Crops ›› 2025, Vol. 41 ›› Issue (1): 54-65.doi: 10.16035/j.issn.1001-7283.2025.01.007

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Identification and Expression Analysis of Dof Gene Family in Sorghum

Fu Senjie1(), Song Yinghui1, Zhu Cancan1, Ye Zhenyan1, Qin Na1, Dai Shutao1, Liu Haixia2, Wang Chunyi1, Li Junxia1()   

  1. 1Cereal Crops Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China
    2Changge Agriculture and Rural Bureau, Xuchang 461500, Henan, China
  • Received:2023-11-02 Revised:2024-01-24 Online:2025-02-15 Published:2025-02-12

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Abstract:

DNA binding with one finger (Dof) is a unique transcription factor in plants, which is involved in regulating physiological and biochemical processes such as plant tissue differentiation, seed germination, stress resistance and metabolism. Using a bioinformatics approach, the basic gene structure, physical and chemical characteristics, conserved motifs, promoter cis-acting elements, tissue-specific expression, and drought-stress expression of the sorghum Dof transcription factor family members were examined at the whole genome level in order to identify and examine the members of the family. Following a 20% PEG6000 simulated drought stress treatment of Yuliang 10 seedlings, the expression of Dof gene family members in response to drought stress at various time points was examined using qPCR. Results showed that a total of 30 Dof genes were identified and distributed on nine chromosomes. The results of gene conservation analysis showed that Motif1 (zinc finger structure) was the conserved protein sequence of sorghum Dof gene family. Among them, 29 genes contained CX2CX21CX2C conserved motif, while the SbDof15 gene was CX20CX2C. The structure of promoter analysis showed that the promoter region of Dof contained ABA, MYB, MeJA, low temperature and other stress response elements. The results of evolutionary tree analysis showed that the homology of sorghum Dof protein was higher than that of maize, and heat map analysis showed that Dof family members were expressed in different parts of sorghum. The results of qRT-PCR indicated that Dof gene family members may be involved in the response of sorghum to drought stress, and different Dof gene members may have different regulatory mechanisms in response to drought stress.

Key words: Sorghum bicolor, Dof gene family, Transcription factor, Whole genome-wide identification, PEG processing

Table 1

Primer sequences for qRT-PCR amplification of Dof genes of sorghum"

基因Gene 登录号Accession number 上游引物序列Upstream primer sequence 下游引物序列Downstream primer sequence
SbDof-1 Sobic.001G034300 GTCGTCCAAGTCAAACTCGTC TCAGTCCGGGGAACCCTAA
SbDof-4 Sobic.001G179300 CGACTACCACCACCAGCAG CAGCTTCCAGTGCAGATCCT
SbDof-8 Sobic.001G489900 CTCATCAAGCTGTTCGGCAAG GTCTTCAGTGTCCGCAACCT
SbDof-10 Sobic.002G313800 TCCATGAACCCTGCGGTTAG TAGAAGAGCGTGGCAATGGA
SbDof-11 Sobic.002G421900 GAGCTGCGTCCCCTCG ACCCTCCGTCTTGGCTATCT
SbDof-13 Sobic.003G121400 CCTGGGATCAAGCTCTTCGG GGCGCATCGACCTTCATTTC
SbDof-24 Sobic.007G223200 ACAACTACAACACCTCCCAGC GTGTCTGTGACACCACTGGC
SbDof-25 Sobic.008G001700 TCTCAGGCTCTGGTTCCTCT CGGGAGCACATTGGGGAATA
Actin LOC110436378 TGAAGTGCGACGTGGATATTAGGA GCTGGAATGTGCTGAGAGATGC

Fig.1

Location of sorghum Dof family genes on chromosomes"

Table 2

Basic information of sorghum Dof gene family"

