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United States Department of Agriculture

Agricultural Research Service

Title: Development and Mapping of Type-I (Gene-Related) Markers in the Bovine Genome by Large-Scale Expressed Sequence Tag (Est) Sequencing and Single Nucleotide Polymorphism (Snp) Detection

item Grosse, William
item Stone, Roger
item Keele, John
item Bennett, Gary
item Fahrenkrug, Scott
item Casas, Eduardo
item Smith, Timothy

Submitted to: Animal Genetics International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: March 14, 2000
Publication Date: N/A

Technical Abstract: Genetic linkage maps of the bovine genome, consisting mainly of Type-II (microsatellite) markers, have been applied to identify chromosomal regions carrying loci that affect production traits (quantitative trait loci; QTL). In order to populate the linkage map with gene-related markers, providing a source of positional candidate genes and tying the bovine map to the more highly developed human map, we have initiated a program to develop SNPs from expressed gene loci. The EST sequencing phase of this program utilizes four normalized libraries constructed with RNA pooled from multiple tissues having importance to production traits. As of the abstract deadline, over 32,000 bovine EST sequences had been deposited in GenBank, with approximately 2,500 new sequences collected each week. Sequences are compared with GenBank using BLASTN, to identify clones with orthologs on the human map. In the SNP discovery phase, BLAST output is used to design primers predicted to flank introns in target loci. Amplicons of primers that successfully amplify bovine genomic DNA (approximately 60% of primers designed) are sequenced to identify polymorphisms in the MARC mapping population. The first 34 amplicons sequenced have identified 21 with SNPs. Mapping ESTs is the final phase and uses MALDI-TOF mass spectrometry-based assays to genotype the reference population. Our goal is to generate sequence from 40-50,000 independent bovine genes, and map 500-1,000 ESTs on the bovine genome. This program will significantly improve the comparative map of cattle with other mammals and provide a resource for SNP-based high throughput genotyping.

Last Modified: 4/21/2015