Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage

Identification of candidate regulators of the response to early heat stress in climate-adapted wheat landraces via transcriptomic and co-expression network analyses

Introduction

Climate change is likely to lead to not only increased global temperatures but also a more variable climate where unseasonal periods of heat stress are more prevalent. This has been evidenced by the observation of spring-time temperatures approaching 40°C in some of the main spring-wheat producing countries, such as the USA, in recent years. With an optimum growth temperature of around 20°C, wheat is particularly prone to damage by heat stress. A warming climate with increasingly common fluctuations in temperature therefore threatens wheat crops and subsequently the lives and livelihoods of billions of people who depend on the crop for food. To futureproof wheat against a variable climate, a better understanding of the response to early heat stress is required.

Methods

Here, we utilised DESeq2 to identify 7,827 genes which were differentially expressed in wheat landraces after early heat stress exposure. Candidate hub genes, which may regulate the transcriptional response to early heat stress, were identified via weighted gene co-expression network analysis (WGCNA), and validated by qRT-PCR.

Results

Two of the most promising candidate hub genes (TraesCS3B02G409300 and TraesCS1B02G384900) may downregulate the expression of genes involved in the drought, salinity, and cold responses-genes which are unlikely to be required under heat stress-as well as photosynthesis genes and stress hormone signalling repressors, respectively. We also suggest a role for a poorly characterised sHSP hub gene (TraesCS4D02G212300), as an activator of the heat stress response, potentially inducing the expression of a vast suite of heat shock proteins and transcription factors known to play key roles in the heat stress response.

Discussion

The present work represents an exploratory examination of the heat-induced transcriptional change in wheat landrace seedlings and identifies several candidate hub genes which may act as regulators of this response and, thus, may be targets for breeders in the production of thermotolerant wheat varieties.

Elevated CO2 increases biomass of Sorghum bicolor green prop roots under drought conditions via soluble sugar accumulation and photosynthetic activity

Elevated [CO2 ] (E[CO2 ]) mitigates agricultural losses of C4 plants under drought. Although several studies have described the molecular responses of the C4 plant species Sorghum bicolor during drought exposure, few have reported the combined effects of drought and E[CO2 ] (E[CO2 ]/D) on the roots. A previous study showed that, among plant organs, green prop roots (GPRs) under E[CO2 ]/D presented the second highest increase in biomass after leaves compared with ambient [CO2 ]/D. GPRs are photosynthetically active and sensitive to drought. To understand which mechanisms are involved in the increase in biomass of GPRs, we performed transcriptome analyses of GPRs under E[CO2 ]/D. Whole-transcriptome analysis revealed several pathways altered under E[CO2 ]/D, among which photosynthesis was strongly affected. We also used previous metabolome data to support our transcriptome data. Activities associated with photosynthesis and central metabolism increased, as seen by the upregulation of photosynthesis-related genes, a rise in glucose and polyol contents, and increased contents of chlorophyll a and carotenoids. Protein-protein interaction networks revealed that proliferation, biogenesis, and homeostasis categories were enriched and contained mainly upregulated genes. The findings suggest that the previously reported increase in GPR biomass of plants grown under E[CO2 ]/D is mainly attributed to glucose and polyol accumulation, as well as photosynthesis activity and carbon provided by respiratory CO2 refixation. Our findings reveal that an intriguing and complex metabolic process occurs in GPRs under E[CO2 ]/D, showing the crucial role of these organs in plant drought /tolerance.

Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress

BACKGROUND

Rice is one of the most important cereals consumed worldwide. Two major abiotic factors affecting rice plants in different growth stages are flooding stress and cold stress. These abiotic stresses can take place independently or simultaneously and significantly affect rice plants during germination and seedling growth. Fortunately, a wide array of phenotypic responses conferring flooding stress and chilling stress tolerance exist within the rice germplasm, indicating the presence of different molecular mechanisms underlying tolerance to these stresses. Understanding these differences may assist in developing improved rice cultivars having higher tolerance to both stresses. In this study, we conducted a comparative global gene expression analysis of two rice genotypes with contrasting phenotypes under cold stress, anaerobic stress, and combined cold and anaerobic stress during germination.

