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Table 1 Differentially regulated transcripts in DRNL::GFP-positive protoplasts (fold change ≥ 1.5; p ≤ 0.01) compared to DRNL::GFP− protoplasts that have functions associated with meristem maintenance and identity, polarity, boundary formation, hormones, vasculature, epigenetic changes and that generate miRNAs

From: The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem

Gene Alias Locus Fold change
Meristem maintenance and identity/floral markers
ASYMMETRIC LEAVES2 AS2 At1g65620 +2.55
FLOWERING PROMOTING FACTOR1 FPF1 At5g24860 +2.38
SHORT VEGETATIVE PHASE SVP At2g22540 +2.16
REPRODUCTIVE MERISTEM1 REM1 At3g19184 +2.10
AINTEGMUMENTA ANT At4g37750 +2.08
LEAFY LFY At5g61850 +1.98
AINTEGUMENTA-LIKE6 AIL6 At5g10510 +1.96
PISTILLATA PI At5g20240 +1.93
REGULATOR OF AXILLARY MERISTEMS1/MYB37 RAX1 At5g23000 +1.86
BASIC PENTACYSTEINE 3 BPC3 At1g68120 +1.85
UNUSUAL FLORAL ORGANS UFO At1g30950 +1.85
BRCA1-ASSOCIATED RING DOMAIN1 BARD1 At1g04020 +1.83
CAULIFLOWER CAL At1g26310 +1.82
REPRODUCTIVE MERISTEM3 REM3 At5g58280 +1.82
LATERAL MERISTEM IDENTITY1 LMI1 At5g03790 +1.79
ULTRAPETALA1 ULT1 At4g28190 +1.77
APETALA1 AP1 At1g69120 +1.60
LATERAL MERISTEM IDENTITY2 LMI2 At3g61250 + 1.55
TUBBY8 TUB8 At1g16070 +1.52
SHOOTMERISTEMLESS STM At1g62360 −1.54
BARELY ANY MERISTEM3 BAM3 At4g20270 −2.89
BREVIPEDICELLUS/KNAT1 BP At4g08150 −3.57
Polarity
YABBY5 YAB5 At2g26580 +14.01
NUBBIN NUB At1g13400 +5.81
BLADE-ON-PETIOLE2 BOP2 At2g41370 + 5.44
BLADE-ON-PETIOLE1 BOP1 At3g57130 + 5.19
FILAMENTOUS FLOWER (YABBY1) FIL At2g45190 +4.37
JAGGED JAG At1g68480 + 3.32
PUCHI PUCHI At5g18560 + 3.25
KNOX ARABIDOPSIS THALIANA MEINOX KNATM At1g14760 +3.17
HOMEOBOX GENE1 ATH1 At4g32980 +2.90
PRESSED FLOWER PRS At2g28610 +2.40
YABBY3 YAB3 At4g00180 +2.14
ETTIN ETT At2g33860 +1.87
KANADI3 KAN3 At4g17695 −3.52
Boundary genes
SUPERMAN SUP At3g23130 +3.07
JAGGED LATERAL ORGANS (LBD30) JLO At4g00220 +2.38
LATERAL BOUNDARY DOMAIN18 LBD18 At2g45420 +2.21
GROWTH REGULATING FACTOR2 GRF2 At4g37740 +1.95
GROWTH REGULATING FACTOR5 GRF5 At3g13960 +1.86
LATERAL ORGAN JUNCTION LOJ At2g39230 +1.68
GROWTH REGULATING FACTOR1 GRF1 At2g22840 +1.63
CUP-SHAPED COTYLEDON1 CUC1 At3g15170 +1.54
PETAL LOSS PTL At5g03680 −1.63
LATERAL ORGAN BOUNDARY LOB At5g63090 −8.87
Auxin
MONOPTEROS MP At1g19850 +1.67
IAA CARBOXYLMETHYLTRANSFERASE1 IAMT 1 At5g55250 −4.64
