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作物学报 ›› 2019, Vol. 45 ›› Issue (12): 1841-1850.doi: 10.3724/SP.J.1006.2019.94049

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

藜麦GRF转录因子家族的鉴定及表达分析

时丕彪1,何冰2,费月跃1,王军1,王伟义1,魏福友1,吕远大2,顾闽峰1,*()   

  1. 1 盐城市新洋农业试验站, 江苏盐城 224049
    2 江苏省农业科学院种质资源与生物技术研究所, 江苏南京 210014
  • 收稿日期:2019-03-22 接受日期:2019-06-22 出版日期:2019-12-12 网络出版日期:2019-07-13
  • 通讯作者: 顾闽峰
  • 作者简介:时丕彪, E-mail: 1032175660@qq.com
  • 基金资助:
    本研究由江苏现代农业(蔬菜)产业技术体系(盐城)推广示范基地项目(JATS(2018)137);江苏省农业科学院探索性颠覆性创新计划项目(ZX(17)2015)

Identification and expression analysis of GRF transcription factor family of Chenopodium quinoa

Pi-Biao SHI1,Bing HE2,Yue-Yue FEI1,Jun WANG1,Wei-Yi WANG1,Fu-You WEI1,Yuan-Da LYU2,Min-Feng GU1,*()   

  1. 1 Xinyang Agricultural Experiment Station of Yancheng City, Yancheng 224049, Jiangsu, China
    2 Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
  • Received:2019-03-22 Accepted:2019-06-22 Published:2019-12-12 Published online:2019-07-13
  • Contact: Min-Feng GU
  • Supported by:
    This study was supported by the Promotion Demonstration Base Program (Yancheng) of Jiangsu Modern Agriculture (Vegetable) Industry Technology System(JATS(2018)137);Exploratory and Disruptive Innovation Program of Jiangsu Academy of Agricultural Sciences(ZX(17)2015)

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摘要：

生长调控因子(growth-regulating factor, GRF)是植物特有的一类转录因子, 对植物的生长发育起重要的调控作用。藜麦是一种单体植物即可满足人体基本营养需求的食物, 也是未来最具潜力的农作物之一。但是关于藜麦GRF基因家族的研究至今尚缺乏报道。因此, 本研究利用生物信息学方法, 对藜麦GRF基因进行全基因组鉴定, 并对其理化性质、基因结构、保守结构域、系统发育关系及组织表达进行分析。结果表明, 藜麦中共有18个GRF转录因子, 蛋白长度77~621 aa, 分子量8.81~67.38 kD, 等电点5.23~9.37; 每个成员含有1~4个内含子及2~5个外显子, 这些GRF蛋白都具有由31~35个氨基酸组成的QLQ保守结构域或由25~43个氨基酸组成的WRC保守结构域。系统进化分析表明, 藜麦与拟南芥的GRF转录因子亲缘关系比水稻更近。表达图谱显示, 藜麦GRF基因具有明显的组织表达特异性, 总体在种子中的表达量较高, 其次是在花序和根中, 在其他组织中的表达量相对较低。

关键词: 藜麦, GRF转录因子, 进化分析, 表达分析

Abstract:

Growth-regulating factors (GRFs) are plant-specific proteins which play an important role in regulating plant growth and development. Quinoa is one of the plant sources that can meet human daily nutritional needs and is also considered as one of the most promising crops in the future. However, no systematical study about GRF gene family has been performed in quinoa to date. In this study, the GRFs in the whole genome of quinoa were identified by bioinformatics method, and their physicochemical properties, gene structure, conserved domain, phylogenetic relationship and tissue expression were analyzed. There were 18 GRF transcription factors in quinoa, with the protein length from 77 to 621 aa, the molecular weight from 8.81 to 67.38 kD and the isoelectric point from 5.23 to 9.37. Each member contained 1-4 introns and 2-5 exons. And all 18 GRF proteins possessed highly conserved QLQ domain composed of 31-35 aa or WRC domain composed of 25-43 aa. Phylogenetic analysis showed that the GRF transcription factors were more closely related between quinoa and Arabidopsis than between quinoa and rice. The expression level of GRFs was higher in seed, moderate in inflorescence and root, and relatively lower in other tissues, showing obvious tissue expression specificity.

