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Kangayam and Tharparkar cattle exhibit higher duplications in innate immune genes compared to Sahiwal, Gir, Karan Fries, and Holstein Friesian: insights from an array comparative genomic hybridization.

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Title: Kangayam and Tharparkar cattle exhibit higher duplications in innate immune genes compared to Sahiwal, Gir, Karan Fries, and Holstein Friesian: insights from an array comparative genomic hybridization.
Authors: Roshan M; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India., Vats A; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India., Bajwa KK; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India., Sharma S; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India., Thambiraja M; Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India., Sodhi M; Animal Biotechnology Division, ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India., Singh D; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India. drdheer.singh@gmail.com., Yennamalli RM; Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India. ragothaman@scbt.sastra.ac.in., Onteru SK; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India. suneelvet@gmail.com.
Source: Mammalian genome : official journal of the International Mammalian Genome Society [Mamm Genome] 2025 Sep; Vol. 36 (3), pp. 812-826. Date of Electronic Publication: 2025 May 31.
Publication Type: Journal Article; Research Support, Non-U.S. Gov't
Language: English
Journal Info: Publisher: Springer-Verlag Country of Publication: United States NLM ID: 9100916 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1432-1777 (Electronic) Linking ISSN: 09388990 NLM ISO Abbreviation: Mamm Genome Subsets: MEDLINE
Imprint Name(s): Publication: New York, NY : Springer-Verlag
Original Publication: New York, NY, USA : Springer International, c1991-
MeSH Terms: Immunity, Innate*/genetics , Comparative Genomic Hybridization* , Gene Duplication*, Cattle/genetics ; Cattle/immunology ; Animals ; DNA Copy Number Variations ; India ; Breeding
Abstract: Innate immunity, the primary defence mechanism, encompasses a range of protective processes like anatomical barriers, cytokine secretion, and the action of various immune cells. Cattle breeds might differ in these processes because of their genetic differences such as copy number variations (CNVs). Therefore, the present investigation employed an array comparative genomic hybridisation (aCGH) approach on breed representative pooled DNA samples to evaluate CNVs across six cattle breeds: four indigenous Indian breeds, Kangayam (KNG), Tharparkar (TP), Sahiwal (SW), Gir (GIR), one crossbred Karan Fries (KF), and one exotic breed, Holstein Friesian (HF). In aCGH, HF DNA was used as control, while test DNA was from the other breeds. Each pooled test DNA sample was a representative of 18 animals belonging to three distinct geographical locations of India. The study using Aberration Detection Method 2 (ADM-2) of Agilent Genomic Workbench revealed the highest number of duplications in KNG (1189 genes), followed by TP (534 genes), and the greatest number of deletions in SW (774 genes). Among these genes, 183 and 76 innate immune genes with hub genes TGF-β1, CD79A, and IL4 showed duplications in KNG and TP, respectively. In SW, 113 innate immune genes with hub genes PSMC5, MAPK1, and AXIN1 showed deletions. In contrast, KF and HF showed no genes with deletions and fewer duplicated innate immunity genes, reflecting either lower genetic variability in their immune gene repertoire or a potential bias due to HF DNA as a control in aCGH. Functional enrichment of innate immune genes revealed duplications in KNG enriched in interleukin-1 receptor (IL1R) activity (p = 9.9 × 10-3) and nucleobase metabolism (p = 2.88 × 10⁻11), while duplications in TP were linked to DNA-binding transcription factor activity (p = 2.34 × 10⁻14). The KEGG pathway analysis highlighted Th17 cell differentiation (p = 1.3 × 10⁻4) in KNG and Hippo signalling (p = 3.7 × 10-2) in TP. Overall, these findings highlight the importance of genetic diversity in shaping innate immunity in indigenous Indian cattle breeds, favouring a balanced crossbreeding to sustain the Indian dairy sector.
(© 2025. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
Competing Interests: Declarations. Competing interest: The authors declare no competing interests.
