Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach

Integrated transcriptome, proteome and metabolome analyses revealed secondary metabolites and auxiliary carbohydrate metabolism augmenting drought tolerance in rice

Drought is one of the major consequences of climate change and a serious threat to rice production. Drought stress activates interactions among genes, proteins and metabolites at the molecular level. A comparative multi-omics analysis of drought-tolerant and drought-sensitive rice cultivars can decipher the molecular mechanisms involved in drought tolerance/response. Here, we characterized the global-level transcriptome, proteome, and metabolome profiles, and performed integrated analyses thereof in a drought-sensitive (IR64) and a drought-tolerant (Nagina 22) rice cultivar under control and drought-stress conditions. The transcriptional dynamics and its integration with proteome analysis revealed the role of transporters in regulation of drought stress. The proteome response illustrated the contribution of translational machinery to drought tolerance in N22. The metabolite profiling revealed that aromatic amino acids and soluble sugars contribute majorly to drought tolerance in rice. The integrated transcriptome, proteome and metabolome analysis performed using statistical and knowledge-based methods revealed the preference for auxiliary carbohydrate metabolism through glycolysis and pentose phosphate pathway contributed to drought tolerance in N22. In addition, L-phenylalanine and the genes/proteins responsible for its biosynthesis were also found to contribute to drought tolerance in N22. In conclusion, our study provided mechanistic insights into the drought response/adaptation mechanism and is expected to facilitate engineering of drought tolerance in rice.

Unearth of small open reading frames (sORFs) in drought stress transcriptome of Oryza sativa subsp. indica

Drought is a major abiotic stress that influences rice production. Although the transcriptomic data of rice against drought is widely available, the regulation of small open reading frames (sORFs) in response to drought stress in rice is yet to be investigated. Different levels of drought stress have different regulatory mechanisms in plants. In this study, drought stress was imposed on four-leaf stage rice, divided into two treatments, 40% and 30% soil moisture content (SMC). The RNAs of the samples were extracted, followed by the RNA sequencing analysis on their sORF expression changes under 40%_SMC and 30%_SMC, and lastly, the expression was validated through NanoString. A total of 122 and 143 sORFs were differentially expressed (DE) in 40%_SMC and 30%_SMC, respectively. In 40%_SMC, 69 sORFs out of 696 (9%) DEGs were found to be upregulated. On the other hand, 69 sORFs out of 449 DEGs (11%) were significantly downregulated. The trend seemed to be higher in 30%_SMC, where 112 (12%) sORFs were found to be upregulated from 928 significantly upregulated DEGs. However, only 8% (31 sORFs out of 385 DEGs) sORFs were downregulated in 30%_SMC. Among the identified sORFs, 110 sORFs with high similarity to rice proteome in the PsORF database were detected in 40%_SMC, while 126 were detected in 30%_SMC. The Gene Ontology (GO) enrichment analysis of DE sORFs revealed their involvement in defense-related biological processes, such as defense response, response to biotic stimulus, and cellular homeostasis, whereas enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that DE sORFs were associated with tryptophan and phenylalanine metabolisms. Several DE sORFs were identified, including the top five sORFs (OsisORF_3394, OsisORF_0050, OsisORF_3007, OsisORF_6407, and OsisORF_7805), which have yet to be characterised. Since these sORFs were responsive to drought stress, they might hold significant potential as targets for future climate-resilient rice development.

Stress-induced F-Box protein-coding gene OsFBX257 modulates drought stress adaptations and ABA responses in rice

F-box (FB) proteins that form part of SKP1-CUL1-F-box (SCF) type of E3 ubiquitin ligases are important components of plant growth and development. Here we characterized OsFBX257, a rice FB protein-coding gene that is differentially expressed under drought conditions and other abiotic stresses. Population genomics analysis suggest that OsFBX257 shows high allelic diversity in aus accessions and has been under positive selection in some japonica, aromatic and indica cultivars. Interestingly, allelic variation at OsFBX257 in aus cultivar Nagina22 is associated with an alternatively spliced transcript. Conserved among land plants, OsFBX257 is a component of the SCF complex, can form homomers and interact molecularly with the 14-3-3 rice proteins GF14b and GF14c. OsFBX257 is co-expressed in a network involving protein kinases and phosphatases. We show that OsFBX257 can bind the kinases OsCDPK1 and OsSAPK2, and that its phosphorylation can be reversed by phosphatase OsPP2C08. OsFBX257 expression level modulates root architecture and drought stress tolerance in rice. OsFBX257 knockdown (OsFBX257^KD ) lines show reduced total root length and depth, crown root number, panicle size and survival under stress. In contrast, its overexpression (OsFBX257^OE ) increases root depth, leaf and grain length, number of panicles, and grain yield in rice. OsFBX257 is a promising breeding target for alleviating drought stress-induced damage in rice.

