Transcriptomic Insights into Phenological Development and Cold Tolerance of Wheat Grown in the Field

Harnessing de novo transcriptome sequencing to identify and characterize genes regulating carbohydrate biosynthesis pathways in Salvia guaranitica L

Introduction

Carbohydrate compounds serve multifaceted roles, from energy sources to stress protectants, found across diverse organisms including bacteria, fungi, and plants. Despite this broad importance, the molecular genetic framework underlying carbohydrate biosynthesis pathways, such as starch, sucrose, and glycolysis/gluconeogenesis in Salvia guaranitica, remains largely unexplored.

Methods

In this study, the Illumina-HiSeq 2500 platform was used to sequence the transcripts of S. guaranitica leaves, generating approximately 8.2 Gb of raw data. After filtering and removing adapter sequences, 38 million reads comprising 210 million high-quality nucleotide bases were obtained. De novo assembly resulted in 75,100 unigenes, which were annotated to establish a comprehensive database for investigating starch, sucrose, and glycolysis biosynthesis. Functional analyses of glucose-6-phosphate isomerase (SgGPI), trehalose-6-phosphate synthase/phosphatase (SgT6PS), and sucrose synthase (SgSUS) were performed using transgenic Arabidopsis thaliana.

Results

Among the unigenes, 410 were identified as putatively involved in these metabolic pathways, including 175 related to glycolysis/gluconeogenesis and 235 to starch and sucrose biosynthesis. Overexpression of SgGPI, SgT6PS, and SgSUS in transgenic A. thaliana enhanced leaf area, accelerated flower formation, and promoted overall growth compared to wild-type plants.

Discussion

These findings lay a foundation for understanding the roles of starch, sucrose, and glycolysis biosynthesis genes in S. guaranitica, offering insights into future metabolic engineering strategies for enhancing the production of valuable carbohydrate compounds in S. guaranitica or other plants.

Deacclimation and reacclimation processes in winter wheat: novel perspectives from time-series transcriptome analysis

Winter wheat achieves freezing tolerance (FT) through cold acclimation (CA) - a process which is induced by low positive temperatures in autumn. The increasing occurrences of temperature fluctuations in winter lead to deacclimation (DEA), causing premature loss of FT, and the cultivars capable of reacclimation (REA) are more likely to survive the subsequent cold spells. The genetic mechanisms of DEA and REA remain poorly understood, necessitating further research to bolster climate resilience in winter wheat. Here, we selected two winter wheat genotypes with contrasting levels of FT and conducted a ten-week-long experiment imitating low-temperature fluctuations after CA under controlled conditions. Crown and leaf tissue samples for RNA-sequencing were collected at CA, DEA, and REA time-points. It is the first transcriptomic study covering both short- and long-term responses to DEA and REA in winter wheat. The study provides novel knowledge regarding CA, DEA, and REA and discusses the gene expression patterns conferring FT under temperature fluctuations. The freezing-tolerant genotype "Lakaja DS" showed elevated photosynthetic activity in leaf tissue and upregulated cryoprotective protein-encoding genes in crowns after CA when compared to the freezing-susceptible "KWS Ferrum". "Lakaja DS" also expressed cold acclimation-associated transcripts at a significantly higher level after 1 week of DEA. Following REA, "Lakaja DS" continued to upregulate dehydrin-related genes in crowns and exhibited significantly higher expression of chitinase transcripts in leaves, when compared to "KWS Ferrum". The findings of this study shed light on the genetic mechanisms governing DEA and REA in winter wheat, thus addressing the gaps in knowledge regarding FT under low-temperature fluctuations. The identified genes should be further examined as potential molecular markers for breeding strategies focused on developing freezing-tolerant winter-type crops. Publicly available datasets generated in this study are valuable resources for further research into DEA and REA, contributing towards the enhancement of winter wheat under global climate change.

Transcriptome analysis during vernalization in wheat (Triticum aestivum L.)

BACKGROUND

Vernalization, as a vital process in the life cycle of winter cereal, has important effects on floral organ formation and flowering time. Many morphological changes together with molecular changes occur during the vernalization period. Here, we used transcriptome sequencing to analyze the transcriptomic changes in wheat leaves before, during and after vernalization using the winter wheat cultivar 'Shiluan02-1'.