RESULTS

The differential gene expression analysis revealed that 5571 differentially expressed genes (DEGs), 7206 DEGs, and 13279 DEGs were identified under anaerobic stress, cold stress, and combined stress, respectively. Genes involved in the carbohydrate metabolic process, glucosyltransferase activity, regulation of nitrogen compound metabolic process, protein metabolic process, lipid metabolic process, cellular nitrogen compound biosynthetic process, lipid biosynthetic process, and a microtubule-based process were enriched across all stresses. Notably, the common Gene Ontology (GO) analysis identified three hub genes, namely Os08g0176800 (similar to mRNA-associated protein mrnp 41), Os11g0454200 (dehydrin), and OS10g0505900 (expressed protein).

CONCLUSION

A large number of differentially expressed genes were identified under anaerobic, cold conditions during germination and the combination of the two stress conditions in rice. These results will assist in the identification of promising candidate genes for possible manipulation toward rice crops that are more tolerant under flooding and cold during germination, both independently and concurrently.

Comparative transcriptomics and co-expression networks reveal cultivar-specific molecular signatures associated with reproductive-stage cold stress in rice

The resistance of Huaidao5 results from the high constitutive expression of tolerance genes, while that of Huaidao9 is due to the cold-induced resistance in flag leaves and panicles. The regulation mechanism of rice seedlings' cold tolerance is relatively clear, and knowledge of its underlying mechanisms at the reproductive stage is limited. We performed differential expression and co-expression network analyses to transcriptomes from panicle and flag leaf tissues of a cold-tolerant cultivar (Huaidao5), and a sensitive cultivar (Huaidao9), under reproductive-stage cold stress. The results revealed that the expression levels of genes in stress-related pathways such as MAPK signaling pathway, diterpenoid biosynthesis, glutathione metabolism, plant-pathogen interaction and plant hormone signal transduction were constitutively highly expressed in Huaidao5, especially in panicles. Moreover, the Hudaidao5's panicle sample-specific (under cold) module contained some genes related to rice yield, such as GW5L, GGC2, SG1 and CTPS1. However, the resistance of Huaidao9 was derived from the induced resistance to cold in flag leaves and panicles. In the flag leaves, the responses included a series of stress response and signal transduction, while in the panicles nitrogen metabolism was severely affected, especially 66 endosperm-specific genes. Through integrating differential expression with co-expression networks, we predicted 161 candidate genes (79 cold-responsive genes common to both cultivars and 82 cold-tolerance genes associated with differences in cold tolerance between cultivars) potentially affecting cold response/tolerance, among which 85 (52.80%) were known to be cold-related genes. Moreover, 52 (65.82%) cold-responsive genes (e.g., TIFY11C, LSK1 and LPA) could be confirmed by previous transcriptome studies and 72 (87.80%) cold-tolerance genes (e.g., APX5, OsFbox17 and OsSTA109) were located within QTLs associated with cold tolerance. This study provides an efficient strategy for further discovery of mechanisms of cold tolerance in rice.

Proteome and phosphoproteome analysis of 2,4-epibrassinolide-mediated cold stress response in cucumber seedlings

The 2, 4-epibrassinolide (EBR) significantly increased plants cold tolerance. However, mechanisms of EBR in regulating cold tolerance in phosphoproteome and proteome levels have not been reported. The mechanism of EBR regulating cold response in cucumber was studied by multiple omics analysis. In this study, phosphoproteome analysis showed that cucumber responded to cold stress through multi-site serine phosphorylation, while EBR further upregulated single-site phosphorylation for most of cold-responsive phosphoproteins. Association analysis of the proteome and phosphoproteome revealed that EBR reprogrammed proteins in response to cold stress by negatively regulating protein phosphorylation and protein content, and phosphorylation negatively regulated protein content in cucumber. Further functional enrichment analysis of proteome and phosphoproteome showed that cucumber mainly upregulated phosphoproteins related to spliceosome, nucleotide binding and photosynthetic pathways in response to cold stress. However, different from the EBR regulation in omics level, hypergeometric analysis showed that EBR further upregulated 16 cold-up-responsive phosphoproteins participated photosynthetic and nucleotide binding pathways in response to cold stress, suggested their important function in cold tolerance. Analysis of cold-responsive transcription factors (TFs) by correlation between proteome and phosphoproteome showed that cucumber regulated eight class TFs may through protein phosphorylation under cold stress. Further combined with cold-related transcriptome found that cucumber phosphorylated eight class TFs, and mainly through targeting major hormone signal genes by bZIP TFs in response to cold stress, while EBR further increased these bZIP TFs (CsABI5.2 and CsABI5.5) phosphorylation level. In conclusion, the EBR mediated schematic of molecule response mechanisms in cucumber under cold stress was proposed.