Key words: Chenopodium quinoa, GRF transcription factor, phylogenetic analysis, expression analysis

表1

定量PCR引物序列"

基因 Gene 正向引物 Forward primer (5°-3°) 反向引物 Reverse primer (5°-3°)
EF1a GTACGCATGGGTGCTTGACAAACTC ATCAGCCTGGGAGGTACCAGTAAT
AUR62001481 TCCCACCTGAACTCTTCTCTGCT ACATCTTCCTGGCTCTGGGTCT
AUR62002094 GGAGGCATGGTCGGGTTTGG GGGATCGTGGACTGGCTGAG
AUR62009885 CCCTTTCACAGCAAGTCAATGGC AGAGAAGAGTCCAGAAGAAGAGGAAGT
AUR62028212 TGCGCCAAAGAAGCCTACCC GACGACACAGAAGCCGTCGT
AUR62033894 TAGTGGTGCCTGGTGGTGGT GCCTTGCATTCCCTGACTGCT
AUR62043106 ACCGGGAAACCCAACATCGG CCCACCGGCACTCCAATTCA

表2

藜麦GRF基因家族成员基本信息"

基因名称
Gene name		 Scaffold位置及基因方向
Scaffold location and gene direction (bp)		 蛋白长度
Length (aa)		 分子量
MW (kDa)		 等电点
pI
AUR62001481 C_Quinoa_2716: 5162638-5164244 (+) 248 28.17 9.15
AUR62002094 C_Quinoa_4480: 2028959-2032889 (-) 331 36.64 8.84
AUR62004030 C_Quinoa_2370: 7633423-7637087 (-) 570 61.48 8.25
AUR62004236 C_Quinoa_4250: 1136571-1139467 (+) 362 40.73 9.32
AUR62006018 C_Quinoa_1001: 1290301-1292042 (-) 273 29.95 5.23
AUR62007068 C_Quinoa_1971: 832455-834729 (+) 369 39.86 8.41
AUR62007538 C_Quinoa_2646: 201458-205187 (-) 621 67.38 8.00
AUR62009885 C_Quinoa_2493: 4358019-4358318 (-) 77 8.81 9.18
AUR62013612 C_Quinoa_1412: 163344-166379 (-) 374 41.77 9.37
基因名称
Gene name		 Scaffold位置及基因方向
Scaffold location and gene direction (bp)		 蛋白长度
Length (aa)		 分子量
MW (kD)		 等电点
pI
AUR62019933 C_Quinoa_1480: 2623570-2625376 (+) 287 30.90 6.25
AUR62024537 C_Quinoa_2876: 5196136-5201404 (+) 541 58.33 9.11
AUR62025191 C_Quinoa_4329: 621270-623166 (-) 302 33.61 6.59
AUR62028212 C_Quinoa_2933: 1647993-1651942 (-) 325 36.02 8.69
AUR62028983 C_Quinoa_2412: 1335673-1337123 (+) 309 34.31 6.45
AUR62033547 C_Quinoa_1776: 1206319-1208711 (-) 268 28.79 7.79
AUR62033894 C_Quinoa_2654: 4420101-4424297 (+) 532 57.33 8.97
AUR62035608 C_Quinoa_2193: 618326-619612 (+) 283 30.81 5.43
AUR62043106 C_Quinoa_1071: 168739-171090 (-) 270 29.22 6.75

图1

藜麦、拟南芥和水稻GRF基因家族系统进化树"

图2

藜麦GRF基因家族进化树与基因结构"

图3

藜麦GRF蛋白保守结构域分析"

图4

藜麦GRF蛋白QLQ (A)和WRC (B)结构域的氨基酸序列比对"

图5

GRF基因在藜麦不同组织中的表达模式分析"

图6

6个GRF基因在藜麦不同组织的表达"

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