Molecular Breeding

, 39:45 | Cite as

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

  • Zhiyong Ren
  • Zeshuang You
  • Shoaib Munir
  • Yuyang Zhang
  • Hanxia Li
  • Junhong Zhang
  • Taotao Wang
  • Wei Zheng
  • Zhibiao YeEmail author


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.


Tomato Molecular marker Late blight Phytophthora infestans Ph-3 Resistance gene 



We are grateful to Dr. Jinshuai Shu for providing the tomato race T1,2,4 of P. infestans and to Xiaoling Yu for guidance on the detached leaf inoculation. We also thank Prof. Tingting Huang for kindly providing the seeds of Wanxia.

Funding information

This project was supported by the grants of the National Key R&D Program of China (2017YFD0101902), China Agriculture Research System (CARS-23-A-03).

Supplementary material

11032_2019_953_Fig4_ESM.png (1.5 mb)
Fig. S1

BLASTN results with Ph-3 CDS and sequences from downstream of CDS as queries from SGN database. Blue line indicates the locations of selected polymorphisms. a, The matched subject sequences (sbjcts) with the highest identity from chromosome 9 of Heinz1706 and contigs of LA1589 by querying with CDS sequence (2556 bp). b, The matched sbjcts with the highest identity from Ph-3 corresponding locus of Heinz1706 and contigs of LA1589 by querying with CDS downstream sequence (1866 bp) (PNG 1508 kb)

11032_2019_953_MOESM1_ESM.tif (27.8 mb)
High Resolution Image (TIF 28467 kb)
11032_2019_953_Fig5_ESM.png (230 kb)
Fig. S2

BLASTN result with sequence of unexpected 1 kb amplicon as query, produced by PCR with newly developed marker Ph-3-GLR/S in HG70 (PNG 230 kb)

11032_2019_953_MOESM2_ESM.tif (5.8 mb)
High Resolution Image (TIF 5951 kb)
11032_2019_953_MOESM3_ESM.doc (43 kb)
Table S1 List of tomato cultivars/lines used in this study and their genotypes at the Ph-3 gene locus (DOC 104 kb)
11032_2019_953_MOESM4_ESM.doc (50 kb)
Table S2 List of sbjcts from SGN blast result querying by Ph-3 sequence (DOC 50 kb)
11032_2019_953_MOESM5_ESM.doc (43 kb)
Table S3 List of sbjcts from SGN blast result queried by 1-kb amplicon sequence from HG70 (DOC 43 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Zhiyong Ren
    • 1
  • Zeshuang You
    • 1
  • Shoaib Munir
    • 1
  • Yuyang Zhang
    • 1
  • Hanxia Li
    • 1
  • Junhong Zhang
    • 1
  • Taotao Wang
    • 1
  • Wei Zheng
    • 2
  • Zhibiao Ye
    • 1
    Email author
  1. 1.Key Laboratory of Horticultural Plant Biology, Ministry of Education, National Center for Vegetable Improvement (Central China), Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
  2. 2.HZAU Chuwei Institute of Advanced SeedsWuhanChina

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