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Updated: May 29, 2025
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Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus
Sarwar Azam1,2, Abhisek Sahu1, Naveen Kumar Pandey1
1National Institute of Animal Biotechnology, Hyderabad, India.
Journal of Animal Science and Biotechnology
|February 6, 2025
Summary
This study reveals novel genetic variations in Indian cattle breeds, creating the first comprehensive pangenome for Bos indicus. These findings enhance our understanding of desi cattle genomics and genetic diversity.
Area of Science:
- Genomics
- Comparative Genomics
- Animal Genetics
Background:
- India possesses the world's largest cattle population with over 50 Bos indicus breeds.
- A single reference genome is insufficient to capture the full genomic diversity of Indian cattle.
- Characterizing genomic variation in Indian dairy breeds is crucial.
Purpose of the Study:
- To identify non-reference sequences in Indian cattle.
- To construct a comprehensive pangenome for Bos indicus dairy breeds.
Main Methods:
- Sequencing of five prominent Indian dairy breeds (Gir, Kankrej, Tharparkar, Sahiwal, Red Sindhi) using 10X Genomics linked-read technology.
- Assembly of genomes and construction of a Bos indicus pangenome via alignment and graph-based comparisons with the Brahman reference genome.
- Identification of Non-reference Unique Insertions (NUIs) and Bos indicus Common Insertions (BICIs).
Main Results:
- A Bos indicus pangenome was constructed, revealing significant novel sequences (8 Mb and 17.7 Mb) and 6,844 NUIs (7.57 Mb).
- Identified 2,312 NUIs (BICIs) common across 98 samples, with 926 BICIs within 682 protein-coding genes, lncRNAs, and pseudogenes.
- BICIs were enriched in genes related to synaptic transmission, cell junctions, and adhesion, and found in QTL regions for milk, reproduction, and health traits. A majority of BICIs contained interspersed repeats and were shared with other species.
Conclusions:
- This study presents the first robust set of NUIs defining the pangenome for Indian Bos indicus breeds.
- The findings provide valuable insights into the genomic landscape of indigenous Indian cattle breeds.
- The identified genetic variations have potential implications for economically important traits in cattle.
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