Genetic markers and their application in poultry breeding.

The current chicken genetic map contains at least 1,965 loci within 50 linkage groups, and it covers about 4,000 cM. About 235 of these loci have homology with known human or mammalian genes. The remaining loci are anonymous molecular DNA markers, including microsatellites, amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD), CR1 elements, and others. A third generation genetic map for human uses single nucleotide polymorphisms (SNP), which have allowed the mapping of complex traits by linkage disequilibrium. One advantage of SNP is that they are usually linked to the gene of interest, and association of the SNP with traits of economic importance can be analyzed using candidate gene approaches. With the tremendous advancements in characterizing chicken expressed sequence tags (EST), the identification of genetic polymorphisms such as SNP in chicken genes has become a reality. Our laboratory has undertaken an in silico analysis of the chicken EST at the University of Delaware by using a Phred/Phrap/Polyphred/Consed pipeline to identify candidate chicken SNP. Initial scanning of 23,427 chicken EST identified a total of 1,209 candidate SNP, with at least 182 non-synonymous SNP that result in an amino acid change observed. Validation of these candidate chicken SNP is ongoing. Placement of the SNP on the chicken genetic map will enhance marker density, thus allowing for mapping of complex traits through linkage analysis and linkage disequilibrium. Application of SNP to identify disease resistance genes in chickens is of special interest to our laboratory, especially in regards to Marek's disease and coccidiosis.