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Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster

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Abstract

Scab, caused by Cladosporium cucumerinum, is an important disease of cucumber, Cucumis sativus. In this study, we conducted fine genetic mapping of the single dominant scab resistance gene, Ccu, with 148 F9 recombinant inbred lines (RILs) and 1,944 F2 plants derived from the resistant cucumber inbred line 9110Gt and the susceptible line 9930, whose draft genome sequence is now available. A framework linkage map was first constructed with simple sequence repeat markers placing Ccu into the terminal 670 kb region of cucumber Chromosome 2. The 9110Gt genome was sequenced at 5× genome coverage with the Solexa next-generation sequencing technology. Sequence analysis of the assembled 9110Gt contigs and the Ccu region of the 9930 genome identified three insertion/deletion (Indel) markers, Indel01, Indel02, and Indel03 that were closely linked with the Ccu locus. On the high-resolution map developed with the F2 population, the two closest flanking markers, Indel01 and Indel02, were 0.14 and 0.15 cM away from the target gene Ccu, respectively, and the physical distance between the two markers was approximately 140 kb. Detailed annotation of the 180 kb region harboring the Ccu locus identified a cluster of six resistance gene analogs (RGAs) that belong to the nucleotide binding site (NBS) type R genes. Four RGAs were in the region delimited by markers Indel01 and Indel02, and thus were possible candidates of Ccu. Comparative DNA analysis of this cucumber Ccu gene region with a melon (C. melo) bacterial artificial chromosome (BAC) clone revealed a high degree of micro-synteny and conservation of the RGA tandem repeats in this region.

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Acknowledgments

This work was supported by the National Key Basic Research and Development Program of China (2009CB119000) and National Natural Science Foundation of China (31030057); We are grateful to Wang Xiaowu for advices in fine mapping of Ccu. Kuang Hanhui, Snyder, John and Yang Haiyuan for critical reading of an early version of the manuscript.

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Authors and Affiliations

  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China

    Houxiang Kang, Yuhong Yang, Zhonghua Zhang, Shengping Zhang, Zhenchuan Mao, Guohua Cheng, Xingfang Gu, Sanwen Huang & Bingyan Xie

  2. Horticulture Department, USDA-ARS Vegetable Crops Research Unit, University of Wisconsin, Madison, WI, 53706, USA

    Yiqun Weng

  3. Key Laboratory of Horticultural Crops Genetic Improvement, Ministry of Agriculture, 100081, Beijing, China

    Houxiang Kang, Yuhong Yang, Zhonghua Zhang, Shengping Zhang, Zhenchuan Mao, Guohua Cheng, Xingfang Gu, Sanwen Huang & Bingyan Xie

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  1. Houxiang Kang
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  2. Yiqun Weng
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  3. Yuhong Yang
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  4. Zhonghua Zhang
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  5. Shengping Zhang
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  6. Zhenchuan Mao
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  7. Guohua Cheng
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  8. Xingfang Gu
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  9. Sanwen Huang
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  10. Bingyan Xie
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Corresponding authors

Correspondence to Sanwen Huang or Bingyan Xie.

Additional information

Communicated by I. Paran.

H. Kang and Y. Weng contributed equally to this work.

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Kang, H., Weng, Y., Yang, Y. et al. Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster. Theor Appl Genet 122, 795–803 (2011). https://doi.org/10.1007/s00122-010-1487-2

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  • DOI: https://doi.org/10.1007/s00122-010-1487-2

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