Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.)

Flexibility of parental-like or maternal-like gene expression under diverse environments contributes to combined drought avoidance and drought tolerance in a water-saving and drought-resistance rice hybrid

KEY MESSAGE

The hybrid rice variety (Hanyou73) exhibits the maternal-like (HH7A) gene expression in roots and parental-like (HH3) gene expression in leaves to obtain both advantages of drought avoidance and drought tolerance from its two parents.

BACKGROUND

Rice is one of the most important crops in the world. Rice production consumes lots of water and significantly suffers from the water deficiency and drought stress. The water-saving and drought-resistance rice (WDR) confers good drought resistance and performs well in the water-saving cultivation.

MAIN FINDINGS

A hybrid WDR variety Hanyou73 (HY73) exhibited superior drought resistance compared with its parents Hanhui3 (HH3) and Huhan7A (HH7A). Studies on drought resistance related traits revealed that HY73 performed like HH3 and HH7A on drought tolerance and drought avoidance, respectively. Transcriptomes were analyzed for samples with various phytohormone treatments and abiotic stresses, in which HY73 was closer to HH3 in leaf samples while HH7A in root samples. HY73 and its parents differed largely in DEGs and GO analysis for DEGs suggested the different pathways of drought response in HH3 and HH7A. Parent-like expression analysis revealed that the higher-parent-like expression pattern was prevailing in HY73. In addition, patterns of the parent-like expression significantly transformed between abiotic-stressed/phytohormone-treated and control samples, which might help HY73 to adapt to different environments. WGCNA analysis for those parent-like expression genes revealed some drought resistant genes that should contribute to the superior drought resistance of HY73. Genetic variation on the promotor sequence was confirmed as the reason for the flexible parent-like gene expression in HY73.

CONCLUSION

Our study uncovered the important roles of complementation of beneficial traits from parents and flexible gene expressions in drought resistance of HY73, which could facilitate the development of new WDR varieties.

Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera

BACKGROUND

In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes.

RESULTS

We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene.

CONCLUSIONS

Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.

Transcriptome analysis reveals key regulatory genes for root growth related to potassium utilization efficiency in rapeseed (Brassica napus L.)

Root system architecture (RSA) is the primary predictor of nutrient intake and significantly influences potassium utilization efficiency (KUE). Uncertainty persists regarding the genetic factors governing root growth in rapeseed. The root transcriptome analysis reveals the genetic basis driving crop root growth. In this study, RNA-seq was used to profile the overall transcriptome in the root tissue of 20 Brassica napus accessions with high and low KUE. 71,437 genes in the roots displayed variable expression profiles between the two contrasting genotype groups. The 212 genes that had varied expression levels between the high and low KUE lines were found using a pairwise comparison approach. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification analysis revealed that the DEGs implicated in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism, were all differently regulated in the rapeseed root system. Additionally, we discovered 33 transcription factors (TFs) that control root development were differentially expressed. By combining differential expression analysis, weighted gene co-expression network analysis (WGCNA), and recent genome-wide association study (GWAS) results, four candidate genes were identified as essential hub genes. These potential genes were located fewer than 100 kb from the peak SNPs of QTL clusters, and it was hypothesized that they regulated the formation of the root system. Three of the four hub genes' homologs-BnaC04G0560400ZS, BnaC04G0560400ZS, and BnaA03G0073500ZS-have been shown to control root development in earlier research. The information produced by our transcriptome profiling could be useful in revealing the molecular processes involved in the growth of rapeseed roots in response to KUE.

PHOSPHORUS-STARVATION TOLERANCE 1 (OsPSTOL1) is prevalent in upland rice and enhances root growth and hastens low phosphate signaling in wheat

