Genome wide landscaping of copy number variations for horse inter-breed variability
Copy number variations (CNVs) have become widely acknowledged as a significant source of genomic variability and phenotypic variance. To understand the genetic variants in horses, CNVs from six Indian horse breeds, namely, Manipuri, Zanskari, Bhutia, Spiti, Kathiawari and Marwari were discovered usi...
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Taylor & Francis Group
2025-12-01
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Online Access: | https://www.tandfonline.com/doi/10.1080/10495398.2024.2446251 |
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author | Nitesh Kumar Sharma Prashant Singh Bibek Saha Anuradha Bhardwaj Mir Asif Iquebal Yash Pal Varij Nayan Sarika Jaiswal Shiv Kumar Giri Ram Avatar Legha T. K. Bhattacharya Dinesh Kumar Anil Rai |
author_facet | Nitesh Kumar Sharma Prashant Singh Bibek Saha Anuradha Bhardwaj Mir Asif Iquebal Yash Pal Varij Nayan Sarika Jaiswal Shiv Kumar Giri Ram Avatar Legha T. K. Bhattacharya Dinesh Kumar Anil Rai |
author_sort | Nitesh Kumar Sharma |
collection | DOAJ |
description | Copy number variations (CNVs) have become widely acknowledged as a significant source of genomic variability and phenotypic variance. To understand the genetic variants in horses, CNVs from six Indian horse breeds, namely, Manipuri, Zanskari, Bhutia, Spiti, Kathiawari and Marwari were discovered using Axiom™ Equine Genotyping Array. These breeds differed in agro-climatic adaptation with distinct phenotypic characters. A total of 2668 autosomal CNVs and 381 CNV regions (CNVRs) were identified with PennCNV tool. DeepCNV was employed to re-validate to get 883 autosomal CNVs, of which 9.06% were singleton type. A total of 180 CNVRs were identified after DeepCNV filtering with the estimated length of 3.12 Kb–4.90 Mb. The functional analysis showed the majority of the CNVRs genes enriched for sensory perception and olfactory receptor activity. An Equine CNVs database, EqCNVdb (http://backlin.cabgrid.res.in/eqcnvdb/) was developed which catalogues detailed information on the horse CNVs, CNVRs and gene content within CNVRs. Also, three random CNVRs were validated with real-time polymerase chain reaction. These findings will aid in the understanding the horse genome and serve as a preliminary foundation for future CNV association research with commercially significant equine traits. The identification of CNVs and CNVRs would lead to better insights into genetic basis of important traits. |
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institution | Kabale University |
issn | 1049-5398 1532-2378 |
language | English |
publishDate | 2025-12-01 |
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spelling | doaj-art-627cd805e71042cf9579942d25854e262025-01-10T12:17:42ZengTaylor & Francis GroupAnimal Biotechnology1049-53981532-23782025-12-0136110.1080/10495398.2024.2446251Genome wide landscaping of copy number variations for horse inter-breed variabilityNitesh Kumar Sharma0Prashant Singh1Bibek Saha2Anuradha Bhardwaj3Mir Asif Iquebal4Yash Pal5Varij Nayan6Sarika Jaiswal7Shiv Kumar Giri8Ram Avatar Legha9T. K. Bhattacharya10Dinesh Kumar11Anil Rai12Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, IndiaICAR-National Research Centre on Equines, Hisar, Haryana, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, IndiaICAR-National Research Centre on Equines, Hisar, Haryana, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, IndiaICAR-National Research Centre on Equines, Hisar, Haryana, IndiaICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, IndiaDepartment of Biotechnology, Maharaja Agrasen University, Baddi (Solan), Himachal Pradesh, IndiaICAR-National Research Centre on Equines, Hisar, Haryana, IndiaICAR-National Research Centre on Equines, Hisar, Haryana, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, IndiaDivision of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, IndiaCopy number variations (CNVs) have become widely acknowledged as a significant source of genomic variability and phenotypic variance. To understand the genetic variants in horses, CNVs from six Indian horse breeds, namely, Manipuri, Zanskari, Bhutia, Spiti, Kathiawari and Marwari were discovered using Axiom™ Equine Genotyping Array. These breeds differed in agro-climatic adaptation with distinct phenotypic characters. A total of 2668 autosomal CNVs and 381 CNV regions (CNVRs) were identified with PennCNV tool. DeepCNV was employed to re-validate to get 883 autosomal CNVs, of which 9.06% were singleton type. A total of 180 CNVRs were identified after DeepCNV filtering with the estimated length of 3.12 Kb–4.90 Mb. The functional analysis showed the majority of the CNVRs genes enriched for sensory perception and olfactory receptor activity. An Equine CNVs database, EqCNVdb (http://backlin.cabgrid.res.in/eqcnvdb/) was developed which catalogues detailed information on the horse CNVs, CNVRs and gene content within CNVRs. Also, three random CNVRs were validated with real-time polymerase chain reaction. These findings will aid in the understanding the horse genome and serve as a preliminary foundation for future CNV association research with commercially significant equine traits. The identification of CNVs and CNVRs would lead to better insights into genetic basis of important traits.https://www.tandfonline.com/doi/10.1080/10495398.2024.2446251Copy number variationcopy number variation regionsequinegenomeweb resource |
spellingShingle | Nitesh Kumar Sharma Prashant Singh Bibek Saha Anuradha Bhardwaj Mir Asif Iquebal Yash Pal Varij Nayan Sarika Jaiswal Shiv Kumar Giri Ram Avatar Legha T. K. Bhattacharya Dinesh Kumar Anil Rai Genome wide landscaping of copy number variations for horse inter-breed variability Animal Biotechnology Copy number variation copy number variation regions equine genome web resource |
title | Genome wide landscaping of copy number variations for horse inter-breed variability |
title_full | Genome wide landscaping of copy number variations for horse inter-breed variability |
title_fullStr | Genome wide landscaping of copy number variations for horse inter-breed variability |
title_full_unstemmed | Genome wide landscaping of copy number variations for horse inter-breed variability |
title_short | Genome wide landscaping of copy number variations for horse inter-breed variability |
title_sort | genome wide landscaping of copy number variations for horse inter breed variability |
topic | Copy number variation copy number variation regions equine genome web resource |
url | https://www.tandfonline.com/doi/10.1080/10495398.2024.2446251 |
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