|本期目录/Table of Contents|

[1]刘蒲东,张舒婷,陈晓慧,等.龙眼GRF家族全基因组鉴定及表达模式[J].应用与环境生物学报,2020,26(02):236-245.[doi:10.19675/j.cnki.1006-687x.2019.06028]
 LIU Pudong,ZHANG Shuting,CHEN Xiaohui,et al.Genomic identification and expression patterns of the longan GRF family[J].Chinese Journal of Applied & Environmental Biology,2020,26(02):236-245.[doi:10.19675/j.cnki.1006-687x.2019.06028]
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龙眼GRF家族全基因组鉴定及表达模式
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《应用与环境生物学报》[ISSN:1006-687X/CN:51-1482/Q]

卷:
26卷
期数:
2020年02期
页码:
236-245
栏目:
研究论文
出版日期:
2020-04-25

文章信息/Info

Title:
Genomic identification and expression patterns of the longan GRF family
作者:
刘蒲东张舒婷陈晓慧苏立遥姚德恒李汉生张梓浩陈裕坤林玉玲赖钟雄
福建农林大学园艺植物生物工程研究所 福州 350002
Author(s):
LIU Pudong ZHANG Shuting CHEN Xiaohui SU Liyao YAO Deheng LI Hansheng ZHANG Zihao CHEN Yukun LIN Yuling & LAI Zhongxiong?
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
关键词:
龙眼生长调节因子(GRF)成员鉴定光质激素实时荧光定量PCR
Keywords:
Dimocarpus longan Lour. growth regulating factor (GRF) member identification light quality hormone qRT-PCR
DOI:
10.19675/j.cnki.1006-687x.2019.06028
摘要:
生长调节因子(growth regulating factor,GRF)是植物体内特有的一种转录因子,在植物生长发育、渗透胁迫中发挥重要的作用. 基于龙眼基因组和转录组数据,采用生物信息学分析的方法对龙眼GRF(DlGRF)家族成员进行鉴定命名;分析其基本理化性质、基因结构、蛋白结构域、启动子序列顺式作用元件;构建系统进化树、预测可能直接调控DlGRF的miRNAs;分析DlGRF家族在龙眼非胚性及胚性培养物、组织器官、光质与激素处理下的表达水平;采用实时荧光定量PCR(qRT-PCR)检测DlGRF的表达模式. 结果显示,龙眼DlGRF家族包含9个成员,均含有QLQ和WRC保守结构域;包含2-5个外显子,以3个为主;分布于四大分支上,与甜橙、拟南芥GRF亲缘关系较近;DlGRF蛋白包含7个motif;启动子序列中包含众多光响应、激素应答、厌氧感应、胁迫响应及其他与生长发育相关的作用元件. 转录组结果显示,DlGRF家族8个成员在球形胚阶段表达量高于其他阶段;各成员均在种子中有较高表达量,对蓝、白光及激素响应明显. qRT-PCR结果显示,DlGRF1-2、DlGRF2-1、DlGRF2-2、DlGRF4、DlGRF5-1及DlGRF7在球形胚阶段表达量最高;DlGRF1-1、DlGRF1-2、DlGRF2-2及DlGRF5-2在脱落酸(ABA)、茉莉酸甲酯(MeJA)和赤霉素(GA3)等激素处理中表达上调. 此外,DlGRF可能受miR396a调控,调控方式为裂解靶标. 本研究表明DlGRF在进化过程中保守性较高,且可能受到蓝光和激素的诱导,参与龙眼非胚性及胚性培养物尤其是球形胚及种子发育形成的过程. (图6 表3 参42)
Abstract:
Growth regulating factor (GRF), a specific transcription factor in plants, plays an important role in plant growth and osmotic stress responses. Based on the longan genome and transcriptome dataset, this study used bioinformatics and quantitative real-time polymerase chain reaction (qRT-PCR) analyses to identify Dimocarpus longan Lour. GRF (DlGRF) family members. Firstly, we analyzed the basic physicochemical properties, gene structure, protein domain, and cis-acting elements of the promoter sequence. Then, we constructed a phylogenetic tree and predicted miRNAs that may directly regulate the DlGRF genes. In addition, we used the transcriptome dataset to analyze the expression levels of the DlGRF gene family in longan non-embryonic and embryogenic cultures, different tissues, different light conditions, and phytohormone treatments. qRT-PCR analysis was also used to detect the expression patterns of DlGRF family members in non-embryonic and embryogenic cultures and different phytohormone treatments. The results showed that the DlGRF family contains 9 members, which contain QLQ and WRC conservative structural domains. The DlGRF family members contained two to five exons and mainly contained three exons. The DlGRF protein contained 7 conservative motifs. The phylogenetic tree analysis found that the DlGRF family distributed among four branches and they were genetically close to Citrus sinensis and Arabidopsis thaliana. The cis-acting element analysis found that the DlGRF family presented massive light response, hormone response, anaerobic induction, stress response, and growth-related elements. An expression pattern analysis (FPKM values) revealed that eight members of the DlGRF family showed the highest expression levels in the global embryo (GE) stage. Additionally, the DlGRF genes were significantly expressed in seeds, and they also responded to light and phytohormone treatments. The qRT-PCR results showed that DlGRF1-2, DlGRF2-1, DlGRF2-2, DlGRF4, DlGRF5-1, and DlGRF7 had the highest expression levels in the GE stage. The expression levels of DlGRF1-1, DlGRF1-2, DlGRF2-2, and DlGRF5-2 were upregulated in the ABA, MeJA, and GA3 treatments. In addition, miR396a may regulate DlGRFs by cleaving their mRNAs. This study indicated that DlGRF is highly conserved in the evolutionary process and may be induced by either blue light or phytohormones, thus these genes may participate in the formation and development of non-embryogenic and embryogenic longan cultures, especially in seeds and during the GE stage.

