Genome scan for transmission ratio distortion regions and its associations with abortion, stillbirth and pre-weaning mortality in Nellore cattle

• Grant number: 24/01909-7
• Support Opportunities: Scholarships abroad - Research Internship - Master's degree
• Effective date (Start): August 01, 2024
• Effective date (End): January 31, 2025
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Maria Eugênia Zerlotti Mercadante
• Grantee: Gustavo Roberto Dias Rodrigues
• Supervisor: Luiz Fernando Brito
• Host Institution: Instituto de Zootecnia. Agência Paulista de Tecnologia dos Agronegócios (APTA). Secretaria de Agricultura e Abastecimento (São Paulo - Estado). Nova Odessa , SP, Brazil
• Research place: Purdue University, United States
• Associated to the scholarship: 23/11176-4 - Mapping candidates for lethal haplotypes and genomic regions associated with the occurrence of abortion and pre-weaning mortality in Nellore cattle, BP.MS

Abstract

Reproductive rate and calf survival are directly related with the profitability and long-term sustainability of the beef cattle industry. A better understanding of the genomic background of reproductive rate and calf survival is paramount for optimizing genetic selection for these traits. The primary objectives of this research project are to i) identify Transmission Ratio Distortion (TRD) regions in the Nellore cattle genome that might contain lethal alleles and/or deleterious genetic variants; and, ii) investigate the effects of TRD regions on abortion, stillbirths, and pre-weaning mortality in Nellore cattle. Data from the Institute of Animal Science (IZ, Sertãozinho/SP) will be used for this study. The genomic dataset comprises 3,226 genotyped animals, including 1,741 males and 1,485 females, corresponding to 1,779 trios and 4,607 unique pairs parent/progeny. A total of 780 animals were genotyped with an HD SNP panel (~770k SNP markers) and 2,446 animals were genotyped with medium density SNP panels (50k and 75k SNP markers). Animals genotyped with the lower density panels were imputed to the HD panel using the FImpute v.3 software, resulting in 612,154 autosomal SNP markers for the TRD analysis. Phenotypic records for abortion, stillbirth, and pre-weaning mortality were measured from 5,105 reproductive records. Two approaches for the identification of TRD regions will be considered: i) allelic parametrization of TRD; and, ii) genotypic parametrization of TRD. The TRD identification will be performed within a Bayesian framework using the TRDscan v.2.0 software. The effects of the TRD regions on abortion, stillbirth, and pre-weaning mortality will be assessed based on an animal model via Bayesian inference considering the systematic effects of breeding season, selection line, and cow's age at breeding with linear and quadratic effects as a covariate, and random effects of additive genetic and permanent environment, and additive genetics obtained exclusively from the TRD regions. The results obtained will provide insights into the potential advantages of incorporating TRD information in animal breeding programs aiming to enhance reproduction efficiency in Brazilian beef cattle production.