AtOFPs regulate cell elongation by modulating microtubule orientation via direct interaction with TONNEAU2

Genome-wide identified VvOFP genes family and VvOFP4 functional characterization provide insight into fruit shape in grape

Ovate Family Proteins (OFPs) are emerging as novel transcriptional regulators of fruit shape. Despite their established role in various species, their involvement in regulating grape fruit shape remains understudied. This study encompassed a comprehensive evaluation of 16 grape OFP genes in total at the whole genome level. Phylogenetic and synteny analyses established a close relationship between grape VvOFP genes and their tomato counterparts. Expression profiling post-treatment with gibberellic acid (GA3) and thidiazuron (TDZ) revealed that certain OFP genes responded to these regulators, with VvOFP4 showing peak expression three days post-anthesis. Functional assays via overexpression of VvOFP4 in tobacco and tomato altered the morphology of both vegetative and reproductive organs, including leaves, stamens, and fruits/pods. Paraffin sections of transgenic tobacco stems and tomato fruits demonstrated that VvOFP4 overexpression modifies cell dimensions, leading to changes in organ morphology. Additionally, treatments with GA3 and TDZ similarly influenced the shape of grape pulp cells and thereby the overall fruit morphology. These findings suggest that the VvOFP4 gene plays a crucial role in fruit shape determination by modulating cell shape and presents a potential target for future grape breeding programs aimed at diversifying fruit shapes.

Identification of QTLs involved in destemming and fruit quality for mechanical harvesting of New Mexico pod-type green chile

Introduction

Domestic production of pepper (Capsicum spp.) is shrinking while demand within the US is growing. Lack of availability and cost of labor often present an obstacle for domestic producers both practically and economically. As a result, switching to harvesting peppers mechanically is anticipated as a key strategy to help domestic producers compete in the international market. Mechanical harvest efficiency can be improved through breeding. One important trait that mechanical harvest compatible material should have is an easy destemming trait: low force separation of the pedicel and calyx from the fruit.

Methods

To detect the genetic sources underlying a novel easy destemming trait for the purpose of future breeding efforts in New Mexico pod-type green chile, we performed QTL analysis on three F2:F3 populations, coming from three New Mexico pod-type varieties: 'NuMex Odyssey,' 'NuMex Iliad,' and 'NuMex Joe E. Parker,' each crossed with a parent with an easy destemming trait: MUC14. Genotyping was done through genotyping by sequencing (GBS) and phenotyping was done for destemming and fruit trait measurements. Correlations between measurements were found through the R package hmisc and QTL analysis was done through R/qtl.

Results

A strong relationship was seen between destemming and aspects of fruit morphology, particularly, destemming force and fruit width (Pearson's correlation coefficient r=0.75). Major QTLs for destemming and fruit size were discovered. Of these, the largest destemming force QTLs for all populations (PVE=34.5-69.9%) were on chromosome 10, and in two populations QTLs for destemming force were found on chromosome 3 (Percent Variance Explained (PVE)=10.7-18.8%). Fruit size-related QTLs in all populations colocalized in these same areas on chromosomes 3 and 10.

Discussion

This suggests that fruit shape may be genetically linked to destemming, and breeders interested in selecting for easy destemming pepper will also have to pay attention to fruit size and shape.

Linkage mapping of root shape traits in two carrot populations

This study investigated the genetic basis of carrot root shape traits using composite interval mapping in two biparental populations (n = 119 and n = 128). The roots of carrot F2:3 progenies were grown over 2 years and analyzed using a digital imaging pipeline to extract root phenotypes that compose market class. Broad-sense heritability on an entry-mean basis ranged from 0.46 to 0.80 for root traits. Reproducible quantitative trait loci (QTL) were identified on chromosomes 2 and 6 on both populations. Colocalization of QTLs for phenotypically correlated root traits was also observed and coincided with previously identified QTLs in published association and linkage mapping studies. Individual QTLs explained between 14 and 27% of total phenotypic variance across traits, while four QTLs for length-to-width ratio collectively accounted for up to 73% of variation. Predicted genes associated with the OFP-TRM (OVATE Family Proteins-TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathway were identified within QTL support intervals. This observation raises the possibility of extending the current regulon model of fruit shape to include carrot storage roots. Nevertheless, the precise molecular mechanisms through which this pathway operates in roots characterized by secondary growth originating from cambium layers remain unknown.

