Genome-wide scan highlights the role of candidate genes on phenotypic plasticity for age at first calving in Nellore heifers

Lucio F M Mota,Guilherme J M Rosa,Roberto Carvalheiro,Lucia G Albuquerque,Ana F B Magalhães,Fernando B Lopes,Gerardo A Fernandes Júnior

doi:10.1038/s41598-020-63516-4

Abstract

Age at first calving (AFC) plays an important role in the economic efficiency of beef cattle production. This trait can be affected by a combination of genetic and environmental factors, leading to physiological changes in response to heifers’ adaptation to a wide range of environments. Genome-wide association studies through the reaction norm model were carried out to identify genomic regions associated with AFC in Nellore heifers, raised under different environmental conditions (EC). The SNP effects for AFC were estimated in three EC levels (Low, Medium, and High, corresponding to average contemporary group effects on yearling body weight equal to 159.40, 228.6 and 297.6 kg, respectively), which unraveled shared and unique genomic regions for AFC in Low, Medium, and High EC levels, that varied according to the genetic correlation between AFC in different EC levels. The significant genomic regions harbored key genes that might play an important biological role in controlling hormone signaling and metabolism. Shared genomic regions among EC levels were identified on BTA 2 and 14, harboring candidate genes associated with energy metabolism (IGFBP2, IGFBP5, SHOX, SMARCAL1, LYN, RPS20, MOS, PLAG1, CHCD7, and SDR16C6). Gene set enrichment analyses identified important biological functions related to growth, hormone levels affecting female fertility, physiological processes involved in female pregnancy, gamete generation, ovulation cycle, and age at puberty. The genomic regions highlighted differences in the physiological processes linked to AFC in different EC levels and metabolic processes that support complex interactions between the gonadotropic axes and sexual precocity in Nellore heifers.

Highlights

Age at first calving (AFC) plays an important role in the economic efficiency of beef cattle production
This study was carried out to evaluate the changes in the Single nucleotide polymorphism (SNP) effect estimates, as well as the biological processes associated with age at first calving in three environmental conditions, combining reaction norm (RN) models and genome-wide association studies (GWAS)
Combining genome-wide scan and reaction norm models helped to identify genomic regions associated with age at first calving (AFC) in Nellore heifers in different environmental conditions

Summary

Introduction

Age at first calving (AFC) plays an important role in the economic efficiency of beef cattle production This trait can be affected by a combination of genetic and environmental factors, leading to physiological changes in response to heifers’ adaptation to a wide range of environments. Www.nature.com/scientificreports pathway and gene network analyses from these results can be performed to uncover mechanisms whereby the environment can potentially affect the sexual precocity in cattle Such knowledge regarding genomic regions and biological pathways involved with GxE interactions in Nellore heifers’ sexual precocity is important to identify molecular mechanisms underlying the phenotypic responses to different environments. This study was carried out to evaluate the changes in the SNP effect estimates, as well as the biological processes associated with age at first calving in three environmental conditions, combining RN models and GWAS

Methods

Results

Conclusion