Dissecting the genomic and shared architecture of growth and reproductive traits in Nellore cattle using imputed whole-genome sequence

Improving growth and early fertility is essential for beef-cattle efficiency, but these complex traits are shaped by complex endocrine, metabolic, and developmental processes. Combining imputed whole-genome sequence (WGS) data with weighted single-step genome-wide association studies (w-ssGWAS) provides dense sequence-level coverage for investigating trait-specific and shared genomic regions affecting productive and reproductive performance. Thus, we used this approach to identify genomic regions, candidate genes, biological pathways, and shared signals associated with average daily gain (ADG), yearling weight (YW), scrotal circumference (SC), heifer early pregnancy at 16 months (HP), and heifer rebreeding (HR). Phenotypes from 905,316 Nellore cattle recorded from 1984 to 2020 were analyzed and 42,591 animals imputed for WGS with 2,591,217 variants after quality control. Genomic regions explaining more than 1% of the additive genetic variance mapped biological mechanisms connecting growth (ADG and YW), and female reproductive traits (HP and HR), whereas no shared region was observed with SC. Genetic correlation estimates supported this pattern, with higher correlation within growth traits (ADG–YW, 0.65 ± 0.04) and female reproductive traits (HP–HR, 0.57 ± 0.04), moderate correlations between growth and early fertility, especially ADG–HP (0.39 ± 0.07), and weak correlations between HR and growth traits or SC. Growth traits (ADG and YW) were mainly associated with endocrine and metabolic regulation ( IGF1R , GHRH , GHRHR , INSR , LPL , MYBPC1 , and MYO5B ). Regions associated with SC highlighted genes involved in testicular development and cellular homeostasis ( SLC9B1 , SLC9B2 , and UBE2D3 ). HP regions indicated roles of IGF and hormone signaling, ovarian development, and metabolic health, involving genes such as IGFBP2 , IGFBP5 , GNRHR , INSR , and FIGLA . HR-associated regions suggested contributions from endocrine recovery, developmental competence, and early placental support, highlighting the genes LEP , FIGLA , GHRH , SOX13 , KCNQ1 , and DHCR7 . Shared windows were detected on BTA14 and BTA7, and enrichment analyses highlighted hormone signaling, MAPK-related processes, growth hormone signaling, cholesterol metabolism, and placental development. Imputed WGS w-ssGWAS in Nellore cattle identifies trait-specific and shared regions linking growth (ADG and YW), puberty traits (HP), and female rebreeding (HR) through endocrine, metabolic, ovarian, and placental mechanisms. These findings provide candidate genes for functional validation and may support genomic selection strategies that jointly improve productivity and reproductive efficiency.