SEQUENCE COMPARISON AND CHARACTERIZATION OF DNA FRAGMENTS AMPLIFIED BY RESISTANCE GENE PRIMERS IN TOMATO

The purpose of this research was to identify and characterize resistance gene analogs (RGAs) in tomato by PCR amplification of genomic DNA using primers designed based on the conserved amino-acid domains of several known plant disease resistance genes (R genes). Amplified DNAs from a Lycopersicon esculentum x L. hirsutum backcross (BC₁) population were separated by denaturing polyacrylamide gel electrophoresis (PAGE). Polymorphic bands were scored as DNA markers and were positioned on a tomato genetic map.
Several markers were located in the vicinity of previously identified tomato R genes and quantitative resistance loci (QRLs). Polymorphic and monomorphic bands were isolated, cloned and sequenced.
Nucleotide sequences of several of the clones revealed homology to known R genes, RGAs, defense-related genes, or other plant genes.
A majority of the clones, however, did not exhibit sequence homology with known R genes in the database, suggesting that PCR amplification using resistance gene primers results in products which are not related to disease resistance.
The utility of PAGE-polymorphic and PAGE-monomorphic bands as genetic markers and potential candidates for positional gene cloning is discussed.