Chin Bull Bot ›› 2018, Vol. 53 ›› Issue (5): 612-624.doi: 10.11983/CBB17117

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Genome-wide Identification of Ethylene Responsive Factor (ERF) Family Genes in Peach and Screening of Genes Related to Germination

Zhao Xuehui1,2, Wang Qingjie1,2, Li Chen1,2, Chen Xiude1,2, Xiao Wei1,2, Gao Dongsheng1,2, Fu Xiling1,2,*()   

  1. 1College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, China;
    2State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China;
  • Received:2017-06-15 Accepted:2017-10-16 Online:2018-11-29 Published:2018-09-01
  • Contact: Fu Xiling E-mail:xilingfu@sdau.edu.cn
  • About author:

    † These authors contributed equally to this paper

Abstract:

In this study, genome-wide identification of ERF family genes in ‘zhongyousihao’ peach was studied by using MEGA 6.0, MEME, GSDS, DNAMAN 6.0. We identified 102 genes, and phylogenetic analyses of the genes indicated that the transcription factors can be classified into 10 different groups (I-X). Gene structure analysis showed that 81 genes had no introns, 20 genes contained an intron, and 1 gene contained 5 introns, which had a large difference from other members. Conservative motif analysis showed that the ERF family contained 20 conserved elements: Motifs 1, 2 and 4 belonged to the APETALA2 (AP2)/ERF domain, and the same conserved motif appeared mainly in the same family; the function of most conserved motifs is unknown. qRT-PCR revealed that the expression of PpeERF068 during dormancy and germination was consistent with the developmental status of leaf buds, which suggested that it might be related to leaf bud germination. The gene expression of peach buds during each period in light culture incubation further showed the relation between PpeERF068 and the germination of leaf buds. So PpeERF068 was named PpeEBB1. We will further study the molecular mechanism of PpeEBB1 to provide theoretical guidance for the cultivation and management of peach.

Key words: peach, ERF family, bud germination, PpeEBB1

Table 1

Primers of qRT-PCR"

Locus name Forward primer (5′-3′) Reverse primer (5′-3′)
Prupe.3g094700 GCGGAGATAAGAGACCGAAT AGAAGATGATGAGCAAGGTGAG
Prupe.1g245500 AGTATCACAGACGACGCAGG ATCGCCCATCACTCAAGA
Prupe.1g212700 TATGCGGCGGAGATAAGA GGGTGAGATAATGGAGGTGA
Prupe.1g139600 TGGATTCTGGGACAACCA GGAACTGATGGAGAGCAAGAG
Prupe.4g176200 GCCCAAACTCCAAAGAGA GTTGTTGTGGCTGTTGATGT
Prupe.4g051400 TCTCGCTCAGGGTGTTAGTA CAGCCGTTGATGAAACTG
Prupe.8g230600 TTGCCTCACACGCTTGTTA GAACGGTTTCTTCTCTTTCCTC
Prupe.4g051200 TCTCTCTCTGGACCTCAACAT CGCCAACATTTCCTACAAC
Prupe.4g222300 AAGCCAAGACCAACTTCCC TGTCCTGAAACCCGTAACC
Prupe.3g209100 TCCTCATCCTCCGTCGTAGA ATCACCACAAACCTCACCG
Actin GTTATTCTTCATCGGCGTCTTCG CTTCACCATTCCAGTTCCATTGTC

Table 2

List of PpeERF family genes and their related information"