Brassinosteroids
BRI1-LIKE1 BRL1 At1g55610 +1.59
BR ENHANCED EXPRESSION2 BEE2 At4g36540 −3.97
BR ENHANCED EXPRESSION1 BEE1 At1g18400 −8.15
Cytokinins
HISTIDINE PHOSPHOTRANSFER PROTEIN6 AHP6 At1g80100 +18.08
ISOPENTENYLTRANSFERASE7 IPT7 At3g23630 −7.25
ISOPENTENYLTRANSFERASE3 IPT3 At3g63110 −13.47
Gibberellins
GIBBERELLIN OXIDASE3 GA3ox3 At4g21690 +4.13
GIBBERELLIN 2-OXIDASE4 GA2ox4 At1g47990 +3.24
GIBBERELLIN 20-OXIDASE2 GA20ox2 At5g51810 +2.16
GIBBERELLIN 3-OXIDASE1 GA3ox1 At1g15550 +1.97
GIBBERELLIN 2-OXIDASE2 GA2ox2 At1g30040 +1.58
Other transcription factors
SHI-RELATED SEQUENCE4 SRS4 At2g18120 +3.61
STYLISH1 STY1 At3g51060 +2.74
SHI-RELATED SEQUENCE7 SRS7 At1g19790 +2.21
INFLORESCENCE DEFICIENT IN ABSCISSION (IDA)-LIKE 2 IDL2 At5g64667 +1.93
SHORT INTERNODES SHI At5g66350 +1.92
MiRNAs and the siRNA precursor TAS3A
TAS3A   At3g17185 −2.21
MiR390A   At2g38325 −2.73
MiR159/159B   At1g18075 −2.86
MiR172D   At3g55512 −3.06
MiR156E   At5g11977 −3.20
MiR172/172B   At5g04275 −5.55
MiR164/164B   At5g01747 −5.88
MiR319/319B   At5g41663 −6.29
MiR160/160C   At5g46845 −8.44
MiR156C   At4g31877 −11.49
MiR172/172A   At2g28056 −21.01
Vascular development
EPIDERMALPATTERNING LIKE FACTOR-LIKE 6 EPFL6 At2g30370 −2.26
REDUCED IN LATERAL GROWTH1 RUL1 At5g05160 −2.44
TDIF-RECEPTOR/PHLOEM INTERCALATED WITH XYLEM TDR/PXY At5g61480 −2.81
CLAVATA3/EMBRYO SURROUNDING REGION41 CLE41 At3g24770 −2.84
XYLEM CYSTEINE PEPTIDASE1 XCP1 At4g35350 −3.02
CLAVATA3/EMBRYO SURROUNDING REGION44 CLE44 At4g13195 −3.24
HIGH CAMBIAL ACTIVITY2 HCA2 At5g62940 −6.05
NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 NST1 At2g46770 −6.45
VASCULAR RELATED NAC DOMAIN6 VND6 At5g62380 −7.53
VASCULAR RELATED NAC DOMAIN7 VND7 At1g71930 −7.76
XYLEM CYSTEINE PEPTIDASE2 XCP2 At1g20850 −7.86
WUSCHEL-RELATED HOMEOBOX4 WOX4 At1g46480 −23.91
Epigenetic regulation
DECREASED DNA METHYLATION1 DDM1 At5g66750 +1.91
SET DOMAIN GROUP4 SDG4 At4g30860 +1.82
VARIANT IN METHYLATION2 VIM2 At1g66050 +1.78
VARIANT IN METHYLATION6 VIM6 At4g08590 +1.77
VARIANT IN METHYLATION1 VIM1 At1g57820 +1.75
VARIANT IN METHYLATION3 VIM3 At5g39550 +1.73
DNA METHYLTRANSFERASE1 MET1 At5g49160 +1.71
CHROMOMETHYLASE3 CMT3 At1g69770 +1.63
KRYPTONITE KYP At5g13960 +1.53
SET DOMAIN PROTEIN35 SDG35 At1g26760 +1.52
DEMETER-LIKE PROTEIN3 DML3 At4g34060 −4.58
  1. Loci in bold represent genes used for the network in Fig. 5