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United States Department of Agriculture

Agricultural Research Service

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Research Project: NOVEL SNP DISCOVERY AND GENOME ASSEMBLY OF WATER BUFFALO

Location: Animal Genomics and Improvement Laboratory

2011 Annual Report


1a.Objectives (from AD-416)
ARS and the Cooperator (The International Water Buffalo Consortium, represented by Parco Tecnologico Padano [PTP] as coordinator and The Department of Animal Science University of Tuscia [UniTus] as administrative center) are interested in developing a first draft sequence assembly of the water buffalo genome based on the bovine species, Bubalis bubalis, which encompasses the prototypical beef and dairy animal in South Asian, Brazilian and Italian production environments. Such a resource is essential for developing informative SNP markers to intensify outputs in current production scenarios and enable selection of locally-adapted breeds in developing-world water buffalo populations. Our Project Plan has two objectives: .
1)generate a 33X genome sequence coverage of DNA sequence from an Italian inbred female to use in building a genome sequence assembly and.
2)generate additional sequence coverage from additional animals to identify SNP for development of a high density SNP assay that contains informative SNP for all breed types of water buffalo. The Cooperator has the funding and genomic DNA material to properly initiate this project, and the expertise and knowledge of the water buffalo production systems to extend application of the results to improve production. ARS has the expertise and facilities to generate the DNA sequence information on next-generation sequencing platforms and characterize the SNP that are potentially informative across all breeds of water buffalo.


1b.Approach (from AD-416)
The project will be managed jointly between ARS and the Cooperator. The Cooperator will evaluate the Water Buffalo herdbook in Italy to guide collection of tissues and/or DNA material from an appropriate buffalo for sequencing. The Cooperator will then provide genomic DNA templates from this animal along with funding to purchase reagents that will generate more than 33X genome equivalent coverage of DNA sequence. ARS will generate the DNA libraries, and provide next-generation DNA sequencing services to generate at least 33X genome coverage of sequence at cost with a small amount for the overhead costs of instrumentation. ARS will analyze, store, and distribute sequence information (as agreed upon with the Cooperator) that will be used for both genome assembly and SNP discovery. Identification of SNP for marker development will be carried out collaboratively by ARS and the Cooperator. Both ARS and the Cooperator will jointly aid development of the genome assembly led by outside parties that possess the necessary advanced expertise for this process. The Cooperator will provide some annotation expertise prepare the data and lead the development of the publication.

All of these activities will be considered true collaborations and thus, by definition, each party will be considered to have provided a true intellectual contribution consistent with authorship.


3.Progress Report

This report documents research conducted under funding received from the International Water Buffalo Consortium being led by Parco Tecnologico Padano in Lodi and funded by University of Tuscia, Milan. ARS exceeded production during completion of objective 1 by producing more than 140 billion bases of sequence data. The genome assembly and annotation is still in progress, which relies on non-funded partners from the University of Maryland for completion. It should be noted that some sequence production contribution and experimental planning was derived from USMARC (Clay Center, NE). Objective 2 is still in progress with various DNA breed samples being collected from the many different international partners in the consortium. Monitoring activities associated with this project included regular email correspondence, face-to-face meetings, workshop in conjunction with an international meeting, and conference calls. This research supported 2 objectives of its related in-house project: .
1)to develop biological resources and computational tools to enhance characterization of the bovine genome sequence (obj. #1) and.
2)to use genotypic data to enhance genetic improvement through development and implementation of whole genome selection and enhanced parentage verification approaches (obj. #2).


Last Modified: 10/1/2014
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