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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (12): 1841-1850.doi: 10.3724/SP.J.1006.2019.94049

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

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 Online:2019-12-12 Published:2019-07-13
  • Contact: Min-Feng GU E-mail:ycgmf@126.com
  • 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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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

Table 1

Primer sequences for RT-qPCR"

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

Table 2

Basic information of GRF gene family members in quinoa"

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

Fig. 1

Phylogenetic tree of GRF gene family in quinoa, Arabidopsis, and rice"

Fig. 2

Phylogenetic tree and gene structure of quinoa GRF gene family"

Fig. 3

Analysis of conserved domains of GRF proteins in quinoa"

Fig. 4

Amino acid sequence alignment of QLQ (A) and WRC (B) domain of quinoa GRF proteins"

Fig. 5

Expression profile analysis of GRF genes in different tissues of quinoa"

Fig. 6

Expression level of six GRF genes in different tissues of quinoa"

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