Sequenciamento de genoma completo do cavalo Nordestino para identificação de variantes genômicas (SNVs e INDELs) e validação em subpopulações remanescentes

Abstract

Genomic variant calling, in order to identify new single nucleotide variants (SNVs) and insertions/deletions (InDELs), potentially associated with the characteristics of rusticity and resistance to arid climate in Nordestino horse breed, based in whole genome sequencing was the strategy used in the present study to understand the adaptive mechanisms of the breed to semiarid climate of Brazilian northeastern. These variations are possibly associated with the resistance exhibited by the breed, through the highly specialized racial pattern for the performance of activities that require strength and endurance, without any damage to its perpetuation. Complete genome sequencing of a typical representative of the breed was carried out, this being the first whole genome sequencing of a Brazilian naturalized equine breed, as a comparative genomics strategy for variants calling with the most recent reference genome equine update (Ensemble EquCab 3.0). Tools based on algorithms for variants calling identified 1,598,210 SNVs and 138,139 InDels (Freebayes software) and 88,838 SNVs and 25,232 InDELs (GATK software). Variants were classified as to the type, location and impact effect and the genomic regions were anoted. High and moderate impact variants were selected to functional enrichment analysis and for population validation in 60 animals from the states of Bahia, Pernambuco and Piaui. High-impact SNVs occurred exclusively in GTPase genes. Olfactory Receptor (OR) genes family containing moderate-impact SNVs had high representativeness in the functional analysis. All 10 loci tested, containing breed-specific SNVs, presented polymorphic alleles in the three populations, with high genotypic frequencies of heterozygous and homozygous with allelic polymorphism. The genotypic frequencies for 8 loci were significantly different between the three populations, suggesting allelic fixation and genetic diversity. The presence of SNVs in OR genes, which are related to adaptive mechanisms, represents important genetic information to understand the adaptation of the breed to the semiarid region of northeastern Brazil and to associate them with the peculiar phenotype exhibited by that breed.