Multi-omics approach reveals the contribution of OsSEH1 to rice cold tolerance

As low environmental temperature adversely affects the growth, development and geographical distribution, plants have evolved multiple mechanisms involving changing physiological and metabolic processes to adapt to cold stress. In this study, we revealed that nucleoporin-coding gene OsSEH1 was a positive regulator of cold stress in rice. Physiological assays showed that the activity of antioxidant enzymes showed a significant difference between osseh1 knock-out lines and wild type under cold stress. Metabolome analysis revealed that the contents of large-scale flavonoids serving as ROS scavengers were lower in osseh1 mutants compared with wild type under cold stress. Transcriptome analysis indicated that the DEGs between osseh1 knock-out lines and wild type plants were enriched in defense response, regulation of hormone levels and oxidation-reduction process. Integration of transcriptomic and metabolic profiling revealed that OsSEH1 plays a role in the oxidation-reduction process by coordinately regulating genes expression and metabolite accumulation involved in phenylpropanoid and flavonoid biosynthetic pathway. In addition, Exogenous ABA application assays indicated that osseh1 lines had hypersensitive phenotypes compared with wild type plants, suggesting that OsSEH1 may mediate cold tolerance by regulating ABA levels.

Cold-adaptive evolution at the reproductive stage in Geng/japonica subspecies reveals the role of OsMAPK3 and OsLEA9

Cold stress at the reproductive stage severely affects the production and geographic distribution of rice. The Geng/japonica subpopulation gradually developed stronger cold adaptation than the Xian/indica subpopulation during the long-term domestication of cultivated rice. However, the evolutionary path and natural alleles underlying the cold adaptability of intra-Geng subspecies remain largely unknown. Here, we identified MITOGEN-ACTIVATED PROTEIN KINASE 3 (OsMAPK3) and LATE EMBRYOGENESIS ABUNDANT PROTEIN 9 (OsLEA9) as two important regulators for the cold adaptation of Geng subspecies from a combination of transcriptome analysis and genome-wide association study. Transgenic validation showed that OsMAPK3 and OsLEA9 confer cold tolerance at the reproductive stage. Selection and evolution analysis suggested that the Geng version of OsMAPK3 (OsMAPK3^Geng ) directly evolved from Chinese Oryza rufipogon III and was largely retained in high-latitude and high-altitude regions with low temperatures during domestication. Later, the functional nucleotide polymorphism (FNP-776) in the Kunmingxiaobaigu and Lijiangxiaoheigu version of the OsLEA9 (OsLEA9^KL ) promoter originated from novel variation of intra-Geng was selected and predominantly retained in temperate Geng to improve the adaptation of Geng together with OsMAPK3^Geng to colder climatic conditions in high-latitude areas. Breeding potential analysis suggested that pyramiding of OsMAPK3^Geng and OsLEA9^KL enhanced the cold tolerance of Geng and promotes the expansion of cultivated rice to colder regions. This study not only highlights the evolutionary path taken by the cold-adaptive differentiation of intra-Geng, but also provides new genetic resources for rice molecular breeding in low-temperature areas.

Different responses of banana classical AGP genes and cell wall AGP components to low-temperature between chilling sensitive and tolerant cultivars

