Impacts of the inclusion of runs of homozygosity in the mating strategy processes in a beef cattle simulated population

Author(s)

Alana Selli

• Document type: Master's Dissertation
• Press: Pirassununga.
• Institution: Universidade de São Paulo (USP). Faculdade de Medicina Veterinária e Zootecnia (FMVZ/SBD)
• Defense date: 2024-03-19

Examining board members

Ricardo Vieira Ventura; Fernando de Oliveira Bussiman; Hinayah Rojas de Oliveira

• Advisor: Ricardo Vieira Ventura; Luiz Fernando Brito; Marcos Eli Buzanskas

Abstract

This work aimed to apply different selection strategies in relation to runs of homozygosity profiles in a population (via simulated data), in addition to investigating the impact of such strategies on the increase or decrease of the Estimated Breeding Value (EBV) of a trait and other parameters related to the genetic variability of the population. For this, a population of beef cattle was simulated with the R package AlphaSimR, containing 5 chromosomes with different sizes and numbers of Quantitative Trait Loci (QTL), corresponding to an additive trait with heritability of 0.3. From the initial simulation, three selection and mating strategies were tested. (1) EBV + Fped: genetic values estimated through pedigree and phenotype, and the inbreeding coefficient based on Pedigree. (2) GEBV + Fg: genetic values estimated through information from Single Nucleotide Polymorphism (SNP) markers, and genomic inbreeding coefficient. (3) GEBV + Froh: genetic values estimated through information from SNP genetic markers, and inbreeding coefficient based on homozygosity runs. The GEBV + Froh strategy consistently produced superior true breeding values and phenotypes. Fg was lower when using the GEBV + Fg strategy, however the same strategy promoted the formation of larger and more frequent runs of homozygosity in the genome. The most efficient strategy to minimize the percentage of the genome covered by ROHs, however, was EBV + Fped. The genetic evaluations of each animal in the population, as well as the respective inbreeding coefficients, were developed via a mix of real-time activations of existing software (BLUF90, PLINK), through an interface developed in R language. Some limitations were highlighted, such as the population size used and the adequacy of certain simulation parameters, and possible solutions were proposed. (AU)

• FAPESP's process: 21/11156-8 - Impacts of the inclusion of runs of homozygosity in the mating strategy processes in a beef cattle simulated population
• Grantee: Alana Selli
• Support Opportunities: Scholarships in Brazil - Master