Estimation of genotype-environment interaction using genomic reaction norm and analysis of gene network for reproductive traits in Nellore cattle

Genotype-environment (GxE) interactions could be an important source of variation in reproductive traits with a striking effect on the onset of animal puberty. Thus, the objectives of the present study were: i) to assess the GxE interaction in Nellore sexual precocity indicator traits under different environmental conditions (EC) and ii) to identify, genomic regions and biological pathways associated to Nellore sexual precocity indicator traits and to investigate whether their effects changes according to EC levels. Phenotypic records for age at first calving (AFC), heifer early pregnancy (HP), heifer rebreeding (HR) and scrotal circumference (SC) were collected on 128,994; 85,339; 90,831 and 151,053 animals, respectively. From those, 1800 heifers, 3050 young bulls, and 800 sires were genotyped with BovineHD BeadChip. A reaction norm model was used to estimate the animal’s response to environmental conditions changes. To assess the predictive ability the younger scheme and environment-specific scheme were used. For genome-wide scan, the SNP effects for reproductive traits were estimated in three EC levels: Low (EC = -3.0), Medium (EC = 0.0) and High (EC = 3.0) using a linear transformation of the genomic breeding values. The pleiotropic regions associated to reproductive traits (AFC, SC, HP and HR) in three EC levels, were identified using the statistical combination of the single-trait GWAS results and considered significant when –log10(p-valor)>6.0. The inclusion of genomic information combined with pedigree, lead to variance components and genetic parameter estimates more accurate than that considering pedigree information. The GxE interaction had an important effect on heifer early pregnancy and scrotal circumference leading to genomic breeding value sensitivity in different environmental condition. In addition, a strong SNP marker-environment interaction was observed for Nellore sexual precocity indicator traits with changes in their effect and explained variance in different EC levels. The younger scheme leads to a higher predictive ability for SC and EP compared to environment-specific scheme. Using the statistical combination of single-trait GWAS were identified, a total of 56 SNP markers with pleiotropic effect for reproductive traits in different EC levels. Those SNP markers were distributed on Bos Taurus autosome (BTA) 5, 7, 10, 14, 16, and 29 and showed changes in their effect according to environmental condition changes. A total of 45 genes were mapped within 200 kb and show a striking effect in biological process associated to fat deposition, embryonic growth, decreasing in hormonal levels and decreasing female and male fertility (mainly on decreased oocyte number and spermatogenesis). In summary, this study pointed to the effect of GxE interaction on breeding value of reproductive traits in Nellore cattle. In addition, genomic regions identified show a key role in biological mechanisms that encode the major reproductive pathways, and that the environmental conditions changes have important effects on its expression. These results contribute to a better understanding of differences in reproductive performance of Nellore cattle raised under different environmental conditions, might aid the genetic improvement of reproductive traits in Nellore cattle. (AU)