Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle

Curtis P Van Tassell,Marcos VB Da Silva,Gábor Mészáros,Tad S Sonstegard,José Fernando Garcia,George E Liu,Yuri T Utsunomiya,Johann Sölkner,Derek M Bickhart,Ana M Pérez O’Brien

doi:10.1186/1297-9686-46-19

Abstract

BackgroundSignatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns.MethodsBy comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation.ResultsFor all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1.ConclusionsThe VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance.

Highlights

Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes
The most distinct peaks were observed for the ANG/Brown Swiss (BSW) and the GIR/NEL comparisons, which show that the largest VarLD scores are found when comparing different production types within a subspecies
Some of the genes found in the indicine and taurine (I/T) comparisons indicate potential adaptive signatures, while the dairy and beef (D/B) comparisons point out genomic regions related to production of milk and beef

Summary

Introduction

Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. When a part of the genome that confers enhanced fitness or productive ability is preferentially kept in a population by increasing the frequency of favorable alleles, neutral loci that surround this region and that are in linkage disequilibrium (LD) with it, are retained, driving the frequency of particular haplotypes in the region towards fixation in a pattern that decays progressively with distance from the causative location [1,2,3,4] Such a selective sweep can be detected by reduced haplotype diversity and a different LD pattern when compared to those of the surrounding background [2,5]. The amount of LD that exists in genomic regions within a population is a key parameter to trace selective sweeps [2,3] and differences in decay of LD between bovine populations have been reported [9,10,11,12].

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Discussion

Conclusion