5. Genetic Resources for Improved Functional Insights and Prediction of Relevant Traits in Livestock.

Abstract Functional insights into economically important traits in agricultural species are essential for both advancing our biological understanding and improving the accuracy of selection predictions. Achieving this goal requires expanded genomic resources together with precise phenotypic data for the traits of interest. Telomere-to-telomere (T2T) genome assemblies now provide complete, highly accurate genomic information that includes variation beyond single nucleotide polymorphisms (SNPs). Complementary pangenomes further broaden the breadth of genomic variations by capturing diversity beyond that of a single reference genome. Comprehensive functional annotations including the identification of environmentally responsive and tissue specific regulatory elements that are linked to key biological processes are fundamental for bridging genome to phenome. Integrating these genomic and functional data will deepen our understanding of how variation and regulatory modifications control physiological processes, thereby transforming our ability to predict trait performance. To unravel complex biological processes, we must obtain precise measurements of physiological responses and interactions across critical developmental windows and under diverse external stimuli. Such detailed knowledge will enable more accurate modeling of genotype by environment interactions in agricultural species.