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Tillering is one of the most important determinants of biomass and yield in rice (Oryza sativa L.). The capacity of plants to develop tillers from primordial meristems or buds is determined not only by the genotype but also by environmental cues. Here, we characterized the function of rice grassy tiller1 (OsGT1) and its interaction with other genetic and biological factors involved in tiller bud outgrowth in rice by generating OsGT1 RNA interference (RNAi) and overexpression (OX) lines. The tiller number was increased in OsGT1-RNAi mutants but strongly suppressed in OsGT1-OX lines. Expression analysis of OsGT1 in rice phyB mutants and in genotypes carrying various genetic combinations of GT1 RNAi and phyB demonstrated that OsGT1 is not involved in phyB-mediated suppression of tiller development in rice. Expression analysis of fine culm1 (fc1), a rice tb1 homolog, and molecular assays demonstrated that FC1 enhances the expression of OsGT1 by directly binding to its promoter. Comparison of the transcriptomic profiles of fc1 and OsGT1-RNAi mutants revealed differentially expressed genes (DEGs) common to both genotypes. Finally, analysis of tillering phenotypes of OX and RNAi seedlings treated with various phytohormones implied a possible role of OsGT1 in strigolactone-mediated tiller outgrowth. Overall, this study enhances our understanding of the diverse mechanisms of tiller development in grasses.

The AMT1 family comprises major ammonium transporters in rice roots. In this study, we utilized AMT1 RNAi mutants (amt1) to explore how AMT1 affects NH4+- and NO3–-mediated morphological development and NH4+-responsive gene expression in roots. In the presence of NH4+, amt1 showed inhibition of NO3–- dependent lateral root development. The inhibitory action of NH4+ on lateral root growth was independent of the NO3– concentrations supplied to amt1 roots. The results of split root assays indicated that NH4+ exerts systemic action in inhibiting NO3–-dependent lateral root development in amt1. Further study with NAA and NOA, a potent auxin flux inhibitor, suggested that perturbation of membrane dynamics might not be the primary cause of the inhibitory action of NH4+ on NO3–-mediated lateral root growth in amt1 mutants. RNA-seq analysis of NH4+-responsive genes showed that approximately half of DEGs observed in wild-type roots were not detected in the DEGs of amt1 roots. Gene ontology enrichment analysis suggested that the expression of specific functional gene groups were affected by amt1 during the early response to NH4+. Auxin-responsive gene expression and root gravity responses were altered in amt1. This study demonstrated that AMT1 affects the interactions not only between ammonium and nitrate in lateral root growth but also between auxin and NH4+ in rice roots.

The ripening pattern of strawberry (Fragaria × ananassa) is different from other fruits, primarily because plant hormones affect the fruit’s quality in a different way than in other fruits. However, most studies on strawberries have focused on cultivation methods, control of pests and diseases, and breeding, and considerably less research has been done on hormones that determine strawberry internal quality. Even though strawberries have good indicators for gauging external quality, there is not enough data to for it to be related to internal quality. As such, we sought to better understand quality as strawberry fruit in specific six progressive developmental stages: flower buds, flowering, green fruits (GF), white fruits, pink fruits, and red fruits (RF). The internal quality and hormonal changes of ‘Seolhyang’ and ‘Maehyang’ cultivars were investigated on the basis of these developmental stages. This report highlights the changes in plant hormones that affect fruit ripening of ‘Seolhyang’ and ‘Maehyang’ cultivars. ABA, cytokinin, JA, and SA content increased gradually with maturity from the GF to the RF stage, while auxin content decreased gradually from GF to RF. Meanwhile, cytokinin and GA3 content exhibited fluctuations and differences between ‘Seolhyang’ and ‘Maehyang’ cultivars. The quality of strawberries was highest at the sixth (RF) stage in the both cultivars. Our results reveal that plant hormones play a role in the maturation of strawberry fruits and provide a foundation for their agricultural use in controlling the maturity of fruits.