RESULTS

A total of 16,370 differentially expressed genes were obtained across different vernalization periods. Gene Ontology enrichment analysis revealed that photoperiodism, photoprotection, photosynthesis, lipid transport and biosynthetic process, and chlorophyll metabolic process were closely related to vernalization. In addition, AP2/ERF, C2H2, bHLH, WRKY, MYB, MYB-related, and NAC transcription factors were significantly enriched during vernalization, and the transcription factor expression patterns suggested the intricate regulation of transcription factor modules in plant vernalization pathways. Analysis of gene expression patterns of the MADS-box transcription factor genes showed different expression patterns during vernalization phases, among which VERNALIZATION1 (VRN1) genes were found to gradually increase during vernalization periods from V0 to V35, while decline in the V42 phase, then increase after vernalization. The Tavrt-2 gene cooperated with Tavrn1 to regulate flowering induced by vernalization, and its expression level was rapidly increased by vernalization but declined in the V42 phase and then increased after vernalization. Some genes from the ICE-CBF-COR pathway were also identified, and additional analysis indicated that some key genes related to phytohormone biosynthesis and signal transduction were enriched during the vernalization period, such as gibberellic acid, ethylene, abscisic acid and jasmonic acid biosynthesis and signaling pathway genes.

CONCLUSIONS

Our study provides valuable molecular information for future studies on wheat vernalization regulation and also serves as an excellent reference for future wheat breeding.

CaREM1.4 interacts with CaRIN4 to regulate Ralstonia solanacearum tolerance by triggering cell death in pepper

Remorins, plant-specific proteins, have a significant role in conferring on plants the ability to adapt to adverse environments. However, the precise function of remorins in resistance to biological stress remains largely unknown. Eighteen CaREM genes were identified in pepper genome sequences based on the C-terminal conserved domain that is specific to remorin proteins in this research. Phylogenetic relations, chromosomal localization, motif, gene structures, and promoter regions of these remorins were analyzed and a remorin gene, CaREM1.4, was cloned for further study. The transcription of CaREM1.4 in pepper was induced by infection with Ralstonia solanacearum. Knocking down CaREM1.4 in pepper using virus-induced gene silencing (VIGS) technologies reduced the resistance of pepper plants to R. solanacearum and downregulated the expression of immunity-associated genes. Conversely, transient overexpression of CaREM1.4 in pepper and Nicotiana benthamiana plants triggered hypersensitive response-mediated cell death and upregulated expression of defense-related genes. In addition, CaRIN4-12, which interacted with CaREM1.4 at the plasma membrane and cell nucleus, was knocked down with VIGS, decreasing the susceptibility of Capsicum annuum to R. solanacearum. Furthermore, CaREM1.4 reduced ROS production by interacting with CaRIN4-12 upon co-injection in pepper. Taken together, our findings suggest that CaREM1.4 may function as a positive regulator of the hypersensitive response, and it interacts with CaRIN4-12, which negatively regulates plant immune responses of pepper to R. solanacearum. Our study provides new evidence for comprehending the molecular regulatory network of plant cell death.

A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement

Gene regulation is central to all aspects of organism growth, and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops. However, the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking. In this study, we constructed a wheat integrative gene regulatory network (wGRN) by combining an updated genome annotation and diverse complementary functional datasets, including gene expression, sequence motif, transcription factor (TF) binding, chromatin accessibility, and evolutionarily conserved regulation. wGRN contains 7.2 million genome-wide interactions covering 5947 TFs and 127 439 target genes, which were further verified using known regulatory relationships, condition-specific expression, gene functional information, and experiments. We used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies. In addition, wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks. We further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions. Finally, we developed an interactive webserver, wGRN (http://wheat.cau.edu.cn/wGRN), for the community to explore gene regulation and discover trait-associated genes. Collectively, this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.

Asymmetric gene expression in grain development of reciprocal crosses between tetraploid and hexaploid wheats

Production of viable progeny from interploid crosses requires precise regulation of gene expression from maternal and paternal chromosomes, yet the transcripts contributed to hybrid seeds from polyploid parent species have rarely been explored. To investigate the genome-wide maternal and paternal contributions to polyploid grain development, we analyzed the transcriptomes of developing embryos, from zygote to maturity, alongside endosperm in two stages of development, using reciprocal crosses between tetraploid and hexaploid wheats. Reciprocal crosses between species with varied levels of ploidy displayed broad impacts on gene expression, including shifts in alternative splicing events in select crosses, as illustrated by active splicing events, enhanced protein synthesis and chromatin remodeling. Homoeologous gene expression was repressed on the univalent D genome in pentaploids, but this suppression was attenuated in crosses with a higher ploidy maternal parent. Imprinted genes were identified in endosperm and early embryo tissues, supporting predominant maternal effects on early embryogenesis. By systematically investigating the complex transcriptional networks in reciprocal-cross hybrids, this study presents a framework for understanding the genomic incompatibility and transcriptome shock that results from interspecific hybridization and uncovers the transcriptional impacts on hybrid seeds created from agriculturally-relevant polyploid species.

