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

Elisa Peripolli,Johannes Geibel,Andréa Alves Do Egito,João Cláudio Do Carmo Panetto,Fernando Baldi,Henner Simianer,Marco Antonio Machado,Ngoc-Thuy Ha,Christian Reimer,Marcos Vinícius Gualberto Barbosa Da Silva

doi:10.1186/s12864-020-07035-6

Abstract

BackgroundThe 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.ResultsA 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.ConclusionThe 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.

Highlights

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
We explored common signals between runs of homozygosity (ROH) hotspots and the top 1% putative sweep regions retrieved from both de-correlated composite of multiple signals (DCMS) statistics to increase the power of signals
By using whole-genome re-sequencing data, we identified candidate sweep regions in indicine and Brazilian locally adapted taurine cattle breeds, of which the latter have been exposed to a process of natural selection for several generations in extremely variable environments

Summary

Introduction

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. The first cattle herds were brought to Brazil by Portuguese conquerors in 1534 during the Brazilian colonization period [1] These cattle have undergone to a process of natural selection for more than 450 years in a wide range of ecosystems throughout the country [2]. Influenced by the environment and shaped by natural selection, these animals acquired very particular traits to thrive in distinct ecosystems, which has presumably left detectable signatures of selection within their genomes In this regard, Brazilian locally adapted cattle breeds represent an important genetic 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]. Their productivity is much lower compared to highly-specialized breeds under intensive production systems [7, 8], great efforts have been made to improve our knowledge of locally adapted breeds [5, 9, 10] and their use in crossbred schemes

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Conclusion