Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development
Abstract
:1. Introduction
2. Results
2.1. Construction of TF-PHOTO, a C. Endivia Leaf Database for Transcription Factors and Photosynthesis-Related Genes
2.2. Finding Expression Patterns in Leaves Using K-Means Cluster Analysis
2.3. Analysis of Gene Co-expression Networks of C. endivia Leaves
2.4. Interplay Between Shape and Function: Photosynthetic Parameters in Relation to Morphological Leaf Diversity
2.5. Interplay Between Development and Function: Developmental Genes Related to the Photosynthetic Regulatory Pathway
2.6. TF-PHOTO Genes Differentially Expressed in Broad Versus Curly Leaves
3. Discussion
3.1. The Regulatory Network of Photosynthesis in the Leaves of C. endivia
3.2. Developmental Genes in Cluster Three Linked to Positive Regulation of Photosynthesis
3.3. Developmental Genes in Cluster Six Antagonistic to Photosynthesis
3.4. Transcription Factors that Are Differentially Expressed Between Broad- and Curly-Leaved C. endivia Cultivars
4. Materials and Methods
4.1. Biological Material and Morphological Analysis
4.2. RNA Isolation, Sequencing, and Expression Analysis
4.3. TF-PHOTO Database Construction
4.4. K-Means Cluster Analysis and Gene Co-Expression Network Construction
4.5. Chlorophyll Fluorescence Measurements
4.6. Determination of Chlorophyll and Total Carotenoids Content
4.7. Measurements of Spectral Reflectance and Spectral Reflectance Indices
4.8. Measurement of Lipid Peroxidation Levels
4.9. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Cultivar | Parameters1 | |||||
---|---|---|---|---|---|---|
Fv/Fm (Relative Units) | Φ PSII (Relative Units) | ETR (μmol elec. m−2 s−1) | Abs (Relative Units) | Chlorophyll Content (µg cm−2) | PRI (Relative Units) | |
Domari | 0.793 ± 0.001 c | 0.405 ± 0.004 b | 55.73 ± 0.53 b | 0.746 ± 0.006 b | 19.87 ± 0.96 b | 0.043 ± 0.001 a |
Myrna | 0.807 ± 0.001 b | 0.375 ± 0.003 c | 49.42 ± 0.47 c | 0.715 ± 0.002 c | 17.25 ± 1.98 bc | 0.038 ± 0.001 ab |
Flester | 0.828 ± 0.001 a | 0.375 ± 0.003 c | 46.64 ± 0.47 d | 0.675 ± 0.009 d | 14.51 ± 1.01 c | 0.033 ± 0.001 b |
Confiance | 0.781 ± 0.001 d | 0.419 ± 0.005 a | 60.16 ± 0.76 a | 0.778 ± 0.002 a | 23.57 ± 0.58 a | 0.042 ± 0.001 a |
P | 0.001 | 0.001 | 0.001 | 0.003 | 0.002 | 0.005 |
Ce ID | Category | Ath ID | Gene Symbol | Score to Core | K | Ce Gene Name |
---|---|---|---|---|---|---|
Ce_contig37589 | TF | AT4G30080 | AUXIN RESPONSE FACTOR 16 (ARF16) | 0.925 | 3 | ARF_11 |
Ce_contig68433 | TF | AT2G25180 | RESPONSE REGULATOR 12 (RR12) | 0.964 | 3 | ARR-B_7 |
Ce_contig18469 | TF | AT1G14920 | GIBBERELLIC ACID INSENSITIVE (GAI) | 0.936 | 3 | GRAS_16 |
Ce_contig31926 | TF | AT5G17490 | RGA-LIKE PROTEIN 3 (RGL3) | 0.972 | 3 | GRAS_23 |
Ce_contig82634 | TF | AT4G00150 | LOST MERISTEMS 3 (LOM3/SCL6-IV) | 0.918 | 3 | GRAS_43 |
Ce_contig6575 | TF | AT4G00150 | LOST MERISTEMS 3 (LOM3/SCL6-IV) | 0.948 | 3 | GRAS_7 |
Ce_contig71598 | TF | AT3G13960 | GROWTH-REGULATING FACTOR 5 (GRF5) | 0.941 | 3 | GRF_8 |
Ce_contig83059 | TF | AT4G32880 | ATHB-8 | 0.933 | 3 | HD-ZIP_41 |
Ce_contig21296 | TF | AT2G22540 | SHORT VEGETATIVE PHASE (SVP) | 0.938 | 3 | MIKC-MADS_10 |
