Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using w
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RESEARCH ARTICLE
Open Access
Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using wholegenome re-sequencing data Elisa Peripolli1, Christian Reimer2,3, Ngoc-Thuy Ha2,3, Johannes Geibel2,3, Marco Antonio Machado4,5, João Cláudio do Carmo Panetto5, Andréa Alves do Egito6, Fernando Baldi1, Henner Simianer2,3 and Marcos Vinícius Gualberto Barbosa da Silva4,5*
Abstract Background: The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. Results: A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations’ historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. 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. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions. Keywords: Bos taurus indicus, Bos taurus taurus, Signatures of selection, Local adaptation, Next-generation sequencing
* Correspondence: [email protected] 4 National Council for Scientific and Technological Development (CNPq), Lago Sul 71605-001, Brazil 5 Embrapa Dairy Cattle, Juiz de Fora 36038-330, Brazil Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons lic
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