Identificação de assinaturas de seleção em bovinos da raça Nelore, Gir e Sindi por meio da homozigose do haplótipo estendido

Abstract

Selection signatures analysis is a promising tool for identifying traces of artificial selection, which can elucidate genetic mechanisms related to morphological, physiological and productive traits specific to each breed. Thus, the objectives of this study were to verify the existence of genomic regions corresponding to the selection signatures in target populations of the Nelore, Gir and Sindhi breeds from Brazil, however using as reference genotypes of these same breeds but from the Asian continent; and at the end, to identify possible genes and SNPs (Single Nucleotide Polymorphisms) present in these regions, related to traits of economic interest and their relationship with the breeding objectives. After the quality control of the samples, 52 Nelore animals from Brazil, 48 Gir animals from Brazil, 49 Sindhi animals from Brazil, 50 Nelore animals from India, 27 Gir animals from India and 9 Sindhi animals from Pakistan were studied, where the Illumina BovineHD BeadChip panel (777,962 SNP - Single Nucleotide Polymorphism markers) was considered. To identify the selection signatures, the rehh package present in the R statistical program was used, through the XP-EHH and Rsb methods. To define the selection signature regions, the 40 largest windows were considered, with a size of 50kb (50,000 base pairs), with no overlap between windows and with at least 2 SNPs per window. The Pearson correlation between the methods in the Nelore, Gir and Sindhi breeds, from Brazil and the Asian continent, was equal to 0.73, 0.73 and 0.81, respectively. However, only common selection signatures were verified in both methodologies for the 40 largest windows in animals of the Gir and Sindi breeds. A total of 652 SNPs were identified in the Rsb methodology and 567 SNPs in the XP-EHH methodology in Nelore animals with no correspondence between them. For the Gir breed, 443 and 441 SNPs were identified using the Rsb and XP-EHH methods and, in common between both methodologies, 290 SNPs were verified. For Sindhi, 702 and 660 SNPs were found in selection signature regions using the Rsb and XP-EHH methods and, in common between both methodologies, 315 SNPs were found. It can be concluded that it was possible to identify selection signatures in cattle from Brazil using genotypes from animals from the Asian continent. The selection signatures identified in Nelore, Gir and Sindi animals corroborate with the selection objectives considered by genetic evaluation programs for breeds in Brazil. It can be highlighted in this study the identification of genes associated with immunological processes, which may be related to the adaptability of these breeds to the production system in Brazil.