Scientia Agricultura Sinica ›› 2014, Vol. 47 ›› Issue (10): 1985-1994.doi: 10.3864/j.issn.0578-1752.2014.10.012

• HORTICULTURE • Previous Articles     Next Articles

Genome-wide Identification and Expression Analysis of Auxin Response Factor (ARF) Family in Cucumber

 SHENG  Hui-1, 2 , QIN  Zhi-Wei-1, LI  Wen-Bin-3, ZHOU  Xiu-Yan-1, WU  Tao-1, XIN  Ming-1   

  1. 1、College of Horticulture, Northeast Agricultural University/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in Northeast China, Ministry of Agriculture, Harbin 150030;
    2、Harbin Academy of Agricultural Sciences,  Harbin 150029;
    3、College of Agriculture, Northeast Agricultural University, Harbin 150030
  • Received:2013-10-16 Online:2014-05-20 Published:2014-03-15

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Abstract: 【Objective】 The objective of this study is to identify the cucumber auxin response factor (ARF), forecast the small RNAs and verify the relationship between ARF with small RNAs and auxin. The expression pattern of ARF during seed germination was analyzed and the effect of ARF on the process of parthenocarpy and seed germination was deduced. 【Method】 The Arabidopsis and rice ARF proteins were used to search the cucumber genome database. Then, the retrieved cucumber ARF family structure was analyzed and the small RNAs were predicted. The predicted gma-MIR160o precursur was built into the pCAMBIA2301. By Agrobacterium-mediated method, it was imported into parthenocarpy cucumber varieties. Transgenic plants were validated by RT-PCR. Using real-time RT-PCR method, the expression patterns of ARF were analyzed in auxin treatment, flowing and seed germination. 【Result】 By comparison with the Arabidopsis and rice ARF protein sequences, there are 18 cucumber ARF protein sequences. ARF proteins were divided into four classes. The number of exons varied from 2 to 18, and the structure was similar among the same class. Phylogenetic tree showed that the similarity of 18 genes was not high. Small RNAs corresponds to ARF genes in cucumber were found. Csa010564, Csa011935, Csa015176, Csa020560 and Csa022361 were miR160 targets. Transgenic test further exhibited mRNA abundance of Csa010564, Csa011935 and Csa015176 decreased, while Csa020560 and Csa022361 rose slightly, indicating that Csa010564, Csa011935 and Csa015176 were miR160 targets. The results of real-time RT-PCR exhibited that mRNA abundance of Csa007296, Csa011935 and Csa015176 in roots, stems and leaves were higher than wild type, indicating the expressions of these genes were positively regulated by auxin. Meanwhile, the expressions in leaves and female flowers were decreased on the second flowering day, while the expression of the ovary was the opposite, especially Csa011935 and Csa015176, indicating that ARF genes play a crucial role in the development of the ovary. In the experiment of the auxin treatment, the expressions in different tissues were up-regulated. The expression of ARF genes in the seed germination was analyzed. The results showed that the expression peak of most genes were 12 h and 48 h in imbibition. 【Conclusion】 The ARF genes were regulated by auxin and the corresponding small RNAs. ARF genes may play a key role in the parthenocarpy and seed germination of cucumber .

Key words: cucumber , ARF , small RNAs , auxin , expression patterns

[1]Lee D J, Park J W, Lee H W, Kim J. Genome-wide analysis of the auxin-responsive transcriptome downstream of iaa1 and its expression analysis reveal the diversity and complexity of auxin-regulated gene expression. Journal of Experimental Botany, 2009, 60(13): 3935-3957.

[2]苏绍坤, 刘宏宇, 秦智伟. 农杆菌介导iaaM基因黄瓜遗传转化体系的建立. 东北农业大学学报，2006, 37(3): 289-293

Su S K, Liu H Y, Qin Z W. Establishment of genetic transformation system by Agrobacterium-mediated parthenocarpy gene of cucumber. Journal of Northeast Agricultural University, 2006, 37(3): 289-293. (in Chinese)

[3]Abel S, Theologis A. Early genes and auxin action. Plant Physiology, 1996, 111: 9-17.

[4]Guilfoyle T, Hagen G, Ulmasov T, Murfett J. How does auxin turn on genes? Plant Physiology, 1998, 118: 341-347.

[5]Chapman E J, Greenham K, Castillejo C, Sartor R, Bialy A, Sun T P, Estelle M. Hypocotyl transcriptome reveals auxin regulation of growth-promoting genes through GA-dependent and independent pathways. PLoS ONE, 2012, 7(5): e36210.

