Altering Plant Architecture to Improve Performance and Resistance

Plant hormone homeostasis modulates plant architecture, crop yield, and resistance to environmental stresses. miRNAs, phytohormones, key transcription factors, and other important signaling proteins form complex networks to regulate plant hormone homeostasis. Some transcription factors act as system integrators of internal and external signals to regulate lateral organ angles and/or orientations and/or branch and tiller numbers. Modification of plant architecture by fine-tuning the expression of key genes has proved to be a promising strategy to improve yield and/or stress resistance. High-stress resistance and yield are major goals in crop cultivation, which can be addressed by modifying plant architecture. Significant progress has been made in recent years to understand how plant architecture is controlled under various growth conditions, recognizing the central role phytohormones play in response to environmental stresses. miRNAs, transcription factors, and other associated proteins regulate plant architecture, mainly via the modulation of hormone homeostasis and signaling. To generate crop plants of ideal architecture, we propose simultaneous editing of multiple genes involved in the regulatory networks associated with plant architecture as a feasible strategy. This strategy can help to address the need to increase grain yield and/or stress resistance under the pressures of the ever-increasing world population and climate change. High-stress resistance and yield are major goals in crop cultivation, which can be addressed by modifying plant architecture. Significant progress has been made in recent years to understand how plant architecture is controlled under various growth conditions, recognizing the central role phytohormones play in response to environmental stresses. miRNAs, transcription factors, and other associated proteins regulate plant architecture, mainly via the modulation of hormone homeostasis and signaling. To generate crop plants of ideal architecture, we propose simultaneous editing of multiple genes involved in the regulatory networks associated with plant architecture as a feasible strategy. This strategy can help to address the need to increase grain yield and/or stress resistance under the pressures of the ever-increasing world population and climate change. APETALA 2 (AP2) DNA-binding domain-containing TFs. AUXIN RESPONSE FACTOR 7, a TF-regulating, auxin-mediated transcriptional activation or repression. ARABIDOPSIS RESPONSE REGULATOR, key regulators of cytokinin (CK) responses. BETAINE ALDEHYDE DEHYDROGENASE 2, encoding betaine aldehyde dehydrogenase involved in the inhibition of the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. the basic local alignment search tool (BLAST) used to query nucleotide sequences against nucleotide sequence databases. Brassica napus MORE AXILLARY GROWTH 1, encoding a carotenoid cleavage dioxygenase regulating plant height and axillary bud outgrowth in rapeseed. BRANCHED 1/TB1 (TEOSINTE BRANCHED 1), TF negatively modulating shoot branching. BRASSINOSTEROID C-6 OXIDASE 1, encoding a brassinosteroids (BR) C-6 oxidase, which catalyzes the final steps of BR synthesis. BASIC LEUCINE ZIPPERTF, a TF family involved in plant growth. CLAVATA 3, a regulator controlling the meristem development of shoot and floral. CONSTITUTIVE PHOTOMORPHOGENIC 1, a RING E3 ubiquitin ligase with a function as a central repressor of photomorphogenesis in higher plants. clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease 9 system, widely used in genome editing. CYTOCHROME P450 MONOOXYGENASE 1, a carlactone oxidase catalyzing the last step of strigolactone (SL) biosynthesis. DWARF 53, encoding a repressor of SL signaling; SLs induce its degradation. DENSE AND ERECT PANICLE 1, encoding a G protein γ subunit contributing to the regulation of erect panicle architecture. DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 1A, encoding a transcriptional activator. DEEPER ROOTING 1, a major quantitative trait locus (QTL) involved in deep rooting of rice. ERECT PANICLE 3, a rice gene encoding a peptide homologous to the arabidopsis F-box protein HAWAIIAN SKIRT. EXOCYST SUBUNIT EXO70 FAMILY PROTEIN A3, encoding a putative subunit of the octameric vesicle-tethering EXOCYST complex. EXPANSIN A3, encoding EXPANSIN-A3 involved in loosening and extension of plant cell walls. GA REQUIRING 5, encoding a rate-limiting gibberellin (GA) biosynthetic enzyme. GAMMA-GLUTAMYL PEPTIDASE 1, encoding a gamma-glutamyl peptidase involved in ascorbic acid synthesis. GRF-INTERACTING FACTOR 1, a transcriptional coactivator. Glycine max Dt2, a soybean MADS-box TF. GRAIN NUMBER 1a, encoding an enzyme that degrades CKs. GROWTH-REGULATING FACTOR 4, a plant-specific TF targeted by miR396s. GRAIN SIZE ON CHROMOSOME 3, a rice QTL involved in regulation grain size. GRAIN WEIGHT 2, a rice QTL involved in regulating grain weight. HOMEOBOX) genes, encoding TFs containing conserved