GENOMIC REACTION NORM MODELS AND GENETIC NETWORK ANALYSIS EXPLORING THE EFFECTS OF GENOTYPE X ENVIRONMENT INTERACTION ON FEED EFFICIENCY TRAITS IN NELORE CATTLE

• Grant number: 22/15385-4
• Support Opportunities: Scholarships in Brazil - Doctorate
• Effective date (Start): April 01, 2023
• Status: Discontinued
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Fernando Sebastián Baldi Rey
• Grantee: João Barbosa da Silva Neto
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated scholarship(s): 23/13417-9 - Investigating the effect of heat stress on feed efficiency-related traits in Nellore cattle based on genomic reaction norm models, BE.EP.DR

Abstract

This research project aims to: 1) verify the occurrence of GxE interaction for the traits dry matter intake (DMI) and residual feed intake (RAC) in Nelore cattle, by means of reaction norm models evaluating the effect of feed efficiency tests to assess the genetic variation of DMI and CAR in different environmental gradients; 2) evaluate the effect of GxE interaction on SNP markers in different environmental gradients. The data set used in this study will be composed of animals of the Nelore breed, from the Nelore Brazil genetic improvement program, coordinated by the National Association of Breeders and Researchers (ANCP, Ribeirão Preto, SP, Brazil). The data encompass 158 feed efficiency trials, with 12,958 phenotypic records for the traits dry matter intake (DMI) and residual feed intake (CAR). Approximately 40,000 animals were genotyped with the CLARIFIDE® Nelore 3.0 low-density panel containing over 30,000 markers. The low density genotyped animals will be imputed for a HD 735,044 marker panel using a reference population of 945 sires genotyped with a panel of 777,000 (excluding sex chromosomes and mitochondrial chromosomes) using FIMPUTE 2.2 software removing animals and markers with call rate < 0.05. Monomorphic SNPs with redundant position and those located on non-autosomal chromosomes will be removed, as well as, SNPs with Mendelian conflicts > 1% will also be excluded. A two-step genomic reaction norm model will be considered in the present study. The first step will use the single-step animal model (GBLUP) combining pedigree and genomic information (ssGBLUP) to obtain the BLUE (best linear non-biased estimates) solutions for the contemporary group for average daily weight gain (ADG) and the environmental descriptors (EC) will be determined as the normalized BLUE solutions. The second step will use the multi-characteristic reaction norm model considering pedigree and genomic information in order to obtain the genetic parameters for IMS and CAR for the different levels of EC. The effects of SNP markers will be estimated at each level of EC from a linear transformation of the predicted genomic genetic values for the genotyped animals in each environmental group. Based on these effects, possible changes or pleiotropic effects of candidate genes as well as of the biological pathways of major importance on the expression of feed efficiency indicator traits (IMS and CAR) will be investigated. Therefore, the results of the present study provide the opportunity to evaluate the estimates of genetic parameters for the traits IMS and CAR in different environmental conditions and if they can be considered the same in environmental conditions, considering each trial as environment and the solution of the GC of the weight gain in trial (GPP) as environmental gradient; to verify which genes and metabolic pathways influence the expression of IMS and CAR in different environmental levels; and to verify which prediction equation to use for these traits. As well as the possibility to evaluate the impact of differences regarding aspects that affect the productive performance and that can lead to an effect on the indicator traits of feed efficiency.