Abstract
Sika deer is indigenous to East Asia. Currently the species is extinct or are nearing the verge of extinction, in numerous places. Reduced population size is sensitive to climate change and has poor adaptation as a result of inbreeding. In this study genome-wide Single nucleotide polymorphisms (SNPs) were identified using double-digest restriction site associated digestion (ddRAD) approach and annotated further to identify genes related to fitness. A total 85,001 SNPs were retained following the quality control. Composite Likelihood Ratio (CLR) statistics found 13 stronger selective sweeps, identified sweeps overlapped with genes related to adaptation, reproduction, cellular functions. Average heterozygosity and nucleotide diversity were 0.27 and 0.29 respectively. Admixture analysis furnished a single cluster indicating no further sub-divergence of Sika deer. These findings would help fabricate appropriate genetic improvement programs by inclusion in the SNP chips, in order to get deeper insights into deer genetics, evolution, domestication and conservation.
Graphical Abstract
Bioinformatic analysis for unravelling genomic variants and selective sweep regions in Cervus nippon
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Acknowledgements
The authors thank the Director, ICAR-National Dairy Research Institute for the support to carry out this research work. We would also like to extend our gratitude to Hengxing Ba for allowing us to use their data in our research/project. Without their contributions, this work would not have been possible.
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NS, MS and KK conceived concept. NS, RG, MS and KK analyzed the data. NS, RG, PB, AD and KJ wrote the main manuscript text. PR, MS and KJ prepared tables and figures. All authors reviewed the manuscript.
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Sukhija, N., Goli, R.C., Sukhija, M. et al. Evolutionary stamps for adaptation traced in Cervus nippon genome using reduced representation sequencing. Conservation Genet Resour 16, 135–146 (2024). https://doi.org/10.1007/s12686-023-01339-x
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DOI: https://doi.org/10.1007/s12686-023-01339-x