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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01080

A mini-atlas of gene expression for the domestic goat (Capra hircus)

Charity Muriuki1, 2,  Stephen J. Bush1, 3,  Mazdak Salavati1, 2,  Mary E. McCulloch1,  Zofia Lisowski1, Morris Agaba4, Appolinaire Djikeng1, 2,  David Hume5 and  Emily L. Clark1, 2*
  • 1Roslin Institute, University of Edinburgh, United Kingdom
  • 2Centre for Tropical Livestock Genetics and Health, Kenya
  • 3Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, United Kingdom
  • 4Biosciences eastern and central Africa, International Livestock Research Institute (BecA - ILRI), Kenya
  • 5Mater Research Institute, University of Queensland, Australia

Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 22 transcriptionally rich tissues and cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis we grouped genes according to their expression patterns and assigned those groups of co-expressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional similarities between macrophage-associated signatures in the sheep and goats sampled in this study. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

Keywords: Ruminant, Goat (capra hircus), RNA-Seq - RNA sequencing, Gene expression atlas, Sheep, Immunity, FAANG, Allele-specific expression (ASE), Network analysis, Transcriptomics, comparative genomics

Received: 24 Jul 2019; Accepted: 09 Oct 2019.

Copyright: © 2019 Muriuki, Bush, Salavati, McCulloch, Lisowski, Agaba, Djikeng, Hume and Clark. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Emily L. Clark, Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, Scotland, United Kingdom,