Physiology and Molecular Breeding in Sustaining Wheat Grain Setting and Quality under Spring Cold Stress

Spring cold stress (SCS) compromises the reproductive growth of wheat, being a major constraint in achieving high grain yield and quality in winter wheat. To sustain wheat productivity in SCS conditions, breeding cultivars conferring cold tolerance is key. In this review, we examine how grain setting and quality traits are affected by SCS, which may occur at the pre-anthesis stage. We have investigated the physiological and molecular mechanisms involved in floret and spikelet SCS tolerance. It includes the protective enzymes scavenging reactive oxygen species (ROS), hormonal adjustment, and carbohydrate metabolism. Lastly, we explored quantitative trait loci (QTLs) that regulate SCS for identifying candidate genes for breeding. The existing cultivars for SCS tolerance were primarily bred on agronomic and morphophysiological traits and lacked in molecular investigations. Therefore, breeding novel wheat cultivars based on QTLs and associated genes underlying the fundamental resistance mechanism is urgently needed to sustain grain setting and quality under SCS.

Computational genomics insights into cold acclimation in wheat

Development of cold acclimation in crops involves transcriptomic reprograming, metabolic shift, and physiological changes. Cold responses in transcriptome and lipid metabolism has been examined in separate studies for various crops. In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptomics and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

Transcriptome-based gene regulatory network analyses of differential cold tolerance of two tobacco cultivars

BACKGROUND

Cold is one of the main abiotic stresses that severely affect plant growth and development, and crop productivity as well. Transcriptional changes during cold stress have already been intensively studied in various plant species. However, the gene networks involved in the regulation of differential cold tolerance between tobacco varieties with contrasting cold resistance are quite limited.

RESULTS

Here, we conducted multiple time-point transcriptomic analyses using Tai tobacco (TT, cold susceptibility) and Yan tobacco (YT, cold resistance) with contrasting cold responses. We identified similar DEGs in both cultivars after comparing with the corresponding control (without cold treatment), which were mainly involved in response to abiotic stimuli, metabolic processes, kinase activities. Through comparison of the two cultivars at each time point, in contrast to TT, YT had higher expression levels of the genes responsible for environmental stresses. By applying Weighted Gene Co-Expression Network Analysis (WGCNA), we identified two main modules: the pink module was similar while the brown module was distinct between the two cultivars. Moreover, we obtained 100 hub genes, including 11 important transcription factors (TFs) potentially involved in cold stress, 3 key TFs in the brown module and 8 key TFs in the pink module. More importantly, according to the genetic regulatory networks (GRNs) between TFs and other genes or TFs by using GENIE3, we identified 3 TFs (ABI3/VP1, ARR-B and WRKY) mainly functioning in differential cold responses between two cultivars, and 3 key TFs (GRAS, AP2-EREBP and C2H2) primarily involved in cold responses.

CONCLUSION

Collectively, our study provides valuable resources for transcriptome- based gene network studies of cold responses in tobacco. It helps to reveal how key cold responsive TFs or other genes are regulated through network. It also helps to identify the potential key cold responsive genes for the genetic manipulation of tobacco cultivars with enhanced cold tolerance in the future.

Comparative Transcriptome Analysis Revealed the Freezing Tolerance Signaling Events in Winter Rapeseed (Brassica rapa L.)

Winter rapeseed (Brassica rapa L.) is an important oilseed crop in northwest China. Freezing stress severely limits its production and geographical distribution, and frequent extreme freezing events caused by climate change are increasing the chances of winter freeze-injury. However, the underlying mechanism of B. rapa response to freezing stress remains elusive. Here, B. rapa genome (v3.0) was used as a reference for the comparative transcriptomic analysis of Longyou 6 and Tianyou 2 (strong and weak cold tolerance, respectively) under different freezing stress. Before and after freezing stress, 5,982 and 11,630 unique differentially expressed genes (DEGs) between two cultivars were identified, respectively. After freezing stress, the GO terms in Tianyou 2 were mainly involved in "macromolecule biosynthetic process", and those in Longyou 6 were involved in "response to stimulus" and "oxidoreductase activity". Morphological and physiological results indicated that Longyou 6 retained a higher basal freezing resistance than Tinayou 2, and that cold acclimation could strengthen the basal freezing resistance. Freezing stress could activate the MAPK signal cascades, and the phosphorylation level of Longyou 6 showed a higher increase in response to freezing treatment than Tianyou 2. Based on our findings, it was speculated that the cell membrane of B. rapa perceives external signals under freezing stress, which are then transmitted to the nucleus through the cold-activated MAPK cascades and Ca²⁺-related protein kinase pathway, thus leading to activation of downstream target genes to enhance the freezing resistance of B. rapa.