Group name Gene name Locus name ORF length (bp) Size (aa) Molecular weight (Da) PI EST hitting
I PpeERF#001 Prupe.6g182200 1122 373 41331.3 6.56 13
I PpeERF#002 Prupe.3g009400 642 213 23101.2 9.79 7
I PpeERF#003 Prupe.1g513600 1137 378 41236.8 6.37 9
I PpeERF#004 Prupe.5g117800 933 310 34377.6 8.34 9
I PpeERF#005 Prupe.3g157100 1386 461 51713.0 5.97 0
I PpeERF#006 Prupe.1g008400 1230 409 45352.9 7.81 2
I PpeERF#007 Prupe.8g198700 696 231 26301.6 9.19 0
II PpeERF#008 Prupe.6g176400 540 179 20308.7 9.51 0
II PpeERF#009 Prupe.1g432000 528 175 19844.9 9.39 1
II PpeERF#010 Prupe.1g464400 453 150 17240.2 9.42 2
II PpeERF#011 Prupe.6g231500 501 166 17849.1 8.72 0
II PpeERF#012 Prupe.1g546100 501 166 17890.7 5.62 0
II PpeERF#013 Prupe.1g500900 726 241 26308.4 5.61 0
II PpeERF#014 Prupe.7g194400 648 215 23980.2 5.16 0
II PpeERF#015 Prupe.1g001700 552 183 20044.5 7.74 0
III PpeERF#016 Prupe.5g090700 558 185 19627.0 4.89 0
III PpeERF#017 Prupe.5g090600 537 178 19407.7 5.67 0
III PpeERF#018 Prupe.5g090400 543 180 19547.0 5.50 0
III PpeERF#019 Prupe.5g090300 543 180 19510.8 5.50 0
III PpeERF#020 Prupe.5g090800 555 184 19705.9 4.64 0
III PpeERF#021 Prupe.2g289600 696 231 24485.1 4.83 0
III PpeERF#022 Prupe.7g116300 609 202 21536.7 4.91 0
III PpeERF#023 Prupe.2g190200 609 202 22713.9 5.87 1
III PpeERF#024 Prupe.2g123200 831 276 30098.8 4.94 0
III PpeERF#025 Prupe.5g065300 762 253 28183.5 4.91 0
III PpeERF#026 Prupe.1g448600 771 256 27960.9 5.11 0
III PpeERF#027 Prupe.7g222700 789 262 28536.4 4.94 0
III PpeERF#028 Prupe.3g062800 732 243 26436.2 6.67 1
III PpeERF#029 Prupe.7g115900 606 201 22481.2 4.95 0
III PpeERF#030 Prupe.2g289500 690 229 24976.9 5.14 7
III PpeERF#031 Prupe.5g090500 723 240 27217.8 7.69 0
III PpeERF#032 Prupe.5g090100 711 236 26352.7 5.17 0
III PpeERF#033 Prupe.5g090000 693 230 25658.8 5.13 7
III PpeERF#034 Prupe.5g090200 699 232 26157.5 5.03 1
III PpeERF#035 Prupe.5g089900 693 230 25521.9 7.78 0
III PpeERF#036 Prupe.1g545700 522 173 19078.3 5.44 0
III PpeERF#037 Prupe.1g545400 600 199 22101.0 5.54 0
IV PpeERF#038 Prupe.2g253000 1041 346 37474.1 6.52 0
IV PpeERF#039 Prupe.6g284400 1554 517 58370.7 4.74 0
IV PpeERF#040 Prupe.2g256900 1167 388 42473.1 4.64 3
IV PpeERF#041 Prupe.3g223300 591 196 21305.5 8.32 0
IV PpeERF#042 Prupe.7g066700 858 285 32054.9 5.73 0
Group name Gene name Locus name ORF length (bp) Size (aa) Molecular weight (Da) PI EST hitting
IV PpeERF#043 Prupe.6g354000 672 223 23337.9 8.50 0
IV PpeERF#044 Prupe.1g372100 768 255 28137.6 6.55 0
V PpeERF#045 Prupe.3g096000 639 212 24310.2 5.94 0
V PpeERF#046 Prupe.1g390800 588 195 22413.4 6.66 6
V PpeERF#047 Prupe.1g480400 672 223 24759.7 9.10 0
V PpeERF#048 Prupe.7g243600 732 243 26570.6 7.02 0
V PpeERF#049 Prupe.3g084600 567 188 20855.3 5.97 0
V PpeERF#050 Prupe.7g004900 945 314 34636.3 5.44 0
V PpeERF#051 Prupe.6g004400 867 288 31688.5 6.01 0
V PpeERF#052 Prupe.3g263000 1275 424 46904.3 4.58 0
V PpeERF#053 Prupe.5g136200 939 312 33152.5 6.13 0
V PpeERF#054 Prupe.1g084800 936 311 33626.0 8.92 0
V PpeERF#055 Prupe.5g213800 675 224 25367.4 8.71 0
VI PpeERF#056 Prupe.5g114100 1002 333 37019.0 4.98 0
VI PpeERF#057 Prupe.2g306400 1098 365 41098.9 4.75 2
