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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (3): 608-623.doi: 10.3724/SP.J.1006.2022.14004

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

Genome-wide characterization and expression analysis of Dof family genes in sweetpotato

JIN Rong1(), JIANG Wei1, LIU Ming1, ZHAO Peng1, ZHANG Qiang-Qiang1, LI Tie-Xin2, WANG Dan-Feng1, FAN Wen-Jing2, ZHANG Ai-Jun1, TANG Zhong-Hou1,*()   

  1. 1Xuzhou Institute of Agricultural Sciences of Xuhuai District of Jiangsu Province/Xuzhou Sweetpotato Research Center of Jiangsu Province/Key Laboratory of Sweetpotato Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Xuzhou 221131, Jiangsu, China
    2Anhui Agricultural University, Hefei 230036, Anhui, China
  • Received:2021-01-11 Accepted:2021-04-26 Online:2021-05-20 Published:2021-05-20
  • Contact: TANG Zhong-Hou E-mail:jinrong_2012@126.com;zhonghoutang@sina.com
  • Supported by:
    China Agriculture Research System(CARS-11-B-13);Open Project of Ministry of Agriculture and Rural Affairs: Key Laboratory of Biology, Genetics and Breeding of Potato Crops(NYBSL201802)

Abstract:

DNA-binding One Zinc Finger (Dof) transcription factors are widely involved in various life activities of plants. Forty-six IbDof genes from sweetpotato cv. Taizhong 6 with a highly conserved Dof domain structured as a C2C2-type zinc finger were identified and named from IbDof1 to IbDof46 according to their position on the chromosomes. IbDof family could be divided into four subgroups (A-D), which shared the similar motifs and gene structures. Motif 1 and Motf 2 occurred in all of the identified IbDofs, Motif 5 and Motif 9 only occurred in subgroup A, and Motif 6-Motif 8 and Motif 10 only occurred in subgroup D. Twelve segment duplicated gene pairs and five tandem duplicated gene pairs of IbDofs (IbDof2/IbDof3, IbDof12/IbDof13, IbDof9/IbDof10, IbDof28/IbDof29, and IbDof32/IbDof33) contributed to the expansion of IbDof family in sweetpotato. The average divergence times of segmental duplication gene pairs and tandem duplicated gene pairs seemed to have emerged 35.22 MYA and 1.86 MYA, and the Ka/Ks ratios of the paralogous IbDofs were range from 0.07 (IbDof12/IbDof13) to 0.68 (IbDof6/IbDof25). Tirty-eight orthologous IbDof gene pairs between sweetpotato and their wild relative species Ipomoea trifida were involved in duplicated genomic blocks based on synteny analysis. Transcriptome analysis indicated different subgroups expressed specifically in various tissues, and IbDofs in the same subgroup also revealed different expression tends. Various hormones and stresses response element were identified in the promoters of IbDof genes, and qRT-PCR demonstrated specific IbDof genes responded to various environmental stresses, including cold, drought, salt, and H2O2. Most IbDof genes were regulated by cold treatment; IbDof10 and IbDof14 were up-regulated by drought treatment; IbDof-2, -14, -37, -41, -43 were up regulated by high salt stress; and IbDof-8, -10, -25, -41 were up regulated by H2O2 treatment. In summary, our result indicated that IbDof family genes coordinately regulated the growth and development of sweetpotato and been involved in the various abiotic stresses process.

Key words: sweetpotato, Dof gene family, evolution analysis, gene expression profiling

Table 1

Primers for qRT-PCR used in this study"

基因名称
Gene name
正向引物序列
Forward sequence (5'-3')
反向引物序列
Reverse sequence (5'-3')
Dof2 GCTGTTGTTGTTGGATTATC CGTTGTTAGGTAGAGTTGTC
Dof5 CTCATTGCCGTCATATTACC TCCTGCCATAGAACTTGTAG
Dof8 GCTGGAGATAATGGAGATGA AACTGCGGTCAATGGATAA
Dof10 GGTTGTGGAGAATGTTGTG GAGGAAGAAGATGATAAGGAAG
Dof14 GAAGGTGATGATGACAACAG CCATGCCAAGAAGAACCA
Dof15 GCTTCATCTCCTCCTCCT GTTCCTTCATCCTCTTCACT
Dof17 CAACTATGGCGACTGATAATC GATGTTCCTCCTCCTCCT
Dof21 TTACTGTCGAACATGCAGACGC GTGGTTGGAGTTGAGGTAGTGA
基因名称
Gene name
正向引物序列
Forward sequence (5'-3')
反向引物序列
Reverse sequence (5'-3')
Dof24 CGACGAGATATTGGAACCTT GGCTGGCTCTGTTGAATC
Dof25 CTACAACAACTACAACCTCTC AGCAATGACGTGAAGGAG
Dof33 TCCGTTCCTCGATCCAAT TGATGGTGTGATTGTTGTTG
Dof37 CGACCAAGACTGAAGATGA GGTGATGTGGCAATGAGA
Dof40 CTCCATCATCATCATCATCATC GGCAGCAGTAGTCATTCC
Dof41 CATCATCATCATCATCTCCATC GGCAGCAGTAGTCATTCC
Dof43 TTCTGTTACGACACCTTCC TACTGCTTCTACCGACTCT

