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Strategies for genomic prediction in multiracial zebu populations using the single step genomic BLUP method

Grant number: 20/14275-5
Support Opportunities:Scholarships in Brazil - Doctorate
Effective date (Start): October 01, 2022
Field of knowledge:Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
Principal Investigator:Fernando Sebastián Baldi Rey
Grantee:Marisol Londoño Gil
Host Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil
Associated scholarship(s):22/15168-3 - Indirect predictions based on genomic evaluation of indicine multibreed populations using the single step GBLUP method with metafounders, BE.EP.DR


The aim of this work is to evaluate different strategies for the evaluation of a metapopulation composed of several breeds such as Nellore, Brahman and Guzerá using the BLUP single-step genomic method for growth traits such as weaning weight (P210) and weight adjusted at 15 months of age ( P450). The specific objectives are: a) To evaluate different strategies for obtaining matrix G, implemented in the ssGBLUP method, in Nellore, Guzerá and Brahman cattle, considering 1) G1: traditional approach (default) of ssGBLUP; 2) G2: G matrix will be centered on allelic frequencies specific to each breed; 3) G3: The G matrix will be centered and scaled to the specific allelic frequencies of each breed; b) To investigate the effect of using different number of metafounders on genomic predictions for P210 and P450 in Nellore, Guzerá and Brahman breeds, through the accuracy and bias of GEBVs; c) The impact of the use of metafounders and weighted genomic matrices on genomic predictions, bias and prediction ability in young animals genotyped for P210 and P450 will be verified. Phenotypic and genotypic information will be used from the breeding programs of Nellore (Nellore Brazil program), Guzerá (Guzerá Brazil program), and Brahman (Brahman Brazil program) breeds of the Association of Breeders and Researchers (ANCP), Ribeirão Preto, SP. For the three breeds, phenotypic information of adjusted weight at 210 and 450 days of age from farms located in the Southeast, Midwest and North regions of Brazil will be used. For the studied traits there is a database available in the Nellore breed, with approximately 900,000 and 600,000 phenotypic observations for P210 (190±32 kg) and P450 (285±58 kg), respectively, distributed in 294 properties. For the Brahman breed, there is a database with approximately 150,000 and 130,000 phenotypic observations for P210 (183±32 kg) and P450 (273±56 kg), respectively, distributed in 35 farms. For the Guzerat breed, there is a database with approximately 60,000 and 50,000 phenotypic observations for P210 (188±36 kg) and P450 (288±65 kg), respectively, distributed in 25 farms. There is a genotype database of approximately 100,000 Nellore animals that were genotyped using the Zoetis SNP Chip ZL5 Low Density Panel, which has approximately 30,000 SNP-type markers. For the Brahman breed there is a database with about 760 animals genotyped, 120 with the SNP Chip ZL5 panel, and 600 bulls with the Illumina GeneSeek® Genomic Profiler (GGP) panel Indicus 50K from Neogen company. For the Guzerá breed there is a database with about 200 animals genotyped with the Illumina GGP panel with approximately 30,000 SNPs, 120 animals genotyped in the GGP Indicus 35K panel from the company Neogen and 600 bulls with the Neogen company GGP Indicus 50K panel. The results of this project will allow to: Evaluate the impact of the implementation of multibreed genomic evaluation of beef zebu breeds using different approaches; Forming and consolidating a work team at the national and international level, made up of different specialists of recognized trajectory, which should form a solid platform for the realization of future research projects; Implement statistical methodologies for the use of genomic data in animal breeding aiming at multibreed evaluation in Zebu breeds; Around 2 to 3 scientific papers will be produced to be published in high-impact journals in the area.

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