Genomic reaction norm models exploiting genotype x environment interaction on sexual precocity indicator traits in Nellore cattle

Author(s)

Mota, L. F. M. ^[1] ; Fernandes, Jr., G. A. ^[1] ; Herrera, A. C. ^[1] ; Scalez, D. C. B. ^[1] ; Espigolan, R. ^[1] ; Magalhaes, A. F. B. ^[1] ; Carvalheiro, R. ^{[2, 1]} ; Baldi, F. ^[1] ; Albuquerque, L. G. ^{[2, 1]}

Affiliation

^[1] Sao Paulo State Univ UNESP, Sch Agr & Veterinarian Sci, Via Acesso Prof Paulo Donato Castelane, BR-14884900 Jaboticabal - Brazil

^[2] Natl Council Sci & Technol Dev, BR-71605001 Brasilia, DF - Brazil

• Document type: Journal article
• Source: ANIMAL GENETICS; v. 51, n. 2, p. 210-223, MAR 2020.
• Web of Science Citations: 1

Abstract

Brazilian beef cattle are raised predominantly on pasture in a wide range of environments. In this scenario, genotype by environment (GxE) interaction is an important source of phenotypic variation in the reproductive traits. Hence, the evaluation of GxE interactions for heifer's early pregnancy (HP) and scrotal circumference (SC) traits in Nellore cattle, belonging to three breeding programs, was carried out to determine the animal's sensitivity to the environmental conditions (EC). The dataset consisted of 85 874 records for HP and 151 553 records for SC, from which 1800 heifers and 3343 young bulls were genotyped with the BovineHD BeadChip. Genotypic information for 826 sires was also used in the analyses. EC levels were based on the contemporary group solutions for yearling body weight. Linear reaction norm models (RNM), using pedigree information (RNM\_A) or pedigree and genomic information (RNM\_H), were used to infer GxE interactions. Two validation schemes were used to assess the predictive ability, with the following training populations: (a) forward scheme-dataset was split based on year of birth from 2008 for HP and from 2011 for SC; and (b) environment-specific scheme-low EC (-3.0 and -1.5) and high EC (1.5 and 3.0). The inclusion of the H matrix in RNM increased the genetic variance of the intercept and slope by 18.55 and 23.00% on average respectively, and provided genetic parameter estimates that were more accurate than those considering pedigree only. The same trend was observed for heritability estimates, which were 0.28-0.56 for SC and 0.26-0.49 for HP, using RNM\_H, and 0.26-0.52 for SC and 0.22-0.45 for HP, using RNM\_A. The lowest correlation observed between unfavorable (-3.0) and favorable (3.0) EC levels were 0.30 for HP and -0.12 for SC, indicating the presence of GxE interaction. The GxE interaction effect implied differences in animals' genetic merit and re-ranking of animals on different environmental conditions. SNP marker-environment interaction was detected for Nellore sexual precocity indicator traits with changes in effect and variance across EC levels. The RNM\_H captured GxE interaction effects better than RNM\_A and improved the predictive ability by around 14.04% for SC and 21.31% for HP. Using the forward scheme increased the overall predictive ability for SC (20.55%) and HP (11.06%) compared with the environment-specific scheme. The results suggest that the inclusion of genomic information combined with the pedigree to assess the GxE interaction leads to more accurate variance components and genetic parameter estimates. (AU)

• FAPESP's process: 17/02291-3 - A search for pleotropic effects on reproductive traits in Nellore cattle considering genotype by environment interaction
• Grantee: Lúcio Flávio Macedo Mota
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 09/16118-5 - Genomic tools to genetic improvement of direct economic important traits in Nelore cattle
• Grantee: Lucia Galvão de Albuquerque
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 15/25356-8 - Estimation of genotype-environment interaction using genomic reaction norm and analysis of gene network for reproductive traits in Nellore cattle
• Grantee: Lúcio Flávio Macedo Mota
• Support Opportunities: Scholarships in Brazil - Doctorate