Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using wholegenome re-sequencing data.

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.

Bibliographic Details

Main Authors:	PERIPOLLI, E., REIMER, C., HA, NGOC-THUY, GEIBEL. J., MACHADO, M. A., PANETTO, J. C. do C., EGITO, A. A. do, BALDI, F., SIMIANER, H., SILVA, M. V. G. B.
Other Authors:	Elisa Peripolli; Christian Reimer; Ngoc-Thuy Ha; Johannes Geibel; MARCO ANTONIO MACHADO, CNPGL; JOAO CLAUDIO DO CARMO PANETTO, CNPGL; ANDREA ALVES DO EGITO, CNPGC; Fernando Baldi; Henner Simianer; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL.
Format:	Artigo de periódico biblioteca
Language:	Ingles English
Published:	2021-02-08
Subjects:	Bos taurus indicus, Bos taurus taurus, Signatures of selection, Local adaptation, Next-generation sequencing,
Online Access:	http://www.alice.cnptia.embrapa.br/alice/handle/doc/1129869 https://doi.org/10.1186/s12864-020-07035-6
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