide association studies. The first study investigated functional longevity, expressed as stayability, in Italian Charolais and Limousine cattle using single-step genomic prediction under linear and threshold models. Heritability estimates were moderate (0.11–0.21), with higher values under threshold models, confirming that longevity can be improved through selection. Spearman rank correlations between early and late calvings were positive but declined with increasing parity, while re-ranking of genotyped sires suggested that stayability across calvings represents genetically distinct traits. Negative correlations between stayability and fertility traits (age at first calving and first calving interval) indicated that earlier and more fertile cows tend to remain productive longer. In Limousine cattle, positive genetic associations between stayability and body conformation traits reflected the contribution of morphological soundness to resilience and longevity, whereas some body traits in Charolais, such as rump convexity, were unfavorably associated with longevity. The second study conducted a single-step genome-wide association analysis for longevity, fertility, and conformation traits in Limousine cattle, identifying genomic regions associated with immune regulation, reproductive efficiency, growth, and energy metabolism. The overlapping of different genes across longevity, fertility, and conformation highlights the polygenic nature of these complex traits. These candidate genes highlighted biological mechanisms underlying female productivity, adaptability, and overall resilience. The third study evaluated inbreeding depression across growth, fertility, and survival traits using both pedigree- and genome-based coefficients. Significant phenotypic depression was observed for growth, fertility traits, and longevity. Genomic inbreeding explained a higher proportion of variance than pedigree-based estimates, underscoring the importance of managing both recent and ancient inbreeding to preserve genetic diversity in the studied population. The fourth study assessed genotype-by-environment interaction for growth traits (average daily gain, weaning weight, and yearling weight) across different climatic environments in Limousine cattle using a multiple-trait model. Results revealed genetic heterogeneity in environmental sensitivity, identifying genotypes capable of maintaining stable growth under heat stress conditions. Overall, this thesis demonstrates that combining genomic prediction, association analyses, and environmental modelling provides an effective framework for identifying animals that are productive, resilient, and well adapted to diverse conditions. These findings provide scientific and practical foundations for future breeding programs that promote productivity, animal welfare, and long-term sustainability in modern beef production systems.