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Title: Fine genetic mapping of target leaf spot resistance gene cca-3 in cucumber, Cucumis sativus L

Author
item WEN, CHANGLONG - Beijing Academy Of Agricultural Sciences
item MAO, AIJUN - Beijing Academy Of Agricultural Sciences
item DONG, CONGJUAN - Beijing Academy Of Agricultural Sciences
item LIU, HUYU - Beijing Academy Of Agricultural Sciences
item YU, SHUANCANG - Beijing Academy Of Agricultural Sciences
item GUO, YANG-DONG - China Agricultural University
item Weng, Yiqun
item XU, YONG - Beijing Academy Of Agricultural Sciences

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2015
Publication Date: 9/5/2015
Publication URL: http://handle.nal.usda.gov/10113/61671
Citation: Wen, C., Mao, A., Dong, C., Liu, H., Yu, S., Guo, Y., Weng, Y., Xu, Y. 2015. Fine genetic mapping of target leaf spot resistance gene cca-3 in cucumber, Cucumis sativus L. Theoretical and Applied Genetics. 128(12):2495-2506. doi: 10.1007/s00122-015-2604-z.

Interpretive Summary: The target leaf spot (TLS) is one of the most important foliar diseases in cucumber (Cucumis sativus L.). In this study, we conducted fine genetic mapping of a simply inherited recessive resistance gene, cca-2 against TLS with 193 F2:3 families and 890 F2 plants derived from the resistant cucumber inbred line D31 and the susceptible line D5. Initial mapping with microsatellite markers and bulked sergeant analysis placed cca-2 in a 2.5 Mbp region of cucumber chromosome 6. The D5 and D31 lines were re-sequenced at 10×genome coverage to explore new markers in the target region. Genetic mapping in the large F2 population delimited the cca-2 locus in a 79kb region with flanking markers Indel16874230 and Indel16953846. Additional fine mapping and gene annotation in this region revealed that a CC-NB-ARC type resistance gene analog, Csa6M375370, seems to be the candidate gene for cca-2. One single nucleotide polymorphism (SNP) was found in the NB-ARC domain of this candidate gene sequences between D31 and D5 that may lead to amino acid change, thus altering the function of the conserved NB-ARC motif. This SNP was validated in the segregating populations as well as 24 cucumber lines with different responses to TLS infection. There was significantly higher level of expression for this candidate gene in the leaves of the susceptible parent (D5) than in the resistant D31, and the expression level was positively correlated with the areas of necrotic spots on leaves after inoculation. It seems the cca-2 resistance gene was able to induce hypersensitive responses to the infection by TLS pathogen.

Technical Abstract: The target leaf spot (TLS) is a very important fungal disease in cucumber. In this study, we conducted fine genetic mapping of a recessively inherited resistance gene, cca-2 against TLS with 1,083 F2 plants derived from the resistant cucumber inbred line D31 and the susceptible line D5. Initial mapping with molecular markers placed cca-2 in a 2.5 Mbp region of cucumber chromosome 6. The D5 and D31 lines were re-sequenced with the next generation sequencing technologies to find new markers in the target region. Genetic mapping allowed delimiting cca-2 gene in a 79kb region that contains nine genes. Additional fine mapping and gene annotation in this region revealed that a NB-LRR type resistance gene analog seems to be the candidate gene for cca-2. One single nucleotide polymorphism was found within this gene that may lead to amino acid change, thus altering the function of this candidate gene. This SNP was validated in the segregating populations as well as 24 cucumber lines. There was significantly higher level of expression for this candidate gene in the leaves of the susceptible parent than in the resistant one, and the expression level was positively correlated with the areas of necrotic spots on leaves after inoculation.