Time-course transcriptome profiling revealed the specific expression patterns of MADS-box genes associated with the distinct developmental processes between winter and spring wheat

The shoot apex is a region where new cells are produced and elongate. The developmental state of the wheat shoot apex under low temperature affects its cold resistance. In this study, the morphology of shoot apex before overwintering was characterized for 24 wheat line with different winter and spring characteristics. Our research showed that the shoot apex of autumn-sown spring wheat lines reached the temperature sensitive double-ridge stage before overwintering, whereas shoot apex of winter wheat lines are found in temperature-insensitive vegetative or elongation stages. In order to explore how gene expression is associated with shoot apex differentiation in winter and spring wheat, we used strand-specific RNA sequencing to profile the gene expression patterns at four time-points between 14 after germination and 45 days after germination in the winter wheat cultivar Dongnongdongmai No. 1 (DM1) and in the spring wheat cultivar China Spring (CS). We identified 11,848 differentially expressed genes between the two cultivars. Most up-regulated genes in CS were involved in energy metabolism and transport during the seedling stage, whereas up-regulated genes in DM1 were involved in protein and DNA synthesis. MADS-box genes affect plant growth and development. In this study, MADS-boxes with differential expression between CS and DM1 were screened and evolutionary tree analysis was conducted. During all sampling periods, CS highly expressed MADS-box genes that induce flowering promotion genes such as VRN1, VRT and AG, while lowly expressed MADS-box genes that induce flowering-inhibiting homologous genes such as SVP. TaVRN1 composition in DM1 and CS was vrn-A1, vrn-B1, and Vrn-D1b. Analysis of the sequence of TaVRN1 (TraesCS5A01G391700) from DM1 and CS revealed 5 SNP differences in the promoter regions and 3 SNP deletions in the intron regions. The expression levels of cold resistant genes in DM1 were significantly higher than those in CS at seedling stage (neither DM1 nor CS experienced cold in this study), including CBF, cold induced protein,acid desaturase and proline rich proteins. Additionally, the expression levels of auxin-related genes were significantly higher in CS than those in DM1 at 45 days after germination. Our study identified candidate genes associated with the process of differentiation of the shoot apex in winter and spring wheat at the seedling stage and also raised an internal stress tolerance model for winter wheat to endogenously anticipate the coming stressful conditions in winter.

Differential Gene Expression Analysis of SoCBL Family Calcineurin B-like Proteins: Potential Involvement in Sugarcane Cold Stress

Sugarcan e is a major crop for sugar and biofuel production and is cultivated in tropical and subtropical areas worldwide. Sugarcane growth is constrained because of winter’s low-temperature stress, and cold resistance is an important limitation in sugarcane growth enhancement. Therefore, in this study, we identified a gene involved in the low-temperature stress response of sugarcane. Calcineurin B-like (CBL) protein is a calcium signal receptor involved in the cold stress response. Five sugarcane CBL genes were cloned, sequenced, and named SoCBL1, SoCBL3, SoCBL5, SoCBL6, and SoCBL9. The protein sequences of these genes were analyzed. The calculated molecular weight of these proteins was 24.5, 25.9, 25.2, 25.6, and 26.3 kD, respectively. Subcellular localization analysis revealed that SoCBL1, SoCBL3, SoCBL6, and SoCBL9 were situated in the cytoplasm, while SoCBL5 was present in mitochondria. Secondary structure analysis showed that these five CBL proteins had similar secondary structures. Conserved domain analysis displayed that each sugarcane CBL protein contained three conserved EF domains. According to the self-expanding values of the phylogenetic tree, the CBL gene family was divided into four groups. The CBL1 and CBL9 genes were classified into one group, illustrating that these two genes might possess a similar function. The expression analysis of the SoCBL gene under low temperatures showed that SoCBL3 and SoCBL5 were affected significantly, while SoCBL1 and SoCBL9 were less affected. These results demonstrate that the CBL genes in sugarcane have similar characteristics and present differences in genetic diversity and gene expression response to low temperatures. Therefore, these genes might be novel candidates for fighting cold stress in sugarcane.

