The Buffalo Expression Atlas

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 have generated 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 (riverine) water buffalo (Mediterranean, Pandharpuri and Bhadawari breeds). RNA was isolated from a subset of tissues and stranded libraries generated for RNA-Seq at high depth for ten key tissues and at medium depth for the remaining thirty tissues. Whole genome sequence data were also generated from each animal. The RNA-Seq data were quantified and co-expressed genes visualised using the network analysis tool, Miru. Co-expression of unannotated genes with genes of known function will be used to infer their function. The atlas data are also being used to analyse alternative splicing, candidate expressed SNPs and allelic expression imbalance and compared to other ruminant species. The sample metadata have been loaded into BioSamples and the sequence data are being deposited in ENA. This will be a valuable resource for the international Functional Annotation of Animal Genomes (FAANG) initiative. Potential variation identified between domestic breeds will form the basis for the development of predictive marker-assisted selection and breed improvement in the buffalo industry.