Gray leaf spot (GLS) disease, caused by the Stemphylium (Sm) fungus, affects a wide range of horticultural crops including tomato. In this study, the South Korean Sm isolate (PNU-SM01) was identified, and the applicability of Sm-resistance gene (Sm)-linked DNA markers in marker-assisted selection was validated. ITS/gpd sequencing and morphological observation identified the isolate as S. lycopersici. A GLS disease assay was conducted on 80 tomato varieties, including commercial F1 hybrids and elite inbred lines. The reference line ‘Motelle’ was highly resistant (R, DSI = 4.0), whereas the ‘Moneymaker’ line was susceptible (S) and showed severe disease symptoms (DSI = 79.3). Among 30 commercial F1 hybrids, five were scored as S by DSI; whereas the rest, including all 17 hybrids claimed as Sm-resistant by the supplier, were R or moderately resistant (MR). Among 48 inbred lines, four were scored as S and 44, including five Lycopersicon accessions reported as R, were R or MR. Three known Sm-linked DNA markers (CT55, D5, and Sm-InDel) were genotyped in all 80 cultivars; the highest match (92.5%) to the GLS disease assay was observed for Sm-InDel. We converted the recessive marker CT55 into a codominant marker (CT55-Co) and developed dCAPS (Sm-SNP) and KASP (Sm-KASP) markers from a previously identified Sm-linked SNP. Sm-SNP and Sm-KASP showed a similar level of phenotype to marker genotype association as Sm-InDel, whereas CT55-Co displayed a high level of mismatch. To screen for the source of Sm resistance, 138 tomato accessions were genotyped with Sm-InDel and Sm-SNP: 15 were homozygous for the resistance allele of both markers. In this study, resistance to the Korean isolate of S. lycopersici in commercial F1 hybrids and breeding sources was characterized to reveal which DNA markers can be effectively applied for marker-assisted selection of Sm-resistance.

BR signaling pathways facilitate xylem differentiation and wood formation by fine tuning SlBZR1/SlBZR2-mediated gene expression networks involved in plant secondary growth. Brassinosteroid (BR) signaling and BR crosstalk with diverse signaling cues are involved in the pleiotropic regulation of plant growth and development. Recent studies reported the critical roles of BR biosynthesis and signaling in vascular bundle development and plant secondary growth; however, the molecular bases of these roles are unclear. Here, we performed comparative physiological and anatomical analyses of shoot morphological growth in a cultivated wild-type tomato (Solanum lycopersicum cv. BGA) and a BR biosynthetic mutant [Micro Tom (MT)]. We observed that the canonical BR signaling pathway was essential for xylem differentiation and sequential wood formation by facilitating plant secondary growth. The gradual retardation of xylem development phenotypes during shoot vegetative growth in the BR-deficient MT tomato mutant recovered completely in response to exogenous BR treatment or genetic complementation of the BR biosynthetic DWARF (D) gene. By contrast, overexpression of the tomato Glycogen synthase kinase 3 (SlGSK3) or CRISPR-Cas9 (CR)-mediated knockout of the tomato Brassinosteroid-insensitive 1 (SlBRI1) impaired BR signaling and resulted in severely defective xylem differentiation and secondary growth. Genetic modulation of the transcriptional activity of the tomato Brassinazole-resistant 1/2 (SlBZR1/SlBZR2) confirmed the positive roles of BR signaling pathways for xylem differentiation and secondary growth. Our data indicate that BR signaling pathways directly promote xylem differentiation and wood formation by canonical BR-activated SlBZR1/SlBZR2.

