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Exploring association of copy number variations in Wild African goats (Capra nubiana) adaptations

Vivien J Chebii1,3*, Emmanuel Mpolya1, Samuel O. Oyola3, Jean-Baka Domelevo Entfellner 3, J. Musembi Mutuku3, Morris Agaba1,4.

1Nelson Mandela Africa Institution of Science and Technology, Arusha, Tanzania, 3International Livestock Research Institute, Nairobi, Kenya , 4Sarissa Limited, Kampala, Uganda

Capra nubiana is a wild goat species inhabiting the Sahara and Arabia deserts characterized by extreme temperatures, scarcity of feed and water. The genetic basis of its' adaptation to these environments remains unknown. In this study, we explored the possible role of copy number variations in the evolution of Capra species with a focus in the adaptation of Capra nubiana to its' environments. Copy number variations (CNV) are gain or loss of genomic segments greater than 1,000 bp between genomes. CNV have been implicated in phenotypic variations between species and might have a role in species differentiation and adaptations.

Based on Capra nubiana paired-end Illumina Hiseq reads sequenced to a coverage of 30x, we detected CNV relative to the domestic goat reference genome using a combination of read depth and split read approach. We identified 1,622 CNV loci overlapping with 343 protein-coding genes. Functional annotation of the protein-coding genes overlapping with the CNV showed that majority of them were immune response, signal transduction, and metabolism genes. Interferons, major histocompatibility complex proteins, and UL16 binding protein 21 which confer resistance against microbial infections were high copy number variable and significantly enriched. Lower density lipoprotein receptor-related protein 11 (Lrp11) which plays a role in stress adaptation resulting from extreme temperatures, water deprivation, and starvation were also high copy number variable. We suggest that the copy number variations of the immune response genes and Lrp11 possibly have a role in Capra nubiana adaptation to their environments.

This study is the first to shed insights on the possible role of the CNV in Capra nubiana adaptation to its' environments. The candidate copy number variable genes identified could be used upon functional confirmation as markers in animal breeding studies aimed at improving livestock health and productivity.

Keywords: Capra nubiana, gene copy number variations, adaptations, harsh environments, whole genome sequencing, Read depth method