Regulation Of Plant Height Research Articles

Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice.

Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.

Transcriptome analysis reveals potential genes associated with plant height in rice

Plant height (PH) is a complex trait regulated by the environment and multiple genes. PH directly affects crop yield, harvest index, and lodging resistance. From plant dwarf mutants, many genes related to PH have been identified and described. Nonetheless, the molecular mechanism of height regulation in high-culm rice mutants has not been well studied. By using transcriptome and weighted gene co-expression network analysis (WGCNA), we identified the differentially expressed genes (DEGs) between high-culm rice mutants (MUT) and wild-type (WT) and explored the key pathways and potential candidate genes involved in PH regulation. Transcriptome analysis identified a total of 2,184 DEGs, of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage. Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction, ABC transportation, and steroid hormone biosynthesis. Among these metabolic pathways, LOC_Os05g43910 and LOC_Os01g35030 were auxin (IAA)-related genes, up-regulated in MUT and LOC_Os02g08500 (LEPTO1), LOC_Os11g04720, and LOC_Os12g04500 were cytokinin (CK)-related genes, down-regulated in MUT. The WGCNA identified four modules (light cyan, dark grey, grey, and pale turquoise) closely related to PH, and seven key genes were screened from these modules, of which two were up-regulated cell wall-related genes (LOC_Os01g26174 (OsWAK5), LOC_Os06g05050) in MUT, and one gibberellic acid (GA) gene (LOC_Os06g37364, OsKO2) was also up-regulated. These genes might be closely related to PH regulation. These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.

DDG1 and G Protein α Subunit RGA1 Interaction Regulates Plant Height and Senescence in Rice (Oryza sativa)

Many studies have already shown that dwarfism and moderate delayed leaf senescence positively impact rice yield, but the underlying molecular mechanism of dwarfism and leaf senescence remains largely unknown. Here, using map-based cloning, we identified an allele of <i>DEP2</i>, <i>DDG1</i>, which controls plant height and leaf senescence in rice. The <i>ddg1</i> mutant displayed dwarfism, short panicles, and delayed leaf senescence. Compared with the wild-type, <i>ddg1</i> was insensitive to exogenous gibberellins (GA) and brassinolide (BR). <i>DDG1</i> is expressed in various organs, especially in stems and panicles. Yeast two-hybrid assay, bimolecular fluorescent complementation and luciferase complementation image assay showed that DDG1 interacts with the α-subunit of the heterotrimeric G protein. Disruption of <i>RGA1</i> resulted in dwarfism, short panicles, and darker-green leaves. Furthermore, we found that <i>ddg1</i> and the <i>RGA1</i> mutant was more sensitive to salt treatment, suggesting that DDG1 and RGA1 are involved in regulating salt stress response in rice. Our results show that DDG1/DEP2 regulates plant height and leaf senescence through interacting with RGA1.

Transcriptomic and metabolomic analyses reveal the mechanism of uniconazole inducing hypocotyl dwarfing by suppressing BrbZIP39-BrPAL4 module mediating lignin biosynthesis in flowering Chinese cabbage.

Uniconazole, a triazole plant growth regulator, is widely used to regulate plant height and prevent the overgrowth of seedlings. However, the underlying molecular mechanism of uniconazole in inhibiting the hypocotyl elongation of seedlings is still largely unclear, and there has been little research on the integration of transcriptomic and metabolomic data to investigate the mechanisms of hypocotyl elonga-tion. Herein we observed that the hypocotyl elongation of flowering Chinese cabbage seedings was significantly inhibited by uniconazole. Interestingly, based on combined transcriptome and metabolome analyses, we found that the "phenylpropanoid biosynthesis" pathway was significantly affected by uniconazole. In this pathway, only one member of the portal enzyme gene family, named BrPAL4, was remarkably downregulated, which was related to lignin biosynthesis. Furthermore, the yeast one-hybrid and dual-luciferase assays showed that BrbZIP39 could directly bind to the promoter region of BrPAL4 and activate its transcript. The virus-induced gene silencing system further demonstrated that BrbZIP39 could positively regulate hypocotyl elongation and the lignin biosynthesis of hypocotyl. Our findings provide a novel insight into the molecular regulatory mechanism of uniconazole inhibiting hypocotyl elongation in flowering Chinese cabbage and confirm, for the first time, that uniconazole decreases lignin content through repressing the BrbZIP39-BrPAL4 module-mediated phenylpropanoid biosynthesis, which leads to the hypocotyl dwarfing of flowering Chinese cabbage seedlings.