Pelargonidin is a natural compound that exists widely in fruits, and exerts antioxidant, anti-atherosclerotic, anti-inflammatory, anti-hyperglycemic, and anti-diabetic activities. However, there have not been any studies concerning its anti-obesity potential to date. Therefore, we evaluated the anti-obesity potential of pelargonidin via inhibition of adipogenesis in 3T3-L1 cells. The cellular oil droplet content was decreased to 68.14%, 56.75%, and 48.39% and triglyceride accumulation decreased to 74.53%, 61.54%, and 47.86% after incubation with 5 μM, 10 μM, and 20 μM pelargonidin, respectively, when compared with DMSO group. Furthermore, pelargonidin treatment led to decrease in glucose consumption. Western blot assay illustrated that the expression of PPAR-γ was suppressed to 63.25%, 47.52%, and 21.23% after incubation with 5 μM, 10 μM, and 20 μM pelargonidin when compared with DMSO group. Then, we measured the expression of some target proteins of PPAR-γ, and found that pelargonidin decreased the expressions of HMGCR, LPL, Glut4, and A-FABP. Besides, the result of Luciferase Reporter Assay indicated that pelargonidin inhibited PPAR-γ transcription activity. These results indicated that pelargonidin exerts anti-adipogenic activity in 3T3-L1 cells through inhibition of PPAR-γ signaling pathway, and pelargonidin could be used as a potential anti-obesity agent.

Reductions in growth and quality due to powdery mildew (PM) disease cause significant economic losses in tomato production. Oidium neolycopersici was identified as the fungal species responsible for tomato PM disease in South Korea in the present study, based on morphological and internal transcribed spacer DNA sequence analyses of PM samples collected from two remote regions (Muju and Miryang). The genes involved in resistance to this pathogen in the tomato accession ‘KNU-12’ (Solanum lycopersicum var. cerasiforme) were evaluated, and the inheritance of PM resistance in ‘KNU-12’ was found to be conferred via simple Mendelian inheritance of a mutant allele of the PM susceptibility locus Ol-2 (SlMlo1). Full-length cDNA analysis of this newly identified mutant allele (Slmlo1.1) showed that a 1-bp deletion in its coding region led to a frameshift mutation possibly resulting in SlMlo1 loss-of-function. An alternatively spliced transcript of Slmlo1.1 was observed in the cDNA sequences of ‘KNU-12’, but its direct influence on PM resistance is unclear. A derived cleaved amplified polymorphic sequence (dCAPS) and a high-resolution melting (HRM) marker were developed based on the 1-bp deletion in Slmlo1.1, and could be used for efficient marker-assisted selection (MAS) using ‘KNU-12’ as the source for durable and broad-spectrum resistance to PM.

This study was conducted to develop an SNP set that can be useful for marker-assisted breeding (MAB) in watermelon (Citrullus. lanatus L) using Genotyping-bysequencing (GBS) analysis of 20 commercial elite watermelon inbreds. The result of GBS showed that 77% of approximately 1.1 billion raw reads were mapped on the watermelon genome with an average mapping region of about 4,000 Kb, which indicated genome coverage of 2.3%. After the filtering process, a total of 2,670 SNPs with an average depth of 31.57 and the PIC (Polymorphic Information Content) value of 0.1~0.38 for 20 elite inbreds were obtained. Among those SNPs, 55 SNPs (5 SNPs per chromosome that are equally distributed on each chromosome) were selected. For the understanding genetic relationship of 20 elite inbreds, PCA (Principal Component Analysis) was carried out with 55 SNPs, which resulted in the classification of inbreds into 4 groups based on PC1 (52%) and PC2 (11%), thus causing differentiation between the inbreds. A similar classification pattern for PCA was observed from hierarchical clustering analysis. The SNP set developed in this study has the potential for application to cultivar identification, F1 seed purity test, and marker-assisted backcross (MABC) not only for 20 elite inbreds but also for diverse resources for watermelon breeding.

