Genomic predictions for traits of productive importance in metapopulations of Zebu beef cattle

• Grant number: 21/04807-2
• Support Opportunities: Regular Research Grants
• Start date: May 01, 2022
• End date: October 31, 2024
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Fernando Sebastián Baldi Rey
• Grantee: Fernando Sebastián Baldi Rey
• Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
• Associated researchers: Daniela Andressa Lino Lourenco ; Danísio Prado Munari ; Ignacio Aguilar ; José Bento Sterman Ferraz ; Marcos Vinicius Gualberto Barbosa da Silva ; Raysildo Barbosa Lôbo

Abstract

The objective is to analyze different strategies for the evaluation of a metapopulation, composed of several breeds such as Nellore, Brahman and Guzerá using the single step genomic BLUP method for growth traits such as weaning weight (W210) and weight adjusted at 15 months of age. (W450). Phenotypic and genotypic information from the Nelore (Nelore Brasil program), Guzerá (Guzerá Brazil program), Brahman (Brahman Brazil program) breeding program from the Association of Breeders and Researchers (ANCP), Ribeirão Preto, SP will be used. For the three breeds, phenotypic information of adjusted weight at 210 and 450 days of age will be used, from farms located in the Southeast, Midwest and North regions of Brazil. For the studied traits there is a database available in the Nelore breed, with approximately 900,000 and 600,000 phenotypic records for W210 (190 ± 32) and W450 (285 ± 58), respectively, distributed in 294 properties. For the Brahman breed, there is a database with approximately 150,000 and 130,000 phenotypic records for W210 (183 ± 32) and W450 (273 ± 56), respectively, distributed in 35 properties. For the Guzerá breed, there is a database with approximately 60,000 and 50,000 phenotypic records for W210 (188 ± 36) and W450 (288 ± 65), respectively, distributed in 25 properties. There is a database of genotypes of approximately 100.000 Nellore animals that have been genotyped using Zoetis' low-density SNP Chip ZL5 panel, which has approximately 30 thousand SNP-type markers. For the Brahman breed, there is a database of about 160 animals genotyped with the SNP Chip ZL5 panel and 600 bulls will be genotyped with more than 20 progenies distributed in more than 2 herds for the traits W210 and W450. For the Guzerá breed, there is a database with about 200 animals genotyped with the Illumina GeneSeek® Genomic Profiler (GGP) panel with approximately 30,000 SNPs, and 120 animals genotyped on the GGP Indicus 35K panel from Neongen. For the Guzerá breed, the 600 most important bulls of the breed with more than 20 progenies distributed in more than 2 herds for the traits W210 and W450 will be genotyped. Different strategies will be evaluated for obtaining the G matrix, implemented in the ssGBLUP method, considering 1) G1: traditional approach (default) of ssGBLUP; 2) G2: the matrix G will be centered on the allele frequencies specific for each breed; 3) G3: Matrix G will be centered and scaled to the allele frequencies specific for each breed. The impact of using a different number of metafounders on genomic predictions in single and multitrait analyzes for W210 and W450 in the Nelore, Guzerá and Brahman breeds will be evaluated, through bias and prediction ability of young genotyped animals. Also, the impact of using metafounders and weighted genomic matrices on the variance components for W210 and W450 will be evaluated. For all single and multitrait analyzes based on pedigree and genomics, the animal model to be used for the estimation of variance components and prediction of genomic values will include the fixed effects of contemporary group, direct additive genetic effects, maternal genetic, permanent environment maternal and residual effect. The maternal genetic effect and maternal permanent environment will be considered only for W210. The maternal genetic effects and maternal permanent environment will be uncorrelated. The results of the present project will allow to evaluate the impact of the implementation of the multibreed genomic evaluation of beef Zebu breeds using ssGBLUP in breeds with reduced size of the reference population. (AU)