Characterization and Comparison of the Leukocyte Transcriptomes of Three Cattle Breeds

Wen Huang,Asif Nadeem,Bao Zhang,Morris Soller,Hasan Khatib,Masroor Babar,Aftab A Ansari

doi:10.1371/journal.pone.0030244

Abstract

In this study, mRNA-Seq was used to characterize and compare the leukocyte transcriptomes from two taurine breeds (Holstein and Jersey), and one indicine breed (Cholistani). At the genomic level, we identified breed-specific base changes in protein coding regions. Among 7,793,425 coding bases, only 165 differed between Holstein and Jersey, and 3,383 (0.04%) differed between Holstein and Cholistani, 817 (25%) of which resulted in amino acid changes in 627 genes. At the transcriptional level, we assembled transcripts and estimated their abundances including those from more than 3,000 unannotated intergeneic regions. Differential gene expression analysis showed a high similarity between Holstein and Jersey, and a much greater difference between the taurine breeds and the indicine breed. We identified gene ontology pathways that were systematically altered, including the electron transport chain and immune response pathways that may contribute to different levels of heat tolerance and disease resistance in taurine and indicine breeds. At the post-transcriptional level, sequencing mRNA allowed us to identify a number of genes undergoing differential alternative splicing among different breeds. This study provided a high-resolution survey of the variation between bovine transcriptomes at different levels and may provide important biological insights into the phenotypic differentiation among cattle breeds.

Highlights

There are two major types of modern cattle breeds which diverged 610,000–850,000 years ago [1]
Sequencing of the bovine transcriptomes To characterize the transcriptomes of cattle breeds, we collected blood samples from Holsteins and Jerseys, and Cholistanis
We aligned sequence reads to the bovine reference genome using Tophat, an RNA-Seq aligner that is capable of discovering splice junctions de novo [14]

Summary

Introduction

There are two major types of modern cattle breeds which diverged 610,000–850,000 years ago [1]. The taurine (Bos taurus) breeds, originating primarily from Europe and the northern parts of Asia, are adapted to temperate climates. The indicine (Bos indicus or Bos taurus indicus) breeds are of South Asian origin and evolved in warm tropical climates [2]. There exists substantial phenotypic difference between taurine and indicine cattle. They differ remarkably in their resistance to thermal stress, parasites, and diseases [3,4]. The transcriptomes of three cattle breeds were investigated. The Cholistani breed is renowned for its remarkable tolerance to heat and resistance to ticks and diseases [5]

Methods

Results

Conclusion