# Anthocyanin Biosynthesis Genes as Model Genes for Genome Editing in Plants **Authors:** Emil Khusnutdinov, Anna Sukhareva, Maria Panfilova, Elena Mikhaylova PMC · DOI: 10.3390/ijms22168752 · International Journal of Molecular Sciences · 2021-08-15 ## TL;DR This paper reviews how CRISPR/Cas genome editing can be tested using anthocyanin biosynthesis genes, which produce visible plant traits and may improve stress resistance. ## Contribution The paper proposes new model genes for CRISPR/Cas editing in plants, focusing on anthocyanin biosynthesis and stress-related traits. ## Key findings - CRISPR/Cas editing of anthocyanin genes like PAP1, DFR, F3H, and F3′H has been successfully tested in multiple plant species. - Genes like Delila, MYB60, and TTG1 are suggested as new model genes due to their roles in anthocyanin biosynthesis and additional traits like drought tolerance and trichome development. - Edited anthocyanin genes may improve plant stress resistance, making them valuable for agricultural applications. ## Abstract CRISPR/Cas, one of the most rapidly developing technologies in the world, has been applied successfully in plant science. To test new nucleases, gRNA expression systems and other inventions in this field, several plant genes with visible phenotypic effects have been constantly used as targets. Anthocyanin pigmentation is one of the most easily identified traits, that does not require any additional treatment. It is also associated with stress resistance, therefore plants with edited anthocyanin genes might be of interest for agriculture. Phenotypic effect of CRISPR/Cas editing of PAP1 and its homologs, DFR, F3H and F3′H genes have been confirmed in several distinct plant species. DFR appears to be a key structural gene of anthocyanin biosynthesis, controlled by various transcription factors. There are still many promising potential model genes that have not been edited yet. Some of them, such as Delila, MYB60, HAT1, UGT79B2, UGT79B3 and miR156, have been shown to regulate drought tolerance in addition to anthocyanin biosynthesis. Genes, also involved in trichome development, such as TTG1, GLABRA2, MYBL2 and CPC, can provide increased visibility. In this review successful events of CRISPR/Cas editing of anthocyanin genes are summarized, and new model genes are proposed. It can be useful for molecular biologists and genetic engineers, crop scientists, plant genetics and physiologists. ## Linked entities - **Genes:** REG3A (regenerating family member 3 alpha) [NCBI Gene 5068], DFR (dihydroflavonol 4-reductase) [NCBI Gene 544150], F3H (flavanone 3-hydroxylase) [NCBI Gene 732548], F3H (flavanone 3-hydroxylase) [NCBI Gene 732548], MYB60 (MYB transcription factor MYB60) [NCBI Gene 778080], HAT1 (histone acetyltransferase 1) [NCBI Gene 8520], MIR156 (microRNA MIR156) [NCBI Gene 143087608], LMO1 (LIM domain only 1) [NCBI Gene 4004], GL2 (HD-ZIP IV family of homeobox-leucine zipper protein with lipid-binding START domain-containing protein) [NCBI Gene 844323], MYBL2 (MYB proto-oncogene like 2) [NCBI Gene 4605], CPC (Homeodomain-like superfamily protein) [NCBI Gene 819249] ## Full-text entities - **Genes:** F3H (flavanone 3-hydroxylase) [NCBI Gene 824287] {aka F3'H, FLAVANONE 3-HYDROXYLASE, TRANSPARENT TESTA 6, TT6, flavanone 3-hydroxylase}, ANT1 (aromatic and neutral transporter 1) [NCBI Gene 820363] {aka aromatic and neutral transporter 1}, R2R3-MYB [NCBI Gene 101263611], MIR870 (ncRNA) [NCBI Gene 6240786] {aka MIR870A, microRNA870A, p_MI0005448}, CPC (Homeodomain-like superfamily protein) [NCBI Gene 819249] {aka