Evolutionary stamps for adaptation traced in Cervus nippon genome using reduced representation sequencing

IF 0.9 4区环境科学与生态学 Q4 BIODIVERSITY CONSERVATION Conservation Genetics Resources Pub Date : 2024-01-27 DOI:10.1007/s12686-023-01339-x

Nidhi Sukhija, Rangasai Chandra Goli, Mukul Sukhija, Pallavi Rathi, Komal Jaglan, Aishwarya Dash, P. B. Nandhini, K. K. Kanaka

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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

Abstract Image

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利用还原表示测序技术追踪海马基因组中的适应进化印记

梅花鹿原产于东亚。目前，该物种在许多地方已经灭绝或濒临灭绝。梅花鹿种群数量的减少对气候变化非常敏感，而且由于近亲繁殖，其适应性很差。在这项研究中，使用双位限制性位点相关消化（ddRAD）方法鉴定了全基因组单核苷酸多态性（SNPs），并进一步注释，以确定与适应性相关的基因。经过质量控制后，共保留了 85 001 个 SNPs。综合似然比（CLR）统计发现了 13 个较强的选择性横扫，所确定的横扫与适应、繁殖和细胞功能相关基因重叠。平均杂合度和核苷酸多样性分别为 0.27 和 0.29。混杂分析得出的单一聚类表明梅花鹿没有进一步的亚分化。这些发现将有助于通过加入 SNP 芯片制定适当的遗传改良计划，从而更深入地了解鹿的遗传学、进化、驯化和保护。图文摘要生物信息学分析揭示梅花鹿基因组变异和选择性扫描区域

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来源期刊

Conservation Genetics Resources BIODIVERSITY CONSERVATION-GENETICS & HEREDITY

CiteScore

2.90

自引率

9.10%

发文量

审稿时长

3-6 weeks

期刊介绍： Conservation Genetics Resources promotes the conservation of genetic diversity and advances the study of conservation genetics by providing rapid publication of technical papers and reviews on methodological innovations or improvements, computer programs, and genomic resources, as well as on the practical application of these resources towards the development of effective conservation policy and practice.