参考文献/References:

1 Kim JH, Kende H. A transcriptional coactivator, AtGIF1, is involved in regulating leaf growth and morphology in Arabidopsis [J]. PNAS, 2004, 101 (36): 13374-13379
2 Kim JH, Choi D, Kende H. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis [J]. Plant J, 2003, 36 (1): 94-104
3 Van der Knaap E, Kim JH, Kende H. A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth [J]. Plant Physiol, 2000, 122 (3): 695-704
4 Choi D, Kim J H, Kende H. Whole genome analysis of the OsGRF gene family encoding plant-specific putative transcription activators in rice (Oryza sativa L.) [J]. Plant Cell Physiol, 2004, 45 (7): 897-904
5 Zhang D, Li B, Jia G. Isolation and characterization of genes encoding GRF transcription factors and GIF transcriptional coactivators in maize (Zea mays L.) [J]. Plant Sci, 2008, 175 (6): 809-817
6 刘倩, 王凤德, 张一卉, 邱念伟, 高建伟. 植物生长调控因子研究进展[J]. 植物生理学报, 2015, 51 (11): 1775-1779 [Liu Q , Wang FD, Zhang YH, Qiu NW, Gao JW. Progress in research on plant growth regulatory factors [J]. Plant Physiol, 2015, 51 (11): 1775-1779]
7 马超, 原佳乐, 张苏, 贾琦石, 冯雅岚. GRF转录因子对植物生长发育及胁迫响应调控的分子机制[J]. 核农学报, 2017, 31 (11): 2145-2153 [Ma C, Yuan JL, Zhang S, Jia QS, Feng YL. Molecular mechanism of GRF transcription factors in response to plant growth and stress [J]. J Nucl Agr Sci, 2017, 31 (11): 2145-2153]
8 Zhou HJ, Wei KL, Jiang C, Zhao YQ, Song XQ, Lu MZ. Negative regulation of GRF1/2d on the formation and development of adventitious roots in Populus alba × P. glandulosa ‘84K’ [J]. Sci Silv Sin, 2017, 53 (3): 33-39
9 袁岐, 张春利, 赵婷婷, 许向阳. 植物中GRF转录因子的研究进展[J]. 基因组学与应用生物学, 2017, 36 (8): 3145-3151 [Yuan Q, Zhang CL, Zhao TT, Xu XY. Advances in GRF transcription factors in plants [J]. Genom Appl Biol, 2017, 36 (8): 3145-3151]
10 阮先乐, 王俊生, 刘红占, 赵锦慧. 油菜GRF基因家族的鉴定和基本特征分析[J]. 分子植物育种, 2018, 16 (8): 2420-2428 [Ruan X L, Wang JS, Liu HZ, Zhao JH. Identification and analysis of GRF gene family in rape [J]. Mol Plant Breed, 2018, 16 (8): 2420-2428]
11 曹珂, 薛灵姿, 王蛟, 方伟超, 朱更瑞, 陈昌文, 王新卫, 王力荣. 桃GRF基因家族的序列及其组织特异性表达分析[J]. 植物遗传资源学报, 2018, 19 (3): 578-586 [Cao K, Xue LZ, Wang J, Fang WC, Chen CW, Wang XW, Wang LR. Sequence and tissue specific expression analysis of GRF gene family in peach [J]. J Plant Genet Resour, 2018, 19 (3): 578-586]
12 Liang G, He H, Li Y. Molecular mechanism of microRNA396 mediating pistil development in Arabidopsis [J]. Plant Physiol, 2014, 164 (1): 249-258
13 袁岐, 张春利, 赵婷婷, 许向阳. 番茄GRF转录因子家族的生物信息学分析[J]. 分子植物育种, 2017, 15 (8): 2949-2956 [Yuan Q, Zhang CL, Zhao TT, Xu XY. Bioinformatics analysis of GRF transcription factor family in tomato [J]. Mol Plant Breed, 2017, 15 (8): 2949-2956]
14 Horiguchi G, Kim G, Tsukaya H. The transcription factor AtGRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana [J]. Plant J, 2005, 43 (1): 68-78