Regulatory networks of the F-box protein FBX206 and OVATE family proteins modulate brassinosteroid biosynthesis to regulate grain size and yield in rice

F-box proteins participate in the regulation of many processes, including cell division, development, and plant hormone responses. Brassinosteroids (BRs) regulate plant growth and development by activating core transcriptional and other multiple factors. In rice, OVATE family proteins (OFPs) participate in BR signalling and regulate grain size. Here we identified an F-box E3 ubiquitin ligase, FBX206, that acts as a negative factor in BR signalling and regulates grain size and yield in rice. Suppressed expression of FBX206 by RNAi leads to promoted plant growth and increased grain yield. Molecular analyses showed that the expression levels of BR biosynthetic genes were up-regulated, whereas those of BR catabolic genes were down-regulated in FBX206-RNAi plants, resulting in the accumulation of 28-homoBL, one of the bioactive BRs. FBX206 interacted with OsOFP8, a positive regulator in BR signalling, and OsOFP19, a negative regulator in BR signalling. SCFFBX206 mediated the degradation of OsOFP8 but suppressed OsOFP19 degradation. OsOFP8 interacted with OsOFP19, and the reciprocal regulation between OsOFP8 and OsOFP19 required the presence of FBX206. FBX206 itself was ubiquitinated and degraded, but interactions of OsOFP8 and OsOFP19 synergistically suppressed the degradation of FBX206. Genetic interactions indicated an additive effect between FBX206 and OsOFP8 and epistatic effects of OsOFP19 on FBX206 and OsOFP8. Our study reveals the regulatory networks of FBX206, OsOFP8, and OsOFP19 in BR signalling that regulate grain size and yield in rice.

Abscisic acid biosynthesis is necessary for full auxin effects on hypocotyl elongation

In concert with other phytohormones, auxin regulates plant growth and development. However, how auxin and other phytohormones coordinately regulate distinct processes is not fully understood. In this work, we uncover an auxin-abscisic acid (ABA) interaction module in Arabidopsis that is specific to coordinating activities of these hormones in the hypocotyl. From our forward genetics screen, we determine that ABA biosynthesis is required for the full effects of auxin on hypocotyl elongation. Our data also suggest that ABA biosynthesis is not required for the inhibitory effects of auxin treatment on root elongation. Our transcriptome analysis identified distinct auxin-responsive genes in root and shoot tissues, which is consistent with differential regulation of growth in these tissues. Further, our data suggest that many gene targets repressed upon auxin treatment require an intact ABA pathway for full repression. Our results support a model in which auxin stimulates ABA biosynthesis to fully regulate hypocotyl elongation.

Overexpression of SlPRE3 alters the plant morphologies in Solanum lycopersicum

KEY MESSAGE

Overexpression of SlPRE3 is detrimental to the photosynthesis and alters plant morphology and root development. SlPRE3 interacts with SlAIF1/SlAIF2/SlPAR1/SlIBH1 to regulate cell expansion. Basic helix-loop-helix (bHLH) transcription factors play crucial roles as regulators in plant growth and development. In this study, we isolated and characterized SlPRE3, an atypical bHLH transcription factor gene. SlPRE3 exhibited predominant expression in the root and moderate expression in the senescent leaves. Comparative analysis with the wild type revealed significant differences in plant morphology in the 35S:SlPRE3 lines. These differences included increased internode length, rolling leaves with reduced chlorophyll accumulation, and elongated yet fewer adventitious roots. Additionally, 35S:SlPRE3 lines displayed elevated levels of GA3 (gibberellin A3) and reduced starch accumulation. Furthermore, utilizing the Y2H (Yeast two-hybrid) and the BiFC (Bimolecular Fluorescent Complimentary) techniques, we identified physical interactions between SlPRE3 and SlAIF1 (ATBS1-interacting factor 1)/SlAIF2 (ATBS1-interacting factor 2)/SlPAR1 (PHYTOCHROME RAPIDLY REGULATED 1)/SlIBH1 (ILI1-binding bHLH 1). RNA-seq analysis of root tissues revealed significant alterations in transcript levels of genes involved in gibberellin metabolism and signal transduction, cell expansion, and root development. In summary, our study sheds light on the crucial regulatory role of SlPRE3 in determining plant morphology and root development.

