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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: Next Generation Sequencing of a Bos taurus indicus (Nellore) animal: Genome Assembly and SNP Analysis

Author
item Sonstegard, Tad

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: March 8, 2011
Publication Date: N/A

Technical Abstract: A de novo genome assembly of the Bos taurus indicus sub-species is essential to better evaluate the genetic variation underlying the prototypical beef and dairy cattle of tropical and sub-tropical production environments. A linebred Nelore bull (Futuro) was selected for genome sequencing based on validation of indicine lineage from mtDNA sequence analysis and a relatively low BovineSNP50 average heterozygosity index of 0.16 (max = 0.40). Genome sequence data for assembly (>120 Gb) was produced from Roche FLX454 and Illumina GAIIx platforms using paired-end reads from long (5 and 20 kb) and short (300 and 500 bp) insert libraries and single-end shotgun reads. After trimming for redundancy and chimeric sequences, long insert mate-pair reads yielded 175X clone (distance) coverage of the genome, while short libraries yielded 27X sequence (depth) coverage. An additional 1X and 3X sequence coverage was generated with 350 and 80 bp shotgun reads, respectively. Sequence data are being assembled into super-reads before using the Celera assembler to build sequence contigs and scaffolds. The final assembly will be annotated by NCBI with RNAseq information generated from tissues harvested from full-sibs to improve gene models. SNP discovery analysis from Futuro’s sequence combined with data from 9 other breeds and the taurine reference assembly identified approximately 41 million SNPs. About 36% of these SNPs segregate only within indicine cattle, while 1% represents fixed allelic differences between the sub-species. These two groups of SNP potentially contain the variation underlying tropical adaptation.

Last Modified: 12/18/2014