15 Kim JH, Lee BH. Growth-regulating factor4 of Arabidopsis thaliana is required for development of leaves, cotyledons, and shoot apical meristem [J]. J Plant Biol, 2006, 49 (6): 463
16 Liu J, Hua W, Yang H. The BnGRF2 gene (GRF2-like gene from Brassica napus) enhances seed oil production through regulating cell number and plant photosynthesis [J]. J Exp Bot, 2012, 63 (10): 3727-3740
17 Debernardi JM, Mecchia MA, Vercruyssen L. Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity [J]. Plant J, 2014, 79 (3): 413-426
18 Kuijt SJH, Greco R, Agalou A. Interaction between the growth-regulating factor and knotted1-like homeobox families of transcription factors [J]. Plant Physiol, 2014, 164 (4): 1952-1966
19 Duan P, Ni S, Wang J. Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice [J]. Nat Plants, 2015, 2 (1): 15203
20 Li S, Gao F, Xie K. The OsmiR396c-OsGRF4-OsGIF1 regulatory module determines grain size and yield in rice [J]. Plant Biotechnol J, 2016, 14 (11): 2134-2146
21 Sun P, Zhang W, Wang Y. OsGRF4 controls grain shape, panicle length and seed shattering in rice [J]. J Integr Plant Biol, 2016, 58 (10): 836-847
22 Cao D, Wang J, Ju Z. Regulations on growth and development in tomato cotyledon, flower and fruit via destruction of miR396 with short tandem target mimic [J]. Plant Sci, 2016, 247: 1-12
23 Vercruyssen L, Tognetti V B, Gonzalez N. Growth-regulating factor5 stimulates Arabidopsis chloroplast division, photosynthesis, and leaf longevity [J]. Plant Physiol, 2015, 167 (3): 817-832
24 张晓卫, 曹蔚, 王玉琨, 王四旺. 龙眼的化学成分及药理作用研究进展[J]. 西北药学杂志, 2012, 27 (5): 493-496 [Zhang XW, Cao W, Wang YK, Wang SW. Study of the progress on chemical constituents and pharmacological activities of longan [J]. NW Pharm J, 2012, 27 (5): 493-496
25 陈晓慧, 白玉, 李汉生, 陈旭, 林玉玲, 赖钟雄. 龙眼DCL家族基因的启动子分析及时空表达[J]. 西北植物学报, 2017, 37 (10): 1926-1933 [Chen XH, Bai Y, Li HS, Chen X, Lin YL, Lai ZX. Promoter analysis and spatio-temporal expression of DCL family genes in longan [J]. Acta Bot Sin NW, 2017, 37 (10): 1926-1933]
26 Lin YL, Min JM, Lai RL, Wu ZY, Chen YK, Yu LL, Cheng CZ, Jin YC, Tian QL, Hu Y, Zhang DM, Minkyaw Thu, Zhang ZH, Liu SC, Zhong CS, Fang XD, Wang J, Yang HM, Varshney RK, Yin Y, Lai ZX. Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics [J]. Giga Sci, 2017, 6 (5): 1-14
27 徐小萍, 陈晓慧, 吕科良, 陈旭, 陈裕坤, 林玉玲, 赖钟雄. 龙眼漆酶家族成员全基因组结构与功能分析[J]. 应用与环境生物学报, 2018, 24 (4): 833-844 [Xu XP, Chen XH, Lü KL, Chen X, Chen YK, Lin YL, Lai ZX. Analysis of genome-wide structure and function of laccase family members of longan [J]. Chin J Appl Environ Biol, 2018, 24 (4): 833-844]
28 赖钟雄, 潘良镇, 陈振光. 龙眼胚性细胞系的建立与保持[J]. 福建农业大学学报, 1997 (2): 33-40 [Lai ZX, Pan LZ, Chen ZG. Establishment and maintenance of embryogenic cell lines in longan [J]. J Fujian Agric Univ, 1997 (2): 33-40]
29 陈春玲, 赖钟雄. 龙眼胚性愈伤组织体胚发生同步化调控及组织细胞学观察[J]. 福建农林大学学报(自然科学版), 2002 (2): 192-194 [Chen CL, Lai ZX. Synchrony regulation and tissue cytology observation of embryogenic callus in longan [J]. J Fujian A&F Univ (Nat Sci Ed), 2002 (02): 192-194]