Complex origin, evolution, and diversification of non-canonically organized OVATE-OFP and OVATE-Like OFP gene pair across Embryophyta

Ovate Family Proteins (OFP) is a plant-specific gene family of negative transcriptional regulators. Till-date, a handful of in-silico studies have provided glimpses into family size, expansion patterns, and genic features across all major plant lineages. A major lacuna exists in understanding origin of organisation complexity of members such as those arranged in a head-to-head manner which may lead to transcriptional co-regulation via a common bi-directional promoter. To address this gap, we investigated the origin, organization and evolution of two head-to-head arranged gene pairs of homologs of AtOFP2-AtOFP17, and, AtOFP4-AtOFP20 across Archaeplastida. The ancestral forms of AtOFP2, AtOFP4, AtOFP17, and AtOFP20 are likely to have evolved in last common ancestors of Embryophyta (land plants) given their complete absence in Rhodophyta and Chlorophyta. The OFP gene family originated and expanded in Bryophyta, including protein variants with complete (OVATE-OFP) or partial (OVATE-Like OFP) OVATE domain; with head-to-head organization present only in Spermatophyta (gymnosperms and angiosperms). Ancestral State Reconstruction revealed the origin of head-to-head organized gene pair in gymnosperms, with both genes being OVATE-OFP (homologs of AtOFP2/4). Phylogenetic reconstruction and copy number analysis suggests the presence of a single copy of the head-to-head arranged pair of OFP2/4 (OVATE)-OFP17/20 (OVATE-Like) in all angiosperms except Brassicaceae, and a duplication event in last common ancestor of core Brassicaceae approximately 32-54 MYA leading to origin of AtOFP2-AtOFP17 and AtOFP4-AtOFP20 as paralogs. Synteny analysis of genomic regions harbouring homologs of AtOFP2-AtOFP17, AtOFP4-AtOFP20 and AtOFP2/4-AtOFP17/20 across angiosperms suggested ancestral nature of AtOFP2-AtOFP17 gene pair. The present study thus establishes the orthology and evolutionary history of two non-canonically organised gene pairs with variation in their OVATE domain. The non-canonical organisation, atleast in Brassicaceae, has the potential of generating complex transcriptional regulation mediated via a common bi-directional promoter. The study thus lays down a framework to understand evolution of gene and protein structure, transcriptional regulation and function across a phylogenetic lineage through comparative analyses.

Molecular and genetic regulations of fleshy fruit shape and lessons from Arabidopsis and rice

Fleshy fruit shape is an important external quality trait influencing the usage of fruits and consumer preference. Thus, modification of fruit shape has become one of the major objectives for crop improvement. However, the underlying mechanisms of fruit shape regulation are poorly understood. In this review we summarize recent progress in the genetic basis of fleshy fruit shape regulation using tomato, cucumber, and peach as examples. Comparative analyses suggest that the OFP-TRM (OVATE Family Protein - TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathways are probably conserved in regulating fruit shape by primarily modulating cell division patterns across fleshy fruit species. Interestingly, cucumber homologs of FRUITFULL (FUL1), CRABS CLAW (CRC) and 1-aminocyclopropane-1-carboxylate synthase 2 (ACS2) were found to regulate fruit elongation. We also outline the recent progress in fruit shape regulation mediated by OFP-TRM and IQD pathways in Arabidopsis and rice, and propose that the OFP-TRM pathway and IQD pathway coordinate regulate fruit shape through integration of phytohormones, including brassinosteroids, gibberellic acids, and auxin, and microtubule organization. In addition, functional redundancy and divergence of the members of each of the OFP, TRM, and IQD families are also shown. This review provides a general overview of current knowledge in fruit shape regulation and discusses the possible mechanisms that need to be addressed in future studies.