NH4+ is an important nitrogen resource for rice plants in paddy soil. Therefore, it is likely that NH4+-triggered plant growth interacts with phytohormone-mediated developmental mechanisms. Our previous transcriptomic analysis revealed that many genes involved in auxin signaling and efflux are sensitive to NH4+. In the current study, we found that NH4+ treatment causes a delayed gravity response in rice roots. To further elucidate the interlocking relationship between NH4+ and auxin signaling during root development, we utilized mutants and overexpressors of a key NH4+ signaling transcription factor INDETERMINATE DOMAIN 10 (IDD10), encoding a transcription factor that regulates the expression of NH4+ uptake and N-assimilation genes. We obtained several lines of evidence that auxin affects NH4+-mediated gene expression and root development in rice plants via IDD10. First, the gravity response was delayed in idd10 roots and accelerated in IDD10 overexpressor (IDD10 OX) roots in the absence and (especially) presence of NH4+. Second, idd10 plants showed strong root coiling only in the presence of NH4+. However, treatment of 1-N-naphthylphthalamic acid (NPA), a polar auxin transport inhibitor suppressed the NH4+-specific root phenotype of idd10. Third, the expression of NH4+-responsive auxin-related genes was affected in idd10 and IDD10 overexpressors. Finally, IDD10 expression was induced by IAA and suppressed by NPA. These findings suggest that the gene expression patterns and phenotypes triggered by NH4+ are influenced by the actions of auxin during root development, pointing to a regulatory circuit between NH4+ and auxin signaling that functions in root development in rice.

Rice (Oryza sativa) is the most important consumed staple food for a large and diverse population worldwide. Since databases of genomic sequences became available, functional genomics and genetic manipulations have been widely practiced in rice research communities. Insertional mutants are the most common genetic materials utilized to analyze gene function. To mutagenize rice genomes, we exploited the transpositional activity of an Activator/Dissociation (Ac/Ds) system in rice. To mobilize Ds in rice genomes, a maize Ac cDNA was expressed under the CaMV35S promoter, and a gene trap Ds was utilized to detect expression of host genes via the reporter gene GUS. Conventional transposon-mediated gene-tagging systems rely on genetic crossing and selection markers. Furthermore, the activities of transposases have to be monitored. By taking advantage of the fact that Ds becomes highly active during tissue culture, a plant regeneration system employing tissue culture was employed to generate a large Ds transposant population in rice. This system overcomes the requirement for markers and the monitoring of Ac activity. In the regenerated populations, more than 70% of the plant lines contained independent Ds insertions and 12% expressed GUS at seedling stages. This protocol describes the method for producing a Ds-mediated insertional population via tissue culture regeneration systems. © 2016 by John Wiley & Sons, Inc.

Rice blast disease, caused by Magnaporthe oryzae, is one of the major constraints to rice production, which feeds half of the world’s population. Proteomic technologies have been used as effective tools in plant−pathogen interactions to study the biological pathways involved in pathogen infection, plant response, and disease progression. Advancements in mass spectrometry (MS) and apoplastic and plasma membrane protein isolation methods facilitated the identification and quantification of subcellular proteomes during plant-pathogen interaction. Proteomic studies conducted during rice−M. oryzae interaction have led to the identification of several proteins eminently involved in pathogen perception, signal transduction, and the adjustment of metabolism to prevent plant disease. Some of these proteins include receptor-like kinases (RLKs), mitogen-activated protein kinases (MAPKs), and proteins related to reactive oxygen species (ROS) signaling and scavenging, hormone signaling, photosynthesis, secondary metabolism, protein degradation, and other defense responses. Moreover, post−translational modifications (PTMs), such as phosphoproteomics and ubiquitin proteomics, during rice−M. oryzae interaction are also summarized in this review. In essence, proteomic studies carried out to date delineated the molecular mechanisms underlying rice-M. oryzae interactions and provided candidate proteins for the breeding of rice blast resistant cultivars.

Shoot meristems are maintained by pluripotent stem cells that are controlled by CLAVATA-WUSCHEL feedback signaling. This pathway, which coordinates stem cell proliferation with differentiation, was first identified in Arabidopsis, but appears to be conserved in diverse higher plant species. In this Review, we highlight the commonalities and differences between CLAVATA-WUSCHEL pathways in different species, with an emphasis on Arabidopsis, maize, rice and tomato. We focus on stem cell control in shoot meristems, but also briefly discuss the role of these signaling components in root meristems.