Ce_contig36777 | TF | AT5G65060 | MADS AFFECTING FLOWERING 3 (MAF3) | 0.973 | 3 | MIKC-MADS_13 |
Ce_contig30145 | TF | AT5G60440 | AGAMOUS-LIKE 62 (AGL62) | 0.936 | 3 | Mtype_MADS_10 |
Ce_contig1183 | TF | AT3G61250 | MYB DOMAIN PROTEIN 17 (MYB17) | 0.898 | 3 | MYB_2 |
Ce_contig13510 | PHOTO | AT2G18790 | PHYTOCHROME B (PHYB) | 0.928 | 3 | PHYB |
Ce_contig73618 | TF | AT2G33810 | SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 (SPL3) | 0.899 | 3 | SBP_14 |
Ce_contig85637 | TF | AT2G36990 | SIGMA FACTOR 6 (SIG6) | 0.955 | 3 | SIG_5 |
Ce_contig49086 | TF | AT3G27010 | TEOSINTE BRANCHED 1, CYCLOIDEA, PCF (TCP) 20 (TCP20) | 0.908 | 3 | TCP_12 |
Ce_contig33120 | TF | AT3G47620 | TEOSINTE BRANCHED, CYCLOIDEA, PCF (TCP) 14 (TCP14) | 0.986 | 3 | TCP_7 |
Ce_contig38256 | TF | AT1G19850 | MONOPTEROS (MP) | 0.947 | 6 | ARF_12 |
Ce_contig18795 | TF | AT1G27730 | SALT TOLERANCE ZINC FINGER (STZ) (ZAT10) | 0.985 | 6 | C2H2_22 |
Ce_contig46000 | TF | AT1G27730 | SALT TOLERANCE ZINC FINGER (STZ) (ZAT10) | 0.955 | 6 | C2H2_40 |
Ce_contig76425 | TF | AT1G27730 | SALT TOLERANCE ZINC FINGER (STZ) (ZAT10) | 0.967 | 6 | C2H2_62 |
Ce_contig81969 | TF | AT1G27730 | SALT TOLERANCE ZINC FINGER (STZ) (ZAT10) | 0.988 | 6 | C2H2_71 |
Ce_contig56990 | TF | AT4G34410 | REDOX RESPONSIVE TRANSCRIPTION FACTOR 1 (RRTF1) | 0.976 | 6 | ERF_75 |
Ce_contig5939 | TF | AT5G48150 | PHYTOCHROME A SIGNAL TRANSDUCTION 1 (PAT1) | 0.946 | 6 | GRAS_6 |
Ce_contig26571 | TF | AT4G37740 | GROWTH-REGULATING FACTOR 2 (GRF2) | 0.954 | 6 | GRF_1 |
Ce_contig19510 | TF | AT5G66870 | ASYMMETRIC LEAVES 2-LIKE 1 (ASL1) | 0.934 | 6 | LBD_6 |
Ce_contig49004 | TF | AT4G21440 | MYB-LIKE 102 (MYB102) | 0.974 | 6 | MYB_36 |
Ce_contig8173 | TF | AT2G31180 | MYB DOMAIN PROTEIN 14 (MYB14) | 0.945 | 6 | MYB_9 |
Ce_contig7 | TF | AT3G10500 | NAC DOMAIN CONTAINING PROTEIN 53 (NAC053) | 0.971 | 6 | NAC_1 |
Ce_contig47321 | TF | AT5G13180 | VND-INTERACTING 2 (VNI2) | 0.990 | 6 | NAC_49 |
Ce_contig85206 | TF | AT2G27990 | BEL1-LIKE HOMEODOMAIN PROTEIN 8 (BLH8) | 0.893 | 6 | TALE_22 |
Ce_contig23430 | TF | AT4G01250 | WRKY22 | 0.957 | 6 | WRKY_25 |
Ce_contig27558 | TF | AT4G23810 | WRKY53 | 0.974 | 6 | WRKY_29 |
Ce_contig33086 | TF | AT3G56400 | WRKY70 | 0.963 | 6 | WRKY_34 |
Ce_contig60019 | TF | AT4G01250 | WRKY22 | 0.909 | 6 | WRKY_50 |
Ce_contig75830 | TF | AT5G13080 | WRKY75 | 0.913 | 6 | WRKY_59 |
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Testone, G.; Baldoni, E.; Iannelli, M.A.; Nicolodi, C.; Di Giacomo, E.; Pietrini, F.; Mele, G.; Giannino, D.; Frugis, G. Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development. Plants 2019, 8, 531. https://doi.org/10.3390/plants8120531
Testone G, Baldoni E, Iannelli MA, Nicolodi C, Di Giacomo E, Pietrini F, Mele G, Giannino D, Frugis G. Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development. Plants. 2019; 8(12):531. https://doi.org/10.3390/plants8120531
Chicago/Turabian StyleTestone, Giulio, Elena Baldoni, Maria Adelaide Iannelli, Chiara Nicolodi, Elisabetta Di Giacomo, Fabrizio Pietrini, Giovanni Mele, Donato Giannino, and Giovanna Frugis. 2019. "Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development" Plants 8, no. 12: 531. https://doi.org/10.3390/plants8120531