Redundant mechanisms in division plane positioning

Redundancies in plant cell division contribute to the maintenance of proper division plane orientation. Here we highlight three types of redundancy: 1) Temporal redundancy, or correction of earlier defects that results in proper final positioning, 2) Genetic redundancy, or functional compensation by homologous genes, and 3) Synthetic redundancy, or redundancy within or between pathways that contribute to proper division plane orientation. Understanding the types of redundant mechanisms involved provides insight into current models of division plane orientation and opens up new avenues for exploration.

A combinatorial TRM-OFP module bilaterally fine-tunes tomato fruit shape

The mechanisms that regulate the vast diversity of plant organ shapes such as the fruit remain to be fully elucidated. TONNEAU1 Recruiting Motif proteins (TRMs) have been implicated in the control of organ shapes in a number of plant species, including tomato. However, the role of many of them is unknown. TRMs interact with Ovate Family Proteins (OFPs) via the M8 domain. However, the in planta function of the TRM-OFP interaction in regulating shape is unknown. We used CRISPR/Cas9 to generate knockout mutants in TRM proteins from different subclades and in-frame mutants within the M8 domain to investigate their roles in organ shape and interactions with OFPs. Our findings indicate that TRMs impact organ shape along both the mediolateral and proximo-distal axes of growth. Mutations in Sltrm3/4 and Sltrm5 act additively to rescue the elongated fruit phenotype of ovate/Slofp20 (o/s) to a round shape. Contrary, mutations in Sltrm19 and Sltrm17/20a result in fruit elongation and further enhance the obovoid phenotype in the o/s mutant. This study supports a combinatorial role of the TRM-OFP regulon where OFPs and TRMs expressed throughout development have both redundant and opposing roles in regulating organ shape.

Transcription Factor AtOFP1 Involved in ABA-Mediated Seed Germination and Root Growth through Modulation of ROS Homeostasis in Arabidopsis

Ovate family proteins (OFPs) are valued as a family of transcription factors that are unique to plants, and they play a pluripotent regulatory role in plant growth and development, including secondary-cell-wall synthesis, DNA repair, gibberellin synthesis, and other biological processes, via their interaction with TALE family proteins. In this study, CHIP-SEQ was used to detect the potential target genes of AtOFP1 and its signal-regulation pathways. On the other hand, Y2H and BIFC were employed to prove that AtOFP1 can participate in ABA signal transduction by interacting with one of the TALE family protein called AtKNAT3. ABA response genes are not only significantly upregulated in the 35S::HAOFP1 OE line, but they also show hypersensitivity to ABA in terms of seed germination and early seedling root elongation. In addition, the AtOFP1-regulated target genes are mainly mitochondrial membranes that are involved in the oxidative–phosphorylation pathway. Further qRT-PCR results showed that the inefficient splicing of the respiratory complex I subunit genes NAD4 and NAD7 may lead to ROS accumulation in 35S::HA-AtOFP1 OE lines. In conclusion, we speculated that the overexpression of AtOFP1 may cause the ABA hypersensitivity response by increasing the intracellular ROS content generated from damage to the intima systems of mitochondria.

A cryptic variation in a member of the Ovate Family Proteins is underlying the melon fruit shape QTL fsqs8.1

