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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Main Authors: 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
Format: Article
Language:English
Published: Taylor & Francis Group 2025-12-01
Series:Animal Biotechnology
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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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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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