CAPRICE, F11C10.10, MYB FAMILY TRANSCRIPTION FACTOR CPC}, TTG1 (Transducin/WD40 repeat-like superfamily protein) [NCBI Gene 832523] {aka ATTTG1, K18P6.4, K18P6_4, TRANSPARENT TESTA GLABRA 1, TTG, UNARMED 23}, TT4 (Chalcone and stilbene synthase family protein) [NCBI Gene 831241] {aka ATCHS, CHALCONE SYNTHASE, CHALCONE/STILBENE SYNTHASE, CHS, MAC12.28, MAC12_28}, DFR (dihydroflavonol 4-reductase) [NCBI Gene 544150] {aka FNR}, SPL13A (Squamosa promoter-binding protein-like (SBP domain) transcription factor family protein) [NCBI Gene 835126] {aka MBA10.13, MBA10_13, SPL13, SQUAMOSA PROMOTER-BINDING PROTEIN LIKE 13, SQUAMOSA PROMOTER-BINDING PROTEIN LIKE 13A}, HAT1 (histone acetyltransferase 1) [NCBI Gene 8520] {aka KAT1}, MYB57 (myb domain protein 57) [NCBI Gene 821113] {aka ATMYB57, F4P13.8, F4P13_8, myb domain protein 57}, GAD (glutamate decarboxylase) [NCBI Gene 831599] {aka GAD1, GLUTAMATE DECARBOXYLASE, GLUTAMATE DECARBOXYLASE 1, MKP11.30, MKP11_30, glutamate decarboxylase}, C4H (cinnamate-4-hydroxylase) [NCBI Gene 817599] {aka ATC4H, CINNAMATE 4-HYDROXYLASE, CINNAMATE-4-HYDROXYLASE, CYP73A5, REDUCED EPRDERMAL FLUORESCENCE 3, REF3}, MYBA7 (R2R3 MYB transcription factor) [NCBI Gene 100265568], PAP1 [NCBI Gene 543510], LBD39 (LOB domain-containing protein 39) [NCBI Gene 829909] {aka F19F18.30, F19F18_30, LOB domain-containing protein 39}, EIN3 (Ethylene insensitive 3 family protein) [NCBI Gene 821625] {aka AtEIN3, ETHYLENE-INSENSITIVE3}, FUS3 (AP2/B3-like transcriptional factor family protein) [NCBI Gene 822293] {aka FUSCA 3}, AGL44 (AGAMOUS-like 44) [NCBI Gene 815907] {aka AGAMOUS-like 44, ANR1, ARABIDOPSIS NITRATE REGULATED 1, F15N24.5, F15N24_5}, DFR (dihydroflavonol 4-reductase) [NCBI Gene 834291] {aka DIHYDROFLAVONOL 4-REDUCTASE, DIHYDROKAEMPFEROL 4-REDUCTASE, M318, MJB21.18, MJB21_18, TT3}, CaS (calcium sensing receptor) [NCBI Gene 832370] {aka MYJ24.5, MYJ24_5, calcium sensing receptor}, DFR [NCBI Gene 106447075], NAC042 (NAC domain containing protein 42) [NCBI Gene 818902] {aka ANAC042, F23E6.1, F23E6_1, JUB1, JUNGBRUNNEN 1, NAC domain containing protein 42}, MYB0 (myb domain protein 0) [NCBI Gene 822415] {aka ATGL1, ATMYB0, GL1, GLABRA 1, TRICHOME DIFFERENTIATION PROTEIN GL1, myb domain protein 0}, MYB10 (myb domain protein 10) [NCBI Gene 820464] {aka AtMYB10, myb domain protein 10}, MIR165a (ncRNA) [NCBI Gene 3766638] {aka MICRORNA 165, MIR165, microRNA165A, p_MI0000199}, TRY (Homeodomain-like superfamily protein) [NCBI Gene 835401] {aka MFH8.14, MFH8_14, TRIPTYCHON}, AT3G25795 (ncRNA) [NCBI Gene 6240732] {aka TAS4, trans acting siRNA 4}, PRPF6 (pre-mRNA processing factor 6) [NCBI Gene 24148] {aka ANT-1, ANT1, C20orf14, Prp6, RP60, SNRNP102}, NAC019 (NAC domain containing protein 19) [NCBI Gene 841722] {aka ANAC019, F14G24.16, F14G24_16, NAC domain containing protein 19}, PAP1 (production of anthocyanin pigment 1) [NCBI Gene 842120] {aka ATMYB75, F25P12.92, F25P12_92, MYB DOMAIN PROTEIN 75, MYB75, MYELOBLASTOSIS PROTEIN 75}, LMO1 (LIM domain only 1) [NCBI Gene 4004] {aka RBTN1, RHOM1, TTG1}, GL3 (basic helix-loop-helix (bHLH) DNA-binding superfamily protein) [NCBI Gene 834133] {aka GLABRA 3, GLABROUS 3, MYC6.2}, MYB113 (myb domain protein 113) [NCBI Gene 842955] {aka AtMYB113, T27F4.12, T27F4_12, myb domain protein 113}, TT7 (Cytochrome P450 superfamily protein) [NCBI Gene 830693] {aka CYP75B1, CYTOCHROME P450 75B1, D501, F13G24.190, F13G24_190, F3'H}, MYB90 (myb domain protein 90) [NCBI Gene 842957] {aka ATMYB90, PAP2, PRODUCTION OF ANTHOCYANIN PIGMENT 2, T27F4.14, T27F4_14, myb domain protein 90}, PAP12 (purple acid phosphatase 12) [NCBI