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Acta Agronomica Sinica ›› 2026, Vol. 52 ›› Issue (1): 28-43.doi: 10.3724/SP.J.1006.2026.51069

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

Identification and expression pattern analysis of RopGEF family genes in Chenopodium quinoa

Jing Xiu-Qing1,2,3,*(), Cai Yong-Duo1, Deng Ning1, Zhao Xiao-Dong1,2, Zhai Fei-Hong1,2, Zeng Qun4   

  1. 1College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong 030619, Shanxi, China
    2Shanxi Key Laboratory of Earth Surface Processes and Resource Ecology Security in Fenhe River Basin, Taiyuan Normal University, Jinzhong 030619, Shanxi, China
    3College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
    4School of Basic Medical, Shanxi University of Chinese Medicine, Jinzhong 030619, Shanxi, China
  • Received:2025-07-22 Accepted:2025-10-30 Online:2026-01-12 Published:2025-11-10
  • Contact: *E-mail: xiuqingjing@tynu.edu.cn
  • Supported by:
    Fundamental Research Programs of Shanxi Province(202203021212186);Graduate Education and Innovation Projects of Taiyuan Normal University(SYYJSYC-2431);College Student Innovation and Entrepreneurship Training Program of Taiyuan Normal University(CXCY25104)

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Abstract:

In plants, RopGEF-mediated ROP signaling plays a crucial role in cellular signaling pathways. In this study, seven RopGEF family members were identified in Chenopodium quinoa through bioinformatics analysis and were found to be distributed across six chromosomes. Based on phylogenetic relationships and structural characteristics, 90 RopGEFs from six crop species, including Arabidopsis thaliana and rice, were classified into four subfamilies. Evolutionary analysis revealed that CqRopGEF5 is closely related to AtRopGEF1 and OsRopGEF1. Structural analysis indicated that the exon-intron organization, protein motif composition, and secondary and three-dimensional structures of CqRopGEFs are highly conserved. qRT-PCR analysis showed that most CqRopGEFs were highly expressed during seed germination, with expression levels in seedling roots being higher than in stems and leaves. Their expression was significantly induced by exogenous abscisic acid (ABA) and abiotic stresses. For instance, the expression of CqRopGEF2, CqRopGEF3, CqRopGEF4, and CqRopGEF7 initially increased and then decreased under ABA treatment, while CqRopGEF7 was strongly downregulated under both cold and heat stress. In conclusion, the CqRopGEF gene family exhibits conserved evolutionary structure and may play important roles in quinoa growth and development, ABA signaling, and responses to abiotic stress.

Key words: Chenopodium quinoa, RopGEFs, phylogenetic analysis, gene expression, abiotic stresses

Table 1

Primer sequences for qRT-PCR"

引物名称
Primer name		 引物序列
Primer sequence (5'-3')
CqActin-F CCCCTGCTATGTATGTTGCAATTC
CqActin-R AGTGGTCTGTTAGGTCACGACCAG
CqRopGEF1-F GTCAGAACCGGATAGGAATGACA
CqRopGEF1-R TTCTAAGATTGCTTGGCCGACG
CqRopGEF2-F GTCAAGTGCTGAGCGTAGAA
CqRopGEF2-R AGAGTAGGCGAAACAGAGGA
CqRopGEF3-F TGATTCAGGGCTTGATGAATTAG
CqRopGEF3-R CTGCAGTACATACACCTTTCCC
CqRopGEF4-F AAGATCACTCGAGCAATCCCAA
CqRopGEF4-R CTTATATGTGGGTTGCCTATGG
CqRopGEF5-F TCTCCCGATCCAAAAACGCA
CqRopGEF5-R ATCTAGGGCTTCCTCCAGCA
CqRopGEF6-F CTGCTCGACATTGACAAGAGAC
CqRopGEF6-R AACAAGTGCTTTCTCTCTCGC
CqRopGEF7-F GAGAAGTCCAACAGCTCGACA
CqRopGEF7-R AGGGAAGTTAAAACTGTTGAGGA

Fig. 1

Chromosome distribution of RopGEF family genes in Chenopodium quinoa"

Table 2

Identification of RopGEF family genes in Chenopodium quinoa"

命名
Name		 基因ID
Gene ID		 染色体定位
Genomic location		 方向
Orientation		 DNA
(bp)		 mRNA
(bp)		 CDS
(bp)		 蛋白质
Protein (aa)
CqRopGEF1 AUR62022562 Chromosome 1A: 2964588-2967787 正向Forward 3200 2059 1344 447
CqRopGEF2 AUR62022802 Chromosome 2A: 55459754-55456379 反向Reverse 3377 2493 1806 601
CqRopGEF3 AUR62004356 Chromosome 2B: 72815241-72818458 正向Forward 3218 2102 1347 448
CqRopGEF4 AUR62017402 Chromosome 5B: 11732273-11725942 反向Reverse 8837 2220 1668 555
CqRopGEF5 AUR62012977 Chromosome 7B: 2293460-2296982 正向Forward 3525 2278 1716 571
CqRopGEF6 AUR62016478 Chromosome 7B: 11948979-11952944 正向Forward 3949 1657 1344 447
CqRopGEF7 AUR62011650 Chromosome 9A: 47835328-47832045 正向Forward 3288 2087 1656 551

