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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Multi-platform next generation sequencing of a high quality genome assembly for the goat

Authors
item Sonstegard, Tad
item Smith, Timothy
item Schroeder, Steven
item Huson, Heather
item Zimin, Aleksey -
item Woodward-Greene, Jennifer
item Mujibi, Denis -
item McClure, Matthew
item Silverstein, Jeff
item Van Tassell, Curtis
item Sayre, Brian -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: December 26, 2012
Publication Date: January 12, 2013
Citation: Sonstegard, T.S., Smith, T.P., Schroeder, S.G., Huson, H.J., Zimin, A., Woodward Greene, M.J., Mujibi, D.F., Mcclure, M.C., Silverstein, J., Van Tassell, C.P., Sayre, B.L. 2013. Multi-platform next generation sequencing of a high quality genome assembly for the goat. Plant Animal Genome XXI, paper W417, pp. 171.

Technical Abstract: The goat is adapted to most of the environmental conditions found around the world. The species has evolved to be tolerant to diseases, productive in tropical or arid regions, and culturally and economically important in developing countries. Characterization of these genetic adaptations and development of SNP-based tools for genetic improvement in indigenous goats requires a high quality reference genome sequence. Male goats from breeds or populations expected to have a high level of inbreeding were screened with the Illumina GoatSNP50. Fifteen male goats from four breeds (San Clemente, Boer, Myotonic, Kiko) were evaluated for genomic coefficients of inbreeding (FROH) using runs of homozygosity. This analysis identified "Papadom", a San Clemente buck, as the most inbred male goat for deep sequencing (FROH=0.46). Paired end reads from long (5 and 20 kb) and short (300 and 500 bp) insert libraries and single end shotgun reads are being sequenced using Roche FLX454 and Illumina MiSeq and HiSeq platforms. A de novo assembly of the sequence data will be completed with the University of Maryland short read assembler. The goat genome sequence will be used for SNP discovery in African and European goat populations and genome comparison to the bezoar, which is a potential source of domestication.

Last Modified: 10/24/2014
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