Development of a highly specific co-dominant marker for genotyping the Ph-3 (tomato late blight resistance) locus by comparing cultivated and wild ancestor species

Late blight is a devastating disease for tomato especially in areas with high humidity and low temperature caused by Phytophthora infestans . A late blight resistance gene, Ph-3 , has been widely used in tomato breeding program as it confers incomplete dominant resistance to a wide range of P. infestans isolates of tomato. This gene was derived from a wild ancestor species of cultivated tomato, Solanum pimpinellifolium accession L3708, and located in a resistance ( R ) gene cluster. Although this gene was cloned a few years ago, and some markers have been developed and used, the effectiveness of these markers was not evaluated with a diverse cultivars panel. Based on the comparative analysis of the Ph-3 locus sequences from L3708, cultivar Heinz1706 and S. pimpinellifolium accession LA1589, we developed a robust co-dominant PCR-based marker Ph-3-GLR/S for the Ph-3 locus. We performed a comparison about efficiency and accuracy of Ph-3-GLR/S with two cleaved amplified polymorphic sequence (CAPS) markers Ph3.gsm/ Hinc II and TG328 developed previously. Ph-3-GLR/S exhibited robust co-dominant patterns compared to Ph3.gsm/ Hinc II. For certain accessions, TG328 and Ph-3-GLR/S yielded the contrast genotyping result. To clarify this discrepancy, disease resistance evaluation by detached leaf inoculation supported the consistency between Ph-3-GLR/S genotyping and resistance phonotype, showing Ph-3-GLR/S was more accurate than TG328. All these findings indicated that our marker Ph-3-GLR/S could serve as a highly specific and robust co-dominant marker for marker-assisted selection of Ph-3 .