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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

Ren, Zhiyong, You, Zeshuang, Munir, Shoaib, Zhang, Yuyang, Li, Hanxia, Zhang, Junhong, Wang, Taotao, Zheng, Wei, Ye, Zhibiao
Molecular breeding 2019 v.39 no.3 pp. 45
Phytophthora infestans, Solanum pimpinellifolium, ancestry, breeding programs, cultivars, disease resistance, genotyping, humidity, leaves, loci, marker-assisted selection, molecular cloning, multigene family, polymerase chain reaction, resistance genes, temperature, tomatoes
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/HincII and TG328 developed previously. Ph-3-GLR/S exhibited robust co-dominant patterns compared to Ph3.gsm/HincII. 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.