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Cell Signal. 2025 Mar;127:111616. (PMID: 39848456)
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J Biol Chem. 2017 Jul 7;292(27):11413-11422. (PMID: 28515320)
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Funct Integr Genomics. 2012 Mar;12(1):81-92. (PMID: 21928070)
Int J Mol Sci. 2017 Mar 10;18(3):. (PMID: 28287439)
Drug Discov Today. 2008 Sep;13(17-18):760-70. (PMID: 18617013)
Arch Pathol Lab Med. 2017 Jun;141(6):751-758. (PMID: 28557599)
Nucleic Acids Res. 2022 Jul 5;50(W1):W216-W221. (PMID: 35325185)
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J Allergy Clin Immunol. 2010 Feb;125(2 Suppl 2):S24-32. (PMID: 19932920)
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Grant Information: F. 572 No. NASF/SUTRA-02/2022-23/50 Indian Council of Agricultural Research-National Agricultural Science Fund (ICAR-NASF)
Entry Date(s): Date Created: 20250531 Date Completed: 20250904 Latest Revision: 20261010
Update Code: 20261010
DOI: 10.1007/s00335-025-10136-w
PMID: 40448838
Database: MEDLINE
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  – Url: https://dx.doi.org/doi:10.1007/s00335-025-10136-w
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  Label: Title
  Group: Ti
  Data: Kangayam and Tharparkar cattle exhibit higher duplications in innate immune genes compared to Sahiwal, Gir, Karan Fries, and Holstein Friesian: insights from an array comparative genomic hybridization.
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  Data: <searchLink fieldCode="AU" term="%22Roshan+M%22">Roshan M</searchLink>; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India.<br /><searchLink fieldCode="AU" term="%22Vats+A%22">Vats A</searchLink>; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India.<br /><searchLink fieldCode="AU" term="%22Bajwa+KK%22">Bajwa KK</searchLink>; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India.<br /><searchLink fieldCode="AU" term="%22Sharma+S%22">Sharma S</searchLink>; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India.<br /><searchLink fieldCode="AU" term="%22Thambiraja+M%22">Thambiraja M</searchLink>; Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India.<br /><searchLink fieldCode="AU" term="%22Sodhi+M%22">Sodhi M</searchLink>; Animal Biotechnology Division, ICAR - National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.<br /><searchLink fieldCode="AU" term="%22Singh+D%22">Singh D</searchLink>; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India. drdheer.singh@gmail.com.<br /><searchLink fieldCode="AU" term="%22Yennamalli+RM%22">Yennamalli RM</searchLink>; Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India. ragothaman@scbt.sastra.ac.in.<br /><searchLink fieldCode="AU" term="%22Onteru+SK%22">Onteru SK</searchLink>; Animal Biochemistry Division, Functional Genomics and Systems Biology Laboratory, ICAR - National Dairy Research Institute, Karnal, Haryana, 132001, India. suneelvet@gmail.com.
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  Data: <searchLink fieldCode="JN" term="%229100916%22">Mammalian genome : official journal of the International Mammalian Genome Society</searchLink> [Mamm Genome] 2025 Sep; Vol. 36 (3), pp. 812-826. <i>Date of Electronic Publication: </i>2025 May 31.
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Springer-Verlag%22">Springer-Verlag </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>9100916 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1432-1777 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2209388990%22">09388990 </searchLink><i>NLM ISO Abbreviation: </i>Mamm Genome <i>Subsets: </i>MEDLINE
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  Data: <searchLink fieldCode="MM" term="%22Immunity%2C+Innate%22">Immunity, Innate*</searchLink>/<searchLink fieldCode="MM" term="%22Immunity%2C+Innate+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Comparative+Genomic+Hybridization%22">Comparative Genomic Hybridization*</searchLink> <br /><searchLink fieldCode="MM" term="%22Gene+Duplication%22">Gene Duplication*</searchLink><br /><searchLink fieldCode="MH" term="%22Cattle%22">Cattle</searchLink>/<searchLink fieldCode="MH" term="%22Cattle+genetics%22">genetics</searchLink> ; <searchLink fieldCode="MH" term="%22Cattle%22">Cattle</searchLink>/<searchLink fieldCode="MH" term="%22Cattle+immunology%22">immunology</searchLink> ; <searchLink fieldCode="MH" term="%22Animals%22">Animals</searchLink> ; <searchLink fieldCode="MH" term="%22DNA+Copy+Number+Variations%22">DNA Copy Number Variations</searchLink> ; <searchLink fieldCode="MH" term="%22India%22">India</searchLink> ; <searchLink fieldCode="MH" term="%22Breeding%22">Breeding</searchLink>
– Name: Abstract
  Label: Abstract
