Expressed sequence tags for the chicken genome from a normalized 10-day-old white leghorn whole embryo cDNA library: 1. DNA sequence characterizationand linkage analysis

Expressed sequence tags (ESTs) provide a rapid and reliable method for gene discovery as well as a resource for the large-scale analysis of gene expre ssion of known and unknown genes. Here we describe a normalized cDNA librar y developed from a 10-day-old White Leghorn chicken whole embryo. The utili ty of the library was evaluated by partial sequencing of 99 randomly select ed insert-containing clones and the analysis of EST-targeted genomic region s for single nucleotide polymorphisms (SNPs) in the East Lansing chicken re ference DNA mapping panel. Using stringent match criteria of percent identi ty of 80 or higher across a length of 50 or more bases, 46 ESTs matched dat abase sequences including previously reported Gallus gallus genes. Thirty-s even of the 50 primer pairs developed from 50 unique ESTs amplified a singl e fragment. The size of the 37 amplicons ranged from 276 to 693 bp for a to tal of 17,508 and an average of 473, About 70% of the SNPs detected were ei ther G-->A or C-->T transition. The number of SNPs detected within the ampl icons from EST-targeted genomic regions ranged from 0 to 4 for a total of 6 5 and a frequency of about 1 every 470 bases. About 35% of the amplicons co ntained only 1 SNP, while 19% had 4 SNPs, Using the SNPs that were informat ive in the East Lansing reference panel, 17 ESTs were mapped on the East La nsing chicken genetic map. The ESTs described, as well as the nucleotide va riants identified within the EST-targeted genomic regions, represent signif icant resources for genome analysis in the chicken.