[6]王垒, 陈劲枫, 娄丽娜, 娄群峰. 黄瓜ARF 家族序列特征及部分成员在果实发育早期的表达分析. 园艺学报, 2011, 38(4): 717-724.

Wang L, Chen J F, Lou L N, Lou Q F. Sequence characteristics of ARF gene family of cucumber and an expression analysis of some members during early development of fruits. Acta Horticulturae Sinica, 2011, 38(4): 717-724. (in Chinese)

[7]王飞燕, 吴健, 张佳景, 程琳, 孔福苓, 彭真, 卢钢. 番茄生长素应答因子SlARF8‐1 的分离与SlARFs 表达特征分析. 浙江大学学报: 农业与生命科学版, 2011, 37(3): 237-244.

Wang F Y, Wu J, Zhang J J, Cheng L, Kong F L, Peng Z, Lu G. Identification of auxin response factor SlARF8-1 gene and characterization of expression pattern of some SlARFs in Solanum lycopersicum. Journal of Zhejiang University: Agricultural and Life Edition, 2011, 37(3): 237-244. (in Chinese)

[8]Shin R, Burch A Y, Huppert K A, Tiwari S B, Murphy A S, Guilfoyle T J, Schachtman D P. The Arabidopsis transcription factor MYB77 modulates auxin signal transduction. The Plant Cell, 2007, 19: 2440-2453.

[9]Okushima Y, Overvoorde P J, Arima K, Alonso J M, Chan A, Chang C, Ecker J R, Hughes B, Lui,A, Nguyen D, Onodera C, Quach H, Smith A, Yu G X, Theologisa A. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: Unique and Overlapping Functions of ARF7 and ARF19. Plant Cell, 2005, 17: 444-463.

[10]Xing H Y, Pudake R N, Guo G G, Xing G F, Hu Z R, Zhang Y R, Sun Q X, Ni Z F. Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize. BMC Genomics, 2011, 12:178.

[11]陈哲皓，鲍林文，王利琳. 黄瓜生长素受体同源基因的克隆、序列特征及表达模式分析. 农业生物技术学报, 2013, 21(8): 931-939.

Chen Z H, Bao L W, Wang L L. Cloning of homologous auxin receptor genes in cucumber (Cucumis sativus L.), and analysis of their sequence characteristics and expression patterns. Journal of Agricultural Biotechnology, 2013, 21(8): 931-939. (in Chinese)

[12]冯媛媛, 李颖楠, 侯佩, 张景荣, 汪松虎, 刘永胜. 番茄ARF4基因果实特异RNAi载体的构建及遗传转化. 应用与环境生物学报, 2012, 18(2): 206-211.

Feng Y Y, Li Y N, Hou P, Zhang J R, Wang S H, Liu Y S. Construction and genetic transformation of tomato ARF4 RNA interference expression vector with fruit specific promoter. Chinese Journal of Applied Environmental Biology, 2012, 18(2): 206-211. (in Chinese)

[13]Mallory A C, Bartel D P, Bartelc B. MicroRNA-directed Regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. The Plant Cell, 2005, 17: 1360-1375.

[14]盛慧. DREB2A、SCMRP基因双价植物表达载体的构建及对苜蓿的遗传转化[D]. 哈尔滨: 东北农业大学, 2006.

Sheng hui. Construction of plant expressive vectors of DREB2A、SCMRP gene and genetic transformation into Alfalfa. Harbin: Northeast Agricultural University, 2006. ( in Chinese)

[15]闫立英, 娄丽娜, 冯志红, 娄群峰, 李晓丽, 陈劲枫. 不同生态环境下雌雄同株黄瓜单性结实性遗传的比较. 应用生态学报, 2010, 21(1): 61-66.

Yan L Y, Lou L N, Feng Z H, Lou Q F, Li X L, Chen J F. Inheritance of parthenocarpy in monoecious cucumber (Cucumis sativus L.) under different eco-environments. Chinese Journal of Applied Ecology, 2010, 21(1): 61-66. (in Chinese)

[16]王垒, 娄丽娜, 闫立英, 娄群峰, 陈劲枫. 黄瓜果实发育早期Aux/IAA家族部分基因的差异表达分析. 南京农业大学学报，2011, 34(4): 13-17.