Shoot apical meristems are stem cell niches that balance proliferation with the incorporation of daughter cells into organ primordia. This balance is maintained by CLAVATA-WUSCHEL feedback signaling between the stem cells at the tip of the meristem and the underlying organizing center. Signals that provide feedback from organ primordia to control the stem cell niche in plants have also been hypothesized, but their identities are unknown. Here we report FASCIATED EAR3 (FEA3), a leucine-rich-repeat receptor that functions in stem cell control and responds to a CLAVATA3/ESR-related (CLE) peptide expressed in organ primordia. We modeled our results to propose a regulatory system that transmits signals from differentiating cells in organ primordia back to the stem cell niche and that appears to function broadly in the plant kingdom. Furthermore, we demonstrate an application of this new signaling feedback, by showing that weak alleles of fea3 enhance hybrid maize yield traits.

Meristems contain groups of indeterminate stem cells, which are maintained by a feedback loop between CLAVATA (CLV) and WUSCHEL (WUS) signaling. CLV signaling involves the secretion of the CLV3 peptide and its perception by a number of Leucine-Rich-Repeat (LRR) receptors, including the receptor-like kinase CLV1 and the receptor-like protein CLV2 coupled with the CORYNE (CRN) pseudokinase. CLV2, and its maize ortholog FASCIATED EAR2 (FEA2) appear to function in signaling by CLV3 and several related CLV3/EMBRYO-SURROUNDING REGION (CLE) peptide ligands. Nevertheless, how signaling specificity is achieved remains unknown. Here we show that FEA2 transmits signaling from two distinct CLE peptides, the maize CLV3 ortholog ZmCLE7 and ZmFON2-LIKE CLE PROTEIN1 (ZmFCP1) through two different candidate downstream effectors, the alpha subunit of the maize heterotrimeric G protein COMPACT PLANT2 (CT2), and ZmCRN. Our data provide a novel framework to understand how diverse signaling peptides can activate different downstream pathways through common receptor proteins., eLife digest Like animals, plants are made up of many different types of cells, which descend from undifferentiated cells called stem cells. Thanks to these cells, plants are able to grow and develop throughout their lives. Stem cells live at the tips of the plant’s shoots and roots. They constantly divide to produce new cells to self-renew or replace specific plant cells in need of repair. Over time, they change – or differentiate – to go on to become part of tissues like leaves, roots, stems, shoots, flowers or fruits. To maintain a continuous pool of undifferentiated stem cells and to make sure that stem cells divide at the correct pace, neighbouring cells emit signals that control the activity of stem cells. The new stem cells that remain close to these ‘maintenance signals’ continue to behave like stem cells, but those displaced away begin to differentiate. Stem cells can receive many different types of signals, but how are these signals filtered and passed onto different places within the cell? To test this, Je, Xu et al. created maize plants that contained mutations in a number of known signalling molecules to see if these molecules used the same communication pathway. The results showed that stem cells could integrate the different signals. Even if the signals pass through the same receiver (a receptor protein called FASCIATED EAR2), each signal exits the receptor as a different message, and attaches to a different messenger protein to relay specific information about stem cell maintenance to the cell. A next step will be to test if other plants use the same signalling pathways in the same ways to send messages between cells. A better knowledge about stem cell signals in plants could help to develop more productive crops. Previous work has found that precise control of stem cell pathways can help breed crops with more seeds or bigger fruits. These kinds of changes have been selected naturally by humans since the dawn of civilization, but we need to accelerate these advances to help meet the needs of the growing world population and improve agricultural sustainability.