PHOSPHORUS-STARVATION TOLERANCE 1 (OsPSTOL1) is a variably present gene that benefits crown root growth and phosphorus (P) sufficiency in rice (Oryza sativa). To explore the ecophysiological importance of this gene, we performed a biogeographic survey of landraces and cultivars, confirming that functional OsPSTOL1 alleles prevail in low nutrient and drought-prone rainfed ecosystems, whereas loss-of-function and absence haplotypes predominate in control-irrigated paddy varieties of east Asia. An evolutionary history analysis of OsPSTOL1 and related genes in cereal, determined it and other genes are kinase-only domain derivatives of membrane-associated receptor like kinases. Finally, to evaluate the potential value of this kinase of unknown function in another Gramineae, wheat (Triticum aestivum) lines overexpressing OsPSTOL1 were evaluated under field and controlled low P conditions. OsPSTOL1 enhances growth, crown root number, and overall root plasticity under low P in wheat. Survey of root and shoot crown transcriptomes at two developmental stages identifies transcription factors that are differentially regulated in OsPSTOL1 wheat that are similarly controlled by the gene in rice. In wheat, OsPSTOL1 alters the timing and amplitude of regulators of root development in dry soils and hastens induction of the core P-starvation response. OsPSTOL1 and related genes may aid more sustainable cultivation of cereal crops.

Overexpression of a novel small auxin-up RNA gene, OsSAUR11, enhances rice deep rootedness

BACKGROUND

Deep rooting is an important factor affecting rice drought resistance. However, few genes have been identified to control this trait in rice. Previously, we identified several candidate genes by QTL mapping of the ratio of deep rooting and gene expression analysis in rice.

RESULTS

In the present work, we cloned one of these candidate genes, OsSAUR11, which encodes a small auxin-up RNA (SAUR) protein. Overexpression of OsSAUR11 significantly enhanced the ratio of deep rooting of transgenic rice, but knockout of this gene did not significantly affect deep rooting. The expression of OsSAUR11 in rice root was induced by auxin and drought, and OsSAUR11-GFP was localized both in the plasma membrane and cell nucleus. Through an electrophoretic mobility shift assay and gene expression analysis in transgenic rice, we found that the transcription factor OsbZIP62 can bind to the promoter of OsSAUR11 and promote its expression. A luciferase complementary test showed that OsSAUR11 interacts with the protein phosphatase OsPP36. Additionally, expression of several auxin synthesis and transport genes (e.g., OsYUC5 and OsPIN2) were down-regulated in OsSAUR11-overexpressing rice plants.

CONCLUSIONS

This study revealed a novel gene OsSAUR11 positively regulates deep rooting in rice, which provides an empirical basis for future improvement of rice root architecture and drought resistance.

Combined metabolomic and transcriptomic analysis reveals key components of OsCIPK17 overexpression improves drought tolerance in rice

Oryza Sativa is one of the most important food crops in China, which is easily affected by drought during its growth and development. As a member of the calcium signaling pathway, CBL-interacting protein kinase (CIPK) plays an important role in plant growth and development as well as environmental stress. However, there is no report on the function and mechanism of OsCIPK17 in rice drought resistance. We combined transcriptional and metabonomic analysis to clarify the specific mechanism of OsCIPK17 in response to rice drought tolerance. The results showed that OsCIPK17 improved drought resistance of rice by regulating deep roots under drought stress; Response to drought by regulating the energy metabolism pathway and controlling the accumulation of citric acid in the tricarboxylic acid (TCA) cycle; Our exogenous experiments also proved that OsCIPK17 responds to citric acid, and this process involves the auxin metabolism pathway; Exogenous citric acid can improve the drought resistance of overexpression plants. Our research reveals that OsCIPK17 positively regulates rice drought resistance and participates in the accumulation of citric acid in the TCA cycle, providing new insights for rice drought resistance.

WGCNA Analysis Revealed the Hub Genes Related to Soil Cadmium Stress in Maize Kernel (Zea mays L.)

Soil contamination by heavy metals has become a prevalent topic due to their widespread release from industry, agriculture, and other human activities. Great progress has been made in elucidating the uptake and translocation of cadmium (Cd) accumulation in rice. However, there is still little known about corresponding progress in maize. In the current study, we performed a comparative RNA-Seq-based approach to identify differentially expressed genes (DEGs) of maize immature kernel related to Cd stress. In total, 55, 92, 22, and 542 DEGs responsive to high cadmium concentration soil were identified between XNY22-CHS-8 vs. XNY22-YA-8, XNY22-CHS-24 vs. XNY22-YA-24, XNY27-CHS-8 vs. XNY27-YA-8, and XNY27-CHS-24 vs. XNY27-YA-24, respectively. The weighted gene co-expression network analysis (WGCNA) categorized the 9599 Cd stress-responsive hub genes into 37 different gene network modules. Combining the hub genes and DEGs, we obtained 71 candidate genes. Gene Ontology (GO) enrichment analysis of genes in the greenyellow module in XNY27-YA-24 and connectivity genes of these 71 candidate hub genes showed that the responses to metal ion, inorganic substance, abiotic stimulus, hydrogen peroxide, oxidative stress, stimulus, and other processes were enrichment. Moreover, five candidate genes that were responsive to Cd stress in maize kernel were detected. These results provided the putative key genes and pathways to response to Cd stress in maize kernel, and a useful dataset for unraveling the underlying mechanism of Cd accumulation in maize kernel.