Identification of Drought Tolerant Rice (Oryza Sativa L.) Genotypes with Asian and African Backgrounds

Drought is among the major abiotic stresses on rice production that can cause yield losses of up to 100% under severe drought conditions. Neither of the rice varieties currently grown in Burundi can withstand very low and irregular precipitation. This study identified genotypes that have putative quantitative trait loci (QTLs) associated with drought tolerance and determined their performance in the field. Two hundred and fifteen genotypes were grown in the field under both drought and irrigated conditions. Genomic deoxyribonucleic acid (DNA) was extracted from rice leaves for further genotypic screening. The results revealed the presence of the QTLs qDTY12.1, qDTY3.1, qDTY2-2_1, and qDTY1.1 in 90%, 85%, 53%, and 22% of the evaluated genotypes, respectively. The results of the phenotypic evaluation showed a significant yield reduction due to drought stress. Yield components and other agronomic traits were also negatively affected by drought. Genotypes having high yield best linear unbiased predictions (BLUPs) with two or more major QTLs for drought tolerance, including IR 108044-B-B-B-3-B-B, IR 92522-45-3-1-4, and BRRI DHAN 55 are of great interest for breeding programs to improve the drought tolerance of lines or varieties with other preferred traits.

Targeted and untargeted metabolomics reveals deep analysis of drought stress responses in needles and roots of Pinus taeda seedlings

Drought stress is one of major environmental stresses affecting plant growth and yield. Although Pinus taeda trees are planted in rainy southern China, local drought sometime occurs and can last several months, further affecting their growth and resin production. In this study, P. taeda seedlings were treated with long-term drought (42 d), and then targeted and untargeted metabolomics analysis were carried out to evaluate drought tolerance of P. taeda. Targeted metabolomics analysis showed that levels of some sugars, phytohormones, and amino acids significantly increased in the roots and needles of water-stressed (WS) P. taeda seedlings, compared with well-watered (WW) pine seedlings. These metabolites included sucrose in pine roots, the phytohormones abscisic acid and sacylic acid in pine needles, the phytohormone gibberellin (GA4) and the two amino acids, glycine and asparagine, in WS pine roots. Compared with WW pine seedlings, the neurotransmitter acetylcholine significantly increased in needles of WS pine seedlings, but significantly reduced in their roots. The neurotransmitters L-glutamine and hydroxytyramine significantly increased in roots and needles of WS pine seedlings, respectively, compared with WW pine seedlings, but the neurotransmitter noradrenaline significantly reduced in needles of WS pine seedlings. Levels of some unsaturated fatty acids significantly reduced in roots or needles of WS pine seedlings, compared with WW pine seedlings, such as linoleic acid, oleic acid, myristelaidic acid, myristoleic acid in WS pine roots, and palmitelaidic acid, erucic acid, and alpha-linolenic acid in WS pine needles. However, three saturated fatty acids significantly increased in WS pine seedlings, i.e., dodecanoic acid in WS pine needles, tricosanoic acid and heptadecanoic acid in WS pine roots. Untargeted metabolomics analysis showed that levels of some metabolites increased in WS pine seedlings, especially sugars, long-chain lipids, flavonoids, and terpenoids. A few of specific metabolites increased greatly, such as androsin, piceatanol, and panaxatriol in roots and needles of WS pine seedlings. Comparing with WW pine seedlings, it was found that the most enriched pathways in WS pine needles included flavone and flavonol biosynthesis, ABC transporters, diterpenoid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis; in WS pine roots, the most enriched pathways included tryptophan metabolism, caffeine metabolism, sesquiterpenoid and triterpenoid biosynthesis, plant hormone signal transduction, biosynthesis of phenylalanine, tyrosine, and tryptophan. Under long-term drought stress, P. taeda seedlings showed their own metabolomics characteristics, and some new metabolites and biosynthesis pathways were found, providing a guideline for breeding drought-tolerant cultivars of P. taeda.

Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable "occupancy" in the pan-genome - genes which are either present in all studied genotypes or missing in some genotypes - show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.

Characterization of Transcription Regulatory Domains of OsMADS29: Identification of Proximal Auxin-Responsive Domains and a Strong Distal Negative Element

OsMADS29 (M29) is a seed-specific MADS-box transcription factor involved in programmed cell death of nucellar tissue and maintaining auxin:cytokinin homeostasis. It affects embryo and endosperm development and starch filling during seed development in rice. Its expression seems to be tightly regulated by developmental, spatial, and temporal cues; however, cis- and trans-regulatory factors that affect its expression are largely unknown. In silico analysis of the 1.7 kb upstream regulatory region (URR) consisting of 1,290 bp promoter and 425 bp 5'-UTR regions revealed several auxin-responsive and seed-specific cis-regulatory elements distributed across the URR. In this study, the analysis of four URR deletions fused to a downstream β-glucuronidase (GUS) reporter in transgenic rice has revealed the presence of several proximal positive elements and a strong distal negative element (NE). The promoter regions containing auxin-responsive elements responded positively to the exogenous application of auxins to transgenic seedlings. The proximal positive elements are capable of driving reporter expression in both vegetative and reproductive tissues. In contrast, the NE strongly suppresses reporter gene expression in both vegetative and reproductive tissues. In a transient onion peel assay system, the NE could reduce the efficacy of a 2x CaMV 35S promoter by ∼90%. Our results indicate the existence of a complex array of positive and negative regulatory regions along with auxin-responsive elements guiding the development-dependent and spatial expression of M29.

