Constructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing
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Abstract
Abstract Background Indian cattle known as desi cattle, renowned for their adaptability to harsh environments and diverse phenotypic traits, represent a valuable genetic resource. While reference genome assemblies have been instrumental in advancing cattle genomics, they often fail to capture the full spectrum of genetic variation present within diverse populations. To address this limitation, we aimed to construct a pangenome for desi cattle by identifying and characterizing Non-Reference Novel Sequences (NRNS). Findings We sequenced 68 desi cattle genomes representing seven distinct breeds, generating 48.35 billion short reads. A PanGenome Analysis (PanGA) pipeline was developed in Bash scripts to process these data to identify NRNS missing in the reference genome. A total of 13,065 NRNS with a cumulative length of ∼41 Mbp were identified that exhibited substantial variation across the population. These NRNS were found to be exclusive to Indian desi cattle, matching only 4.1% with the Chinese indicine pangenome. However, a significant proportion (∼40%) of NRNS displayed ancestral origins within the Bos genus. These sequences were enriched in genic regions, suggesting functional roles, and were associated with quantitative trait loci (QTLs), particularly for milk production. Compared to a single reference genome, the pangenome approach significantly enhanced read mapping accuracy, reduced spurious SNP calls, and facilitated the discovery of novel genetic variants. Conclusions This study has successfully established a within-species cattle pangenome specifically focused on desi cattle breeds from India. Our findings highlight the importance of pangenome based analyses for understanding the complex genetic architecture of desi cattle.
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Azam et al. identified 7.5 Mb of high-confidence non-reference unique insertions and 41 Mb of non-reference novel sequences in Indian cattle, enriched in immune-related gene clusters.
“Similarly, Azam et al. [185,186] identified 7.5 Mb of high-confidence non-reference unique insertions (NUIs) and 41Mb of non-reference novel sequences in Indian cattle. These insertions are enriched in immune-related gene clusters, further highlighting that indicine immune systems possess a genomic repertoire distinct from the taurine reference genome [186].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [185]
The Abstract reports approximately 41 Mb of non-reference novel sequences in Indian cattle. Results (GO enrichment analysis; no page available) reports immune-related enrichment for genes associated with core-like NRNS contigs, but not enrichment of the insertions in immune-related gene clusters. The Results table on NRNS presence and absence gives 7,165,905 bases of private insertions; the cited paper does not identify 7.5 Mb of high-confidence non-reference unique insertions. (LLM, conf=0.88)
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- Authors
- Azam, S., Sahu, A., Pandey, N. K., Neupane, M., Van Tassell, C. P., Rosen, B. D., Gandham, R. K., Rath, S. N., & Majumdar, S. S.
- Affiliations
- National Institute of Animal Biotechnology (IN)
- Agricultural Research Service (US)
- Indian Institute of Technology Hyderabad (IN)
- Corresponding author
- Rosen, Benjamin D.
- Majumdar, Subeer S.
- ORCID
- Venue
- Communications Biology
- Published
- 2025-04-13
- Volume
- 8
- Issue
- 1
- Pages
- 605-605
- ISSN
- 2399-3642 (ISSN-L)
- PMC
- PMC11994783
- OpenAlex
- W4409393941
- Cited by
- 5
- References
- 62
- Citations by year
- 2026: 5
- FWCI
- 2.94
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Communications Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. Department of Agriculture
- Department of Biotechnology, Ministry of Science and Technology, India (BT/PR26466/AAQ/1/704/2017)
- Agricultural Research Service (8042-31000-112-000-D)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- pan-genome, Bos indicus, cattle breeds, novel genetic variants
- MeSH terms
- Animals, Cattle, India, Genetic Variation, Genome, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genomics, Quantitative Trait Loci, High-Throughput Nucleotide Sequencing
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