homeodomain. HEADING DATE 1, a flowering time-related gene. HEAT STRESS TRANSCRIPTION FACTOR 2D, a transcriptional activator specifically binding DNA of heat shock promoter elements. ELONGATED HYPOCOTYL 5, a master regulator of photomorphogenesis. IDEAL PLANT ARCHITECTURE 1, a semidominant rice QTL encoding OsSPL14 and being involved in regulation of crop yield by modifying plant architecture. ISOPENTENYL-TRANSFERASE genes, encoding adenosine phosphate-isopentenyltransferases involved in the biosynthesis of CKs. JASMONATE-ZIM DOMAIN, repressor of jasmonic acid (JA) signaling. LOOSE PLANT ARCHITECTURE 1, an INDETERMINATE DOMAIN protein involved in shoot gravitropism. MONOCULM 1, a TF of the plant-specific GRAS family. a basic helix–loop–helix TF modulating JA signaling pathway. NADH-DEPENDENT GLUTAMATE SYNTHASE, a glutamate synthase playing a crucial role in assimilating ammonium. NINE-CIS-EPOXICAROTENOID DIOXIGENASE 3, an enzyme catalyzing the first step of abscisic acid (ABA) biosynthesis from carotenoids. NITRATE TRANSPORTER 2.1, encoding a high-affinity nitrate transporter. Oryza sativa BRASSINAZOLE RESISTANT 1, encoding a master regulator controlling BR-related gene expression in rice. Oryza sativa CYTOKININ OXIDASE/DEHYDROGENASE 9, encoding an enzyme involved in CK catabolism. Oryza sativa GATA7, encoding a GATA TF modulating BR-mediated rice growth. Oryza sativa GRETCHEN HAGEN 3.8, encoding an acyl-acid-amido synthetase catalyzing the ATP-dependent formation of amino acid conjugates with phytohormones. Oryza sativa GLYCOGEN SYNTHASE KINASE3-LIKE GENE 2, encoding a glycogen synthase kinase with negative regulation in BR signaling in rice. Oryza sativa HUA ENHANCER 1, encoding a small RNA methyltransferase, which is a potential target of the transcription activator-like (TAL) effector Tal9a. Oryza sativa NAC DOMAIN CONTAINING PROTEIN 2, encoding a rice NAC (for NAM, ATAF1/2, and CUC2) TF with a highly conserved N terminal NAC domain. Oryza sativa OVATE FAMILY PROTEIN 1, encoding a rice TF regulating BR responses. PHYTOCHROME B, a regulatory photoreceptor. PHYTOCHROMEINTERACTING FACTOR 4, encoding a TF mediating cell growth in response to light and temperature. PIN-FORMED 3, a predicted secondary transporter with the function of auxin efflux from cells. PLETHORA 1, encoding an auxin-responsive AP2-domain TF. PYRABACTIN RESISTANCE 1-LIKE proteins, ABA receptors. a rapid mapping of plant QTLs by using whole-genome resequencing of DNAs from two bulked populations. REGULATORY-ASSOCIATED PROTEIN OF mTOR, a regulatory associated protein of the TOR complex. the DELLA protein REPRESSOR OF GA 1-3, a repressor of GA response that appears to undergo GA-stimulated protein degradation. RCC1-LIKE DOMAIN protein,: the protein containing one or more RCC1-like domains. RNA interference, a technology used to repress the activity of given gene(s) in the cells. SMALL AUXIN UP RNA 19, an early auxin-responsive gene. SHORT HYPOCOTYL 2, a transcriptional repressor of the PIN auxin transporter genes. SLENDER RICE 1, a repressor of GA signaling in rice. STEROL 4α-METHYL OXIDASE 1, a key enzyme of the sterol biosynthetic pathway. SUCROE NON-FERMENTING 1-RELATED PROTEIN KINASES 2, protein kinases and the central components of ABA and osmotic stress signaling pathways. SELF PRUNING, a major regulator controlling the vegetative-reproductive switch along the compound shoot of tomato. SELF-PRUNING 5G, a major locus influencing day-length adaptation of tomato. SQUAMOSA PROMOTER-BINDING-PROTEIN-LIKE, encoding TFs involved in regulating shoot branching or tillering or panicle branching. a post-translational modification process that enzymatically attaches SUMOs (SMALL UBIQUITIN-LIKE MODIFIER) to a target protein. trehalose-6 phosphate, intermediate of trehalose biosynthesis. TILLER ANGLE CONTROL 1, a protein belonging to the IGT family. TILLERING AND DWARF 1, a coactivator of the anaphase-promoting complex, a multi-subunit E3 ligase. transcription activator-like effector 9a, a type III effector of the rice pathogen Xanthomonas oryzae. Triticum aestivum STRESS-RESPONSIVE NAC8-6A, encoding a drought- and ABA-responsive NAC TF in wheat. TCP INTERACTOR CONTAINING EAR MOTIF PROTEIN 1, a nuclear transcriptional repressor controlling shoot branching. TILLER INCLINED GROWTH 1, a TCP transcriptional activator controlling the tiller angle in rice. tiller number 1, a QTL containing a gene that encodes a TF regulating tillering. TRANSPORT INHIBITOR RESPONSE 1, encoding an auxin receptor. TARGET OF RAPAMYCIN, an atypical Ser/Thr protein kinase controlling cell growth. TOPLESS/TPR (TOPLESS-RELATED), a group of transcriptional corepressors that are recruited by diverse DNA-binding TFs or other transcriptional regulators. TASSELS REPLACE UPPER EARS 1, an ankyrin-repeat-domain protein. WUSCHEL RELATED HOMEOBOX 6, a TF critical for embryo development. WUSCHEL, a central regulator of axillary meristem formation. Zea mays RELATED TO ABI3/VP1RAV-LIKE 1,: a B3-domain TF regulating BR biosynthesis in maize.