Table 3

Physicochemical properties of RopGEF family proteins in Chenopodium quinoa"

名称
Name		 蛋白质分子量
MV (Da)		 等电点
pI		 电荷
Charge		 不稳定指数
II		 脂肪指数
AI		 总平均亲水性
GRAVY		 主要氨基酸含量
Major amino acids content (%)
CqRopGEF1 50733.64 5.64 -5.0 44.12 69.46 -0.532 Ser (9.8), Leu (9.4), Glu (7.8)
CqRopGEF2 67003.52 8.91 15.5 51.88 82.10 -0.468 Ser (12.0), Leu (10.1), Lys (7.0)
CqRopGEF3 50820.74 5.65 -5.0 47.32 68.86 -0.549 Ser (9.8), Leu (9.4), Glu (8.0)
CqRopGEF4 61739.50 5.42 -8.5 50.76 75.59 -0.447 Ser (13.2), Leu (8.1), Glu (7.6)
CqRopGEF5 63181.72 5.43 -7.0 53.29 79.98 -0.343 Ser (11.0), Leu (10.7), Ala (8.2)
CqRopGEF6 49940.71 5.82 -2.5 44.40 83.18 -0.568 Leu (10.3), Ser (8.7), Lys (8.1)
CqRopGEF7 61880.51 6.72 2.5 46.90 85.35 -0.543 Leu (10.0), Ser (9.1), Lys (8.3)

Fig. 2

Phylogenetic analysis of RopGEF family members from Arabidopsis, rice, and Chenopodium quinoa"

Fig. 3

Motif composition of CqRopGEF family proteins"

Fig. 4

Exon-intron structure of CqRopGEF family genes"

Fig. 5

Predicted secondary structure of CqRopGEF family proteins"

Table 4

Proportion of secondary structure of CqRopGEF family proteins (%)"

蛋白名称
Protein name		 α-螺旋
Alpha helix		 延伸链
Extended strand		 β-折叠
Beta turn		 无规则卷曲
Random coil
CqRopGEF1 48.55 9.40 6.26 35.79
CqRopGEF2 39.60 11.81 5.16 43.43
CqRopGEF3 49.33 9.38 6.47 34.82
CqRopGEF4 39.46 13.51 5.77 41.26
CqRopGEF5 45.01 11.73 5.78 37.48
CqRopGEF6 50.56 10.29 5.82 33.33
CqRopGEF7 48.46 12.89 6.53 32.12

Fig. 6

3D structural model of CqRopGEF family proteins"

Fig. 7

Tissue-specific expression patterns of CqRopGEFs The X-axis represents different genes derived from various tissues, while the Y-axis shows the relative expression levels of each gene, where the expression level of the corresponding gene in the seedling-stage leaf control group serves as the reference. Error bars represent the standard deviations (SD) of three independent biological replicates, indicating variability in the data. Lowercase letters above columns indicate statistically significant differences among groups (P < 0.05)."

Table S1

Tissue-specific relative expression levels of CqRopGEFs"

藜麦的不同组织
Different tissues of Chenopodium quinoa		 CqRopGEF1 CqRopGEF2 CqRopGEF3 CqRopGEF4 CqRopGEF5 CqRopGEF6 CqRopGEF7
萌发期的种子
Seeds at the
germination stage		 4.878203 2.278607 2.754176 16.890020 2.797100 11.876840 19.897840
3.766052 3.312942 4.805450 15.268320 3.482195 9.355844 16.520080
6.100269 3.838499 6.404784 18.461560 3.013842 5.053957 23.091410
幼苗期的根
Roots at the
seedling stage		 6.807494 1.331894 0.460650 21.580820 3.284094 4.173666 6.313694
3.532024 1.830430 2.551489 20.974230 4.843827 5.355065 6.104382
5.169742 1.199528 0.971060 22.187410 5.968582 6.533347 5.893400
幼苗期的茎
Stems at the
seedling stage		 4.733415 1.770585 1.180153 4.127276 0.713631 0.588344 0.717597
6.430234 1.379614 1.270806 5.117608 2.263214 0.303270 0.691531
1.542182 0.988338 0.902921 4.178092 0.824355 0.451662 0.728712
幼苗期的叶
Leaves at the
seedling stage		 0.518102 1.125639 1.652672 1.051103 1.411523 1.807061 1.370787
0.936619 0.608740 0.535888 0.935297 0.857690 1.133261 0.897113
1.573340 1.642738 1.129119 1.017196 0.826002 0.488311 0.813173

