Expressed Sequence Tag Polymorphisms
Orthology describes the evolutionary origin of a locus. Loci in two species are said to be orthologous (identical by descent) when they have arisen from the same locus of a common ancestor. For example, gene A in Species 1 and 2 are orthologous, whereas gene B1, which has arisen by gene duplication in species 2, is paralogous to gene B in Species 1. Clearly, comparative mapping in species groups having large genomes with abundant multigene families, such as pines, can be confounded by the mapping of paralogous loci.
Along with David E. Harry, Berhanu Temesgen and Garth Brown (Harry et al., 1998; Temesgen et al., 2001; Brown et al., 2001), we have developed a set of primer pairs from loblolly pine expressed sequence tags (ESTs) that can serve as a framework around which comparative genetic maps can be built for pines and other conifers. Polymorphisms in these PCR-based markers are quite easily detected using denaturing gradient gel electrophoresis and other means. By targeting PCR amplification to the 3″ end of genes, the EST polymorphisms (ESTPs) mapped to date appear to be orthologous even though the cDNAs from which the primer sequences were derived represent gene families in loblolly pine. The pedigrees of CCGP collaborators have been screened for successful PCR amplification and polymorphism and the results can be found here.
In addition, a group of cDNAs that are single or low copy in loblolly pine and other pine species have been identified. These markers, listed below and suitable for constructing comparative maps using RFLPs, are freely available upon request.
Loblolly Pine cDNAs Likely to Reveal Orthologous Loci In Other Species