1a. Objectives (from AD-416)
ARS and the COOPERATOR (UNESP-Aracatuba) are interested in developing a second draft sequence assembly of the bovine genome based on the bovine sub-species, Bos indicus, which encompasses the prototypical beef and dairy animal in tropical and sub-tropical 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 cattle populations. Our Project Plan has two objectives: 1) generate a 40X genome coverage of DNA sequence from a linebred Nelore bull to use in building a genome sequence assembly and 2) generate 10X coverage from 10 additional Nelore animals (1X each animal) to identify SNP for development of a 660K SNP assay that contains informative SNP for all breed types of cattle. The COOPERATOR has the funding and genomic DNA material to properly initiate this project, and the expertise and knowledge of the extensive cattle 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 cattle.
1b. Approach (from AD-416)
The project will be managed jointly between ARS and the COOPERATOR. The COOPERATOR will evaluate the Nelore herdbook and mtDNA sequence to guide collection of appropriate tissues and/or DNA material for sequencing. ARS will analyze the heterozygosity indices of candidate animals using BovineSNP50 data. This analysis will aid final selection by the COOPERATOR of the appropriate animal for genome sequencing. The COOPERATOR will then provide genomic DNA templates from this animal and 10 additional Nelore animals (for 1X coverage sequencing/animal) along with funding to purchase reagents that will generate a 40X genome equivalent of DNA sequence. ARS will generate the DNA libraries, and provide next-generation DNA sequencing services to generate 50X genome coverage of sequence at cost. 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 done by ARS. 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 to help prepare the data for 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
The two objectives of this project were to: 1) generate a 40X genome coverage of DNA sequence (116 billion base pairs) from a linebred Nelore bull to use in building a de novo genome sequence assembly and 2) generate 10X coverage from 10 additional Nelore animals (1X each animal) to identify SNP for development of high density SNP assays that contains informative SNP for all breed types of cattle. All ARS objectives have been completed and only the genome assembly and annotation is still in progress, which relies on non-funded partners from the University of Maryland and Università Cattolica del S. Cuore for completion. It should be noted that some sequence production contribution and experimental planning was derived from USMARC (Clay Center, NE) and production of cDNA libraries to improve annotation was completed at USDA, LARRL (Miles City, MT). Monitoring activities associated with this project included regular email correspondence, face-to-face meetings, one international workshop, and conference calls. This research supported two 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).