CCGP ESTPs

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
PtIFG_66
PtIFG_138
PtIFG_606
PtIFG_624
PtIFG_653
PtIFG_669
PtIFG_1454
PtIFG_1584
PtIFG_1633
PtIFG_1635
PtIFG_1643
PtIFG_1672
PtIFG_1849
PtIFG_1917
PtIFG_1950
PtIFG_1955
PtIFG_1956
PtIFG_2006
PtIFG_2020
PtIFG_2022
PtIFG_2068
PtIFG_2113
PtIFG_2150
PtIFG_2220
PtIFG_2253
PtIFG_2274
PtIFG_2291
PtIFG_2358
PtIFG_2442
PtIFG_2540
PtIFG_2547
PtIFG_2564
PtIFG_2610
PtIFG_2697
PtIFG_2707
PtIFG_2723
PtIFG_2897
PtIFG_2986