A gene expression atlas in domestic water buffalo

Rachel Young, Lucas Lefevre, Stephen J. Bush, John Williams, Suresh B. Gokhale, Satish Kumar, Stephen Bishop, Alan L. Archibald, David A. Hume

Research output: Contribution to conferenceAbstract

Abstract

The domestic water buffalo (Bubalus bubalis) contributes significantly to the global agricultural economy through milk, meat, hides and draught power. A larger part of the human population depends on domestic water buffalo than on any other livestock species in the world (FAO & UNEP 2000). Despite its agricultural importance, the buffalo genome is not fully annotated. We aim to generate a fine scale gene expression atlas to improve knowledge of the buffalo transcriptome and annotate the reference genome. Various tissue and cell types were collected from eight adult water buffalo (Mediterranean, Pandharpuri and Bhadawari breeds). RNA was isolated from a subset of tissues and stranded libraries generated for RNAseq (125 base paired-end reads) at high depth (>100 million reads) for ten key tissues and at medium depth (>25 million reads) for the remaining thirty tissues. Whole genome sequence data were also generated from each breed. Analysis of the preliminary RNAseq data is underway. We aim to use this data to analyse alternative splicing, candidate expressed SNPs, monoallelic expression and allelic imbalance in buffalo. RNAseq data generated by the atlas will be deposited in public domain sequence repositories, the data will also be a valuable resource for the international Functional Annotation of Animal Genomes (FAANG) initiative. This RNAseq-based expression atlas will be used to improve knowledge of the buffalo genome and transcriptome. Potential variation identified between domestic breeds can form the basis for the development of predictive marker-assisted selection and breed improvement in the buffalo industry.
Original languageEnglish
Publication statusPublished - 9 Jan 2016
EventPlant and Animal Genome XXIV - Town and Country Hotel, San Diego, United States
Duration: 8 Jan 201613 Jan 2016

Conference

ConferencePlant and Animal Genome XXIV
Country/TerritoryUnited States
CitySan Diego
Period8/01/1613/01/16

Keywords

  • Water buffalo
  • RNA-seq
  • FAANG
  • functional annotation
  • gene expression atlas

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