TaVrt2, an SVP-like gene, cooperates with TaVrn1 to regulate vernalization-induced flowering in wheat

TaVrn1, encoding a MADS-box transcription factor (TF), is the central regulator of wheat vernalization-induced flowering. Considering that the MADS-box TF usually works by forming hetero- or homodimers, we conducted yeast-two-hybrid screening and identified an SVP-like MADS-box protein TaVrt2 interacting with TaVrn1. However, the specific function of TaVrt2 and the biological implication of its interaction with TaVrn1 remained unknown. We validated the function of TaVrt2 and TaVrn1 by wheat transgenic experiments and their interaction through multiple protein-binding assays. Population genetic analysis also was used to display their interplay. Transcriptomic sequencing and chromatin immunoprecipitation assays were performed to identify their common targets. TaVrt2 and TaVrn1 are flowering promoters in the vernalization pathway and interact physically in vitro, in planta and in wheat cells. Additionally, TaVrt2 and TaVrn1 were significantly induced in leaves by vernalization, suggesting their spatio-temporal interaction during vernalization. Genetic analysis indicated that TaVrt2 and TaVrn1 had significant epistatic effects on flowering time. Furthermore, native TaVrn1 was up-regulated significantly in TaVrn1-OE (overexpression) and TaVrt2-OE lines. Moreover, TaVrt2 could bind with TaVrn1 promoter directly. A TaVrt2-mediated positive feedback loop of TaVrn1 during vernalization was proposed, providing additional understanding on the regulatory mechanism underlying vernalization-induced flowering.

Elucidating the biochemical basis of trans-16:1 fatty acid change in leaves during cold acclimation in wheat

In plant cells, phosphatidylglycerol (PG) in the chloroplast has a characteristic trans-∆3-hexadecenoic acid (t16:1) at the sn-2 position. The t16:1 content in wheat leaf tissues decreases during cold treatment, but the significance of this fatty acid compositional change and the underlying biochemical mechanism remains poorly understood. Using a large collection of wheat cultivars displaying a varying capacity of freezing tolerance, we show for the first time under field conditions that this low temperature induced t16:1 change is associated with winter hardiness. To explore the metabolic mechanism responsible for the reduction of t16:1, we performed detailed lipid analysis and comparative transcriptome study with four selected wheat lines under cold acclimation. Our results show that wheat leaf tissues experience a gradual decrease in chloroplast lipid pathway activity during cold acclimation and that the decline in chloroplast lipid synthesis manifests itself in the decrease of t16:1 in PG. Comparative RNA-seq analyses with leaf tissues further reveal concerted transcriptome shifts indicating a rebalancing of chloroplast and cytosolic lipid synthesis during cold acclimation. Our study, thus, provides mechanistic understanding on chloroplast lipid adjustments as a "molecular ideotype" and the t16:1 change as a specific metabolite marker for screening freezing tolerance in wheat.

COR/LEA Proteins as Indicators of Frost Tolerance in Triticeae: A Comparison of Controlled versus Field Conditions

Low temperatures in the autumn induce enhanced expression/relative accumulation of several cold-inducible transcripts/proteins with protective functions from Late-embryogenesis-abundant (LEA) superfamily including dehydrins. Several studies dealing with plants grown under controlled conditions revealed a correlation (significant quantitative relationship) between dehydrin transcript/protein relative accumulation and plant frost tolerance. However, to apply these results in breeding, field experiments are necessary. The aim of the review is to provide a summary of the studies dealing with the relationships between plant acquired frost tolerance and COR/LEA transcripts/proteins relative accumulation in cereals grown in controlled and field conditions. The impacts of cold acclimation and vernalisation processes on the ability of winter-type Triticeae to accumulate COR/LEA proteins are discussed. The factors determining dehydrin relative accumulation under controlled cold acclimation treatments versus field trials during winter seasons are discussed. In conclusion, it can be stated that dehydrins could be used as suitable indicators of winter survival in field-grown winter cereals but only in plant prior to the fulfilment of vernalisation requirement.