Genome-wide association study reveals a GLYCOGEN SYNTHASE KINASE 3 gene regulating plant height in Brassica napus.

Rapeseed (Brassica napus) is an allotetraploid crop that is the main source of edible oils and feed proteins in the world. The ideal plant architecture breeding is a major objective of rapeseed breeding and determining the appropriate plant height is a key element of the ideal plant architecture. Therefore, this study aims to improve the understanding of the genetic controls underlying plant height. The plant heights of 230 rapeseed accessions collected worldwide were investigated in field experiments over two consecutive years in Wuhan, China. Whole-genome resequencing of these accessions yielded a total of 1,707,194 informative single nucleotide polymorphisms (SNPs) that were used for genome-wide association analysis (GWAS). GWAS and haplotype analysis showed that BnaA01g09530D, which encodes BRASSINOSTEROID-INSENSITIVE 2 and belongs to the GLYCOGEN SYNTHASE KINASE 3 (GSK3) family, was significantly associated with plant height in B. napus. Moreover, a total of 31 BnGSK3s with complete domains were identified from B. napus genome and clustered into four groups according to phylogenetic analysis, gene structure, and motif distribution. The expression patterns showed that BnGSK3s exhibited significant differences in 13 developmental tissues in B. napus, suggesting that BnGSK3s may be involved in tissue-specific development. Sixteen BnGSK3 genes were highly expressed the in shoot apical meristem, which may be related to plant height or architecture development. These results are important for providing new haplotypes of plant height in B. napus and for extending valuable genetic information for rapeseed genetic improvement of plant architecture.

OsDREB2B, an AP2/ERF transcription factor, negatively regulates plant height by conferring GA metabolism in rice.

The AP2/ERF family is a large group of plant-specific transcription factors that play an important role in many biological processes, such as growth, development, and abiotic stress responses. OsDREB2B, a dehydration responsive factor (DRE/CRT) in the DREB subgroup of the AP2/ERF family, is associated with abiotic stress responses, such as cold, drought, salt, and heat stress, in Arabidopsis or rice. However, its role in regulating plant growth and development in rice is unclear. In this study, we reported a new function of OsDREB2B, which negatively regulates plant height in rice. Compared with wild type (WT), OsDREB2B-overexpressing (OE) rice exhibited dwarf phenotypes, such as reduction in plant height, internode length, and seed length, as well as grain yield, while the knockout mutants developed by CRISPR/Cas9 technology exhibited similar phenotypes. Spatial expression analysis revealed that OsDREB2B was highly expressed in the leaf sheaths. Under exogenous GA3 application, OsDREB2B expression was induced, and the length of the second leaf sheath of the OsDREB2B-OE lines recovered to that of the WT. OsDREB2B localized to the nucleus of the rice protoplast acted as a transcription activator and upregulated OsAP2-39 by directly binding to its promoter. OsDREB2B-OE lines reduced endogenous bioactive GA levels by downregulating seven GA biosynthesis genes and upregulating eight GA deactivation genes but not GA signaling genes. The yeast two-hybrid assay and bimolecular fluorescence complementation assay showed that OsDREB2B interacted with OsWRKY21. In summary, our study suggests that OsDREB2B plays a negative role in rice growth and development by regulating GA metabolic gene expression, which is mediated by OsAP2-39 and OsWRKY21, thereby reducing GA content and rice plant height.

OsHLS1 regulates plant height and development by controlling active gibberellin accumulation in rice (Oryza sativa L.)