Comparative Physiology of Indica and Japonica Rice under Salinity and Drought Stress: An Intrinsic Study on Osmotic Adjustment, Oxidative Stress, Antioxidant Defense and Methylglyoxal Detoxification

Salinity and drought stress are significant environmental threats, alone or in combination. The current study was conducted to investigate the morpho-physiology, osmotic adjustment, oxidative stress, antioxidant defense and methylglyoxal detoxification of three rice genotypes from the indica (cv. BRRI dhan29 and BRRI dhan48) and japonica (cv. Koshihikari) groups. Eighteen-day-old seedlings of these genotypes were exposed to either in alone salinity (150 mM NaCl) and drought (15% PEG 6000) or in the combination of salinity and drought (150 mM NaCl + 15% PEG 6000) stress in vitro for 72 h. Compared with the control, the water status, biomass and photosynthetic pigments were decreased, where a significant increase was seen in the mortality rate, hydrogen peroxide content, electrolyte leakage, lipoxygenase activity, level of malondialdehyde and methylglyoxal, indicating increased lipid peroxidation in rice genotypes in stress conditions. The non-enzymatic and enzymatic components of the ascorbate-glutathione (AsA-GSH) pool in rice genotypes were disrupted under all stress treatments, resulting imbalance in the redox equilibrium. In contrast, compared to other rice genotypes, BRRI dhan48 revealed a lower Na+/K+ ratio, greater proline (Pro) levels, higher activity of AsA, dehydroascorbate (DHA) and GSH, lower glutathione disulfide (GSSG) and a higher ratio of AsA/DHA and GSH/GSSG, whereas enzymatic components increased monodehydroascorbate reductase, dehydroascorbate reductase, glutathione peroxidase and glyoxalase enzymes. The results showed that a stronger tolerate ability for BRRI dhan48 against stress has been connected to a lower Na+/K+ ratio, an increase in Pro content and an improved performance of the glyoxalase system and antioxidant protection for scavenging of reactive oxygen species. These data can give insight into probable responses to single or combination salinity and drought stress in rice genotypes.

The rice EP3 and OsFBK1 E3 ligases alter plant architecture and flower development, and affect transcript accumulation of microRNA pathway genes and their targets

ERECTA PANICLE 3 (EP3) and ORYZA SATIVA F-BOX KELCH 1 (OsFBK1) proteins share 57% and 54% sequence identity with the Arabidopsis F-box protein HAWAIIAN SKIRT (HWS). Previously we showed that EP3 is a functional orthologue of HWS. Here we demonstrate that OsFBK1 is another functional orthologue of HWS and show the complexity of interaction between EP3 and OsFBK1 genes at different developmental stages of the plant. qRT-PCR expression analyses and studies of EP3-GFP and OsFBK1-RFP promoter reporter lines demonstrate that although EP3 and OsFBK1 expression can be detected in the same tissues some cells exclusively express EP3 or OsFBK1 whilst others co-express both genes. Loss, reduction or gain-of-function lines for EP3 and OsFBK1, show that EP3 and OsFBK1 affect plant architecture, organ size, floral organ number and size, floral morphology, pollen viability, grain size and weight. We have identified the putative orthologue genes of the rice microRNA pathway for ORYZA SATIVA DAWDLE (OsDDL) and ORYZA SATIVA SERRATE (OsSE), and demonstrated that EP3 and OsFBK1 affect their transcript levels as well as those of CROWN ROOT DEFECT 1/ORYZA SATIVA Exportin-5 HASTY (CRD1/OsHST), ORYZA SATIVA DICER-LIKE 1 (OsDCL) and ORYZA SATIVA WEAVY LEAF1 (OsWAF1). We show that EP3 affects OsPri-MIR164, OsNAM1 and OsNAC1 transcript levels. OsNAC1 transcripts are modified by OsFBK1, suggesting two independent regulatory pathways, one via EP3 and OsMIR164 and the other via OsFBK1. Our data propose that EP3 and OsFBK1 conjointly play similar roles in rice to how HWS does in Arabidopsis.

Variety-specific transcript accumulation during reproductive stage in drought-stressed rice

The divergence of natural stress tolerance mechanisms between species is an intriguing phenomenon. To study it in rice, a comparative transcriptome analysis was carried out in 'heading' stage tissue (flag leaf, panicles and roots) of Nagina 22 (N22; drought-tolerant) and IR64 (drought-sensitive) plants subjected to field drought. Interestingly, N22 showed almost double the number of differentially expressed genes (DEGs) than IR64. Many DEGs colocalized within drought-related QTLs responsible for grain yield and drought tolerance and also associated with drought tolerance and critical drought-related plant traits such as leaf rolling, trehalose content, sucrose and cellulose content. Besides, co-expression analysis of the DEGs revealed several 'hub' genes known to actively regulate drought stress response. Strikingly, 1366 DEGs, including 21 'hub' genes, showed a distinct opposite regulation in the two rice varieties under similar drought conditions. Annotation of these variety-specific DEGs (VS-DEGs) revealed that they are distributed in various biological pathways. Furthermore, 103 VS-DEGs were found to physically interact with over 1300 genes, including 32 that physically interact with other VS-DEGs as well. The promoter region of these genes has sequence variations among the two rice varieties, which might be in part responsible for their unique expression pattern.

Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress

Drought tolerance in rice is controlled by several genes and is inherited quantitatively. Low genetic map density and the use of phenotypic traits that do not reflect the corresponding tolerance level have been obstacles in genetic analyses performed to identify genes that control drought-tolerant traits in rice. The current study aimed to construct a genetic map from high-density single-nucleotide polymorphism (SNP) markers generated from genome sequences of recombinant inbred lines (RILs), derived from IR64 × Hawara Bunar. Moreover, it sought to analyze the quantitative trait loci (QTL) and identify the drought tolerance candidate genes. A linkage map along 1980 cM on the 12 rice chromosomes was constructed employing 55,205 SNP markers resulting from the RIL genome sequences. A total of 175 morpho-physiological traits pertaining to drought stress were determined. A total of 41 QTLs were detected in 13 regions on rice chromosomes 1, 3, 6, 8, 9, and 12. Moreover, three hotspot QTL regions were found on chromosomes 6 and 8, along with two major QTL on chromosome 9. Differential gene expression for the loci within the QTL physical map intervals revealed many potential candidate genes. The markers tightly linked to the QTL and their candidate genes can potentially be used for pyramiding in marker-assisted breeding in order to achieve genetic improvement concerning the tolerance of rice to drought stress.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01095-y.

The Divergent Roles of the Rice bcl-2 Associated Athanogene (BAG) Genes in Plant Development and Environmental Responses

Bcl-2-associated athanogene (BAG), a group of proteins evolutionarily conserved and functioned as co-chaperones in plants and animals, is involved in various cell activities and diverse physiological processes. However, the biological functions of this gene family in rice are largely unknown. In this study, we identified a total of six BAG members in rice. These genes were classified into two groups, OsBAG1, -2, -3, and -4 are in group I with a conserved ubiquitin-like structure and OsBAG5 and -6 are in group Ⅱ with a calmodulin-binding domain, in addition to a common BAG domain. The BAG genes exhibited diverse expression patterns, with OsBAG4 showing the highest expression level, followed by OsBAG1 and OsBAG3, and OsBAG6 preferentially expressed in the panicle, endosperm, and calli. The co-expression analysis and the hierarchical cluster analysis indicated that the OsBAG1 and OsBAG3 were co-expressed with primary cell wall-biosynthesizing genes, OsBAG4 was co-expressed with phytohormone and transcriptional factors, and OsBAG6 was co-expressed with disease and shock-associated genes. β-glucuronidase (GUS) staining further indicated that OsBAG3 is mainly involved in primary young tissues under both primary and secondary growth. In addition, the expression of the BAG genes under brown planthopper (BPH) feeding, N, P, and K deficiency, heat, drought and plant hormones treatments was investigated. Our results clearly showed that OsBAGs are multifunctional molecules as inferred by their protein structures, subcellular localizations, and expression profiles. BAGs in group I are mainly involved in plant development, whereas BAGs in group II are reactive in gene regulations and stress responses. Our results provide a solid basis for the further elucidation of the biological functions of plant BAG genes.

Combining Genome and Gene Co-expression Network Analyses for the Identification of Genes Potentially Regulating Salt Tolerance in Rice

Salinity stress tolerance is a complex polygenic trait involving multi-molecular pathways. This study aims to demonstrate an effective transcriptomic approach for identifying genes regulating salt tolerance in rice. The chromosome segment substitution lines (CSSLs) of "Khao Dawk Mali 105 (KDML105)" rice containing various regions of DH212 between markers RM1003 and RM3362 displayed differential salt tolerance at the booting stage. CSSL16 and its nearly isogenic parent, KDML105, were used for transcriptome analysis. Differentially expressed genes in the leaves of seedlings, flag leaves, and second leaves of CSSL16 and KDML105 under normal and salt stress conditions were subjected to analyses based on gene co-expression network (GCN), on two-state co-expression with clustering coefficient (CC), and on weighted gene co-expression network (WGCN). GCN identified 57 genes, while 30 and 59 genes were identified using CC and WGCN, respectively. With the three methods, some of the identified genes overlapped, bringing the maximum number of predicted salt tolerance genes to 92. Among the 92 genes, nine genes, OsNodulin, OsBTBZ1, OsPSB28, OsERD, OsSub34, peroxidase precursor genes, and three expressed protein genes, displayed SNPs between CSSL16 and KDML105. The nine genes were differentially expressed in CSSL16 and KDML105 under normal and salt stress conditions. OsBTBZ1 and OsERD were identified by the three methods. These results suggest that the transcriptomic approach described here effectively identified the genes regulating salt tolerance in rice and support the identification of appropriate QTL for salt tolerance improvement.

Genome-Wide Association Mapping of Mixed Linkage (1,3;1,4)-β-Glucan and Starch Contents in Rice Whole Grain

The glucan content of rice is a key factor defining its nutritional and economic value. Starch and its derivatives have many industrial applications such as in fuel and material production. Non-starch glucans such as (1,3;1,4)-β-D-glucan (mixed-linkage β-glucan, MLG) have many benefits in human health, including lowering cholesterol, boosting the immune system, and modulating the gut microbiome. In this study, the genetic variability of MLG and starch contents were analyzed in rice (Oryza sativa L.) whole grain, by performing a new quantitative analysis of the polysaccharide content of rice grains. The 197 rice accessions investigated had an average MLG content of 252 μg/mg, which was negatively correlated with the grain starch content. A new genome-wide association study revealed seven significant quantitative trait loci (QTLs) associated with the MLG content and two QTLs associated with the starch content in rice whole grain. Novel genes associated with the MLG content were a hexose transporter and anthocyanidin 5,3-O-glucosyltransferase. Also, the novel gene associated with the starch content was a nodulin-like domain. The data pave the way for a better understanding of the genes involved in determining both MLG and starch contents in rice grains and should facilitate future plant breeding programs.