基因编号
Gene code		 基因ID
Gene ID		 氨基酸数
Number of amino acids		 基因长度
Gene length
(bp)		 编码区
Coding
region		 等电点
Isoelectric
point		 蛋白质相对分子质量
Protein relative
molecular mass (Da)		 信号肽分析
Signal peptide
analysis
SbDof1 Sobic.001G034300 435 3309 1572~2879 9.34 43 307.61 0.0031
SbDof2 Sobic.001G078700 380 1995 365~1507 9.23 38 671.80 0.0008
SbDof3 Sobic.001G166200 351 1397 94~1149 8.93 35 519.91 0.0025
SbDof4 Sobic.001G179300 385 1950 419~1576 8.34 38 461.74 0.0143
SbDof5 Sobic.001G206300 261 1535 484~1269 9.32 26 378.44 0.0026
SbDof6 Sobic.001G252800 476 2136 315~1745 6.31 49 778.02 0.0013
SbDof7 Sobic.001G420300 394 1997 298~1485 9.94 40 285.77 0.0015
SbDof8 Sobic.001G489900 424 1810 259~1533 8.65 45 170.80 0.0016
SbDof9 Sobic.002G236600 252 1348 127~1077 9.28 25 792.75 0.0109
SbDof10 Sobic.002G313800 354 2489 547~1611 8.16 34 828.74 0.0137
SbDof11 Sobic.002G421900 484 1980 137~1591 6.35 51 627.69 0.0020
SbDof12 Sobic.003G033500 235 1519 198~1142 9.90 24 113.61 0.0619
SbDof13 Sobic.003G121400 560 2222 208~1890 5.14 61 403.46 0.0005
SbDof14 Sobic.003G131100 512 2359 347~1885 9.04 54 771.55 0.0025
SbDof15 Sobic.003G253200 168 2049 1425~1940 10.27 17 251.49 0.0015
SbDof16 Sobic.003G301700 260 1645 471~1253 9.21 27 855.15 0.0011
SbDof17 Sobic.003G367100 335 1495 218~1225 4.75 35 258.15 0.0260
SbDof18 Sobic.004G254000 304 1476 235~1149 8.81 30 986.43 0.0212
SbDof19 Sobic.004G266200 295 1639 444~1331 8.51 30 934.23 0.0020
SbDof20 Sobic.004G284400 457 2244 460~1833 9.28 45 947.04 0.0002
SbDof21 Sobic.005G001500 340 1527 281~1303 9.11 36 180.21 0.0011
SbDof22 Sobic.006G182300 388 2534 696~1811 8.76 38 945.94 0.0013
SbDof23 Sobic.006G267900 224 1682 702~1376 7.59 23 265.65 0.0374
SbDof24 Sobic.007G223200 265 1502 161~1020 5.86 27 579.64 0.0062
SbDof25 Sobic.008G001700 354 1524 234~1298 9.12 38 038.01 0.0020
SbDof26 Sobic.008G136100 340 2016 610~1632 9.05 34 557.65 0.0100
SbDof27 Sobic.008G148101 275 923 96~923 9.77 28 033.91 0.0214
SbDof28 Sobic.009G014400 385 2066 428~1585 9.07 39 250.54 0.0028
SbDof29 Sobic.009G153400 366 1472 117~1217 5.68 38 488.27 0.0010
SbDof30 Sobic.009G196100 216 1909 419~1087 9.99 22 783.69 0.0014

Table 3

The secondary structure analysis of Dof albumen in sorghum %"

基因号
Gene ID		 α-螺旋
α-helix
(Hh)		 延伸链
Extended
strand (Ee)		 β-转角
β-turn
(Tt)		 无规则卷曲
Random coil
(Cc)		 基因号
Gene ID		 α-螺旋
α-helix
(Hh)		 延伸链
Extended
trand (Ee)		 β-转角
β-turn
(Tt)		 无规则卷曲
Random coil
(Cc)
SbDof1 12.87 8.97 4.37 73.79 SbDof16 16.92 14.23 5.77 63.08
SbDof2 26.05 10.53 5.26 58.16 SbDof17 19.10 8.96 4.48 67.46
SbDof3 23.36 13.96 7.12 55.56 SbDof18 22.37 15.13 4.93 57.57
SbDof4 33.25 11.43 4.94 50.39 SbDof19 24.75 12.88 5.08 57.29
SbDof5 26.05 11.88 5.75 56.32 SbDof20 17.94 15.10 6.13 60.83
SbDof6 17.23 9.24 3.15 70.38 SbDof21 15.88 14.41 4.12 65.59
SbDof7 17.01 12.69 5.58 64.72 SbDof22 11.34 11.60 2.84 74.23
SbDof8 13.68 8.02 1.65 76.65 SbDof23 34.38 8.48 8.04 49.11
SbDof9 11.90 17.46 6.75 63.89 SbDof24 25.28 14.34 10.19 50.19
SbDof10 36.72 9.60 6.50 47.18 SbDof25 14.41 15.54 3.95 66.10
SbDof11 13.84 7.23 1.45 77.48 SbDof26 26.47 11.76 7.94 53.82
SbDof12 13.62 15.32 10.21 60.85 SbDof27 27.64 11.64 7.27 53.45
SbDof13 13.75 6.07 2.14 78.04 SbDof28 24.16 12.47 10.91 52.47
SbDof14 19.73 8.20 3.12 68.95 SbDof29 26.23 12.84 8.47 52.46
SbDof15 30.36 6.55 4.76 58.33 SbDof30 27.78 16.20 5.56 50.46

Fig.2

Comparison and analysis of conserved sequences of SbDof protein family"

Fig.3

Analysis of Dof family gene structure in sorghum"

Fig.4

Analysis of conserved motifs of sorghum Dof family proteins"

Fig.5

Sequence analysis of functional domain of Dof gene in sorghum"

Fig.6

Analysis of cis-regulatory elements of Dof family genes in sorghum"

Fig.7

Phylogenetic tree of Dof gene family in three crops"

Fig.8

The expression patterns of the Dof genes in sorghum"

Table 4

Functional interaction protein prediction of SbDof10"

互作蛋白Interaction protein 基因描述Gene description 互作系数Interaction coefficient 氨基酸数量Number of amino acids
Sb09g006196.1 Loc8065916亚型x1，响应低温胁迫 0.695 384
Sb01g029000.1 WRKY DNA结合域超家族蛋白 0.694 346
Sb03g034780.1 发病机制相关基因转录激活因子PTI5 0.663 178
Sb01g031890.1 锌指蛋白ZAT10 0.622 253
Sb09g027800.1 转录因子MYB 0.663 289

Fig.9

Expression analysis of Dof family genes in sorghum under drought treatments “*”indicates significant difference (P < 0.05),“**”indicates extremely significant difference (P < 0.01)."

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