Wang L, Lou L N, Yan L Y, Lou Q F, Chen J F. Adifferential expression analysis of some Aux/IAA family genes in cucumber fruit during the early development. Journal of Nanjing Agricultural University, 2011, 34(4): 13-17. (in Chinese)

[17]刘世琦, 邢禹贤, 王冰林. 外源激素诱导西瓜单性结实的研究. 中国农业科学, 2003, 36(9): 1071-1075.

Liu S Q，Xing Y X，Wang B L. Study on exogenous hormone inducing parthenocarpy of watermelon. Scientia Agricultura Sinica, 2003, 36(9): 1071 -1075. (in Chinese)

[18]Dorcey E, Urbez C, Blázquez M A., Carbonell J, Perez-Amador M A. Fertilization-dependent auxin response in ovules triggers fruit development through the modulation of gibberellin metabolism in Arabidopsis. The Plant Journal, 2009, 58: 318-332.

[19]Goetz M，Vivian-Smith A，Johnson S D，Koltunow A M. Auxin response factor 8 is a negative regulator of fruit initiation in Arabidopsis. The Plant Cell, 2006, 18: 1873-1886.

[20]Jong M, Wolters-Arts M , Feron R, Mariani C，Vriezen W H. The Solanum lycopersicum auxin response factor 7（SlARF7）regulates auxin signaling during tomato fruit set and development. The Plant Journal, 2009, 57: 160-170.

[21]Woodward A W, Bartel B. A receptor for auxin. Plant Cell, 2005, 17: 2425-2429.

[22]Guilfoyle T. Plant biology: sticking with auxin. Nature, 2007, 446: 621-622.

[23]Ulmasov T, Hagen G, Guilfoyle T J. Activation and repression of transcription by auxin response factors. Proceedings of the National Academy of Sciences USA, 1999, 96: 5844-5849.

[24]Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voinnet O, Jones J D G. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science, 2006, 312: 436-439.

[25]Vernoux T, Brunoud G, Farcot E, Morin V, Daele H V, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc’h S, Cellier C, Parry G, Koumproglou R, Doonan J H, Estelle M, Godin C, Kepinski S, Bennett M, Veylder L D, Traas J. The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Molecular Systems Biology, 2011, 7: 508.

[26]Nemhauser J L, Mockler T C, Chory J. Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biology, 2004, 2(9): e258.

[27]Goda H, Sawa S, Asami T, Fujioka S, Shimada Y, Yoshida S. Comprehensive comparison of auxin-regulated and brassinosteroid- regulated genes in Arabidopsis. Plant Physiology, 2004, 134: 1555-1573.

[28]王垒, 陈劲枫, 娄丽娜, 娄群峰, 贾利. 黄瓜果实中ARF和Aux/IAA基因对外源激素的应答. 西北植物学报, 2011, 31(6): 1127-1131.

Wang L , Chen J F, Lou L N, Lou Q F, Jia L. Expression analysis about some ARF an d Aux/ IAA family members in fruits of cucumber with exogenous hormones. Acta Botanica Boreali-Occidentalia Sinica, 2011, 31(6): 1127-1131. (in Chinese)

[29]皮冬梅, 刘悦萍. 植物生长素受体蛋白研究现状. 生物技术通报, 2011(6): 7-11.

Pi D M, Liu Y P. Plant auxin receptor proteins research status. Biotechnology Bulletin, 2011(6): 7-11. (in Chinese)

[30]史梦雅, 李阳, 张巍, 刘悦萍. 生长素反应因子作用机制研究进展. 生物技术通报, 2012(8): 24-28.

Shi M Y, Li Y, Zhang W, Liu Y P. Progress in mechanism of auxin response factors. Biotechnology Bulletin, 2012(8): 24-28. (in Chinese)

[31]江海洋, 魏巍, 刘艳, 朱苏文, 程备久. 高粱生长素反应因子(ARF)基因的全基因组分析与进化研究. 安徽农业大学学报, 2010, 37(3): 395-400.

Jiang H Y, Wei W, Liu Y, Zhu S W, Cheng B J. Genome - wide analysis and evolution of the auxin response factor ( ARF ) gene family in Sorghum bicolor. Journal of Anhui Agricultural University, 2010, 37(3): 395-400. (in Chinese)

[32]Audran-Delalande C, Bassa C, Mila I, Regad F, Zouine M, Bouzayen M. Genome-Wide identification, functional analysis and expression profiling of the Aux/IAA gene family in tomato. Plant Cell Physiology, 2012, 53(4): 659-672.
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