Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India
Abstract Crossbreeding in India has been widely adopted to address low sustainability and poor productivity in non-descript cattle. This study analyzed Vrindavani (VRI) crossbred cattle and their parental populations (Holstein Friesian (HOL), Jersey (JER), Brown Swiss (BSW), Hariana (HAR) using SNP...
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Nature Portfolio
2025-05-01
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| Online Access: | https://doi.org/10.1038/s41598-025-01971-7 |
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| author | Rangasai Chandra Goli Kiyevi G. Chishi Karan Mahar Indrajit Ganguly Sanjeev Singh S. P. Dixit Oguru Sai Sruthi Sonu Choudhary Vikas Diwakar Pallavi Rathi Chandana Sree Chinnareddyvari Mahesh Dige Muralidhar Metta Amit Kumar Ganesh N. Aderao Nidhi Sukhija K. K. Kanaka |
| author_facet | Rangasai Chandra Goli Kiyevi G. Chishi Karan Mahar Indrajit Ganguly Sanjeev Singh S. P. Dixit Oguru Sai Sruthi Sonu Choudhary Vikas Diwakar Pallavi Rathi Chandana Sree Chinnareddyvari Mahesh Dige Muralidhar Metta Amit Kumar Ganesh N. Aderao Nidhi Sukhija K. K. Kanaka |
| author_sort | Rangasai Chandra Goli |
| collection | DOAJ |
| description | Abstract Crossbreeding in India has been widely adopted to address low sustainability and poor productivity in non-descript cattle. This study analyzed Vrindavani (VRI) crossbred cattle and their parental populations (Holstein Friesian (HOL), Jersey (JER), Brown Swiss (BSW), Hariana (HAR) using SNP data to characterize locus-specific ancestry in VRI’s genome along with admixture proportions and population stratification. Admixture analysis showed VRI have 67.3% HOL, 20.1% HAR, 8.5% JER, and 4% BSW ancestry. Locus-specific ancestry estimation identified regions with adaptive admixtures, which can be defined as admixed genomic regions favored by evolutionary forces and increased their frequencies, revealed 79.7% Bos taurus and 20.3% Bos indicus ancestry. Notably, regions on chromosome (chr) 2, 3, 4, 5, 7, 10, 12, 13, 14, 16, 17, 19, 20, 21, 22, 23, and 24 were associated with disease resistance contributed by indicine ancestry and chr 1, 6, 9, 11, 15, 18, 27, and 28 related to production which were contributed by taurine ancestry. The study concluded that increased taurine ancestry contributes to higher milk yield in VRI crosses, while indicine ancestry confers disease resistance and adaptability to tropical climates. This comprehensive genomic analysis suggests that while taurine inheritance enhances milk yield, a balance with indicine traits is essential for resilience. Understanding locus-specific ancestry patterns can aid in refining breeding strategies by selectively promoting beneficial alleles. Future advancements in genomic tools may enable controlled inheritance of desirable traits, maximizing heterosis in structured breeding programs for sustainable cattle production. |
| format | Article |
| id | doaj-art-763b2316b0fc4757832ef010c5ec29f8 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-05-01 |
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| spelling | doaj-art-763b2316b0fc4757832ef010c5ec29f82025-08-20T03:48:05ZengNature PortfolioScientific Reports2045-23222025-05-0115111510.1038/s41598-025-01971-7Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of IndiaRangasai Chandra Goli0Kiyevi G. Chishi1Karan Mahar2Indrajit Ganguly3Sanjeev Singh4S. P. Dixit5Oguru Sai Sruthi6Sonu Choudhary7Vikas Diwakar8Pallavi Rathi9Chandana Sree Chinnareddyvari10Mahesh Dige11Muralidhar Metta12Amit Kumar13Ganesh N. Aderao14Nidhi Sukhija15K. K. Kanaka16ICAR-National Dairy Research InstituteICAR-National Dairy Research InstituteICAR-National Dairy Research InstituteICAR-National Bureau of Animal Genetic ResourcesICAR-National Bureau of Animal Genetic ResourcesICAR-National Bureau of Animal Genetic ResourcesSri Venkateswara Veterinary UniversityICAR-National Dairy Research InstituteICAR-National Dairy Research InstituteICAR-National Dairy Research InstituteICAR-National Dairy Research InstituteICAR-National Bureau of Animal Genetic ResourcesSri Venkateswara Veterinary UniversityICAR- Indian Institute of Agricultural BiotechnologyICAR- Indian Institute of Agricultural BiotechnologyCSB-Central Tasar Research and Training InstituteICAR- Indian Institute of Agricultural BiotechnologyAbstract Crossbreeding in India has been widely adopted to address low sustainability and poor productivity in non-descript cattle. This study analyzed Vrindavani (VRI) crossbred cattle and their parental populations (Holstein Friesian (HOL), Jersey (JER), Brown Swiss (BSW), Hariana (HAR) using SNP data to characterize locus-specific ancestry in VRI’s genome along with admixture proportions and population stratification. Admixture analysis showed VRI have 67.3% HOL, 20.1% HAR, 8.5% JER, and 4% BSW ancestry. Locus-specific ancestry estimation identified regions with adaptive admixtures, which can be defined as admixed genomic regions favored by evolutionary forces and increased their frequencies, revealed 79.7% Bos taurus and 20.3% Bos indicus ancestry. Notably, regions on chromosome (chr) 2, 3, 4, 5, 7, 10, 12, 13, 14, 16, 17, 19, 20, 21, 22, 23, and 24 were associated with disease resistance contributed by indicine ancestry and chr 1, 6, 9, 11, 15, 18, 27, and 28 related to production which were contributed by taurine ancestry. The study concluded that increased taurine ancestry contributes to higher milk yield in VRI crosses, while indicine ancestry confers disease resistance and adaptability to tropical climates. This comprehensive genomic analysis suggests that while taurine inheritance enhances milk yield, a balance with indicine traits is essential for resilience. Understanding locus-specific ancestry patterns can aid in refining breeding strategies by selectively promoting beneficial alleles. Future advancements in genomic tools may enable controlled inheritance of desirable traits, maximizing heterosis in structured breeding programs for sustainable cattle production.https://doi.org/10.1038/s41598-025-01971-7VrindavaniLocus-specific ancestryBos taurusBos indicusHeterosis |
| spellingShingle | Rangasai Chandra Goli Kiyevi G. Chishi Karan Mahar Indrajit Ganguly Sanjeev Singh S. P. Dixit Oguru Sai Sruthi Sonu Choudhary Vikas Diwakar Pallavi Rathi Chandana Sree Chinnareddyvari Mahesh Dige Muralidhar Metta Amit Kumar Ganesh N. Aderao Nidhi Sukhija K. K. Kanaka Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India Scientific Reports Vrindavani Locus-specific ancestry Bos taurus Bos indicus Heterosis |
| title | Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India |
| title_full | Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India |
| title_fullStr | Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India |
| title_full_unstemmed | Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India |
| title_short | Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India |
| title_sort | genome wide locus specific ancestry analysis revealed adaptive admixtures in crossbred cattle of india |
| topic | Vrindavani Locus-specific ancestry Bos taurus Bos indicus Heterosis |
| url | https://doi.org/10.1038/s41598-025-01971-7 |
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