- Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics.. - Conclusion: The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. - Full list of author information is available at the end of the article. - By the end of the nineteenth century, the increasing de- mand for food supply triggered the imports of exotic and more productive breeds of indicine origin [3, 4]. - In this regard, Brazilian locally adapted cattle breeds represent an important gen- etic resource for the understanding of the role of natural selection in diverse environments, providing new insights into the genetic mechanisms inherent to adaptation and survivorship [6]. - According to Utsunomiya et al. - Potential bio- logical functions of the genes screened within the puta- tive candidate regions were also examined to better elucidate the phenotypic variation related to adaptation shaped by natural selection.. - Of the total SNPs identified (n SNPs), most of them were located in intergenic (67.17%) and intronic (25.85%) regions (Additional file 1). - The population structure among breeds was dissected by analyzing the first two principal components, which accounted for roughly 20% of the genetic variability and divided the populations into three clusters (Fig. - A total of 499 putative sweep regions encompassing 221 genes were identified from the top 1% of the empirical dis- tribution generated by the within-population de- correlated composite of multiple signals (DCMS) statistic [20] (Fig. - For the cross-population DCMS statistic, the top 1% of the empirical distribution revealed 503 putative sweep regions comprehending 242 genes (Additional file 6). - The functional importance of the annotated genes was assessed by performing GO and KEGG pathway en- richment analysis separately for each DCMS statistic and its respective retrieved gene list. - Each sample is denoted by a single vertical bar partitioned into K colors according to its proportion of ancestry in each of the clusters. - Five genomic regions overlapped between the candi- date sweep regions of the within-population and cross- population DCMS statistics (BTA BTA BTA BTA and BTA11:. - Reds dots correspond to the top 1% of the empirical distribution generated by the DCMS statistics. - Several putative sweep regions identified from the top 1% of the empirical distribution generated by the within-. - As a result of the domestication process and selective breeding over time, the cattle can be classi- fied into temperate (Bos taurus taurus or taurine) and tropical (Bos taurus indicus or indicine) based on the common adaptive and evolutionary traits they have ac- quired [57]. - This gene flow reinforces the concept that the import of exotic breeds at the beginning of the twentieth century [3] led to the miscegenation of the locally adapted breeds due to crossbreeding prac- tices, resulting nearly in their extinction [4]. - Concurring with our findings, Egito et al. - [16] and Egito et al. - As already stated, the Brazilian locally adapted cattle breeds nearly disappeared between the late 19th and be- ginning of the twentieth century, and most of them are nowadays threatened with extinction [3, 5]. - Most of the locally adapted cattle breeds in Brazil de- veloped from a narrow genetic base, and in such cases, inbreeding can increase over generations and reduce genetic variability [65]. - Egito et al. - [15] attributed such re- sults to the formation of new PAN herds from 2009 onwards while Pezzini et al. - Further, Egito et al. - According to Marras et al. - Presumptively, these two concomi- tant events led to the dissemination of the breed, allow- ing formerly closed herds to start using semen of proven sires, increasing the overall genetic exchange and redu- cing the average inbreeding over time.. - The genes and QTLs identified within the candidate regions provide a hint about the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. - The greatest number of the putative sweep regions iden- tified from the top 1% of the within-population DCMS statistic overlapped with candidate regions under posi- tive selection previously reported in five cattle breeds. - selected for dairy production [54], comprehending roughly 22% (n = 52) of the overlapping regions. - For the top 1% of the cross-population DCMS statistic, the greatest number was described for native cattle breeds from Siberia, eastern and northern Europe [46], totaling nearly 17% (n = 50) of the overlapping regions. - Remark- ably, in both statistics, the majority of the shared signals within those reported in the literature was found associ- ated with specialized cattle breeds (i.e. - According to Gutiérrez-Gil et al. - The greater number (seven out of 11) of the putative sweep regions shared between ROH hotspots and the top 1% putative sweep regions retrieved from both DCMS statistics overlapped with regions previously de- scribed on local and native cattle breeds . - Besides, some scan methodologies based on site fre- quency spectrum and population differentiation may be more likely to ascertainment bias than others compromising the power of the tests and may yielding to flawed results [107] when compared to those obtained from whole-genome re-sequencing data.. - The sig- natures of selection across the genome could provide im- portant insights for the understanding of the adaptive process and the differences in the breeding history under- lying such breeds. - Our findings suggest that admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds, and the stratifi- cation results revealed the genetic structure integrity of the dairy populations sampled in this study. - The candidate sweeps regions and the gene list retrieved from them can improve our understanding of the biological mechanisms underlying important pheno- typic variation related to adaptation to hostile environ- ments and selective pressures events to which these breeds have undergone. - Variant annotation and predicted functional impacts A functional annotation analysis of the called variants was performed to assess their possible biological im- pact using the Variant Effect Predictor (VEP, [114]) together with the Ensembl cow gene set 94 release.. - A PCA implemented with a custom R script was used to examine the genetic structure of the four breeds.. - Genomic inbreeding coefficients based on runs of homo- zygosity (F ROH ) were estimated for every animal accord- ing to the genome autozygotic proportion described by McQuillan et al. - where S i ROH is the sum of ROH across the genome for the i th animals and L GEN is the total length of the auto- somes covered by SNPs. - F ST [125] was calculated between all six pairwise com- binations of the four breeds with custom R scripts as follows:. - The ancestral allele in- formation was assessed from a cattle reference allele list retrieved from Rocha et al. - The iHS scores were calculated within each breed and XP-EHH between all six pairwise combi- nations of the four breeds. - Candidate sweep regions under selec- tion were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics.. - Candidate sweep regions revealed from the top 1% of the empirical distribution generated by the DCMS. - ROH formerly identified to estimate F ROH were applied, and ROH hotspots were determined by selecting segments shared by more than 50% of the samples within each breed.. - Functional annotation of the candidate regions. - Distribution of the functional consequences of the called variants ( n SNPs) using the Variant Effect Predictor (VEP) tool.. - Annotated candidate sweep regions for the within- population statistic retrieved from the top 1% of the empirical distribu- tion generated by the DCMS statistic.. - Annotated candidate sweep regions for the cross- population statistic retrieved from the top 1% of the empirical distribu- tion generated by the DCMS statistic.. - Overlapping of the putative sweep regions identified from the top 1% of the within-population DCMS statistic with candidate regions under positive selection previously reported in other cattle populations.. - Overlapping of the putative sweep regions identified from the top 1% of the cross-population DCMS statistic with candidate regions under positive selection previously reported in other cattle populations.. - of the within-population DCMS statistic with the candidate regions under positive selection previously reported in other cattle populations.. - of the cross-population DCMS statistic with the candidate regions under positive selection previously reported in other cattle populations.. - Brazilian geographical regions of the four cattle breeds sampled in the study (Adapted from https://pt.wikipedia.org/wiki/. - Manhattan plot of the independent results for each selective sweep statistical method and population.. - EP, CR, HS, FB, and MVGBS contributed to the conceptualization of the manuscript. - However, data are available for sharing upon reasonable request and with permission of the. - Kim J, Hanotte O, Mwai OA, Dessie T, Salim B, Diallo B, et al. - Cardoso CC, Lima FG, Fioravanti MCS, Egito AA, Paula e Silva FC, Tanure CB, et al. - Qanbari S, Pausch H, Jansen S, Somel M, Strom TM, Fries R, et al. - Wang X, Liu J, Zhou G, Guo J, Yan H, Niu Y, et al. - Egito AA, Martinez AM, Juliano RS, Landi V, Moura MI, Silva MC, et al.. - 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