Variation in genes involved in epigenetic processes offers insights into tropically adapted cattle diversity.

Laercio R Porto-Neto,Antonio Reverter,Sigrid A Lehnert,Sean M Mcwilliam,Marina R S Fortes

doi:10.3389/fgene.2014.00089

Abstract

We evaluated the relevance of the BovineHD Illumina SNP chip with respect to genes involved in epigenetic processes. Genotypes for 729,068 SNP on two tropical cattle breeds of Australia were used: Brahman (n = 2112) and Tropical Composite (n = 2550). We used data mining approaches to compile a list of bovine protein-coding genes involved in epigenetic processes. These genes represent 9 functional categories that contain between one (histone demethylases) and 99 (chromatin remodeling factors) genes. A total of 3091 SNP mapped to positions within 3000 bp of the 193 coding regions of those genes, including 113 SNP in transcribed regions, 2738 in intronic regions and 240 in up- or down-stream regions. For all these SNP categories, we observed differences in the allelic frequencies between Brahman and Tropical Composite cattle. These differences were larger than those observed for the entire set of 729,068 SNP (P = 1.79 x 10−5). A multidimensional scaling analysis using only the 113 SNP in transcribed regions allowed for the separation of the two populations and this separation was comparable to the one obtained with a random set of 113 SNP (Principal Component 1 r2 > 0.84). To further characterize the differences between the breeds we defined a gene-differentiation metric based on the average genotypic frequencies of SNP connected to each gene and compared both cattle populations. The 10% most differentiated genes were distributed across 10 chromosomes, with significant (P < 0.05) enrichment on BTA 3 and 10. The 10% most conserved genes were located in 12 chromosomes. We conclude that there is variation between cattle populations in genes connected to epigenetic processes, and this variation can be used to differentiate cattle breeds. More research is needed to fully characterize the use of these SNP and its potential as means to further our understanding of biological variation and epigenetic processes.

Highlights

Differences in gene transcriptional regulation between individuals are likely to contribute to quantitative variation in important livestock production traits such as growth, metabolic efficiency, immunological competence, and reproductive performance
A recent example is the mutation on the Bos taurus autosome (BTA) 14 that regulates the expression of various genes in the PLAG1 region and is associated with many production traits as well as reproductive phenotypes (Karim et al, 2011; Fortes et al, 2013)
In an example with promising relevance to livestock productivity, Lomniczi et al (2013) have shown that the timing of female puberty in rats is driven by transcriptional activation of the KISS1 promoter in the hypothalamus in a complex interplay of several components of the epigenetic machinery: DNA methylation, Polycomb Group (PcG) proteins, and histone modifications

Summary

Introduction

Differences in gene transcriptional regulation between individuals are likely to contribute to quantitative variation in important livestock production traits such as growth, metabolic efficiency, immunological competence, and reproductive performance. Variations in transcriptional activity have been linked to a number of epigenetic processes including: differences in DNA methylation (Doerfler, 1983), the incorporation of histone variants into chromatin (Jin et al, 2009), histone modifications such as methylation and acetylation (Barth and Imhof, 2010), and Polycomb Group (PcG) proteins (Leeb et al, 2010). In an example with promising relevance to livestock productivity, Lomniczi et al (2013) have shown that the timing of female puberty in rats is driven by transcriptional activation of the KISS1 promoter in the hypothalamus in a complex interplay of several components of the epigenetic machinery: DNA methylation, PcG proteins, and histone modifications. Regulatory transcription factors associated with cattle puberty and heifer pregnancy have been proposed previously (Fortes et al, 2010, 2011, 2012)

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