Deciphering transcriptional regulators of banana fruit ripening by regulatory network analysis

Fruit ripening is a critical phase in the production and marketing of fruits. Previous studies have indicated that fruit ripening is a highly coordinated process, mainly regulated at the transcriptional level, in which transcription factors play essential roles. Thus, identifying key transcription factors regulating fruit ripening as well as their associated regulatory networks promises to contribute to a better understanding of fruit ripening. In this study, temporal gene expression analyses were performed to investigate banana fruit ripening with the aim to discern the global architecture of gene regulatory networks underlying fruit ripening. Eight time points were profiled covering dynamic changes of phenotypes, the associated physiology and levels of known ripening marker genes. Combining results from a weighted gene co-expression network analysis (WGCNA) as well as cis-motif analysis and supported by EMSA, Y1H, tobacco-, banana-transactivation experimental results, the regulatory network of banana fruit ripening was constructed, from which 25 transcription factors were identified as prime candidates to regulate the ripening process by modulating different ripening-related pathways. Our study presents the first global view of the gene regulatory network involved in banana fruit ripening, which may provide the basis for a targeted manipulation of fruit ripening to attain higher banana and loss-reduced banana commercialization.

Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress

Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Results showed that a total of 118,015 genes and 6,034 of these differentially expressed genes (DEGs) were screened. Protein–protein interaction (PPI) analyses revealed that ABA signaling via protein phosphatase 2Cs was the most important signal transduction pathway and late embryogenesis abundant protein was the hub protein associated with adaptation to cold stress. Furthermore, a total of 856 miRNAs were identified in this study and 109 of them were differentially expressed in sugarcane responding to cold stress. Most importantly, the miRNA–gene regulatory networks suggested the complex post-transcriptional regulation in sugarcane under cold stress, including 10 miRNAs−42 genes, 16 miRNAs−70 genes, and three miRNAs−18 genes in CT vs. LT0.5, CT vs. LT1, and CT0.5 vs. LT1, respectively. Specifically, key regulators from 16 genes encoding laccase were targeted by novel-Chr4C_47059 and Novel-Chr4A_40498, while five LRR-RLK genes were targeted by Novel-Chr6B_65233 and Novel-Chr5D_60023, 19 PPR repeat proteins by Novel-Chr5C_57213 and Novel-Chr5D_58065. Our findings suggested that these miRNAs and cell wall-related genes played vital regulatory roles in the responses of sugarcane to cold stress. Overall, the results of this study provide insights into the transcriptional and post-transcriptional regulatory network underlying the responses of sugarcane to cold stress.

Ribosome profiling in plants: what is not lost in translation?

Translation is a highly dynamic cellular process whereby genetic information residing in an mRNA molecule is converted into a protein that in turn executes specific functions. However, pre-synthesized mRNA levels do not always correlate with corresponding protein levels, suggesting that translational control plays an essential role in gene regulation. A better understanding of how gene expression is regulated during translation will enable the discovery of new genes and mechanisms that control important traits in plants. Therefore, in recent years, several methods have been developed to analyse the translatome; that is, all mRNAs being actively translated at a given time, tissue, and/or developmental stage. Ribosome profiling or ribo-seq is one such technology revolutionizing our ability to analyse the translatome and in turn understand translational control of gene expression. Ribo-seq involves isolating mRNA-ribosome complexes, treating them with a RNase, and then identifying ribosome-protected mRNA regions by deep sequencing. Here, we briefly review recent ribosome profiling studies that revealed new insights into plant biology. Manipulation of novel genes identified using ribosome profiling could prove useful for increasing yield through improved biotic and abiotic stress tolerance.

Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.)

The objective of the study is to reveal the freezing tolerance mechanisms of wheat by combining the emerging single-molecule real-time (SMRT) sequencing technology PacBio Sequel and Illumina sequencing. Commercial semiwinter wheat Zhoumai 18 was exposed to -6°C for 4 h at the four-leave stage. Leaves of the control group and freezing-treated group were used to perform cDNA library construction. PacBio SMRT sequencing yielded 51,570 high-quality isoforms from leaves of control sample of Zhoumai 18, encoded by 20,366 gene loci. In total, 73,695 transcript isoforms, corresponding to 23,039 genes, were identified from the freezing-treated leaves. Compared with transcripts from the International Wheat Genome Sequencing Consortium RefSeq v1.1, 57,667 novel isoforms were discovered, which were annotated 21,672 known gene loci, as well as 3,399 novel gene loci. Transcriptome characterization including alterative spliced events, alternative polydenylation sites, transcription factors, and fusion transcripts were also analyzed. Freezing-responsive genes and signals were uncovered and proved that the ICE-ERF-COR pathway and ABA signal transduction play a vital role in the freezing response of wheat. In this study, PacBio sequencing and Illumina sequencing were applied to investigate the freezing tolerance in common wheat, and the transcriptome results provide insights into the molecular regulation mechanisms under freezing treatment.