In this study, we identified a gene related to plant height, leaf, and premature senescence in rice, and named it OsHLS1. Through bioinformatics analysis, it was found that this gene belongs to a new gene family-HLS family, and this gene family exists widely in higher plants. Expression of OsHLS1 was significantly brought about by gibberellin (GA). Subcellular localization showed that OsHLS1 was located in the nucleus. oshls1–3 displayed a GA-deficient phenotype, with dwarf plants. In addition, oshls1–3 also showed premature senescence, shorter and narrower leaves, and pollen abortion. Exogenous GA3 can restore the plant height of oshls1–3. Histomorphological analysis showed that the gene affected the progress of internode cells in the first and third nodes under the rice panicle. Through the verification of the homologous gene AT4G25690 in Arabidopsis, it was found that the mutant at4g25690 lines also showed plant dwarfing, premature senescence, and shortening and narrowing of leaves and pollen abortion. OsHLS1 affected the expression levels of genes involved in the GA metabolic pathway and affected the content of active GA, thereby regulating plant height development in rice. In conclusion, we suggest that OsHLS1 regulates plant height and development by controlling the accumulation of active gibberellins in rice.

DWARF AND ROBUST PLANT regulates plant height via modulating gibberellin biosynthesis in chrysanthemum.

YABBY (YAB) genes are specifically expressed in abaxial cells of lateral organs and determine abaxial cell fate. However, most studies have focused on few model plants, and the molecular mechanisms of YAB genes are not well understood. Here, we identified a YAB transcription factor in chrysanthemum (Chrysanthemum morifolium), Dwarf and Robust Plant (CmDRP), that belongs to a distinct FILAMENTOUS FLOWER (FlL)/YAB3 sub-clade lost in Brassicaceae. CmDRP was expressed in various tissues but did not show any polar distribution in chrysanthemum. Overexpression of CmDRP resulted in a semi-dwarf phenotype with a significantly decreased active GA3 content, while reduced expression generated the opposite phenotype. Furthermore, plant height of transgenic plants was partially rescued through the exogenous application of GA3 and Paclobutrazol, and expression of the GA biosynthesis gene CmGA3ox1 was significantly altered in transgenic plants. Yeast one-hybrid, luciferase, and chromatin immunoprecipitation-qPCR analyses showed that CmDRP could directly bind to the CmGA3ox1 promoter and suppress its expression. Our research reveals a nonpolar expression pattern of a YAB family gene in dicots and demonstrates it regulates plant height through the GA pathway, which will deepen the understanding of the genetic and molecular mechanisms of YAB genes.

The HD-Zip transcription factor GhHB12 represses plant height by regulating the auxin signaling in cotton

Upland cotton (Gossypium hirsutum L.) is the most important natural textile fiber crop worldwide. Plant height (PH) is a significant component of plant architecture, strongly influencing crop cultivation patterns, overall yield, and economic coefficient. However, cotton genes regulating plant height have not been fully identified. Previously, an HD-Zip gene (GhHB12) was isolated and characterized in cotton, which regulates the abiotic and biotic stress responses and the growth and development processes. In this study, we showed that GhHB12 was induced by auxin. Moreover, overexpression of GhHB12 induces the expression of HY5, ATH1, and HAT4, represses the spatial-temporal distribution, polar transport, and signaling of auxin, alters the expression of genes involved in cell wall expansion, and restrains the plant height in cotton. These results suggest a role of GhHB12 in regulating cotton plant height, which could be achieved by affecting the auxin signaling and cell wall expansion.

An APETALA2/ethylene responsive factor transcription factor GmCRF4a regulates plant height and auxin biosynthesis in soybean.

Plant height is one of the key agronomic traits affecting soybean yield. The cytokinin response factors (CRFs), as a branch of the APETALA2/ethylene responsive factor (AP2/ERF) super gene family, have been reported to play important roles in regulating plant growth and development. However, their functions in soybean remain unknown. This study characterized a soybean CRF gene named GmCRF4a by comparing the performance of the homozygous Gmcrf4a-1 mutant, GmCRF4a overexpression (OX) and co-silencing (CS) lines. Phenotypic analysis showed that overexpression of GmCRF4a resulted in taller hypocotyls and epicotyls, more main stem nodes, and higher plant height. While down-regulation of GmCRF4a conferred shorter hypocotyls and epicotyls, as well as a reduction in plant height. The histological analysis results demonstrated that GmCRF4a promotes epicotyl elongation primarily by increasing cell length. Furthermore, GmCRF4a is required for the expression of GmYUCs genes to elevate endogenous auxin levels, which may subsequently enhance stem elongation. Taken together, these observations describe a novel regulatory mechanism in soybean, and provide the basis for elucidating the function of GmCRF4a in auxin biosynthesis pathway and plant heigh regulation in plants.