Transcriptome profiling of two rice genotypes under mild field drought stress during grain-filling stage

Drought is one of the most critical abiotic stresses that threaten crop production worldwide. This stress affects the rice crop in all stages of rice development; however, the occurrence during reproductive and grain-filling stages has the most impact on grain yield. Although many global transcriptomic studies have been performed during the reproductive stage in rice, very limited information is available for the grain-filling stage. Hence, we intend to investigate how the rice plant responds to drought stress during the grain-filling stage and how the responses change over time under field conditions. Two rice genotypes were selected for RNA-seq analysis: '4610', previously reported as a moderately tolerant breeding line, and Rondo, an elite indica rice cultivar susceptible to drought conditions. Additionally, 10 agronomic traits were evaluated under normal irrigated and drought conditions. Leaf tissues were collected during grain-filling stages at two time points, 14 and 21 days after the drought treatment, from both the drought field and normal irrigated field conditions. Based on agronomic performances, '4610' was less negatively affected than Rondo under mild drought conditions, and expression profiling largely aligned with the phenotypic data. The transcriptomic data indicated that, in general, '4610' had much earlier responses than its counterpart in mitigating the impact of drought stress. Several key genes and gene families related to drought stress or stress-related conditions were found differentially expressed in this study, including transcription factors, drought tolerance genes and reactive oxygen species scavengers. Furthermore, this study identified novel differentially expressed genes (DEGs) without function annotations that may play roles in drought tolerance-related functions. Some of the important DEGs detected in this study can be targeted for future research.

Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions

Meta-QTL (MQTL) analysis is a robust approach for genetic dissection of complex quantitative traits. Rice varieties adapted to non-flooded cultivation are highly desirable in breeding programs due to the water deficit global problem. In order to identify stable QTLs for major agronomic traits under water deficit conditions, we performed a comprehensive MQTL analysis on 563 QTLs from 67 rice populations published from 2001 to 2019. Yield and yield-related traits including grain weight, heading date, plant height, tiller number as well as root architecture-related traits including root dry weight, root length, root number, root thickness, the ratio of deep rooting and plant water content under water deficit condition were investigated. A total of 61 stable MQTLs over different genetic backgrounds and environments were identified. The average confidence interval of MQTLs was considerably refined compared to the initial QTLs, resulted in the identification of some well-known functionally characterized genes and several putative novel CGs for investigated traits. Ortho-MQTL mining based on genomic collinearity between rice and maize allowed identification of five ortho-MQTLs between these two cereals. The results can help breeders to improve yield under water deficit conditions.

A comprehensive transcriptome analysis of contrasting rice cultivars highlights the role of auxin and ABA responsive genes in heat stress response

Sensing a change in ambient temperature is key to survival among all living organisms. Temperature fluctuations due to climate change are a matter of grave concern since it adversely affects growth and eventually the yield of crop plants, including two of the major cereals, i.e., rice and wheat. Thus, to understand the response of rice seedlings to elevated temperatures, we performed microarray-based transcriptome analysis of two contrasting rice cultivars, Annapurna (heat tolerant) and IR64 (heat susceptible), by subjecting their seedlings to 37 °C and 42 °C, sequentially. The transcriptome analyses revealed a set of uniquely regulated genes and related pathways in red rice cultivar Annapurna, particularly associated with auxin and ABA as a part of heat stress response in rice. The changes in expression of few auxin and ABA associated genes, such as OsIAA13, OsIAA20, ILL8, OsbZIP12, OsPP2C51, OsDi19-1 and OsHOX24, among others, were validated under high-temperature conditions using RT-qPCR. In particular, the expression of auxin-inducible SAUR genes was enhanced considerably at both elevated temperatures. Further, using genes that expressed inversely under heat vs. cold temperature conditions, we built a regulatory network between transcription factors (TF) such as HSFs, NAC, WRKYs, bHLHs or bZIPs and their target gene pairs and determined regulatory coordination in their expression under varying temperature conditions. Our work thus provides useful insights into temperature-responsive genes, particularly under elevated temperature conditions, and could serve as a resource of candidate genes associated with thermotolerance or downstream components of temperature sensors in rice.

Temporal transcriptomic differences between tolerant and susceptible genotypes contribute to rice drought tolerance

BACKGROUND

Drought-tolerance ensures a crop to maintain life activities and protect cell from damages under dehydration. It refers to diverse mechanisms temporally activated when the crop adapts to drought. However, knowledge about the temporal dynamics of rice transcriptome under drought is limited.