Proteomics and Co-expression Network Analysis Reveal the Importance of Hub Proteins and Metabolic Pathways in Nicotine Synthesis and Accumulation in Tobacco (Nicotiana tabacum L.)

Nicotine is a unique alkaloid present in tobacco that is widely used in cigarettes and in the agricultural, chemical, and pharmaceutical industries. However, the research on nicotine is mostly limited to its synthesis pathways, and only a few studies have explored the effects of other metabolic pathways on nicotine precursors. Regulating the nicotine content in tobacco can greatly promoting the application of nicotine in other fields. In this study, we performed global data-independent acquisition proteomics analysis of four tobacco varieties. Of the four varieties, one had high nicotine content and three had a low nicotine content. A total of 31,259 distinct peptides and 6,018 proteins across two samples were identified. A total of 45 differentially expressed proteins (DEPs) co-existed in the three comparison groups and were mainly involved in the transport and metallic processes of the substances. Most DEPs were enriched in the biosynthesis of secondary metals, glutathione metabolism, carbon metabolism, and glycolysis/gluconeogenesis. In addition, the weighted gene co-expression network analysis identified an expression module closely related to the nicotine content (Brown, r = 0.74, P = 0.006). Gene Ontology annotation and Kyoto Encyclopaedia of Genes and Genomes enrichment analysis showed that the module proteins were mainly involved in the synthesis and metabolism of nicotine precursors such as arginine, ornithine aspartate, proline, and glutathione. The increased levels of these precursors lead to the synthesis and accumulation of nicotine in plants. More importantly, these proteins regulate nicotine synthesis by affecting the formation of putrescine, which is the core intermediate product in nicotine anabolism. Our results provide a reference for tobacco variety selection with a suitable nicotine content and regulation of the nicotine content. Additionally, the results highlight the importance of other precursor metabolism in nicotine synthesis.

Co-expression analysis to identify key modules and hub genes associated with COVID-19 in platelets

Corona virus disease 2019 (COVID-19) increases the risk of cardiovascular occlusive/thrombotic events and is linked to poor outcomes. The underlying pathophysiological processes are complex, and remain poorly understood. To this end, platelets play important roles in regulating the cardiovascular system, including via contributions to coagulation and inflammation. There is ample evidence that circulating platelets are activated in COVID-19 patients, which is a primary driver of the observed thrombotic outcome. However, the comprehensive molecular basis of platelet activation in COVID-19 disease remains elusive, which warrants more investigation. Hence, we employed gene co-expression network analysis combined with pathways enrichment analysis to further investigate the aforementioned issues. Our study revealed three important gene clusters/modules that were closely related to COVID-19. These cluster of genes successfully identify COVID-19 cases, relative to healthy in a separate validation data set using machine learning, thereby validating our findings. Furthermore, enrichment analysis showed that these three modules were mostly related to platelet metabolism, protein translation, mitochondrial activity, and oxidative phosphorylation, as well as regulation of megakaryocyte differentiation, and apoptosis, suggesting a hyperactivation status of platelets in COVID-19. We identified the three hub genes from each of three key modules according to their intramodular connectivity value ranking, namely: COPE, CDC37, CAPNS1, AURKAIP1, LAMTOR2, GABARAP MT-ND1, MT-ND5, and MTRNR2L12. Collectively, our results offer a new and interesting insight into platelet involvement in COVID-19 disease at the molecular level, which might aid in defining new targets for treatment of COVID-19–induced thrombosis.