Fine-tuning OsCPK18/OsCPK4 activity via genome editing of phosphorylation motif improves rice yield and immunity.

Plants have evolved complex signalling networks to regulate growth and defence responses under an ever-changing environment. However, the molecular mechanisms underlying the growth-defence tradeoff are largely unclear. We previously reported that rice CALCIUM-DEPENDENT PROTEIN KINASE 18 (OsCPK18) and MITOGEN-ACTIVATED PROTEIN KINASE 5 (OsMPK5) mutually phosphorylate each other and that OsCPK18 phosphorylates and positively regulates OsMPK5 to suppress rice immunity. In this study, we found that OsCPK18 and its paralog OsCPK4 positively regulate plant height and yield-related traits. Further analysis reveals that OsCPK18 and OsMPK5 synergistically regulate defence-related genes but differentially regulate development-related genes. In vitro and in vivo kinase assays demonstrated that OsMPK5 phosphorylates C-terminal threonine (T505) and serine (S512) residues of OsCPK18 and OsCPK4, respectively. The kinase activity of OsCPK18T505D , in which T505 was replaced by aspartic acid to mimic T505 phosphorylation, displayed less calcium sensitivity than that of wild-type OsCPK18. Interestingly, editing the MAPK phosphorylation motif in OsCPK18 and its paralog OsCPK4, which deprives OsMPK5-mediated phosphorylation but retains calcium-dependent activation of kinase activity, simultaneously increases rice yields and immunity. Thisediting event also changed the last seven amino acid residues of OsCPK18 and attenuated its binding with OsMPK5. This study presents a new regulatory circuit that fine tunes the growth-defence tradeoff by modulating OsCPK18/4 activity and suggests that CRISPR/Cas9-mediated engineering phosphorylation pathways could simultaneously improve crop yield and immunity.

Natural variation of the BRD2 allele affects plant height and grain size in rice.

The zqdm1 identified from a rice mutant is a novel allele of BRD2 and is responsible for regulating rice plant height, grain size and appearance, which has possibilities on improving rice quality. Plant height is an important agronomic trait related to rice yield, and grain size directly determines grain yield in rice (Oryza sativa L.). With the development of molecular biotechnology and genome sequencing technology, more and more key genes associated with plant height and grain size have been cloned and identified in recent years. This study identified the zqdm1 gene from a mutant with reduced plant height and grain size. The zqdm1 gene was revealed to be a new allele of BRASSINOSTEROID DEFICIENT DWARF 2 (BRD2), encoding a FAD-linked oxidoreductase protein involved in the brassinosteroid (BR) biosynthesis pathway, and regulates plant height by reducing cell number of longitudinal sections of the internode and regulates grain size by altering cell expansion. A 369-bp DNA fragment was found inserted at the first exon, resulting in protein-coding termination. This mutation has not been discovered in previous studies. Complementation tests have confirmed that 369-bp insertion in BRD2 was responsible for the plant height and grain size changing in the zqdm1 mutant. Over-expression of BRD2 driven by different promoters into indica rice variety Jiafuzhan (JFZ) results in slender grains, suggesting its function on regulating grain shape. In summary, the current study has identified a new BRD2 allele, which facilitated the further research on the molecular mechanism of this gene on regulating growth and development.