RESULTS

Here, we investigated temporal transcriptomic dynamics in 12 rice genotypes, which varied in drought tolerance (DT), under a naturally occurred drought in fields. The tolerant genotypes possess less differentially expressed genes (DEGs) while they have higher proportions of upregulated DEGs. Tolerant and susceptible genotypes have great differences in temporally activated biological processes (BPs) during the drought period and at the recovery stage based on their DEGs. The DT-featured BPs, which are activated specially (e.g. raffinose, fucose, and trehalose metabolic processes, etc.) or earlier in the tolerant genotypes (e.g. protein and histone deacetylation, protein peptidyl-prolyl isomerization, transcriptional attenuation, ferric iron transport, etc.) shall contribute to DT. Meanwhile, the tolerant genotypes and the susceptible genotypes also present great differences in photosynthesis and cross-talks among phytohormones under drought. A certain transcriptomic tradeoff between DT and productivity is observed. Tolerant genotypes have a better balance between DT and productivity under drought by activating drought-responsive genes appropriately. Twenty hub genes in the gene coexpression network, which are correlated with DT but without potential penalties in productivity, are recommended as good candidates for DT.

CONCLUSIONS

Findings of this study provide us informative cues about rice temporal transcriptomic dynamics under drought and strengthen our system-level understandings in rice DT.

Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice

BACKGROUND

Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling.

RESULTS

The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H₂O₂ (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H₂O₂-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H₂O₂ and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403.

CONCLUSIONS

We speculated that drought-induced photosynthetic inhibition leads to H₂O₂ and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.

Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and efficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in differential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of differential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield.

Proteome Responses to Individual Pathogens and Abiotic Conditions in Rice Seedlings

Rice plants under field conditions experience various biotic and abiotic stresses and are adapted to survive using a molecular cross-talk of genes and their protein products based on the severity of a given stress. Seedlings of cultivated variety ASD16 (resistant to fungal disease, blast; tolerant to abiotic stress, salinity) were subjected to salt, drought, high temperature and low temperature stress as well as infection by Rhizoctonia solani and Xanthomonas oryzae pv. oryzae (causing reemerging diseases such as sheath blight and leaf blight), respectively, the sheath blight and bacterial leaf blight pathogens. Leaf proteome was analyzed using two-dimensional electrophoresis and differentially expressed proteins were identified using mass spectrometry. In addition to many other differentially expressed proteins, acidic endochitinase was found to be upregulated during fungal infection and drought treatment, and a germin-like protein upregulated during fungal infection and high temperature stress. These two proteins were further validated at the gene expression level using reverse transcription-PCR in dual stress experiments. Pot culture plants were subjected to fungal infection followed by drought and drought followed by fungal infection to validate chitinase gene expression. Similarly, plants subjected to fungal infections followed by high temperature stress and vice versa were used to validate the expression of germin-like protein-coding gene. The results of the present study indicate that chitinase and germin-like protein are potential targets for further exploration to develop rice plants resistant or tolerant to biotic and abiotic stresses.

Drought-induced protein (Di19-3) plays a role in auxin signaling by interacting with IAA14 in Arabidopsis

The members of early auxin response gene family, Aux/IAA, encode negative regulators of auxin signaling but play a central role in auxin-mediated plant development. Here we report the interaction of an Aux/IAA protein, AtIAA14, with Drought-induced-19 (Di19-3) protein and its possible role in auxin signaling. The Atdi19-3 mutant seedlings develop short hypocotyl, both in light and dark, and are compromised in temperature-induced hypocotyl elongation. The mutant plants accumulate more IAA and also show altered expression of NIT2, ILL5, and YUCCA genes involved in auxin biosynthesis and homeostasis, along with many auxin responsive genes like AUX1 and MYB77. Atdi19-3 seedlings show enhanced root growth inhibition when grown in the medium supplemented with auxin. Nevertheless, number of lateral roots is low in Atdi19-3 seedlings grown on the basal medium. We have shown that AtIAA14 physically interacts with AtDi19-3 in yeast two-hybrid (Y2H), bimolecular fluorescence complementation, and in vitro pull-down assays. However, the auxin-induced degradation of AtIAA14 in the Atdi19-3 seedlings was delayed. By expressing pIAA14::mIAA14-GFP in Atdi19-3 mutant background, it became apparent that both Di19-3 and AtIAA14 work in the same pathway and influence lateral root development in Arabidopsis. Gain-of-function slr-1/iaa14 (slr) mutant, like Atdi19-3, showed tolerance to abiotic stress in seed germination and cotyledon greening assays. The Atdi19-3 seedlings showed enhanced sensitivity to ethylene in triple response assay and AgNO3, an ethylene inhibitor, caused profuse lateral root formation in the mutant seedlings. These observations suggest that AtDi19-3 interacting with AtIAA14, in all probability, serves as a positive regulator of auxin signaling and also plays a role in some ethylene-mediated responses in Arabidopsis.

SIGNIFICANCE STATEMENT

This study has demonstrated interaction of auxin responsive Aux/IAA with Drought-induced 19 (Di19) protein and its possible implication in abiotic stress response.

OsEUL Lectin Gene Expression in Rice: Stress Regulation, Subcellular Localization and Tissue Specificity

The Euonymus lectin (EUL) family is a unique group of carbohydrate-binding proteins that is omnipresent in plants. Sequences encoding EUL-related lectins have been retrieved from all completely sequenced plant genomes. The rice (Oryza sativa) genome contains 5 functional EUL genes referred to as OsEULS2, OsEULS3, OsEULD1a, OsEULD1b, and OsEULD2. In this study we focused on the tissue specific expression, stress inducibility and subcellular localization of the rice EULs. Even though the EUL domain sequence is highly conserved among the rice EULs (at least 80% sequence similarity) different biotic and abiotic stress treatments yielded unique responses for the different EULs. Transcript levels for OsEULs were differentially affected by drought and salt stress, ABA treatment, pathogen infection or insect infestation. Analysis of promoter activity revealed differential expression and tissue specificity for the 5 OsEUL genes, with most expression observed in the vascular system of roots and shoots, as well as in the root tips and seeds. At cell level, all OsEULs are located in the nucleus whereas OsEULD1b and OsEULD2 also locate to the cytoplasm. This paper contributes to the functional characterization of the EULs and provides insight in the biological importance of this family of proteins for rice.

