Identification of candidate lethal haplotypes in Nelore cattle

Abstract

Pedigree analysis has been used to provide evidence of recessive alleles occurrence in the population. Now, with the inclusion of genomic information, it is possible to detect lethal recessive haplotypes considering the frequency of homozygous individuals in the population. The objectives of the present study are to identify lethal recessive haplotypes, based on expected population frequencies, and to detect candidate genes underlying lethal haplotypes through functional analysis. A total of 4,669 animals were genotyped with a high-density panel (777,962 SNP markers) and 4,094 with a panel containing 70,000 markers, which will be imputed to the HD panel using FImput software v 2.2. Evidence for a haplotype harboring a lethal allele will be evaluated based on the expected frequency of homozygous individuals in the population. To identify the causal variants underlying the putative lethal regions, we will select all the genes in regions of lethal haplotypes using ENSEMBL software. Lethal genes during all stages of life development will be described and marked as candidate genes. This study will generate knowledge to anticipate problems caused by disadvantageous variants through the implementation of selection actions, management of matings and, potentially, gene editing to prevent the emergence of lethal haplotypes in the population. (AU)