Combining QTL mapping and gene co-expression network analysis for prediction of candidate genes and molecular network related to yield in wheat

BackgroundWheat (Triticum aestivum L.) is an important cereal crop. Increasing grain yield for wheat is always a priority. Due to the complex genome of hexaploid wheat with 21 chromosomes, it is difficult to identify underlying genes by traditional genetic approach. The combination of genetics and omics analysis has displayed the powerful capability to identify candidate genes for major quantitative trait loci (QTLs), but such studies have rarely been carried out in wheat. In this study, candidate genes related to yield were predicted by a combined use of linkage mapping and weighted gene co-expression network analysis (WGCNA) in a recombinant inbred line population.ResultsQTL mapping was performed for plant height (PH), spike length (SL) and seed traits. A total of 68 QTLs were identified for them, among which, 12 QTLs were stably identified across different environments. Using RNA sequencing, we scanned the 99,168 genes expression patterns of the whole spike for the recombinant inbred line population. By the combined use of QTL mapping and WGCNA, 29, 47, 20, 26, 54, 46 and 22 candidate genes were predicted for PH, SL, kernel length (KL), kernel width, thousand kernel weight, seed dormancy, and seed vigor, respectively. Candidate genes for different traits had distinct preferences. The known PH regulation genes Rht-B and Rht-D, and the known seed dormancy regulation genes TaMFT can be selected as candidate gene. Moreover, further experiment revealed that there was a SL regulatory QTL located in an interval of about 7 Mbp on chromosome 7A, named TaSL1, which also involved in the regulation of KL.ConclusionsA combination of QTL mapping and WGCNA was applied to predicted wheat candidate genes for PH, SL and seed traits. This strategy will facilitate the identification of candidate genes for related QTLs in wheat. In addition, the QTL TaSL1 that had multi-effect regulation of KL and SL was identified, which can be used for wheat improvement. These results provided valuable molecular marker and gene information for fine mapping and cloning of the yield-related trait loci in the future.

OsFBK4, a novel GA insensitive gene positively regulates plant height in rice (Oryza Sativa L.)

Semi-dwarf is one of the most valuable agronomic characteristics for rice improvement programs because it affects lodging resistance and grain yield. In the present study, a semi-dwarf mutant, RE9586 , exhibits reduced plant height, panicle length and decreased grain yield. Scanning electron microscopic observation results showed that the longitudinal length of the uppermost internode of RE9586 significantly reduced, resulting in a semi-dwarf phenotype. Employing a MutMap-based strategy, LOC_Os02g11790 was preliminarily identified as the candidate gene, which encoded the F-box domain and kelch repeat-containing protein ( OsFBK4 ). A point mutation in the 3rd exon of OsFBK4 resulted in an amino acid change of 414 R→G that was subsequently confirmed by linkage analysis. Real time-PCR showed the OsFBK4 gene was predominantly expressed in the internode. The knockout lines of OsFBK4 by CRISPR/Cas9 showed a short plant height, while OsFBK4 overexpression lines recovered the phenotype of plant height. We have also demonstrated that the expressions of GA-signaling genes such as SRL1 , CIGR , GID1 , GID2 , D1 , and SPY showed clear differences in which SRL1 was down regulated, while other genes were up-regulated in RE9586 mutant. GA biosynthesis genes, OsKAO , OsGA3ox2 , and OsGA2ox2 , also displayed apparent differences in expression level. In addition, the OsFBK4 protein probably localized to the nucleus and plasma membrane. In conclusion, OsFBK4 regulates plant height involving in GA signaling, providing further insights into the mechanisms underlying the regulation of plant height in rice.

The miR528-D3 Module Regulates Plant Height in Rice by Modulating the Gibberellin and Abscisic Acid Metabolisms