Seventeen classical MaAGPs and 9 MbAGPs were identified and analyzed. MaAGP1/2/6/9/16/17, the antigens of JIM13 and LM2 antibodies are likely to be involved in banana chilling tolerance. Classical arabinogalactan proteins (AGPs) belong to glycosylphosphatidylinositol-anchored proteins, which are proved to be involved in signaling and cell wall metabolism upon stresses. However, rare information is available on the roles of classical AGPs in low temperature (LT) tolerance. Cultivation of banana in tropical and subtropical region is seriously threatened by LT stress. In the present study, 17 classical MaAGPs and nine MbAGPs in banana A and B genome were identified and characterized, respectively. Great diversity was present among different classical MaAGP/MbAGP members while five members (AGP3/6/11/13/14) showed 100% identity between these two gene families. We further investigated different responses of classical AGPs to LT between a chilling sensitive (CS) and tolerant (CT) banana cultivars. In addition, different changes in the temporal and spatial distribution of cell wall AGP components under LTs between these two cultivars were compared using immunofluorescence labeling. Seven classical MbAGPs were upregulated by LT(s) in the CT cultivar. Classical MaAGP4/6 was induced by LT(s) in both cultivars while MaAGP1/2/9/16/17 only in the CT cultivar. Moreover, these genes showed significantly higher transcription abundance in the CT cultivar than the CS one under LT(s) except classical MaAGP4. Similar results were observed with the epitopes of JIM13 and LM2 antibodies. The antigens of these antibodies and classical MaAGP1/2/6/9/16/17 might be related to LT tolerance of banana. These results provide additional information about plant classical AGPs and their involvement in LT tolerance, as well as their potential as candidate genes to be targeted when breeding CT banana.

Root responses of contrasting rice genotypes to low temperature stress

Rice (Oryza sativa L.) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the root response to low temperature stress during the early vegetative stage of two rice genotypes contrasting in their cold tolerance (CT, cold-tolerant; and CS, cold-sensitive). Root dry weight and length, as well as the number of root hairs, were higher in CT than CS when exposed to cold treatment. Histochemical analyses indicated that roots of CS genotype present higher levels of lipid peroxidation and H₂O₂ accumulation, along with lower levels of plasma membrane integrity than CT under low temperature stress. RNAseq analyses revealed that the contrasting genotypes present completely different molecular responses to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes might contribute to rice cold tolerance, including the ones related with cell wall remodeling, cytoskeleton and growth, signaling, antioxidant system, lipid metabolism, and stress response. On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Since these two genotypes have a similar genetic background (sister lines), the differentially expressed genes found here can be considered candidate genes for cold tolerance and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.

Transcriptome Sequencing and iTRAQ of Different Rice Cultivars Provide Insight into Molecular Mechanisms of Cold-Tolerance Response in Japonica Rice

BACKGROUND

Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions. However, it has a high sensitivity to cold stress and chilling stress limits its nitrogen uptake and metabolism. To identify the genes and pathways involved in cold tolerance, specifically within nitrogen metabolism pathways, we compared gene and protein expression differences between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10 (SJ).

RESULTS

Using isobaric tags for relative or absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5549 genes and 450 proteins in DN and 6145 genes and 790 proteins in SJ, which were differentially expressed during low water temperature (T_w) treatments. There were 354 transcription factor (TF) genes (212 downregulated, 142 upregulated) and 366 TF genes (220 downregulated, 146 upregulated), including 47 gene families, differentially expressed in DN under control (CKDN) vs. DN under low-T_w (D15DN) and SJ under control (CKSJ) vs. SJ under low-T_w D15SJ, respectively. Genes associated with rice cold-related biosynthesis pathways, particularly the mitogen-activated protein kinase (MAPK) signaling, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) associated with rice cold-related biosynthesis pathways, and particularly glutathione metabolism, were significantly differentially expressed in both rice cultivars. Transcriptome and proteome analysis of the nitrogen metabolism pathways showed that major genes and proteins that participated in γ-aminobutyric acid (GABA) and glutamine synthesis were downregulated under cold stress.

CONCLUSION

Cold stress conditions during reproductive growth, resulted in genes and proteins related to cold stress biosynthesis pathways being significantly differentially expressed in DN and SJ. The present study confirmed the known cold stress-associated genes and identified new putative cold-responsive genes. We also found that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-T_w treatments affected N uptake and N metabolism in rice, as well as promoted Glu metabolism and the synthesis of ornithine and proline in cold-sensitive SJ.

