Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus
Abstract Background India harbors the world’s largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the...
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2025-02-01
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| Series: | Journal of Animal Science and Biotechnology |
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| Online Access: | https://doi.org/10.1186/s40104-024-01133-1 |
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| author | Sarwar Azam Abhisek Sahu Naveen Kumar Pandey Mahesh Neupane Curtis P Van Tassell Benjamin D Rosen Ravi Kumar Gandham Subha Narayan Rath Subeer S Majumdar |
| author_facet | Sarwar Azam Abhisek Sahu Naveen Kumar Pandey Mahesh Neupane Curtis P Van Tassell Benjamin D Rosen Ravi Kumar Gandham Subha Narayan Rath Subeer S Majumdar |
| author_sort | Sarwar Azam |
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| description | Abstract Background India harbors the world’s largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome. Results Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics ‘linked-read’ technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb, comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 Mb was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs encompassing ~ 2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis. The protein-coding genes were found in various prominent quantitative trait locus (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance. Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds. |
| format | Article |
| id | doaj-art-139a9ce656b04db6b15bbadd36d58413 |
| institution | Kabale University |
| issn | 2049-1891 |
| language | English |
| publishDate | 2025-02-01 |
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| series | Journal of Animal Science and Biotechnology |
| spelling | doaj-art-139a9ce656b04db6b15bbadd36d584132025-02-09T12:49:07ZengBMCJournal of Animal Science and Biotechnology2049-18912025-02-0116112010.1186/s40104-024-01133-1Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicusSarwar Azam0Abhisek Sahu1Naveen Kumar Pandey2Mahesh Neupane3Curtis P Van Tassell4Benjamin D Rosen5Ravi Kumar Gandham6Subha Narayan Rath7Subeer S Majumdar8National Institute of Animal BiotechnologyNational Institute of Animal BiotechnologyNational Institute of Animal BiotechnologyAnimal Genomics and Improvement Laboratory, USDA-ARSAnimal Genomics and Improvement Laboratory, USDA-ARSAnimal Genomics and Improvement Laboratory, USDA-ARSNational Institute of Animal BiotechnologyIndian Institute of Technology HyderabadNational Institute of Animal BiotechnologyAbstract Background India harbors the world’s largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome. Results Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics ‘linked-read’ technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb, comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 Mb was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs encompassing ~ 2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis. The protein-coding genes were found in various prominent quantitative trait locus (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance. Conclusions This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.https://doi.org/10.1186/s40104-024-01133-1BICIsBos indicusCattleGenome assemblyLinked-readsNUIs |
| spellingShingle | Sarwar Azam Abhisek Sahu Naveen Kumar Pandey Mahesh Neupane Curtis P Van Tassell Benjamin D Rosen Ravi Kumar Gandham Subha Narayan Rath Subeer S Majumdar Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus Journal of Animal Science and Biotechnology BICIs Bos indicus Cattle Genome assembly Linked-reads NUIs |
| title | Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus |
| title_full | Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus |
| title_fullStr | Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus |
| title_full_unstemmed | Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus |
| title_short | Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus |
| title_sort | advancing the indian cattle pangenome characterizing non reference sequences in bos indicus |
| topic | BICIs Bos indicus Cattle Genome assembly Linked-reads NUIs |
| url | https://doi.org/10.1186/s40104-024-01133-1 |
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