Scientia Agricultura Sinica ›› 2014, Vol. 47 ›› Issue (1): 122-132.doi: 10.3864/j.issn.0578-1752.2014.01.013

• HORTICULTURE • Previous Articles     Next Articles

Molecular Mapping and Candidate Gene Analysis of Black Fruit Spine Gene in Cucumber (Cucumis sativus L.)

 LIU  Shu-Lin-1, GU  Xing-Fang-1, MIAO  Han-1, WANG  Ye-1, YiqunWeng2 , ToddCWehner3 , ZHANG  Sheng-Ping-1   

  1. 1.Institute of Vegetables and Flowers of Chinese Academy of Agricultural Sciences, Beijing 100081;
    2.USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA;
    3.Department of Horticulture Science, North Carolina State University, Raleigh, NC 27695-7609, USA
  • Received:2013-05-03 Online:2014-01-01 Published:2013-08-09

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Abstract: 【Objective】Cucumber (Cucumis sativus L.) is an important fruit vegetables. Fruit quality is always getting more attention in cucumber breeding program. Fruit quality includes inner quality and exterior quality, and fruit exterior quality of cucumber has important influences on its commodification. Spine color is one of the important fruit quality traits in cucumber. The clarification of the inheritance and identification of molecular markers for the fruit spine color gene will provide a theoretical basis for breeding of fruit quality and lay a foundation for fine mapping and gene cloning. 【Method】 Cucumber inbred lines GY14 with white fruit spines and NC76 with black fruit spines were used as the experiment materials for genetic analysis and gene mapping for black fruit spine in this study. Bulked segregation analysis (BSA) was performed in the F2 population using 2112 SSR markers. The sequence and re-sequencing information of 9930 and 100 core germplasms were used to develop new SSR and Indel markers in the primary mapping region of the black spine color gene (B). JoinMap 4.0 and MapInspect software were employed to construct a linkage map for the B gene with SSR markers. Bio-informatics was adopted to predict candidate genes in the genomic region harboring the B gene. A set of 156 recombinant inbred lines (RILs) were used to test the veracity for marker-assisted selection (MAS) of flanking molecular markers linked to the B gene. 【Result】Genetic analysis showed that the trait of black fruit spine in NC76 was qualitative, and a single dominant nuclear gene (B) controlled this trait. Black was dominant to white. In the primary genetic mapping of the B gene, eight SSR markers were screened to be linked with the black fruit spine color locus. The B gene was mapped on the chromosome 4 (Chr.4) of cucumber. The closest linked marker SSR22231 was 10.8 cM away from B. A total of 212 pairs of new SSR primer and 25 pairs of Indel primer were developed based on the sequence information in the primary mapping region of B. Fourteen SSR markers and one Indel marker were identified to be linked with the B gene after analysis of the F2 mapping population using these new developed molecular markers. The two closest flanking markers SSRB-181 and SSRB-130 were 2.0 and 1.6 cM away from B, respectively. The physical distance between SSRB-181 and SSRB-130 was 422.1Kb containing 60 predicted genes. Csa4G003095 and Csa4G001690 were the most possible candidate genes for the black fruit spine trait. The probability of the two flanking SSR markers to predict the spine color for marker-assisted selection (MAS) breeding was 96.8% and 96.2%, respectively. And the accuracy rate for SSRB-181 to predict the black spine color in MAS breeding was 100%.【Conclusion】The black fruit spine trait of NC76 is controlled by one dominant nuclear gene (B). It is located on the Chr.4 of cucumber delimited in a physical distance of 422.1 Kb. The two closest flanking markers SSRB-181 and SSRB-130 could be used in the MAS breeding program. The results in this study will be of great benefit to fine mapping and gene cloning for the B gene and lay a good foundation for cucumber MAS breeding.

Key words: Cucumis sativus L., black fruit spine, molecular mapping, SSR marker, candidate gene

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