Table 2

Information of IbDof gene family members"

基因名称
Gene name
基因编号
Gene ID
染色体定位
Chromosome
CDS长度
Coding domain sequence (bp)
氨基酸长度
Amino acid length
等电点
Isoelectric point (pI)
分子量
Molecular weight (kD)
亚细胞定位
Subcellular location
分组
Group
IbDof1 g1970.t1 1 891 297 6.35 31.96 细胞核 Nucleus D3
IbDof2 g5563.t1 1 807 269 4.94 29.78 细胞核 Nucleus D3
IbDof3 g5605.t1 1 807 269 4.94 29.76 细胞核 Nucleus D3
IbDof4 g6131.t1 1 600 200 9.16 20.99 细胞核 Nucleus C2.2
IbDof5 g9564.t1 2 1164 388 9.33 42.57 细胞核 Nucleus B1
IbDof6 g10705.t1 2 561 187 9.60 21.15 细胞核 Nucleus B2
IbDof7 g11533.t1 3 1542 514 5.28 55.81 细胞核 Nucleus B1
IbDof8 g11556.t1 3 1494 498 5.09 53.53 细胞核 Nucleus B1
IbDof9 g15022.t1 3 759 253 8.15 27.43 细胞核 Nucleus D1
IbDof10 g15141.t1 3 732 244 8.90 26.49 细胞核 Nucleus D1
IbDof11 g17470.t1 4 330 110 9.66 12.60 细胞核 Nucleus B2
IbDof12 g21747.t1 4 960 320 9.20 33.86 细胞核 Nucleus A
IbDof13 g21785.t1 4 957 319 9.20 33.80 细胞核 Nucleus A
IbDof14 g21856.t1 4 846 282 6.78 30.99 细胞核 Nucleus D2
IbDof15 g26198.t1 5 1587 529 6.19 58.14 细胞核 Nucleus B1
IbDof16 g26413.t1 5 786 262 9.18 27.65 细胞核 Nucleus C1
IbDof17 g26723.t1 5 825 275 7.17 29.90 细胞核 Nucleus D1
IbDof18 g27204.t1 5 807 269 5.03 29.57 细胞核 Nucleus D3
IbDof19 g28361.t1 6 498 166 9.73 19.31 细胞核 Nucleus B2
IbDof20 g28392.t1 6 606 202 9.32 22.91 细胞核 Nucleus B2
IbDof21 g28584.t1 6 606 202 8.45 22.54 细胞核 Nucleus B2
IbDof22 g28692.t1 6 687 229 8.79 25.43 细胞核 Nucleus B2
IbDof23 g31777.t1 6 630 210 8.16 22.06 细胞核 Nucleus C2.2
IbDof24 g32164.t1 6 1164 388 9.05 42.28 细胞核 Nucleus C2.2
IbDof26 g34747.t1 7 786 262 8.64 28.71 细胞核 Nucleus D2
IbDof27 g34761.t1 7 786 262 8.49 28.58 细胞核 Nucleus D2
IbDof28 g38905.t1 8 657 219 8.84 23.95 细胞核 Nucleus D1
IbDof29 g38982.t1 8 1038 346 8.83 38.71 细胞核 Nucleus D1
IbDof30 g42311.t1 9 939 313 9.33 34.08 细胞核 Nucleus C3
IbDof31 g42323.t1 9 1014 338 9.14 36.42 细胞核 Nucleus C3
IbDof32 g46228.t1 9 972 324 9.60 33.39 细胞核 Nucleus A
IbDof33 g46266.t1 9 1032 344 9.30 35.94 细胞核 Nucleus A
IbDof34 g48623.t1 10 861 287 6.19 31.08 细胞核 Nucleus D3
IbDof35 g50844.t1 10 1050 350 8.90 37.73 细胞核 Nucleus C3
IbDof36 g50864.t1 10 837 279 6.15 30.23 细胞核 Nucleus B1
IbDof37 g53865.t1 11 1398 466 5.76 50.71 细胞核 Nucleus B1
基因名称
Gene name
基因编号
Gene ID
染色体定位
Chromosome
CDS长度
Coding domain sequence (bp)
氨基酸长度
Amino acid length
等电点
Isoelectric point (pI)
分子量
Molecular weight (kD)
亚细胞定位
Subcellular location
分组
Group
IbDof38 g55460.t1 11 1050 350 6.97 38.44 细胞核 Nucleus D2
IbDof39 g57153.t1 12 1002 334 9.63 35.93 细胞核 Nucleus A
IbDof40 g58686.t1 12 1008 336 8.24 36.37 细胞核 Nucleus D1
IbDof41 g59490.t1 12 1011 337 8.21 36.31 细胞核 Nucleus D1
IbDof42 g59977.t1 12 939 313 9.48 33.42 细胞核 Nucleus A
IbDof43 g65472.t1 14 1317 439 7.22 47.43 细胞核 Nucleus B1
IbDof44 g65553.t1 14 1053 351 8.99 39.00 细胞核 Nucleus B2
IbDof45 g68289.t1 14 804 268 8.24 29.58 细胞核 Nucleus D2
IbDof46 g68388.t1 14 882 294 9.17 30.81 细胞核 Nucleus A

