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

[1]张文珠, 李加旺, 王疆. 日光温室黄瓜新品种津优35号的选育. 中国蔬菜, 2007 (12): 33-35.

Zhang W Z，Li J W，Wang J. A new cucumber F1 hybrid - Jinyou 35. China Vegetables，2007(12):33-35. (in Chinese)

[2]顾兴芳, 张圣平, 王烨, 徐彩清, 苗晗, 郑启功. 日光温室黄瓜新品种‘中农27号’. 园艺学报, 2012, 39(4): 809-810.

Gu X F, Zhang S P, Wang Y, Xu C Q, Miao H, Zhang Q G. A new cucumber hybrid ‘Zhongnong 27’ for solar greenhouse. Acta Horticulturae Sinica, 2012, 39(4): 809-810. (in Chinese)

[3]孟焕文, 程智慧.黄瓜新品种‘农城新玉 1 号’. 园艺学报, 2012, 39(5): 1009-1010.

Meng H W, Cheng Z H. A new cucumber cultivar ‘Nongcheng Xinyu 1’. Acta Horticulturae Sinica, 2012, 39(5): 1009-1010. (in Chinese)

[4]Wellington R. Mendelian inheritance of epidermal characters in the fruit of Cucumis sativus L. Science, 1913, 38: 61-64.

[5]Strong W J. Breeding experiments with the cucumber (Cucumis sativus L.). Scientia Agricola, 1931, 11:333-346. 

[6]Tkachenko N N. Preliminary results of a genetic investigation of the cucumber, Cucumis sativus L. Bul. Applied Plant Breeding, Ser. 2, 1935, 9: 311-356. 

[7]Shanmugasundarum S, Williams P H, Peterson C E. Inheritance of fruit spine color in cucumber. HortScience, 1971, 6: 213-214. 

[8]Cowen N M, Helsel D B. Inheritance of 2 genes for spine color and linkages in a cucumber cross. Journal of Heredity, 1983, 74: 308-310. 

[9]Kennard W C, Poetter K, Dijkhuizen A, Meglic V, Staub J E, Havev J. Linkage among RFLP, RAPD, isozyme, disease-resistance and morphological markers in narrow and wide crosses of cucumber. Theoretical and Applied Genetics, 1994, 89: 42-48.

[10]Heang D, Sato H, Sassa H, Koba T. Detection of two QTLs for fruit weight in cucumber (Cucumis sativus L.). Proc 9th  EUCARPIA 8 Meeting in Genetics and Breeding of Cucurbitaceae. Inra, Avignon, France, 2008: 511-514.

[11]苗晗, 顾兴芳, 张圣平, 张忠华, 黄三文, 王烨, 程周超, 张若纬, 穆生奇, 李曼, 张振贤, 方智远. 黄瓜果实相关性状QTL定位分析.中国农业科学, 2011, 44(24): 5031-5040.

Miao H, Gu X F, Zhang S P, Zhang Z H, Huang S W, Wang Y, Cheng Z C, Zhang R W, Mu S Q, Li M, Zhang Z X, Fang Z Y. Mapping QTLs for fruit-associated traits in Cucumis sativus L. Scientia Agricultura Sinica, 2011, 44(24): 5031-5040. (in Chinese)

[12]Ren Y, Zhang Z H, Liu J H, Staub J E, Han Y H, Cheng Z H, Li X F, Miao H, Kang H X, Xie B Y, Gu X F, Wang X W, Du Y C, Jin W W, Huang S W. An integrated genetic and cytogenetic map of the cucumber genome. Plos One, 2009, 4(6): e5795.

[13]Zhang W W, Pan J S, He H L, Zhang C, Li Z, Zhao J L, Yuan G, Yuan X J, Zhu L H, Huang S W, Cai R. Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.). Theoretical and Applied Genetics, 2012, 124: 249-259.

[14]张圣平,苗晗,程周超,张忠华,武剑,孙日飞,顾兴芳. 黄瓜果实苦味（Bt）基因的插入缺失（Indel）标记. 农业生物技术学报,2011,19(4) : 649-653.

Zhang S P, Miao H, Cheng Z C, Zhang Z H, Wu J, Sun R F, Gu X F. The insertion-deletion (Indel) marker linked to the fruit bitterness gene(Bt) in cucumber. Journal of Agricultural Biotechnology, 2011, 19(4): 649-653.(in Chinese)

[15]Miao H, Zhang S P, Wang X W, Zhang Z H, Li M, Mu S Q, Cheng Z C, Zhang R W, Huang S W, Xie B Y, Fang Z Y, Zhang Z X, Weng Y Q, Gu X F. A linkage map of cultivated cucumber (Cucumis sativus L.) with 248 microsatellite marker loci and seven genes for horticulturally important traits. Euphytica, 2011, 182:167-176.

