Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2024
Publication Date: 9/9/2024
Citation: Pineda, P.S., Flores, E.B., Villamor, L.P., Parac, C.J.M., Khatkar, M.S., Thu, H.T., Smith, T.P.L., Rosen, B.D., Ajmone-Marsan, P., Colli, L., Williams, J.L., Low, W. et al. 2024. Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 buffalo genomes project. Gigascience. 13. Article giae053. https://doi.org/10.1093/gigascience/giae053.
DOI: https://doi.org/10.1093/gigascience/giae053

Interpretive Summary: Water buffalo are a widely used animal for agriculture outside the U.S. but have not benefited substantially from the application of genomic science for improvement. The manuscript describes creation of the most complete water buffalo genome assembly, the basis for implementing genomics for enhancing animal utility, health, and sustainability. The main point of the paper beyond the assembly is the identification of millions of single nucleotide markers called SNP that are used to identify DNA markers for selection of superior genetics within populations. These can be harnessed for genetic improvement of livestock as well as providing information to identify important subpopulations, for example distinguishing between swamp and riverine types of buffalo.

Technical Abstract: More people in the world depend on water buffalo for their livelihoods than on any other domesticated animals, but its genetics is still not extensively explored. The 1000 Buffalo Genomes Project (1000BGP) provides genetic resources for global buffalo population study and tools to breed more sustainable and productive buffaloes. Here we report the most contiguous swamp buffalo genome assembly (PCC_UOA_SB_1v2) with substantial resolution of telomeric and centromeric repeats, ~4-fold more contiguous than the existing reference river buffalo assembly and exceeding a recently published male swamp buffalo genome. This assembly was used along with the current reference to align 140 water buffalo short-read sequences and produce a public genetic resource with an average of ~41 million single nucleotide polymorphisms per swamp and river buffalo genome. Comparison of the swamp and river buffalo sequences showed ~1.5% genetic differences, and estimated divergence time occurred 3.1 million years ago (95% CI, 2.6–4.9). The open science model employed in the 1000BGP provides a key genomic resource and tools for a species with global economic relevance.