Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project
Author:
Pineda Paulene S12ORCID, Flores Ester B2ORCID, Villamor Lilian P2ORCID, Parac Connie Joyce M2ORCID, Khatkar Mehar S1ORCID, Thu Hien To3ORCID, Smith Timothy P L4ORCID, Rosen Benjamin D5ORCID, Ajmone-Marsan Paolo6ORCID, Colli Licia6ORCID, Williams John L16ORCID, Low Wai Yee1ORCID, , Low Lloyd, Khatkar Mehar, Chen Tong, Nguyen Hanh Thi Hong, Tonhati Humberto, de Camargo Gregório Miguel Ferreira, Biffani Stefano, Han Jianlin, Zhang Yi, Liu Mei, Zhou Yang, Gómez Divier Antonio Agudelo, Kumarasamy P, Bhatti Jaswinder Singh, Mukesh Manishi, Priyono Dwi Sendi, Dakhlan Akhmad, Mokhber Mahdi, Williams John, Paolo Ajmone Marsan, Colli Licia, Carpio Mayra Gómez, Cimmino Roberta, Awan Ali Raza, Pineda Paulene S, Villamor Lilian P, Flores Ester B, Parac Connie Joyce, Parnpai Rangsun, Tuk Siri, Soysal M İhsan, Unal Emel Özkan, Isik Raziye, Jiang Zhihua, Lụ’c Ðỗ Ðụ’c, Thinh Nguyen Hoang
Affiliation:
1. The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide , Roseworthy, SA 5371 , Australia 2. Philippine Carabao Center National Headquarters and Genepool , Science City of Muñoz, Nueva Ecija 3120 , Philippines 3. Norwegian University of Life Sciences: NMBU , Universitetstunet 3, 1430 Ås, Norway 4. U.S. Meat Animal Research Center, USDA-ARS , Clay Center, NE 68933 , USA 5. Animal Genomics and Improvement Laboratory , USDA-ARS, Beltsville, MD 20705 , USA 6. Department of Animal Science , Food and Nutrition, Università Cattolica del Sacro Cuore, 29122 Piacenza , Italy
Abstract
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.
Funder
University of Adelaide U.S. Department of Agriculture
Publisher
Oxford University Press (OUP)
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