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<p>Indian <i>desi</i> 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 <i>desi</i> 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 <i>desi</i> 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 <i>desi</i> cattle genomics.</p>

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Constructing a draft Indian cattle pangenome using short-read sequencing

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年4月13日

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  • Sarwar Azam,
  • Abhisek Sahu,
  • Naveen Kumar Pandey,
  • Mahesh Neupane,
  • Curtis P. Van Tassell,
  • Benjamin D. Rosen,
  • Ravi Kumar Gandham,
  • Subha Narayan Rath,
  • Subeer S. Majumdar

摘要

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.