In-Silico Evaluation of a New Gene From Wheat Reveals the Divergent Evolution of the CAP160 Homologous Genes Into Monocots

This study reports the evolutionary history and in-silico functional characterization of a novel water-deficit and ABA-responsive gene in wheat. This gene has remote sequence similarity to known abiotic stress-related genes in different plants, including CAP160 in Spinacia oleracea, RD29B in Arabidopsis thaliana, and CDeT11-24 in Craterostigma plantagineum. The study investigated if these genes form a close homologous relationship or if they are a result of convergent evolutionary processes. The results indicated a closely shared homologous relationship between these genes. Bayesian phylogenetic analysis of the protein sequences of the remotely related CAP160 proteins from various plant species indicated the presence of three distinct clades. Further analyses indicated that CAP160 homologous genes have predominantly evolved through neutral processes, with multiple regions experiencing signatures of purifying selection, while others were indicated to be the result of episodic diversifying selection events. Functional predictions revealed that these genes might share at least two functions related to abiotic stress conditions: one similar to the cryoprotective function of LEA protein, and the other a signalling molecule with phosphatidic acid binding specificity. Studies focused on the identification of cold-responsive genes are essential for the development of cold-tolerant crop plants, if we are to increase agricultural productivity throughout temperate regions.

Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field

Cold acclimation and vegetative/reproductive transition are two important evolutionary adaptive mechanisms for winter wheat surviving the freezing temperature in winter and successful seeds setting in the next year. MicroRNA (miRNA) is a class of regulatory small RNAs (sRNAs), which plays critical roles in the growth and development of plants. However, the regulation mechanism of miRNAs during cold acclimation and vegetative/reproductive transition of winter wheat is not much understood. In this study, four sRNA libraries from leaves of winter wheat grown in the field at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage were analyzed to identify known and novel miRNAs and to understand their potential roles in the growth and development of winter wheat. We examined miRNA expression using a high-throughput sequencing technique. A total of 373 known, 55 novel, and 27 putative novel miRNAs were identified. Ninety-one miRNAs were found to be differentially expressed at the four stages. Among them, the expression of six known and eight novel miRNAs was significantly suppressed at the winter dormancy stage, whereas the expression levels of seven known and eight novel miRNAs were induced at this stage; three known miRNAs and three novel miRNAs were significantly induced at the spring green-up stage; six known miRNAs were induced at the spring green-up stage and reached the highest expression level at the jointing stage; and 20 known miRNAs and 10 novel miRNAs were significantly induced at the jointing stage. Expression of a number of representative differentially expressed miRNAs was verified using quantitative real-time polymerase chain reaction (qRT-PCR). Potential target genes for known and novel miRNAs were predicted. Moreover, six novel target genes for four Pooideae species-specific miRNAs and two novel miRNAs were verified using the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5'RACE) technique. These results indicate that miRNAs are key non-coding regulatory factors modulating the growth and development of wheat. Our study provides valuable information for in-depth understanding of the regulatory mechanism of miRNAs in cold acclimation and vegetative/reproductive transition of winter wheat grown in the field.

Genome-Wide Identification and Characterization of the Wheat Remorin (TaREM) Family during Cold Acclimation

Remorins (REMs) are plant-specific proteins that play an essential role in plant-microbe interactions. However, their roles in vernalization and abiotic stress responses remain speculative. Most remorins have a variable proline-rich -half and a more conserved -half that is predicted to form coils. A search of the wheat ( L.) database revealed the existence of 20 different genes, which we classified into six groups on the basis of whether they shared a common phylogenetic and structural origin. Analysis of the physical genomic distributions demonstrated that genes are dispersed in the wheat genome and have one to seven introns. Promoter analysis of genes revealed the presence of putative -elements related to diverse functions like development, hormonal regulation, and biotic and abiotic stress responsiveness. Expression levels of genes were measured in plants grown under field and controlled conditions and in response to hormone treatment. Our analyses revealed that 12 members of the REM family are regulated during cold acclimation in wheat in four different tissues (roots, crowns, stems, and leaves), with the highest expression in roots. Differential gene expression was found between wheat cultivars with contrasting degrees of cold tolerance, suggesting the implication of genes in cold response and tolerance. Additionally, eight genes were induced in response to abscisic acid and methyl jasmonate treatment. This genome-wide analysis of genes provides valuable resources for functional analysis aimed at understanding their role in stress adaptation.