The promotive effects of brassinosteroids (BRs) on plant growth and development have been widely investigated; however, it is not known whether BRs directly affect nutrient uptake. Here, we explored the possibility of a direct relationship between BRs and ammonium uptake via AMT1-type genes in rice (Oryza sativa). BR treatment increased the expression of AMT1;1 and AMT1;2, whereas in the mutant d61-1, which is defective in the BR-receptor gene BRI1, BR-dependent expression of these genes was suppressed. We then employed Related to ABI3/VP1-Like 1 (RAVL1), which is involved in BR homeostasis, to investigate BR-mediated AMT1 expression and its effect on NH4+ uptake in rice roots. AMT1;2 expression was lower in the ravl1 mutant, but higher in the RAVL1-overexpressing lines. EMSA and ChIP analyses showed that RAVL1 activates the expression of AMT1;2 by directly binding to E-box motifs in its promoter. Moreover, 15NH4+ uptake, cellular ammonium contents, and root responses to methyl-ammonium strongly depended on RAVL1 levels. Analysing AMT1;2 expression levels in different crosses between BRI1 and RAVL1 mutant and overexpression lines indicated that RAVL1 acts downstream of BRI1 in the regulation of AMT1;2. Thus, the present study shows how BRs may be involved in the transcriptional regulation of nutrient transporters to modulate their uptake capacity.

Nitrogen (N) is the most important macronutrient for plant growth and grain yields. For rice crops, nitrate and ammonium are the major N sources. To explore the genomic responses to ammonium supplements in rice roots, we used 17-day-old seedlings grown in the absence of external N that were then exposed to 0.5mM (NH4)2SO4 for 3h. Transcriptomic profiles were examined by microarray experiments. In all, 634 genes were up-regulated at least two-fold by the N-supplement when compared with expression in roots from untreated control plants. Gene Ontology (GO) enrichment analysis revealed that those upregulated genes are associated with 23 GO terms. Among them, metabolic processes for diverse amino acids (i.e., aspartate, threonine, tryptophan, glutamine, l-phenylalanine, and thiamin) as well as nitrogen compounds are highly over-represented, demonstrating that our selected genes are suitable for studying the N-response in roots. This enrichment analysis also indicated that nitrogen is closely linked to diverse transporter activities by primary metabolites, including proteins (amino acids), lipids, and carbohydrates, and is associated with carbohydrate catabolism and cell wall organization. Integration of results from omics analysis of metabolic pathways and transcriptome data using the MapMan tool suggested that the TCA cycle and pathway for mitochondrial electron transport are co-regulated when rice roots are exposed to ammonium. We also investigated the expression of N-responsive marker genes by performing a comparative analysis with root samples from plants grown under different NH4(+) treatments. The diverse responses to such treatment provide useful insight into the global changes related to the shift from an N-deficiency to an enhanced N-supply in rice, a model crop plant.

Highlight LPA1 suppresses auxin signalling that interacts with C-22-hydroxylated and 6-deoxo brassinosteroids, which regulates lamina inclination independently of OsBRI1., Lamina inclination is a key agronomical character that determines plant architecture and is sensitive to auxin and brassinosteroids (BRs). Loose Plant Architecture1 (LPA1) in rice (Oryza sativa) and its Arabidopsis homologues (SGR5/AtIDD15) have been reported to control plant architecture and auxin homeostasis. This study explores the role of LPA1 in determining lamina inclination in rice. LPA1 acts as a positive regulator to suppress lamina bending. Genetic and biochemical data indicate that LPA1 suppresses the auxin signalling that interacts with C-22-hydroxylated and 6-deoxo BRs, which regulates lamina inclination independently of OsBRI1. Mutant lpa1 plants are hypersensitive to indole-3-acetic acid (IAA) during the lamina inclination response, which is suppressed by the brassinazole (Brz) inhibitor of C-22 hydroxylase involved in BR synthesis. A strong synergic effect is detected between lpa1 and d2 (the defective mutant for catalysis of C-23-hydroxylated BRs) during IAA-mediated lamina inclination. No significant interaction between LPA1 and OsBRI1 was identified. The lpa1 mutant is sensitive to C-22-hydroxylated and 6-deoxo BRs in the d61-1 (rice BRI1 mutant) background. We present evidence verifying that two independent pathways function via either BRs or BRI1 to determine IAA-mediated lamina inclination in rice. RNA sequencing analysis and qRT-PCR indicate that LPA1 influences the expression of three OsPIN genes (OsPIN1a, OsPIN1c and OsPIN3a), which suggests that auxin flux might be an important factor in LPA1-mediated lamina inclination in rice.