ARS | Publication request: CONSTRUCTION OF SNP-BASED EST COMPARATIVE MAP OF SWINE, CATTLE, AND HUMAN GENOMES

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: January 5, 2001
Publication Date: N/A

Technical Abstract: Considerable variation in production traits exists within commercial populations of livestock, suggesting the presence of allelic variation in important genes. However, the production of basic tools for genomic research has lagged in these species, and support for development of these tools is much lower than in biomedicine. The most efficient, realistic approach to genomic science in mammalian livestock species is the construction of dense comparative maps with the human and mouse genomes. To construct a comparative map between porcine, bovine, and human genomes, we have undertaken a program of EST sequencing using pooled-tissue, normalized libraries. This effort has produced 72,814 ESTs from cattle and 38,854 from swine to date, deposited in GenBank. The EST sequences are compared to the human sequence database via BLASTN analysis to identify probable intron sites and human map position. This data is used to design primers that amplify intronic sequence within the EST genes. These primers are used to obtain partial gene sequence from the parents of the MARC mapping reference families, and reveal SNPs within the population. At present, over 1,500 primer sets have been tested and more than 2,500 SNPs have been identified. Genotyping of SNPs in the mapping population by MALDI-TOF mass spec has allowed placement of over 300 ESTs on the cattle and swine linkage maps. This program has produced the necessary data and reagents for construction of livestock microarrays, as well as providing a significant advance in the development of mammalian comparative maps.