The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance

Like many cereal crops, barley is also negatively affected by drought stress. However, due to its simple genome as well as enhanced stress resilient nature compared to rice and wheat, barley has been considered as a model to decipher drought tolerance in cereals. In the present study, transcriptomic and hormonal profiles along with several biochemical features were compared between drought-tolerant (Otis) and drought-sensitive (Baronesse) barley genotypes subjected to drought to identify molecular and biochemical differences between the genotypes. The drought-induced decrease in the leaf relative water content, net photosynthesis, and biomass accumulation was relatively low in Otis compared to Baronesse. The hormonal profiles did not reveal significant differences for majority of the compounds other than the GA20 and the cis-zeatin-o-glucoside (c-ZOG), whose levels were greatly increased in Otis compared to Baronesse under drought. The major differences that emerged from the transcriptome analysis are; (1), the overall number of differentially expressed genes was relatively low in drought-tolerant Otis compared to drought-sensitive Baronesse; (2), a wax biosynthesis gene (CER1), and NAC transcription factors were specifically induced in Otis but not in Baronesse; (3), the degree of upregulation of betaine aldehyde dehydrogenase and a homeobox transcription factor (genes with proven roles in imparting drought tolerance), was greater in Otis compared to Baronesse; (4) the extent of downregulation of gene expression profiles for proteins of the reaction center photosystem II (PSII) (D1 and D2) was low in Otis compared to Baronesse; and, (5), alternative splicing (AS) was also found to differ between the genotypes under drought. Taken together, the overall transcriptional responses were low in drought-tolerant Otis but the genes that could confer drought tolerance were either specifically induced or greatly upregulated in the tolerant genotype and these differences could be important for drought tolerance in barley.

Network-based feature selection reveals substructures of gene modules responding to salt stress in rice

Rice, an important food resource, is highly sensitive to salt stress, which is directly related to food security. Although many studies have identified physiological mechanisms that confer tolerance to the osmotic effects of salinity, the link between rice genotype and salt tolerance is not very clear yet. Association of gene co-expression network and rice phenotypic data under stress has penitential to identify stress-responsive genes, but there is no standard method to associate stress phenotype with gene co-expression network. A novel method for integration of gene co-expression network and stress phenotype data was developed to conduct a system analysis to link genotype to phenotype. We applied a LASSO-based method to the gene co-expression network of rice with salt stress to discover key genes and their interactions for salt tolerance-related phenotypes. Submodules in gene modules identified from the co-expression network were selected by the LASSO regression, which establishes a linear relationship between gene expression profiles and physiological responses, that is, sodium/potassium condenses under salt stress. Genes in these submodules have functions related to ion transport, osmotic adjustment, and oxidative tolerance. We argued that these genes in submodules are biologically meaningful and useful for studies on rice salt tolerance. This method can be applied to other studies to efficiently and reliably integrate co-expression network and phenotypic data.

Systematized biosynthesis and catabolism regulate citrulline accumulation in watermelon

Citrulline, a non-protein amino acid, is present in large amounts in watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai Cucurbitaceae) fruits. Amino acid profiling of various tissues of cv. Charleston Gray during plant development confirmed progressive accumulation of citrulline only in the fruit flesh and rind tissues. Citrulline content was positively correlated with precursor (ornithine) and by-product (arginine) amino acids during fruit ripening. Genetic variation in the partitioning of citrulline and related amino acids in the flesh and rind tissues was confirmed in a sub-set of watermelon cultivars. No correlation was established between morphological fruit traits (size and rind properties) and citrulline content. To understand the regulation of citrulline accumulation, we investigated the expression of genes associated with its biosynthesis and catabolism in flesh and rind tissues during fruit development. The expression of ornithine carbamoyltransferase (OTC) involved in the ultimate step of citrulline synthesis remained steady in both tissues. The expression of N-acetylornithine aminotransferase (N-AOA) involved in the production of N-acetylornithine and N-acetylornithine deacetylase (AOD-3) involved in ornithine synthesis coincided with increasing accumulation of citrulline in flesh and rind tissues during fruit development. Down-regulation N-acetylornithine-glutamate acetyltransferase (N-AOGA) suggests the subordinate role of the non-cyclic pathway in citrulline synthesis. Eccentricity between citrulline accumulation and expression of carbamoyl phosphate synthases (CPS-1, CPS-2) during fruit development suggest that the localized synthesis of carbamoyl phosphates may not be required for citrulline synthesis. Most genes involved in citrulline break-down (Argininosuccinate synthases - ASS-1, ASS-2, and ASS-3, Argininosuccinate lyases - ASL-1, Ornithine decarboxylase - ODC, Arginine decarboxylase - ADC) were consistently down-regulated during fruit development.

