Tassell, C. P. V. | Search bioRxiv

bioRxiv2025

Genome assemblies of Indian desi cattle reveals hotspots of rearrangements and immune-related genetic diversity

India, home to the worlds largest cattle population, hosts native dairy breeds essential to its agricultural economy because of their adaptability and resilience. This study characterizes the genomes of five prominent breeds Gir, Kankrej, Red Sindhi, Sahiwal and Tharparkar, highlighting their unique genomic characteristics. The de novo assemblies ranged from 2.70-2.78 Gb in size, with 90% of the genomes assembled in just 56 to 1,663 scaffolds. The use of reference-guided scaffolding further enhanced these genomes, resulting in 93.3-96.7% pseudomolecule coverage with strong BUSCO scores (94.1-95.5%). Comparative analyses revealed 87-95% synteny with the Brahman genome and identified 19.84-153.16 Mb of structural rearrangements per genome, including inversions, translocations, and duplications. Synteny diversity analysis uncovered 10,643 perfectly collinear regions spanning 87.3 Mb and 6,622 hotspots of rearrangement (HOT regions) covering 55.18 Mb. These HOT regions, characterized by high synteny diversity, were significantly enriched with immune-related genes. Moreover, immune-related gene clusters, including MHC, NKC, and LRC, were identified within HOT regions in the desi reference genome. Our findings provide valuable insights into the genetic diversity of desi cattle breeds. The high-quality genome assemblies generated in this study will serve as valuable resources for future research in genetic improvement, disease resistance, and environmental adaptation.

genomics↗

bioRxiv2024

Constructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing

BackgroundIndian 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). FindingsWe 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. ConclusionsThis 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.

genomics↗