Long-term transcriptional memory in rice plants submitted to salt shock

A first salt shock event alters transcriptional and physiological responses to a second event, being possible to identify 26 genes associated with long-term memory. Soil salinity significantly affects rice cultivation, resulting in large losses in growth and productivity. Studies report that a disturbing event can prepare the plant for a subsequent event through memory acquisition, involving physiological and molecular processes. Therefore, genes that provide altered responses in subsequent events define a category known as "memory genes". In this work, the RNA-sequencing (RNA-Seq) technique was used to analyse the transcriptional profile of rice plants subjected to different salt shock events and to characterise genes associated with long-term memory. Plants subjected to recurrent salt shock showed differences in stomatal conductance, chlorophyll index, electrolyte leakage, and the number of differentially expressed genes (DEGs), and they had lower Na⁺/K⁺ ratios than plants that experienced only one stress event. Additionally, the mammalian target of rapamycin (mTOR) pathways, and carbohydrate and amino acid-associated pathways were altered under all conditions. Memory genes can be classified according to their responses during the first event (+ or -) and the second shock event (+ or -), being possible to observe a larger number of transcripts for groups [+ /-] and [-/ +], genes characterised as "revised response." This is the first long-term transcriptional memory study in rice plants under salt shock, providing new insights into the process of plant memory acquisition.

Photosynthetic activity of indica rice sister lines with contrasting cold tolerance

Incidence of cold during early stages is an obstacle for the growing progress of rice plants. Cold stress has strong negative effects on photosynthetic activity. Previously, our group evaluated plant survival of 90 indica rice genotypes after cold treatment. Two sister lines were characterized as cold-tolerant and cold-sensitive. Transcriptomic analyses of the same genotypes had indicated differential expression of genes related to photosynthesis. Previous work with japonica rice had suggested that cold sensitivity was more related to photosystem II (PSII) than to photosystem I (PSI). Using our previously identified contrasting genotypes, we investigated the role of specific steps of the photosynthetic process in cold tolerance/sensitivity of indica rice plants during and after (recovery period) cold exposure. During both cold treatment and recovery period, the photochemical activity (including PSII and PSI) presented higher levels in the low temperature-tolerant genotype, when compared with the sensitive one. The higher photochemical efficiency during the cold treatment appears to be related to a lower fraction of reduced QA - in PSII. We also observed lower transpiration rates and higher water use efficiency in the cold-tolerant genotype, due to stomatal closure. After the recovery period, the higher efficiency in the cold-tolerant genotype seems to be related to a lower fraction of reduced QA - and a larger pool of final electron acceptors at the PSI. This work uncovered changes in photosynthetic performance including both photosystems and improved water use efficiency which may be important components of cold tolerance mechanisms in indica rice.

Quantitative Trait Loci for Freezing Tolerance in a Lowland x Upland Switchgrass Population

Low-temperature related abiotic stress is an important factor affecting winter survival in lowland switchgrass when grown in northern latitudes in the United States. A better understanding of the genetic architecture of freezing tolerance in switchgrass will aid the development of lowland switchgrass cultivars with improved winter survival. The objectives of this study were to conduct a freezing tolerance assessment, generate a genetic map using single nucleotide polymorphism (SNP) markers, and identify QTL (quantitative trait loci) associated with freezing tolerance in a lowland × upland switchgrass population. A pseudo-F2 mapping population was generated from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. The segregating progenies were screened for freezing tolerance in a controlled-environment facility. Two clonal replicates of each genotype were tested at six different treatment temperatures ranging from -15 to -5°C at an interval of 2°C for two time periods. Tiller emergence (days) and tiller number were recorded following the recovery of each genotype with the hypothesis that upland genotype is the source for higher tiller number and early tiller emergence. Survivorship of the pseudo-F2 population ranged from 89% at -5°C to 5% at -15°C with an average LT50 of -9.7°C. Genotype had a significant effect on all traits except tiller number at -15°C. A linkage map was constructed from bi-allelic single nucleotide polymorphism markers generated using exome capture sequencing. The final map consisted of 1618 markers and 2626 cM, with an average inter-marker distance of 1.8 cM. Six significant QTL were identified, one each on chromosomes 1K, 5K, 5N, 6K, 6N, and 9K, for the following traits: tiller number, tiller emergence days and LT50. A comparative genomics study revealed important freezing tolerance genes/proteins, such as COR47, DREB2B, zinc finger-CCCH, WRKY, GIGANTEA, HSP70, and NRT2, among others that reside within the 1.5 LOD confidence interval of the identified QTL.

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.