Insights from homozygous signatures of cervus nippon revealed genetic architecture for components of fitness

This study investigates the genomic landscape of Sika deer populations, emphasizing the detection and characterization of runs of homozygosity (ROH) and their contribution towards components of fitness. Using 85,001 high-confidence SNPs, the investigation into ROH distribution unveiled nuanced patte...

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Bibliographic Details
Published in:Mammalian genome Vol. 35; no. 4; pp. 657 - 672
Main Authors: Goli, Rangasai Chandra, Mahar, Karan, Manohar, Peela Sai, Chishi, Kiyevi G, Prabhu, Immanual Gilwax, Choudhary, Sonu, Rathi, Pallavi, Chinnareddyvari, Chandana Sree, Haritha, Pala, Metta, Muralidhar, Shetkar, Mahantesh, Kumar, Amit, N D, Chethan Patil, Vidyasagar, Sukhija, Nidhi, Kanaka, K. K.
Format: Journal Article
Language:English
Published: New York Springer US 01.12.2024
Springer Nature B.V
Subjects:
Adipogenesis
Animal Genetics and Genomics
Biomedical and Life Sciences
Cell Biology
Cell cycle
Cervus nippon
eyes
Farms
Flagella
Genes
Genetic diversity
genetic recombination
genetic variation
Genomics
heat stress
homozygosity
Human Genetics
Inbreeding
Life Sciences
Population genetics
Population studies
Single-nucleotide polymorphism
Skp2 gene
spermatozoa
vision
vulnerable species
Conservation
Diversity
Inbreeding
ROH
Sika deer
Consensus
Fitness
ISSN:0938-8990, 1432-1777, 1432-1777
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Summary:This study investigates the genomic landscape of Sika deer populations, emphasizing the detection and characterization of runs of homozygosity (ROH) and their contribution towards components of fitness. Using 85,001 high-confidence SNPs, the investigation into ROH distribution unveiled nuanced patterns of autozygosity across individuals especially in 2 out of the 8 farms, exhibiting elevated ROH levels and mean genome coverage under ROH segments. The prevalence of shorter ROH segments (0.5-4 Mb) suggests historical relatedness and potential selective pressures within these populations. Intriguingly, despite observed variations in ROH profiles, the overall genomic inbreeding coefficient (F ROH ) remained relatively low across all farms, indicating a discernible degree of genetic exchange and effective mitigation of inbreeding within the studied Sika deer populations. Consensus ROH (cROH) were found to harbor genes for important functions viz., EGFLAM gene which is involved in the vision function of the eye, SKP2 gene which regulates cell cycle, CAPSL involved in adipogenesis, SPEF2 which is essential for sperm flagellar assembly, DCLK3 involved in the heat stress. This first ever study on ROH in Sika deer, to shed light on the adaptive role of genes in these homozygous regions. The insights garnered from this study have broader implications in the management of genetic diversity in this vulnerable species. Graphical abstract
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ISSN:0938-8990
1432-1777
1432-1777
DOI:10.1007/s00335-024-10064-1