30 Lin YL, Lai ZX. Comparative analysis reveals dynamic changes in miRNAs and their targets and expression during somatic embryogenesis in longan (Dimocarpus longan Lour.) [J]. PLoS ONE, 2013, 8 (4): e60337
31 张舒婷, 朱晨, 王培育, 陈旭, 陈晓慧, 白玉, 张梓浩, 陈裕坤, 赖钟雄, 林玉玲. 龙眼miR172家族成员进化特性及其时空表达分析[J]. 果树学报, 2017 (11): 1385-1393 [Zhang ST , Zhu C, Wang PY, Chen X, Chen XH, Zhang ZH, Chen YK, Lin YL, Lai ZX. Evolutionary characteristics and spatio-temporal expression of miR172 family members in longan [J]. J Fruit Sci, 2017 (11): 1385-1393]
32 Li HS, Lyu YM, Chen XH, Wang CQ, Yao DH, Ni SS, Lin YL, Chen YK, Zhang ZH, Lai ZX. Exploration of the effect of blue light on functional metabolite accumulation in longan embryonic calli via RNA sequencing [J]. Int J Mol Sc, 2019, 20 (2): 441
33 Lin YL, Lai ZX. Reference gene selection for qPCR analysis during somatic embryogenesis in longan tree [J]. Plant Sci, 2010, 178 (4): 359-365
34 方智振, 赖钟雄. 龙眼体胚发生中期发育同步化的初步调控[J]. 中国农学通报, 2009 (1): 152-155 [Fang ZZ, Lai ZX. Preliminary regulation of synchrony of somatic embryo development in longan [J]. Chin Agric Sci Bull, 2009 (1): 152-155]
35 Wang FD, Qiu NW, Ding Q, Li JJ, Zhang YH, Li HY. Genome-wide identification and analysis of the growth-regulating factor family in Chinese cabbage (Brassica rapa L. ssp. pekinensis) [J].BMC Genom, 2014, 15: 807
36 何龙燕, 刘武阳, 娄永峰, 肖复明. 毛竹GRF转录因子家族的全基因组鉴定与分析[J]. 植物科学学报, 2018, 36 (5): 713-720 [He LY, Liu WY, Lou YF, Xiao FM. Genome-wide identification and analysis of GRF transcription factor family in bamboo [J]. Acta Bot Sin, 2018, 36 (5): 713-720]
37 张书芹, 乐愉, 武斐. 陆地棉GRF基因家族的鉴定和生物信息学分析[J]. 分子植物育种, 2019, 17 (12): 3817-3824 [Zhang SQ, Le Y, Wu F. Identification and bioinformatics analysis of GRF gene family in upland cotton [J]. Mol Plant Breed, 2019, 17 (12): 3817-3824]
38 王鹏杰, 郑玉成, 林浥, 周珍, 杨江帆, 叶乃兴. 茶树GRF基因家族的全基因组鉴定及表达分析[J]. 西北植物学报, 2019, 39 (3): 413-421 [Wang PJ, Zheng YC, Lin Y, Zhou Z, Yang JF, Ye NX. Genome-wide identification and expression analysis of tea tree GRF gene family [J]. Acta Bot Sin NW, 2019, 39 (3): 413-421]
39 Liu J, Rice JH, Chen N. Synchronization of developmental processes and defense signaling by growth regulating transcription factors [J]. PLoS ONE, 2014, 9 (5): e98477
40 Glazebrook J. Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens [J]. Annu Rev Phytopathol, 2005, 43 (1): 205-227
41 Zhang J, Xue B, Gai M. Small RNA and transcriptome sequencing reveal a potential miRNA-mediated interaction network that functions during somatic embryogenesis in Lilium pumilum DC. Fisch [J]. Front Plant Sci, 2017, 8: 566
42 Liang G, He H, Li Y. Molecular mechanism of microRNA396 mediating pistil development in Arabidopsis [J]. Plant Physiol, 2014, 164 (1): 249-258

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更新日期/Last Update: 2020-04-25