Azam Sarwar, Sahu Abhisek, Pandey Naveen Kumar, Neupane Mahesh, Van Tassell Curtis P, Rosen Benjamin D, Gandham Ravi Kumar, Rath Subha Narayan, Majumdar Subeer S
National Institute of Animal Biotechnology, Hyderabad, India.
Indian Institute of Technology Hyderabad, Sangareddy, India.
Commun Biol. 2025 Apr 13;8(1):605. doi: 10.1038/s42003-025-07978-0.
Indian desi cattle, known for their adaptability and phenotypic diversity, represent a valuable genetic resource. However, a single reference genome often fails to capture the full extent of their genetic variation. To address this, we construct a pangenome for desi cattle by identifying and characterizing non-reference novel sequences (NRNS). We sequence 68 genomes from seven breeds, generating 48.35 billion short reads. Using the PanGenome Analysis (PanGA) pipeline, we identify 13,065 NRNS (~41 Mbp), with substantial variation across the population. Most NRNS were unique to desi cattle, with minimal overlap (4.1%) with the Chinese indicine pangenome. Approximately 40% of NRNS exhibited ancestral origins within the Bos genus and were enriched in genic regions, suggesting functional roles. These sequences are linked to quantitative trait loci for traits such as milk production. The pangenome approach enhances read mapping accuracy, reduces spurious single nucleotide polymorphism calls, and uncovers novel genetic variants, offering a deeper understanding of desi cattle genomics.
印度本土牛以其适应性和表型多样性而闻名，是一种宝贵的遗传资源。然而，单一的参考基因组往往无法完全捕捉其遗传变异的全貌。为了解决这个问题，我们通过识别和表征非参考新序列（NRNS）构建了本土牛的泛基因组。我们对七个品种的68个基因组进行了测序，产生了483.5亿条短读段。使用泛基因组分析（PanGA）流程，我们识别出13065个NRNS（约41兆碱基对），群体间存在大量变异。大多数NRNS是本土牛特有的，与中国瘤牛泛基因组的重叠极少（4.1%）。约40%的NRNS在牛属内表现出祖先起源，并且在基因区域富集，表明具有功能作用。这些序列与产奶等性状的数量性状位点相关。泛基因组方法提高了读段映射准确性，减少了虚假单核苷酸多态性的调用，并揭示了新的遗传变异，有助于更深入地了解本土牛基因组学。
