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The Journal of Heredity 2001:92(1)
© 2001 The American Genetic Association 92:1-8

Expressed Sequence Tags for the Chicken Genome from a Normalized 10-Day-Old White Leghorn Whole Embryo cDNA Library: 1. DNA Sequence Characterization and Linkage Analysis

E. J. Smith, L. Shi, P. Drummond, L. Rodriguez, R. Hamilton, S. Ramlal, G. Smith, K. Pierce, and J. Foster

From the Comparative Genomics Laboratory, College of Agricultural, Environmental, and Natural Sciences, Tuskegee University, Tuskegee, Alabama.

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 expression of known and unknown genes. Here we describe a normalized cDNA library developed from a 10-day-old White Leghorn chicken whole embryo. The utility of the library was evaluated by partial sequencing of 99 randomly selected insert-containing clones and the analysis of EST-targeted genomic regions for single nucleotide polymorphisms (SNPs) in the East Lansing chicken reference DNA mapping panel. Using stringent match criteria of percent identity of 80 or higher across a length of 50 or more bases, 46 ESTs matched database sequences including previously reported Gallus gallus genes. Thirty-seven of the 50 primer pairs developed from 50 unique ESTs amplified a single fragment. The size of the 37 amplicons ranged from 276 to 693 bp for a total of 17,508 and an average of 473. About 70% of the SNPs detected were either G->A or C->T transition. The number of SNPs detected within the amplicons from EST-targeted genomic regions ranged from 0 to 4 for a total of 65 and a frequency of about 1 every 470 bases. About 35% of the amplicons contained only 1 SNP, while 19% had 4 SNPs. Using the SNPs that were informative in the East Lansing reference panel, 17 ESTs were mapped on the East Lansing chicken genetic map. The ESTs described, as well as the nucleotide variants identified within the EST-targeted genomic regions, represent significant resources for genome analysis in the chicken.


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