Transcriptomic response of durum wheat to cold stress at reproductive stage

Understanding the genetic basis of cold tolerance is a key step towards obtaining new and improved crop varieties. Current geographical distribution of durum wheat in Argentina exposes the plants to frost damage when spikes have already emerged. Biochemical pathways involved in cold tolerance are known to be early activated at above freezing temperatures. In this study we reported the transcriptome of CBW0101 spring durum wheat by merging data from untreated control and cold (5 °C) treated plant samples at reproductive stage. A total of 128,804 unigenes were predicted. Near 62% of the unigenes were annotated in at least one database. In total 876 unigenes were differentially expressed (DEGs), 562 were up-regulated and 314 down-regulated in treated samples. DEGs are involved in many critical processes including, photosynthetic activity, lipid and carbohydrate synthesis and accumulation of amino acids and seed proteins. Twenty-eight transcription factors (TFs) belonging to 14 families resulted differentially expressed from which eight families comprised of only TFs induced by cold. We also found 31 differentially expressed Long non-coding RNAs (lncRNAs), most of them up-regulated in treated plants. Two of these lncRNAs could operate via microRNAs (miRNAs) target mimic. Our results suggest a reprogramming of expression patterns in CBW0101 that affects a number of genes that is closer to the number reported in winter genotypes. These observations could partially explain its moderate tolerance (low proportion of frost-damaged spikes) when exposed to freezing days in the field.

The General Transcription Repressor TaDr1 Is Co-expressed With TaVrn1 and TaFT1 in Bread Wheat Under Drought

The general transcription repressor, TaDr1 gene, was identified during screening of a wheat SNP database using the Amplifluor-like SNP marker KATU-W62. Together with two genes described earlier, TaDr1A and TaDr1B, they represent a set of three homeologous genes in the wheat genome. Under drought, the total expression profiles of all three genes varied between different bread wheat cultivars. Plants of four high-yielding cultivars exposed to drought showed a 2.0-2.4-fold increase in TaDr1 expression compared to controls. Less strong, but significant 1.3-1.8-fold up-regulation of the TaDr1 transcript levels was observed in four low-yielding cultivars. TaVrn1 and TaFT1, which controls the transition to flowering, revealed similar profiles of expression as TaDr1. Expression levels of all three genes were in good correlation with grain yields of evaluated cultivars growing in the field under water-limited conditions. The results could indicate the involvement of all three genes in the same regulatory pathway, where the general transcription repressor TaDr1 may control expression of TaVrn1 and TaFT1 and, consequently, flowering time. The strength of these genes expression can lead to phenological changes that affect plant productivity and hence explain differences in the adaptation of the examined wheat cultivars to the dry environment of Northern and Central Kazakhstan. The Amplifluor-like SNP marker KATU-W62 used in this work can be applied to the identification of wheat cultivars differing in alleles at the TaDr1 locus and in screening hybrids.

Remembering winter through vernalisation

Vernalisation is the programmed physiological process in which prolonged cold-exposure provides competency to flower in plants; widely found in winter and biennial species, such as Arabidopsis, fruit trees, vegetables and wheat. This phenomenon is regulated by diverse genetic networks, and memory of vernalisation in a life cycle mainly depends on epigenetic mechanisms. However, less is known about how to count winter-dosage for flowering in plants. Here, we compare the vernalisation genetic framework between the dicots Arabidopsis, temperate grasses, wheat, barley and Brachypodium. We discuss vernalisation mechanisms involving crosstalk between phosphorylation and O-GlcNAcylation modification of key proteins, and epigenetic modifications of the key gene VRN1 in wheat. We also highlight the potential evolutionary origins of vernalisation in various species. Current progress toward understanding the regulation of vernalisation requirements provides insight that will inform the design of molecular breeding strategies for winter crops.

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat

Wheat spike development is a coordinated process of cell proliferation and differentiation with distinctive phases and architecture changes. However, the dynamic alteration of gene expression in this process remains enigmatic. Here, we characterized and dissected bread wheat spike into six developmental stages, and used genome-wide gene expression profiling, to investigate the underlying regulatory mechanisms. High gene expression correlations between any two given stages indicated that wheat early spike development is controlled by a small subset of genes. Throughout, auxin signaling increased, while cytokinin signaling decreased. Besides, many genes associated with stress responses highly expressed during the double ridge stage. Among the differentially expressed genes (DEGs), were identified 375 transcription factor (TF) genes, of which some homologs in rice or Arabidopsis are proposed to function in meristem maintenance, flowering time, meristem initiation or transition, floral organ development or response to stress. Gene expression profiling demonstrated that these genes had either similar or distinct expression pattern in wheat. Several genes regulating spike development were expressed in the early spike, of which Earliness per se 3 (Eps-3) was found might function in the initiation of spikelet meristem. Our study helps uncover important genes associated with apical meristem morphology and development in wheat.