Fig. 1

Phylogenetic tree of Dof protein in sweetpotato, Arabidopsis, and rice"

Fig. 2

Conserved motif and gene structure of Dof genes in sweetpotato"

Fig. 3

Cis-elements in the promoter regions of Dof genes in sweetpotato"

Table 3

Duplicate Dof genes and their estimated types of duplication in sweetpotato"

基因I
Gene I
基因II
Gene II
复制类型
Type of duplication
同义
替换率
Ka
非同义
替换率
Ks
Ka/Ks 分歧时间(百万年前)
Divergence time (MYA)
IbDof2 IbDof3 串联重复序列 Tandem duplicated gene pairs 0.001611 0.016886 0.095413 0.562876
IbDof4 IbDof25 染色体片段复制 Segmental duplication gene pairs 0.158131 0.233118 0.678330 7.77059
IbDof7 IbDof15 染色体片段复制 Segmental duplication gene pairs 0.275346 0.952055 0.289212 31.73516
IbDof9 IbDof10 串联重复序列 Tandem duplicated gene pairs 0.016325 0.053043 0.307773 1.768089
IbDof10 IbDof17 染色体片段复制 Segmental duplication gene pairs 0.291817 1.563082 0.186693 52.10274
IbDof12 IbDof13 串联重复序列 Tandem duplicated gene pairs 0.006995 0.097434 0.071789 3.247803
IbDof14 IbDof27 染色体片段复制 Segmental duplication gene pairs 0.228799 1.117142 0.204807 37.23806
IbDof28 IbDof29 串联重复序列 Tandem duplicated gene pairs 0.008162 0.020799 0.392429 0.693285
IbDof32 IbDof33 串联重复序列 Tandem duplicated gene pairs 0.030506 0.102014 0.299038 3.400458
IbDof35 IbDof30 染色体片段复制 Segmental duplication gene pairs 0.495625 1.024638 0.483707 34.15461
IbDof39 IbDof12 染色体片段复制 Segmental duplication gene pairs 0.624101 1.595607 0.391137 53.1869
基因I
Gene I
基因II
Gene II
复制类型
Type of duplication
同义
替换率
Ka
非同义
替换率
Ks
Ka/Ks 分歧时间(百万年前)
Divergence time (MYA)
IbDof40 IbDof41 染色体片段复制 Segmental duplication gene pairs 0.006582 0.044195 0.148927 1.47318
IbDof40 IbDof29 染色体片段复制 Segmental duplication gene pairs 0.338989 0.932423 0.363557 31.08075
IbDof45 IbDof14 染色体片段复制 Segmental duplication gene pairs 0.290234 0.953107 0.304514 31.77022
IbDof45 IbDof27 染色体片段复制 Segmental duplication gene pairs 0.287356 1.117214 0.257208 37.24048
IbDof46 IbDof13 染色体片段复制 Segmental duplication gene pairs 0.217848 1.104950 0.197156 36.83168
IbDof46 IbDof12 染色体片段复制 Segmental duplication gene pairs 0.192186 1.127080 0.170517 37.56932

Fig. 4

Chromosome location and duplication events of Dof genes in sweetpotato"

Fig. 5

Synteny relationship of Dof genes between sweetpotato and its relative wild species Ipomoea trifida Lines between the chromosomes in sweetpotato (top) and Ipomoea trifida (bottom) indicate orthologous gene pairs."

Fig. 6

Relative expression profiles of Dof genes in different tissues of sweetpotato A: the relative expression profiles of Dof genes in different tissues of Xushu 22; B: the relative expression profiles of Dof genes in different tissues of Xushu 18. The value of FPKM of Dof genes is presented."

Fig. 7

Relative expression profiles of Dof genes under cold stress treatment in sweetpotato *: P < 0.05; **: P < 0.01."

Fig. 8

Relative expression profiles of Dof genes under drought stress treatment in sweetpotato **: P < 0.01."

Fig. 9

Relative expression profiles of Dof genes under salt stress treatment in sweetpotato *: P < 0.05; **: P < 0.01."

Fig. 10

Relative expression profiles of Dof genes under H2O2 treatment in sweetpotato *: P < 0.05; **: P < 0.01."

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