Whole-genome sequencing of a Brazilian naturalized horse breed resistant to arid climate for identifying single nucleotide variants and insertions/deletions [post]

glacy silva, Danielle Cunha Cardoso, Eduardo Geraldo Alves Coelho, Brenda Neves Porto, Denea de Araújo Fernandes Pires, Denise Aparecida Andrade de Oliveira
2020 unpublished
Background: In this study, we perform a search for variants (SNVs and InDels) in the genome of a Brazilian Naturalized horse breed, using FreeBayes and GATK variant calling tools. This breed presents exclusive adaptive traits of extreme importance to semi-arid conditions, such as those that allow survival under excessive sunlight, rainfall, low forage availability and stony ground. Moreover, these traits are expressed without any detriment to the performance and perpetuation of the breed.
more » ... of the breed. Results: A total of 305,588,364 reads were mapped in the horse reference genome, 1,598,210 single nucleotide variations and 138,139 insertions/deletions were detected by FreeBayes, 88,838 (SNVs) and 25,232 (InDels) by GATK. Both have been used in order to increase the safety of variant calls, identify in which regions of the genome they are present and check for variants in genes possibly associated with the peculiar traits exhibited by the breed. Conclusions: The variants annotation identified numerous non-synonymous SNVs and frameshift InDels, which could affect phenotypic variation. We found 28 and 392 Emsembl gene IDs containing high and moderate impact SNVs, including GTPase family members, olfactory receptors, mitochondrial complex and defense genes. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway were overrepresented.
doi:10.21203/rs.3.rs-21956/v1 fatcat:jhbalo5fmbdpzixo6xqp3fkryu