Use of EST data mining to characterize genetic parameters in the chicken (Gallus gallus)

We have explored chicken expressed sequence tag (EST) data to estimate various parameters of the chicken genome, mainly using in silico analytical methods. The chicken genomic parameters that were explored included single nucleotide polymorphisms (SNPs), domain patterns of the F-box protein family, and total number of genes in the chicken genome. Starting with 23,427 chicken ESTs, we discovered 1,210 potential SNPs using a computational pipeline and among these, 108 candidate nonsynonymous SNPs (nsSNPs) were identified by a double screening method. A searchable SNP database (chicksnps) for the candidate chicken SNPs is available at http://chicksnps.afs.udel.edu. In addition, the 108 nsSNPs were prioritized, based on structural (relative accessibility) and evolutionary characteristics (conservation index), to select nsSNPs that are more likely to affect the phenotype. The functionally important nsSNPs (rank = 1) were mapped onto aldehyde dehydrogenase, serum amyloid B component and ovotransferrin. The remaining nsSNPs were given a priority rank of 2 or 3, dependent on their conservation indices and relative accessibilities. This prioritization of nsSNPs will be useful in mapping of loci that affect quantitative traits in chickens. To characterize the F-box protein families in chicken, we initially mapped and sequenced a chicken gene, with homology to the human F-box only protein 7 (FBXO7) gene. The equivalent chicken gene was located to chromosome I (DEL0001) and the genomic structure had subtle differences compared to other FBXO7 genes. To continue characterizing F-box protein families in the chicken, we identified chicken ESTs that contained F-box domains, by blasting two separate publically available chicken EST data sets against the F-box proteins of other species that were available from non-redundant protein database at the NCBI. Twenty putative F-box proteins were characterized into three categories: FBXWs containing WD40 domains (2), FBXLs containing leucine-rich repeats (5), and FBXOs either containing different protein-protein interaction modules or no recognizable motifs (13). Lastly, the total number of chicken genes was estimated from the EST data to be approximately 29,000 using a method modified by Ewing and Green. The research in this dissertation has made a small, but significant advancement in chicken genomics, and it has demonstrated the useful application of EST data mining as a strategy for characterizing chicken genomic parameters.