Physiological and Metabolic Responses of Rice to Reduced Soil Moisture: Relationship of Water Stress Tolerance and Grain Production

Access to adequate irrigation resources is critical for sustained agricultural production, and rice, a staple cereal grain for half of the world population, is one of the biggest users of irrigation. To reduce water use, several water saving irrigation systems have been developed for rice production, but a reliable system to evaluate cultivars for water stress tolerance is still lacking. Here, seven rice cultivars that have diverse yield potential under water stress were evaluated in a field study using four continuous irrigation regimes varying from saturation to wilting point. To understand the relationship between water stress and yield potential, the physiological and leaf metabolic responses were investigated at the critical transition between vegetative and reproductive growth stages. Twenty-nine metabolite markers including carbohydrates, amino acids and organic acids were found to significantly differ among the seven cultivars in response to increasing water stress levels with amino acids increasing but organic acids and carbohydrates showing mixed responses. Overall, our data suggest that, in response to increasing water stress, rice cultivars that do not show a significant yield loss accumulate carbohydrates (fructose, glucose, and myo-inositol), and this is associated with a moderate reduction in stomatal conductance (g_s), particularly under milder stress conditions. In contrast, cultivars that had significant yield loss due to water stress had the greatest reduction in g_s, relatively lower accumulation of carbohydrates, and relatively high increases in relative chlorophyll content (SPAD) and leaf temperature (Tm). These data demonstrate the existence of genetic variation in yield under different water stress levels which results from a suite of physiological and biochemical responses to water stress. Our study, therefore, suggests that in rice there are different physiological and metabolic strategies that result in tolerance to water stress that should be considered in developing new cultivars for deficit irrigation production systems that use less water.

The OsFBK1 E3 Ligase Subunit Affects Anther and Root Secondary Cell Wall Thickenings by Mediating Turnover of a Cinnamoyl-CoA Reductase

Regulated proteolysis by the ubiquitin-26S proteasome system challenges transcription and phosphorylation in magnitude and is one of the most important regulatory mechanisms in plants. This article describes the characterization of a rice (Oryza sativa) auxin-responsive Kelch-domain-containing F-box protein, OsFBK1, found to be a component of an SCF E3 ligase by interaction studies in yeast. Rice transgenics of OsFBK1 displayed variations in anther and root secondary cell wall content; it could be corroborated by electron/confocal microscopy and lignification studies, with no apparent changes in auxin content/signaling pathway. The presence of U-shaped secondary wall thickenings (or lignin) in the anthers were remarkably less pronounced in plants overexpressing OsFBK1 as compared to wild-type and knockdown transgenics. The roots of the transgenics also displayed differential accumulation of lignin. Yeast two-hybrid anther library screening identified an OsCCR that is a homolog of the well-studied Arabidopsis (Arabidopsis thaliana) IRX4; OsFBK1-OsCCR interaction was confirmed by fluorescence and immunoprecipitation studies. Degradation of OsCCR mediated by SCFOsFBK1 and the 26S proteasome pathway was validated by cell-free experiments in the absence of auxin, indicating that the phenotype observed is due to the direct interaction between OsFBK1 and OsCCR. Interestingly, the OsCCR knockdown transgenics also displayed a decrease in root and anther lignin depositions, suggesting that OsFBK1 plays a role in the development of rice anthers and roots by regulating the cellular levels of a key enzyme controlling lignification.

The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway

In Arabidopsis, the F-box HAWAIIAN SKIRT (HWS) protein is important for organ growth. Loss of function of HWS exhibits pleiotropic phenotypes including sepal fusion. To dissect the HWS role, we EMS-mutagenized hws-1 seeds and screened for mutations that suppress hws-1 associated phenotypes. We identified shs-2 and shs-3 (suppressor of hws-2 and 3) mutants in which the sepal fusion phenotype of hws-1 was suppressed. shs-2 and shs-3 (renamed hst-23/hws-1 and hst-24/hws-1) carry transition mutations that result in premature terminations in the plant homolog of Exportin-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport. Genetic crosses between hws-1 and mutant lines for genes in the miRNA pathway also suppress the phenotypes associated with HWS loss of function, corroborating epistatic relations between the miRNA pathway genes and HWS. In agreement with these data, accumulation of miRNA is modified in HWS loss or gain of function mutants. Our data propose HWS as a new player in the miRNA pathway, important for plant growth.

Citrulline metabolism in plants

Citrulline was chemically isolated more than 100 years ago and is ubiquitous in animals, plants, bacteria, and fungi. Most of the research on plant citrulline metabolism and transport has been carried out in Arabidopsis thaliana and the Cucurbitaceae family, particularly in watermelon which accumulates this non-proteinogenic amino acid to very high levels. Industrially, citrulline is produced via specially optimized microbial strains; however, the amounts present in watermelon render it an economically viable source providing that other high-value compounds can be co-extracted. In this review, we provide an overview of our current understanding of citrulline biosynthesis, transport, and catabolism in plants additionally pointing out significant gaps in our knowledge which need to be closed by future experimentation. This includes the identification of further potential enzymes of citrulline metabolism as well as obtaining a far better spatial resolution of both sub-cellular and long-distance partitioning of citrulline. We further discuss what is known concerning the biological function of citrulline in plants paying particular attention to the proposed roles in scavenging of excess NH₄⁺ and as a compatible solute.