Effect of selection for growth on reproductive traits in Nellore females: Genetic parameters and genome-wide association studies

Abstract

This study aimed to evaluate the effects of selection for post-weaning weight on reproductive traits in Nellore cattle by (i) estimating genetic parameters and trends for birth weight (BIW), body weight at selection (BW), days to calving (DC), and pregnancy rate (PR); and (ii) performing a genome-wide association study (GWAS), gene annotation, and functional enrichment analyses to uncover genomic regions, candidate genes, biological processes, and metabolic pathways underlying DC and PR. The dataset contained 12,865 Nellore animals from the experimental breeding program of the Institute of Animal Science (IZ, Sertãozinho, Brazil), including three selection lines: Nellore Control (NeC, stablishing selection for post-weaning weight), Nellore Selection (NeS, selected for higher post-weaning weight), and Nellore Traditional (NeT, selected for higher post-weaning weight and lower residual feed intake). Genomic data were available for 2,326 animals and 384,521 autosomal SNP markers after quality control. Genetic parameters were estimated using Bayesian inference under the ssGBLUP framework. Genetic trends from 1981 to 2021 were derived from linear regressions considering genomic estimated breeding values (GEBVs). The weighted single-step GWAS (WssGWAS) was used to identify genomic regions that explained more than 1.0% of the additive genetic variance for DC and PR, which were further analyzed for gene annotation and functional enrichment. Heritability estimates were high for BIW (0.46 ± 0.02) and BW (0.41 ± 0.02), and low for DC and PR (0.10 ± 0.02 for both). Moderate genetic correlations were observed between BIW and DC, especially in lines selected for higher growth (NeS: 0.38 ± 0.12; NeT: 0.56 ± 0.09), in contrast, BW showed weak genetic correlations with reproductive traits, with estimates for DC of − 0.11 ± 0.18 (NeC), 0.15 ± 0.15 (NeS), and 0.36 ± 0.14 (NeT), and for PR of 0.25 ± 0.22 (NeC), − 0.12 ± 0.17 (NeS), and − 0.44 ± 0.16 (NeT). Genetic trends indicated consistent increases in BW and BIW in NeS and NeT, while NeC showed more favorable trends for DC and PR. The GWAS identified 13 and 9 genomic windows associated with DC and PR, respectively, with pleiotropic regions on chromosome 14 influencing both traits. Key candidate genes annotated included PLAG1, MOS, MAPK13, MAPK14, and FKBP5. Functional enrichment revealed biological processes related to hormone metabolism, immune modulation, and oocyte development. Selection for increased growth does not directly impair reproductive traits; however, it indirectly influences fertility due to correlated response in BIW, which is genetically associated with DC.