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  Data: Innate immunity, the primary defence mechanism, encompasses a range of protective processes like anatomical barriers, cytokine secretion, and the action of various immune cells. Cattle breeds might differ in these processes because of their genetic differences such as copy number variations (CNVs). Therefore, the present investigation employed an array comparative genomic hybridisation (aCGH) approach on breed representative pooled DNA samples to evaluate CNVs across six cattle breeds: four indigenous Indian breeds, Kangayam (KNG), Tharparkar (TP), Sahiwal (SW), Gir (GIR), one crossbred Karan Fries (KF), and one exotic breed, Holstein Friesian (HF). In aCGH, HF DNA was used as control, while test DNA was from the other breeds. Each pooled test DNA sample was a representative of 18 animals belonging to three distinct geographical locations of India. The study using Aberration Detection Method 2 (ADM-2) of Agilent Genomic Workbench revealed the highest number of duplications in KNG (1189 genes), followed by TP (534 genes), and the greatest number of deletions in SW (774 genes). Among these genes, 183 and 76 innate immune genes with hub genes TGF-β1, CD79A, and IL4 showed duplications in KNG and TP, respectively. In SW, 113 innate immune genes with hub genes PSMC5, MAPK1, and AXIN1 showed deletions. In contrast, KF and HF showed no genes with deletions and fewer duplicated innate immunity genes, reflecting either lower genetic variability in their immune gene repertoire or a potential bias due to HF DNA as a control in aCGH. Functional enrichment of innate immune genes revealed duplications in KNG enriched in interleukin-1 receptor (IL1R) activity (p = 9.9 × 10<superscript>-3</superscript>) and nucleobase metabolism (p = 2.88 × 10⁻<superscript>11</superscript>), while duplications in TP were linked to DNA-binding transcription factor activity (p = 2.34 × 10⁻<superscript>14</superscript>). The KEGG pathway analysis highlighted Th17 cell differentiation (p = 1.3 × 10⁻<superscript>4</superscript>) in KNG and Hippo signalling (p = 3.7 × 10<superscript>-2</superscript>) in TP. Overall, these findings highlight the importance of genetic diversity in shaping innate immunity in indigenous Indian cattle breeds, favouring a balanced crossbreeding to sustain the Indian dairy sector.<br /> (© 2025. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
– Name: Abstract
  Label: Competing Interests
  Group: Ab
  Data: Declarations. Competing interest: The authors declare no competing interests.
– Name: Ref
  Label: References
  Group: RefInfo
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  Data: F. 572 No. NASF/SUTRA-02/2022-23/50 Indian Council of Agricultural Research-National Agricultural Science Fund (ICAR-NASF)
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  Data: <i>Date Created: </i>20250531 <i>Date Completed: </i>20250904 <i>Latest Revision: </i>20261010
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RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1007/s00335-025-10136-w
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        StartPage: 812
    Subjects:
      – SubjectFull: Cattle genetics
        Type: general
      – SubjectFull: Cattle immunology
        Type: general
      – SubjectFull: Animals
        Type: general
      – SubjectFull: DNA Copy Number Variations
        Type: general
      – SubjectFull: India
        Type: general
      – SubjectFull: Breeding
        Type: general
      – SubjectFull: Immunity, Innate genetics
        Type: general
      – SubjectFull: Comparative Genomic Hybridization
        Type: general
      – SubjectFull: Gene Duplication
        Type: general
    Titles:
      – TitleFull: Kangayam and Tharparkar cattle exhibit higher duplications in innate immune genes compared to Sahiwal, Gir, Karan Fries, and Holstein Friesian: insights from an array comparative genomic hybridization.
        Type: main
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      – PersonEntity:
          Name:
            NameFull: Roshan M
      – PersonEntity:
          Name:
            NameFull: Vats A
      – PersonEntity:
          Name:
            NameFull: Bajwa KK
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            NameFull: Sharma S
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            NameFull: Thambiraja M
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            NameFull: Sodhi M
      – PersonEntity:
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            NameFull: Singh D
      – PersonEntity:
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            NameFull: Yennamalli RM
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            NameFull: Onteru SK
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          Dates:
            – D: 01
              M: 09
              Text: 2025 Sep
              Type: published
              Y: 2025
          Identifiers:
            – Type: issn-electronic
              Value: 1432-1777
          Numbering:
            – Type: volume
              Value: 36
            – Type: issue
              Value: 3
          Titles:
            – TitleFull: Mammalian genome : official journal of the International Mammalian Genome Society
              Type: main
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