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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY Title: Fine Genetic Mapping Localizes Cucumber Scab Resistance Gene Ccu into an R Gene Cluster

Authors
item Kang, Houxiang -
item Yang, Yuhong -
item Zhang, Zhonghua -
item Zhang, Shengping -
item Mao, Zhenchuan -
item Cheng, Guohua -
item Gu, Xingfang -
item Huang, Sanwen -
item Weng, Yiqun
item Xie, Bingyan -

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 22, 2010
Publication Date: November 21, 2010
Citation: Kang, H., Yang, Y., Zhang, Z., Zhang, S., Mao, Z., Cheng, G., Gu, X., Huang, S., Weng, Y., Xie, B. 2010. Fine Genetic Mapping Localizes Cucumber Scab Resistance Gene Ccu into an R Gene Cluster. Journal of Theoretical and Applied Genetics. Available: http://www.springerlink.com/content/lqu520225154x357/.

Interpretive Summary: The scab is an important disease of cucumber. In this study, we conducted fine genetic mapping of the scab resistance gene, Ccu, with 148 recombination inbreeding lines (RILs) and 1,944 F2 plants derived from the resistant cucumber inbred line 9110Gt and the susceptible line 9930. A framework genetic map was first constructed with microsatellite markers placing Ccu into the terminal 640 kb region of cucumber Chromosome 2. The 9110Gt genome was sequenced at 5× coverage with the Solexa next-generation sequencing technology. Analysis of the assembled 9110Gt sequences 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, Indel01 and Indel02 were two closest flanking markers that were 0.14 and 0.15 cM away from Ccu, respectively. Both markers were located in the scaffold of the 9930 draft genome that were approximately 140 kb apart. Detailed annotation of the 180 kb region harboring the Ccu gene identified a cluster of six resistance gene analogs (RGAs) which belong to the nucleotide binding site (NBS) type R genes. Four RGAs, three of which were in tandem repeats, were in the region delimited by markers Indel01 and Indel02, and thus were possible candidate of Ccu. This region in cucumber was highly conserved with melon region at DNA level.

Technical Abstract: The 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 recombination inbreeding 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 microsatellite (or simple sequence repeat, SSR) markers placing Ccu into the terminal 640 kb region of cucumber Chromosome 2. The 9110Gt genome was sequenced at 5× coverage with the Solexa next-generation sequencing platform. 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, Indel01 and Indel02 were two closest flanking markers that were 0.14 and 0.15 cM away from Ccu, respectively. Both markers were located in the scaffold of the 9930 draft genome that were approximately 140 kb apart. Detailed annotation of the 180 kb region harboring the Ccu gene identified a cluster of six resistance gene analogs (RGAs) which belong to the nucleotide binding site (NBS) type R genes. Four RGAs, three of which were in tandem repeats, were in the region delimited by markers Indel01 and Indel02, and thus were possible candidate of Ccu. Comparative analysis of this cucumber R gene cluster DNA region with a melon (C. melo) BAC (bacterial artificial chromosome) clone revealed high degree of micro-synteny at the DNA level, and conservation of the RGA tandem repeat between melon and cucumber.

Last Modified: 12/19/2014
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