Fig. 8

Expression profiles of SiRopGEFs in responding to phytohormone ABA The X-axis represents treatments with a concentration of 100 μmol L-1 abscisic acid (ABA); The Y-axis shows the relative expression levels of genes under each treatment, with the gene expression level at 0 h serving as the control for comparison. Error bars indicate the standard deviations from three independent biological replicates, reflecting experimental variability. Lowercase letters above columns denote statistically significant differences among treatments (P < 0.05)."

Table S2

Relative expression level of CqRopGEFs in responding to phytohormone ABA"

脱落酸诱导时间
ABA induction time (h)		 CqRopGEF1 CqRopGEF2 CqRopGEF3 CqRopGEF4 CqRopGEF5 CqRopGEF6 CqRopGEF7
0 0.383349 0.560141 0.854405 0.606571 0.728405 0.728405 1.062129
1.506241 1.269373 1.345321 1.828694 1.029036 1.029036 0.721514
1.731853 1.406414 0.869982 0.901525 1.334125 1.334125 1.304915
0.5 0.983333 1.102365 1.681996 2.789007 1.298839 9.554574 2.288396
1.524082 1.747551 1.203658 2.703967 1.087367 11.379720 1.333165
2.197235 1.325759 2.439122 1.717055 1.389695 10.233450 0.362952
1.0 3.337438 2.589671 5.702759 3.252600 2.760910 9.061889 4.074006
3.772568 1.520832 4.813831 2.026537 3.317331 10.027570 2.866530
3.308728 1.739145 2.253050 1.514832 2.865699 10.617900 3.495186
3.0 1.137558 3.965328 2.342961 3.991537 0.879867 8.917276 2.692579
1.323412 5.386514 2.337639 5.240955 1.371273 10.102700 4.462155
1.509266 4.675921 2.198124 5.679425 1.445019 9.509880 4.253782
6.0 2.052419 3.843384 2.081516 4.373684 0.209642 18.590750 2.624539
2.699639 3.878513 2.878217 4.111525 0.139735 15.317400 4.317009
4.581864 3.860945 1.946418 3.849441 0.254140 11.211030 1.693145
9.0 2.842707 2.123543 1.361779 2.529633 2.378183 7.451357 1.053495
5.334447 2.349829 2.334819 4.288677 2.990309 9.269848 2.691308
6.244401 1.185006 2.165277 3.323484 2.684246 7.931538 1.479827
12.0 1.089972 1.704662 0.582268 1.517851 0.522919 5.989391 2.404398
1.123806 1.002880 0.458469 1.095538 0.452549 6.101458 0.909693
1.463621 1.428291 0.968643 1.940164 0.657857 5.563212 2.143747

Fig. 9

Expression profiles of CqRopGEFs in response to abiotic stresses The X-axis represents treatments, and the Y-axis shows the relative expression levels of genes under each treatment, with the gene expression level at 0 h serving as the control for comparison. Error bars represent standard deviations from three independent biological replicates, indicating data variability. Lowercase letters above columns indicate statistically significant differences among treatments (P < 0.05)."

Table S3

Relative expression level of CqRopGEFs in responding to abiotic stresses"