Plant height, as one of the important agronomic traits of rice, is closely related to yield. In recent years, plant height-related genes have been characterized and identified, among which the DWARF3 (D3) gene is one of the target genes of miR528, and regulates rice plant height and tillering mainly by affecting strigolactone (SL) signal transduction. However, it remains unknown whether the miR528 and D3 interaction functions in controlling plant height, and the underlying regulatory mechanism in rice. In this study, we found that the plant height, internode length, and cell length of internodes of d3 mutants and miR528-overexpressing (OE-miR528) lines were greatly shorter than WT, D3-overexpressing (OE-D3), and miR528 target mimicry (OE-MIM528) transgenic plants. Knockout of D3 gene (d3 mutants) or miR528-overexpressing (OE-miR528) triggers a substantial reduction of gibberellin (GA) content, but a significant increase of abscisic acid (ABA) accumulation than in WT. The d3 and OE-miR528 transgenic plants were much more sensitive to GA, but less sensitive to ABA than WT. Moreover, the expression level of GA biosynthesis-related key genes, including OsCPS1, OsCPS2, OsKO2 and OsKAO was remarkably higher in OE-D3 plants, while the NECD2 expression, a key gene involved in ABA biosynthesis, was significantly higher in d3 mutants than in WT and OE-D3 plants. The results indicate that the miR528-D3 module negatively regulates plant height in rice by modulating the GA and ABA homeostasis, thereby further affecting the elongation of internodes, and resulting in lower plant height, which adds a new regulatory role to the D3-mediated plant height controlling in rice.

The miR166 mediated regulatory module controls plant height by regulating gibberellic acid biosynthesis and catabolism in soybean.

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play critical roles in regulating plant growth and development. Here, we used Short Tandem Target Mimic (STTM) technology to generate soybean (Glycine max (L.) Merr.) miRNA knockdown lines and identify miRNAs that regulate plant height, a key agronomic trait that affects yield. STTM166 successfully silenced miR166 in soybean and upregulated the expression of miR166 target genes, such as ATHB14-LIKE. The miR166 knockdown lines (GmSTTM166) displayed a reduced plant height phenotype. Moreover, GmSTTM166 plants contained lower levels of bioactive gibberellic acid (GA3) than wild-type plants, and application of exogenous GA partially rescued the dwarf phenotype of GmSTTM166. Knockdown of miR166 altered the expression of genes involved in GA biosynthesis and catabolism. Further analysis revealed that ATHB14-LIKE directly represses transcription of the GA biosynthesis genes GmGA1 and GmGA2, while activating transcription of the GA catabolic gene GIBBERLLIN 2 OXIDASE 2 (GmGA2ox2). Collectively, these results reveal a pivotal role for miR166 in the genetic control of plant height in soybean, thereby providing invaluable insights for molecular breeding to improve soybean yield.

Overexpression of GhKTI12 Enhances Seed Yield and Biomass Production in Nicotiana Tabacum.

Crop molecular breeding primarily focuses on increasing the trait of plant yield. An elongator-associated protein, KTI12, is closely associated with plant biomass and yield. KTI12 is involved in developmental processes of most organs, including the leaf, root, flower, and seed, through regulating cell division and differentiation. Previous work has shown that in upland cotton (Gossypium hirsutum), GhKTI12 regulates plant height, flowering, and tolerance to salt and drought stress. However, little is known about the molecular regulation mechanism of GhKTI12 in plant developmental processes. In this study, we identified the main GhKTI12 (Gh_D02G144400) gene and transformed it into tobacco (Nicotonia tabacum cv NC89). From seven transgenic lines, we obtained three (OE5, OE6 and OE8) with high expression of GhKTI12; compared with wild type plants, these three lines exhibited larger plant size, later flowering, and higher seed yield. Microscopic observation revealed that the number of leaf epidermal cells and stem parenchyma cells was increased by ~55%. Biochemical analysis showed that chlorophyll content and starch accumulation were significantly increased in younger leaves at the top canopy of transgenic plants, which may contribute to improved photosynthetic rate and, in turn, increased seed yield. To understand the molecular mechanism of GhKTI12 in transgenic plants development, two lines (OE6 and OE8) with higher expression levels of GhKTI12 were used as representative plants to conduct RNA-seq analysis. Through transcriptome analysis of the plant’s shoot apical meristematic tissue of these two lines, we identified 518 upregulated genes and 406 downregulated genes common to both overexpression lines. A large number of cellular component genes associated with cell division and differentiation, such as RD21, TET8, KTN80, AOX1, AOX2, CP1, and KIC, were found to be upregulated, and genes showing the most downregulation included MADS-box genes related to flowering time, such as MADS6, AP1, AP3, AGL8, AGL6, SEP1, and SEP2. Downregulation of these genes caused delayed flowering time and longer vegetative stage during development. Combined with the upregulation of the yield-related gene RD21, the GhKTI12 transgenic plants could produce a higher seed yield. We here show that the overexpression of GhKTI12 could positively improve key agronomic traits in tobacco by regulating cell proliferation, photosynthesis, and organ development, and suggest that homologs of GhKTI12 may also be important in the genetic improvement of other crop plants.