The gene underlying the melon fruit shape QTL fsqs8.1 is a member of the Ovate Family Proteins. Variation in fruit morphology is caused by changes in gene expression likely due to a cryptic structural variation in this locus. Melon cultivars have a wide range of fruit morphologies. Quantitative trait loci (QTL) have been identified underlying such diversity. This research focuses on the fruit shape QTL fsqs8.1, previously detected in a cross between the accession PI 124112 (CALC, producing elongated fruit) and the cultivar 'Piel de Sapo' (PS, producing oval fruit). The CALC fsqs8.1 allele induced round fruit shape, being responsible for the transgressive segregation for this trait observed in that population. In fact, the introgression line CALC8-1, carrying the fsqs8.1 locus from CALC into the PS genetic background, produced perfect round fruit. Following a map-based cloning approach, we found that the gene underlying fsqs8.1 is a member of the Ovate Family Proteins (OFP), CmOFP13, likely a homologue of AtOFP1 and SlOFP20 from Arabidopsis thaliana and tomato, respectively. The induction of the round shape was due to the higher expression of the CALC allele at the early ovary development stage. The fsqs8.1 locus showed an important structural variation, being CmOFP13 surrounded by two deletions in the CALC genome. The deletions are present at very low frequency in melon germplasm. Deletions and single nucleotide polymorphisms in the fsqs8.1 locus could not be not associated with variation in fruit shape among different melon accessions, what indicates that other genetic factors should be involved to induce the CALC fsqs8.1 allele effects. Therefore, fsqs8.1 is an example of a cryptic variation that alters gene expression, likely due to structural variation, resulting in phenotypic changes in melon fruit morphology.

OVATE Family Protein PpOFP1 Physically Interacts With PpZFHD1 and Confers Salt Tolerance to Tomato and Yeast

The OVATE family protein (OFP) genes (OFPs) have been shown to respond to salt stress in plants. However, the regulatory mechanism for salt tolerance of the peach (Prunus persica) OFP gene PpOFP1 has not been elucidated. In this study, using yeast two-hybrid screening, we isolated a nucleus-localized ZF-HD_dimer domain protein PpZFHD1, which interacts with the PpOFP1 protein in the peach cultivar "Zhongnongpan No.10". A segmentation experiment further suggested that the interaction happens more specifically between the N-terminal, contains ZF-HD_dimer domain, of PpZFHD1 and the C-terminal, consists of OVATE domain, of PpOFP1. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) experiments indicate that transcription of these two genes are induced by 200 mmol/L (mM) NaCl treatment. Heterogeneous transformation experiments suggested that the growth status of transformed yeast strain over-expressing each of these two genes was more robust than that of control (CK). Furthermore, transgenic tomato plants over-expressing PpOFP1 were also more robust. They had a higher content of chlorophyll, soluble proteins, soluble sugars, and proline. Activities of the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in these plants were higher, and tissues from these plants exhibited a lower relative conductivity and malondialdehyde (MDA) content. These results suggest that PpOFP1 physically interacts with PpZFHD1 and confers salt tolerance to tomato and yeast, thus revealing a novel mechanism for regulating salt tolerance in peach and other perennial deciduous trees.

Characterization of the development dynamics within the linear growth bamboo leaf

The leaf is the main photosynthetic organ in plants, such as bamboo. Leaves from bamboo are used as a food additive. However, according to our investigation, to date there have been no reports concerning the leaf development of bamboo. By measuring over 7500 parenchymal cells, we discovered that the linear leaf growth of Pseudosasa japonica could be divided into three growth sections. The first one is a roughly 1-cm long division zone (DZ), containing about 1580 cells, located at the bottom of the leaf; the second one is an about 3-cm long elongation zone (EZ), with ~1905 cells, located above the DZ; and the last is a mature zone (MZ) in which cell elongation is completed. The cell production rate of the DZ was 25.33-35.81 cells per hour, with an average of 29.73; and the cell division rate was ~0.45 cells per cell every 24 h. PacBio and Illumina transcriptome sequencing found 21 933 unigenes expressed in these zones. Further analysis revealed a dynamic transcriptome, with transcripts for cell division in the DZ changing to transcripts for cell elongation, photosynthetic development, secondary metabolism, stress resistance, and nutrition transport toward the leaf distal. Those transcriptome transformations correlated well with the changes of relative water content, biomass accumulation, and cellulose crystal degree and were supported by quantitative polymerase chain reaction data. These results revealed a developmental gradient of the bamboo linear growth leaf, which offers a foundation to elucidate and engineer leaf development in bamboo, an economically valuable plant.