VI PpeERF#058 Prupe.2g183200 864 287 32269.0 4.95 0
VI PpeERF#059 Prupe.3g019900 570 189 20614.4 9.37 0
VI PpeERF#060 Prupe.7g060700 588 195 21933.2 10.37 2
VI PpeERF#061 Prupe.6g039700 927 308 34031.9 5.49 2
VI PpeERF#062 Prupe.5g220700 1311 436 49386.8 6.25 1
VI PpeERF#063 Prupe.1g310100 1020 339 38021.2 4.92 1
VII PpeERF#064 Prupe.8g264900 966 321 35682.6 5.68 4
VII PpeERF#065 Prupe.3g032300 1149 382 42495.9 4.81 84
VII PpeERF#066 Prupe.1g130300 870 289 31564.0 7.66 31
VIII PpeERF#067 Prupe.3g094700 870 289 31781.0 9.56 0
VIII PpeERF#068 Prupe.1g245500 1275 424 46297.0 7.73 0
VIII PpeERF#069 Prupe.1g212700 831 276 29938.4 4.94 0
VIII PpeERF#070 Prupe.1g139600 1092 363 39938.7 5.60 0
VIII PpeERF#071 Prupe.4g176200 687 228 24245.0 9.62 2
VIII PpeERF#072 Prupe.4g051400 795 264 28447.6 9.47 1
VIII PpeERF#073 Prupe.8g230600 546 181 19951.0 9.99 0
VIII PpeERF#074 Prupe.4g051200 519 172 18303.7 9.20 3
VIII PpeERF#075 Prupe.4g222300 696 231 25022.8 7.62 20
VIII PpeERF#076 Prupe.3g209100 708 235 25471.3 6.58 3
IX PpeERF#077 Prupe.2g129700 672 223 24950.8 5.41 0
IX PpeERF#078 Prupe.2g129500 651 216 23968.9 5.99 0
IX PpeERF#079 Prupe.2g129600 714 237 25948.7 5.47 0
IX PpeERF#080 Prupe.2g129300 816 271 29817.0 5.17 0
IX PpeERF#081 Prupe.2g129400 621 206 22559.1 5.97 0
IX PpeERF#082 Prupe.5g061800 846 281 30157.0 9.09 10
IX PpeERF#083 Prupe.6g064700 2115 704 77761.3 9.77 15
IX PpeERF#084 Prupe.2g272300 783 260 29210.8 6.53 3
IX PpeERF#085 Prupe.5g062000 1059 352 39322.2 5.90 5
Group name Gene name Locus name ORF length (bp) Size (aa) Molecular weight (Da) PI EST hitting
IX PpeERF#086 Prupe.2g272400 945 314 35018.8 6.17 21
IX PpeERF#087 Prupe.2g272500 726 241 27069.2 5.92 0
IX PpeERF#088 Prupe.8g224700 540 179 20470.7 6.08 0
IX PpeERF#089 Prupe.1g037800 492 163 18008.7 6.85 0
IX PpeERF#090 Prupe.8g224800 465 154 17059.7 7.79 0
IX PpeERF#091 Prupe.1g037700 417 138 15204.7 6.84 0
IX PpeERF#092 Prupe.4g055600 795 264 29431.3 5.61 0
IX PpeERF#093 Prupe.4g055500 564 187 20369.6 9.51 2
IX PpeERF#094 Prupe.6g348700 744 247 28089.7 4.92 0
IX PpeERF#095 Prupe.8g224600 759 252 28672.0 4.99 1
IX PpeERF#096 Prupe.1g037900 699 232 25950.8 5.54 1
X PpeERF#097 Prupe.8g125100 816 271 30318.2 8.16 0
X PpeERF#098 Prupe.7g134100 801 266 29255.4 7.67 0
X PpeERF#099 Prupe.5g141200 696 231 25763.5 9.21 0
X PpeERF#100 Prupe.6g165700 1215 404 43314.9 7.07 2
X PpeERF#101 Prupe.5g141300 816 271 30005.0 6.16 0
X PpeERF#102 Prupe.1g214900 741 246 27203.7 6.23 1

Figure 1

The phylogenetic tree of peach ERF family genesI-X indicate the 10 different groups of ERF family, respectively; II-L: II-like; VI-L: VI-like"

Figure 2

Amino acids sequence alignment of AP2/ERF domain of ERF family genes in peach"

Figure 3

Conserved motif (A) and structures (B) of ERF genes in peachI-X indicate the 10 different groups of ERF family, respectively."

Figure 4

Bud development process (A) and relative expression of VIII sub-family (B) in peach under natural condition"

Figure 5

Bud development process (A) and relative expression of VIII sub-family genes (B) in peach in light culture incubation"

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