OsGGC2, Gγ Subunit of Heterotrimeric G Protein, Regulates Plant Height by Functionally Overlapping with DEP1 in Rice.

Plant heterotrimeric G proteins have been shown to regulate the size of various organs. There are three types of Gγ subunits in plants: type A, consisting of a canonical Gγ domain; type B, possessing a plant-specific domain at the N-terminus of the Gγ domain; and type C, possessing a plant-specific domain at the C-terminal of the Gγ domain. There is one type A, one type B, and three type C of the five γ-subunits in the rice genome. In type C Gγ subunits, GS3, which controls grain size; DEP1, which controls plant height and panicle branching; and their homolog OsGGC2, which affects grain size, have been reported; however, the function of each gene, their interactions, and molecular mechanisms for the control of plant height have not yet been clarified. In this study, we generated loss-of-function mutants of DEP1 and OsGGC2, which have high homology and similar expression, and investigated their phenotypes. Since both dep1 and osggc2 mutants were dwarfed and the double mutants showed a synergistic phenotype, we concluded that both DEP1 and OsGGC2 are positive regulators of plant height and that their functions are redundant.

Growth Repressor GmRAV Binds to the GmGA3ox Promoter to Negatively Regulate Plant Height Development in Soybean.

Plant height is an important component of plant architecture, and significantly affects crop quality and yield. A soybean GmRAV (Related to ABI3/VP1) transcription factor containing both AP2 and B3 domains is a growth repressor. Three GmRAV-overexpressing (GmRAV-ox) transgenic lines displayed extremely shorter height and shortened internodes compared with control plants, whereas transgenic inhibition of GmRAV expression resulted in increased plant height. GmRAV-ox soybean plants showed a low active gibberellin level and the dwarf phenotype could be rescued by treatment with exogenous GA3 treatment. ChIP (Chromatin immunoprecipitation)-qPCR assay showed that GmRAV could directly regulate the expression of the GA4 biosynthetic genes GA3-oxidase (GmGA3ox) by binding two CAACA motifs in the GmGA3ox promoter. The GmGA3ox promoter was bound by GmRAV, whose expression levels in leaves were both elevated in GmRAV-i-3 and decreased in GmRAV-ox-7 soybean plants. Transient expression assay in N. benthamiana also showed that the proGmRAV:GmRAV-3F6H effector strongly repressed the expression of LUC reporter gene driven by GmGA3ox promoter containing two CAACA motifs. Together, our results suggested that GmRAV protein repressed the expression of GmGA3ox by directly binding to the two CAACA motifs in the promoter to limit soybean plant height.

Finding Stable QTL for Plant Height in Super Hybrid Rice

Plant height (PH) is one of the most important agronomic traits determining plant architecture in rice. To investigate the genetic basis of plant height in the high-yielding hybrid rice variety Nei2You No.6, recombinant inbred sister lines (RISLs) were used to map quantitative trait loci (QTL) over four years. A total of 19 minor/medium-effect QTLs were mapped on eleven chromosomes except chromosome 10, totally explaining 44.61–51.15% phenotypic variance in four environments. Among these, qPH-1a, qPH-1b, qPH-2b, qPH-3b, qPH-6, and qPH-7b were repeatedly detected over four years. Among these, the qPH-6 was mapped to an interval of 22.11–29.41 Mb on chromosome 6L, which showed the highest phenotypic variation explained (PVE) of 10.22–14.05% and additive effect of 3.45–4.63. Subsequently, evaluation of near isogenic lines (NILs) showed that the qPH-6 allele from the restorer line (R8006) could positively regulate plant height, resulting in an 18.50% increase in grain yield. These results offered a basis for further mapping of qPH-6 and molecular breeding in improving plant architecture in rice.