Abstract
Since domestication, horse breeds have adapted to their environments and differentiated from one another. This paper uses two methods to detect selection signatures in 23 horse breeds, eight of which are Brazilian (610 animals), both cold-blooded and warm-blooded, from temperate and tropical regions. These animals were genotyped using the GGP Equine BeadChip and we analysed the data by Principal Component Analysis (PCA). The samples were separated into groups based on their geographical area of origin and PCA results studied. The genomic regions under selection were detected by hapFLK and PCAdapt methodologies, identifying six regions under selection with at least one Brazilian horse breed. These regions contain genes associated with heat tolerance, skin colour, body size, energy production/metabolism, genes involved in protein degradation/turnover/DNA repair, genes reducing the impact of oxidative stress/cellular repair, and transcriptional regulation. This work confirmed LCORL and NCAPG gene regions in previous studies associated with body size on Equine Chromosome Autosome 3 (ECA3). On the same ECA3, a region implicating genes linked to coat colour was identified, also previously related to heat stress. Regions with genes coding heat shock proteins were found on ECA1 and 2, and many candidate genes for oxidation–reduction which are a natural response to heat stress. However, a larger sample size and whole-genome SNPs are needed to understand better and identify new candidate regions as well as their functional relation with heat tolerance.
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Funding
This work was supported by CAPES (Coordination for the Improvement of Higher Education Personnel), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Grant no. 001, Concepta M. McManus), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Grant no. 308929/2020-9, Concepta M. McManus), Ministério da Agricultura, Pecuária e Abastecimento (Grant no. 001, Concepta M. McManus).
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A
) Population tree of horses breeds according to hapFLK results using all autosomes and Swiss Warmblood as outgroup. B) Tree of the groups of horse breeds according to hapFLK results using all autosomes and Warmblood1 as outgroup (TIFF 6592 KB)
438_2022_1862_MOESM3_ESM.tiff
Manhattan plot of SNP p-values based on PCA analysis. The significant SNP for each component (1, 3 and 4) had different colours and shape (TIFF 9492 KB)
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de Faria, D.A., do Prado Paim, T., dos Santos, C.A. et al. Selection signatures for heat tolerance in Brazilian horse breeds. Mol Genet Genomics 297, 449–462 (2022). https://doi.org/10.1007/s00438-022-01862-w
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DOI: https://doi.org/10.1007/s00438-022-01862-w