Gene 817261] {aka ARABIDOPSIS THALIANA PURPLE ACID PHOSPHATASE 1, ATPAP1, ATPAP12, PAP1, PURPLE ACID PHOSPHATASE 1, PURPLE ACID PHOSPHATASE 12}, MYB [NCBI Gene 544113], MYB12 [NCBI Gene 100191123], 4CL3 (4-coumarate:CoA ligase 3) [NCBI Gene 842814] {aka 4-COUMARATE:COA LIGASE, 4-coumarate:CoA ligase 3, F16G16.6, F16G16_6}, PAL4 (phenylalanine ammonia-lyase 4) [NCBI Gene 820196] {aka phenylalanine ammonia-lyase 4}, F3'H [NCBI Gene 100736482], TT2 (Duplicated homeodomain-like superfamily protein) [NCBI Gene 833520] {aka ATMYB123, ATTT2, MOK9.18, MOK9_18, MYB DOMAIN PROTEIN 123, MYB123}, MYB114 (myb domain protein 114) [NCBI Gene 842956] {aka AtMYB114, T27F4.13, T27F4_13, myb domain protein 114}, MYBL2 (MYB proto-oncogene like 2) [NCBI Gene 4605] {aka B-MYB, BMYB}, LBD37 (LOB domain-containing protein 37) [NCBI Gene 836878] {aka ASL39, ASYMMETRIC LEAVES2-LIKE 39, K8K14.16, K8K14_16, LOB domain-containing protein 37}, 4CL5 (4-coumarate:CoA ligase 5) [NCBI Gene 821677] {aka 4-coumarate:CoA ligase 5}, MYB60 (myb domain protein 60) [NCBI Gene 837403] {aka AtMYB60, F22O13.30, F22O13_30, myb domain protein 60}, GL2 (HD-ZIP IV family of homeobox-leucine zipper protein with lipid-binding START domain-containing protein) [NCBI Gene 844323] {aka F19K16.20, F19K16_20, GLABRA 2, HOMEOBOX PROTEIN GLABRA 2}, LDOX (leucoanthocyanidin dioxygenase) [NCBI Gene 828387] {aka ANS, ANTHOCYANIDIN SYNTHASE, F7H19.60, F7H19_60, LEUCOANTHOCYANIDIN DIOXYGENASE, TANNIN DEFICIENT SEED 4}, RP9 (RP9 pre-mRNA splicing factor) [NCBI Gene 6100] {aka PAP-1, PAP1}, PAP2 (Purple acid phosphatases superfamily protein) [NCBI Gene 837949] {aka F16A14.11, F16A14_11, purple acid phosphatase 2}, MYB11 (myb domain protein 11) [NCBI Gene 825435] {aka ATMYB11, PFG2, PRODUCTION OF FLAVONOL GLYCOSIDES 2, myb domain protein 11}, MYB12 (myb domain protein 12) [NCBI Gene 819359] {aka ATMYB12, MYB DOMAIN PROTEIN 12, PFG1, PRODUCTION OF FLAVONOL GLYCOSIDES 1, T30B22.24, myb domain protein 12}, MYBL2 (MYB-like 2) [NCBI Gene 843443] {aka ARABIDOPSIS MYB-LIKE 2, ATMYBL2, F23N20.2, F23N20_2, MYB-like 2}, LEC2 (AP2/B3-like transcriptional factor family protein) [NCBI Gene 839724] {aka AtLEC2, F3H9.5, F3H9_5, LEAFY COTYLEDON 2}, MYB4 (myb domain protein 4) [NCBI Gene 830018] {aka ATMYB4, T9A14.11, myb domain protein 4}, MYB82 (myb domain protein 82) [NCBI Gene 835337] {aka AtMYB82, myb domain protein 82}, LAP1 (Cytosol aminopeptidase family protein) [NCBI Gene 816954] {aka F27D4.11, F27D4_11, leucyl aminopeptidase 1}, PAL1 [NCBI Gene 101261892] - **Diseases:** cyst nematodes (MESH:D009349), salt (MESH:D013651), pigmentation (MESH:D010859), fungal deceases (MESH:D009181), FNS (MESH:D020159), flowers (MESH:C000719190), purple pigmentation (MESH:C000719196), bacterial infections (MESH:D001424) - **Chemicals:** lipid (MESH:D008055), flavone (MESH:C043562), gentiodelphin (MESH:C414932), lignin (MESH:D008031), betalain (MESH:D050858), benzoic acid (MESH:D019817), flavonoid (MESH:D005419), proanthocyanidins (MESH:D044945), kaempherol (MESH:C006552), quercetin (MESH:D011794), Anthocyanin (MESH:D000872), flavones (MESH:D047309), GABA (MESH:D005680), brassinosteroid (MESH:D060406), sucrose (MESH:D013395), flavonols (MESH:D044948), oil (MESH:D009821), shikimate (MESH:C000723335), peonidin (MESH:C473205), (2R,3S,4S)-leucoanthocyanidins (-), heavy metals (MESH:D019216), N (MESH:D009584), flavonol (MESH:C041477), NO3 (MESH:C038619), malvidin (MESH:C065861), Cyanidin (MESH:C017154), delphinidin (MESH:C017185), fat (MESH:D005223), petunidin (MESH:C473206), chlorophyll (MESH:D002734), ATs (MESH:D001246), salt (MESH:D012492), fatty acid (MESH:D005227), pelargonidin (MESH:C066957), proanthocyanidin (MESH:C013221) - **Species:** Medicago truncatula (barrel medic, species) [taxon 3880], Petunia (petunia, genus) [taxon 4101], Nicotiana benthamiana (species) [taxon 4100], Daucus carota (carrot, species) [taxon 4039], Torenia fournieri (bluewings, species) [taxon 68875], Ipomoea nil (Japanese morning glory, species) [taxon 35883], Gentiana scabra (species) [taxon 292393], Oryza sativa (Asian cultivated rice, species) [taxon 4530], Brassica rapa (field mustard, species) [taxon 3711], Allium cepa (onion, species) [taxon 4679], Gerbera hybrid cultivar (species) [taxon 18101], Lycium ruthenicum (species) [taxon 112879], Pyrus pyrifolia (Asian pear, species) [taxon 3767], Prunus armeniaca (apricot, species) [taxon 36596], Eutrema salsugineum (saltwater cress, species) [taxon 72664], Mangifera indica (mango, species) [taxon 29780], Anthurium andraeanum (flamingo-lily, species) [taxon 226677], Ipomoea purpurea (common morning-glory, species) [taxon 4121], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Vaccinium corymbosum (American blueberry, species) [taxon 69266], Litchi chinensis (litchi, species) [taxon 151069], Fragaria vesca (alpine strawberry, species) [taxon 57918], Malus domestica (apple, species) [taxon 3750], Brassica oleracea (wild cabbage, species) [taxon 3712], Beta vulgaris (beet, species) [taxon 161934], Narcissus tazetta (species) [taxon 54860], Paeonia suffruticosa (moutan peony, species) [taxon 45171], Agrobacterium (genus) [taxon 357], Nicotiana tabacum (American tobacco, species) [taxon 4097], Actinidia deliciosa (Chinese gooseberry, species) [taxon 3627], Iochroma (genus) [taxon 304104], Lobelia erinus (species) [taxon 16430], Camelina sativa (false flax, species) [taxon 90675], Lycium barbarum (Duke of Argyll's teatree, species) [taxon 112863], Prunus persica (peach, species) [taxon 3760], Solanum lycopersicum (tomato, species) [taxon 4081], Raphanus sativus (radish, species) [taxon 3726], Lotus corniculatus (species) [taxon 47247], Antirrhinum majus (garden snapdragon, species) [taxon 4151], Apium graveolens (species) [taxon 4045], Fragaria x ananassa (strawberry, species) [taxon 3747], Ipomoea batatas (batate, species) [taxon 4120], Iochroma loxense (species) [taxon 362363], Solanum tuberosum (potatoes, species) [taxon 4113], Euphorbia pulcherrima (poinsettia, species) [taxon 37495], Trifolium repens (creeping white clover, species) [taxon 3899], Petunia nyctaginiflora (species) [taxon 310461], Muscari armeniacum (species) [taxon 156613], Pyrus pyrifolia var. culta (yama-nashi, varietas) [taxon 332388], Medicago sativa (alfalfa, species) [taxon 3879], Populus tomentosa (Chinese white poplar, species) [taxon 118781], Brassica juncea (brown mustard, species) [taxon 3707], Vitis vinifera (wine grape, species) [taxon 29760], Bean yellow dwarf virus (no rank) [taxon 57119], Musa acuminata (banana, species) [taxon 4641], Dendrobium (genus) [taxon 37818], Brassica napus (oilseed rape, species) [taxon 3708], Pyrus x bretschneideri (bai li, species) [taxon 225117], Gentiana triflora (species) [taxon 55190] - **Cell lines:** EDLL-S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232) ## Full text _Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC8395717/full.md ## Figures 1 figure with captions in the complete paper: https://tomesphere.com/paper/PMC8395717/full.md ## References 194 references — full list in the complete paper: https://tomesphere.com/paper/PMC8395717/full.md --- Source: https://tomesphere.com/paper/PMC8395717