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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #418356
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Constructing a draft Indian cattle pangenome using short-read sequencing

Author
item AZAM, SARWAR - Collaborator
item SAHU, ABHISEK - Collaborator
item PANDEY, NAVEEN - Collaborator
item Neupane, Mahesh
item Van Tassell, Curtis
item Rosen, Benjamin
item GANDHAM, RAVI - Collaborator
item RATH, SUBHA - Collaborator
item MAJUMDAR, SUBEER - Collaborator

Submitted to: Communications Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/21/2025
Publication Date: 4/13/2025
Citation: 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. 2025. Constructing a draft Indian cattle pangenome using short-read sequencing. Communications Biology. 8. Article e605. https://doi.org/10.1038/s42003-025-07978-0.
DOI: https://doi.org/10.1038/s42003-025-07978-0

Interpretive Summary: There are many Indian cattle breeds with unique characteristics that can thrive in different, often harsh, environments. We sequenced the genomes of 68 Indian cattle from seven different breeds. These sequences were used to generate an Indian cattle “pangenome” representing the genomes of many individuals. We identified over 13,000 new sequences not found in the cattle reference genome. These sequences are unique to Indian cattle. Many of them play important roles in farming traits such as milk production. Our approach provides more accurate genetic information specific to Indian cattle and helped find new variations that were not detected before. This study highlights the value of using pangenomes to understand the genetic makeup of Indian cattle.

Technical Abstract: 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). 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. 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.