非生物胁迫类型
Abiotic stress types		 诱导时间
Induction time (h)		 CqRopGEF1 CqRopGEF2 CqRopGEF3 CqRopGEF4 CqRopGEF5 CqRopGEF6 CqRopGEF7
盐胁迫
NaCl stress		 0 0.383349 0.560141 0.854405 0.606571 0.728405 0.728405 1.062129
1.506241 1.269373 1.345321 1.828694 1.029036 1.029036 0.721514
1.731853 1.406414 0.869982 0.901525 1.334125 1.334125 1.304915
0.5 0.772326 1.159405 1.773793 1.854496 0.691270 7.582796 1.691677
2.333372 1.381033 1.693753 1.954086 0.719767 10.713740 1.489551
0.906278 2.128215 2.517919 1.878350 0.807654 12.751710 1.440584
1.0 4.021173 1.505571 1.616389 4.601057 0.637286 1.205228 1.654745
3.552205 1.141802 0.760429 1.714344 0.204097 0.749852 0.648161
3.153475 1.869340 1.330379 3.146229 0.274938 0.863148 0.816919
3.0 1.730386 1.712858 2.823156 1.944915 1.290353 1.278683 0.441802
1.743547 0.958481 1.360395 0.609258 0.556973 0.900653 0.231205
1.531246 1.217893 1.133152 1.566374 1.034183 2.563201 0.544648
6.0 7.491243 4.959007 11.984900 14.824110 1.460042 14.339160 1.742513
8.709589 6.226643 11.173230 15.912830 1.610668 20.513880 2.250919
6.730411 5.592825 12.796570 15.055710 1.536903 20.236210 1.996716
9.0 1.550042 2.273255 0.611888 0.814029 0.874245 7.804387 1.216835
1.286587 2.985491 0.669221 0.808121 1.009184 5.403626 0.735552
1.763603 3.697727 0.740158 0.855448 0.901323 2.963197 1.151440
12.0 0.659497 1.284734 1.313399 0.988045 1.204775 8.536256 1.024598
3.250984 2.389733 1.484973 1.884897 1.850079 12.979700 1.120172
1.017229 0.672581 0.837188 0.465141 0.841363 6.292692 0.358020
冷胁迫
Cold stress		 0 0.383349 0.560141 0.854405 0.606571 0.728405 0.728405 1.062129
1.506241 1.269373 1.345321 1.828694 1.029036 1.029036 0.721514
1.731853 1.406414 0.869982 0.901525 1.334125 1.334125 1.304915
0.5 3.067984 0.073947 1.240688 0.905638 0.506053 3.463253 0.041140
2.764997 0.095788 1.552569 0.869109 0.680372 10.269000 0.048050
1.630744 0.025687 2.114081 0.600380 0.674204 4.344438 0.047003
1.0 6.912400 2.331709 2.603918 1.268249 1.842374 9.603889 0.064722
3.522932 4.848282 1.906822 0.534672 1.078122 4.360394 0.037754
1.921253 2.452198 0.514955 0.786965 1.011729 5.216602 0.027871
3.0 4.384372 1.205219 0.984415 1.079580 1.133988 7.848745 0.045085
4.254747 1.864312 1.894010 1.485352 1.642780 9.145513 0.052989
4.014151 2.783633 1.027342 0.985608 1.142598 12.440090 0.072667
6.0 2.086202 1.709914 1.716748 2.497598 1.202176 3.998536 0.074053
1.942518 1.154572 1.937527 2.730446 0.733247 4.476529 0.086771
1.385889 0.834515 1.365975 0.948892 0.348817 3.680676 0.047853
9.0 0.711963 0.238596 0.367345 1.016697 0.872451 1.058060 0.026753
1.105034 0.868088 0.321311 0.587120 1.104628 2.405538 0.033237
1.466575 1.280835 1.849609 1.070318 1.585804 5.327724 0.074461
12.0 5.369742 1.663197 2.324701 2.033130 0.741304 6.911496 0.062350
5.109689 0.758459 2.143919 2.832090 0.686679 5.455784 0.045538
4.807878 1.727933 3.264301 2.993412 0.647229 5.499532 0.046762
热胁迫
Heat stress		 0 0.383349 0.560141 0.854405 0.606571 0.728405 0.728405 1.062129
1.506241 1.269373 1.345321 1.828694 1.029036 1.029036 0.721514
1.731853 1.406414 0.869982 0.901525 1.334125 1.334125 1.304915
0.5 5.698402 0.342630 2.938812 1.912740 3.123081 0.395001 0.030419
6.523212 0.543866 4.800879 3.507437 3.619378 1.669364 0.089216
7.348022 0.435744 1.879438 2.008440 2.626784 0.813130 0.051139
1.0 11.545170 0.967400 0.065129 0.952527 3.284985 0.017801 0.001726
12.091210 0.729950 0.278504 1.931629 2.470521 0.042110 0.002321
12.637250 0.965469 0.173085 2.069349 4.086476 0.058591 0.004358
3.0 3.355991 0.049800 0.829518 3.078433 1.326899 0.576277 0.016437
8.287571 0.134510 3.354101 4.393673 1.842339 1.273716 0.029428
5.315243 0.866220 2.655746 5.708913 1.601412 0.721393 0.018568
6.0 0.043172 0.310586 0.386811 1.060621 2.231053 0.284953 0.006082
0.417197 1.199896 1.531503 2.426767 2.021476 0.704766 0.011086
0.364518 0.590544 1.353164 2.264082 1.811899 0.528078 0.007894
9.0 1.266708 0.243170 0.605378 3.033535 1.584369 0.668059 0.011319
3.190623 0.649720 1.499023 4.901491 1.326435 0.359377 0.018200
0.773340 0.517530 2.008419 3.327380 1.068478 0.485347 0.011061
12.0 0.300956 0.103220 0.158249 1.211129 0.470379 0.254347 0.002693
0.541412 0.579653 1.105782 1.806751 0.616462 0.383229 0.004141
0.320881 0.163824 0.260170 1.228762 0.557374 0.220774 0.003609
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