[16]Cavagnaro P F, Senalik D A, Yang L M, Simon P P, Harkins T T, Kodira C D, Huang S W, Weng Y Q. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics, 2010, 11: 569-587.

[17]Weng Y Q, Johnson V, Staub J E, Huang S W. An extended microsatellite genetic map of cucumber, Cucumis sativus L. HortScience, 2010, 45:880-886.

[18]Zhang W W, He H, Yuan G, Du H, Yuan L H, Li Z, Yao D Q, Pan J S, Cai R. Identification and mapping of molecular markers linked to the tuberculate fruit gene in the cucumber (Cucumis sativus L.). Theoretical and Applied Genetics, 2010, 120(3):645-654.

[19]Bo K L, Song H, Shen J, Qian C T, Staub J E, Simon P W, Lou Q F, Chen J F. Inheritance and mapping of the ore gene controlling the quantity of b-carotene in cucumber (Cucumis sativus L.). Molecular Breeding, 2012, 30: 335-344.

[20]Zhang S P, Miao H, Gu X F ,Yang Y H, Xie B Y, Wang X W, Huang S W, Du Y C, Sun R F, Wehner T C. Genetic mapping of the scab resistance gene (Ccu) in cucumber (Cucumis sativus L.).  Journal of the Society for Horticultural Science, 2010, 135(1):53-58.

[21]Zhang S P, Liu M M, Miao H, Zhang S Q, Yang Y H, Xie B Y, Wehner T C, Gu X F. Chromosomal mapping and QTL analysis of resistance to downy mildew in Cucumis sativus L.. Plant Disease, 2013, 97(2): 245-251.

[22]Zhang S P, Miao H, Sun R F, Wang X W, Huang S W, Wehner T C, Gu X F. Localization of a new gene for bitterness in cucumber. Journal of Heredity, 2013, 104(1): 134-139 .

[23]董邵云, 苗晗, 张圣平, 刘苗苗, 王 晔, 顾兴芳. 黄瓜白色果皮基因遗传规律及定位研究. 西北植物学报, 2012, 32(11):2177-2181.

Dong S Y, Miao H, Zhang S P, Liu M M, Wang Y, Gu X F. Genetic analysis and gene mapping of white fruit skin in cucumber (Cucumis sativus L.). Acta Botanica Boreali-Occidentalia Sinica, 2012, 32(11): 2177-2181. (in Chinese)

[24]Li Y H, Yang L M, Pathak M, Li D W, He X M, Weng Y Q. Fine genetic mapping of cp, a recessive gene for compact (dwarf) plant architecture in cucumber, Cucumis sativus L. Theoretical and Applied Genetics, 2011, 123(6): 973-983.

[25]Kang H X, Weng Y Q, Yang Y H, Zhang Z H, Zhang S P, Mao Z C, Cheng G H, Gu X F, Huang S W, Xie B Y. Fine genetic mapping localizes cucumber scab resistance gene(Ccu) into an R gene cluster. Theoretical and Applied Genetics, 2010, 122(4): 795-803.

[26]南海洋, 李英慧, 常汝镇, 邱丽娟. 基于大豆胞囊线虫病抗性候选基因rhg1的InDel标记的开发与鉴定. 作物学报, 2009, 35(7):1236-1243.

Nan H Y, Li Y H, Chang R Z, Qiu L J. Development and idenfication of InDel marker based on candidate gene rhg1 for resistance to soybean cystnematode. Acta Agronomica Sinica, 2009, 35(7): 1236-1243. (in Chinese)

[27]马玉银, 李磊, 李育红, 左示敏, 殷跃军, 张亚芳, 陈宗祥, 潘学彪. 一个新的水稻隐性高秆突变体的遗传分析和基因定位. 中国农业科学, 2008, 41(12): 3967-3973.

Ma Y Y, Li L, Li Y H, Zuo S M, Yin Y J, Zang Y F, Chen Z X, and Pan X B. Genetic analysis and gene mapping of a new recessive long-culm mutant in rice. Scientia Agricultura Sinica, 2008, 41(12): 3967-3973. (in Chinese)

[28]Singh K B. Transcriptional regulation in plants: the importance of combinational control. Plant Physiology, 1998, 118: 1111-1120.

[29]Ledent V, Vervoot M. The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Research, 2001, 11:754-770.

[30]Smith T F, Gaitatzes C, Saxena K, Neer E J. The WD repeat: a common architecture for diverse functions. Trends in Biochemical Sciences, 1999, 24(5):181-185.

[31]Madrona A Y, Wilson D K. The structure of Ski8p, a protein regulating mRNA degradation: implications for WD protein structure. Protein Science, 2004, 13(6):1557-1565.

[32]Neer E J, Schmidt C J, Nambudripad R, Smith T F. The ancient regulatory-protein family of WD-repeat proteins. Nature, 1994, 371: 297-300.
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