Root Trait Variation in Lentil (Lens culinaris Medikus) Germplasm under Drought Stress

Drought is the most critical environmental factor across the continents affecting food security. Roots are the prime organs for water and nutrient uptake. Fine tuning between water uptake, efficient use and loss determines the genotypic response to water limitations. Targeted breeding for root system architecture needs to be explored to improve water use efficiency in legumes. Hence, the present study was designed to explore root system architecture in lentil germplasm in response to drought. A set of 119 lentil (Lens culinaris Medik.) genotypes was screened in controlled conditions to assess the variability in root traits in relation to drought tolerance at seedling stage. We reported significant variation for different root traits in lentil germplasm. Total root length, surface area, root volume and root diameter were correlated to the survival and growth under drought. Among the studied genotypes, the stress tolerance index varied 0.19–1.0 for survival and 0.09–0.90 for biomass. Based on seedling survival and biomass under control and drought conditions, 11 drought tolerant genotypes were identified, which may be investigated further at a physiological and molecular level for the identification of the genes involved in drought tolerance. Identified lines may also be utilised in a lentil breeding program.

Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress

Coreopsis tinctoria Nutt. (C. tinctoria) is a special tea ingredient that adapts to certain salt stresses and shares the functions of chrysanthemum. With annual expansion of the cultivation area of C. tinctoria in Xinjiang (China), soil salinity may become a constraint for chrysanthemum cultivation. To investigate the response of C. tinctoria to salt stress, physiological and transcriptional changes in C. tinctoria in the early stages of low (50 mM NaCl) and high (200 mM NaCl) salt stress were analyzed and identified. The results showed that the contents of osmotic regulators (free proline, soluble sugar, and soluble protein) and antioxidant enzymes (catalase and peroxidase) under salt stress increased to various extents compared with those of the control (CK) within 72 h, and the increase was higher under 200 mM NaCl treatments. De novo RNA-seq was used to analyze changes in the transcripts under 50 and 200 mM NaCl treatments for up to 48 h. In total, 8,584, 3,760, 7,833, 19,341, 13,233, and 9,224 differentially expressed genes (DEGs) were detected under 12 h, 24 h, and 48 h for 50 and 200 mM NaCl treatments, respectively. Weighted correlation network analysis (WGCNA) was used to analyze the correlations between all DEGs and physiological indexes. We found that the coexpression modules blue2 and Lightskyblue4 highly correlated with osmotic regulators and CAT and identified 20 and 30 hub genes, respectively. The results provide useful data for the further study of salt tolerance in C. tinctoria.

Root-omics for drought tolerance in cool-season grain legumes

Root traits can be exploited to increase the physiological efficiency of crop water use under drought. Root length, root hairs, root branching, root diameter, and root proliferation rate are genetically defined traits that can help to improve the water productivity potential of crops. Recently, high-throughput phenotyping techniques/platforms have been used to screen the germplasm of major cool-season grain legumes for root traits and their impact on different physiological processes, including nutrient uptake and yield potential. Advances in omics approaches have led to the dissection of genomic, proteomic, and metabolomic structures of these traits. This knowledge facilitates breeders to improve the water productivity and nutrient uptake of cultivars under limited soil moisture conditions in major cool-season grain legumes that usually face terminal drought. This review discusses the advances in root traits and their potential for developing drought-tolerant cultivars in cool-season grain legumes.

Hotter, drier, CRISPR: the latest edit on climate change

Integrating CRISPR/Cas9 genome editing into modern breeding programs for crop improvement in cereals. Global climate trends in many agricultural regions have been rapidly changing over the past decades, and major advances in global food systems are required to ensure food security in the face of these emerging challenges. With increasing climate instability due to warmer temperatures and rising CO₂ levels, the productivity of global agriculture will continue to be negatively impacted. To combat these growing concerns, creative approaches will be required, utilising all the tools available to produce more robust and tolerant crops with increased quality and yields under more extreme conditions. The integration of genome editing and transgenics into current breeding strategies is one promising solution to accelerate genetic gains through targeted genetic modifications, producing crops that can overcome the shifting climate realities. This review focuses on how revolutionary genome editing tools can be directly implemented into breeding programs for cereal crop improvement to rapidly counteract many of the issues affecting agriculture production in the years to come.

Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes

Drought response is coordinated through expression changes in a large suite of genes. Interspecific variation in this response is common and associated with drought-tolerant and -sensitive genotypes. The extent to which different genetic networks orchestrate the adjustments to water deficit in tolerant and sensitive genotypes has not been fully elucidated, particularly in non-model or woody plants. Differential expression analysis via RNA-seq was evaluated in root tissue exposed to simulated drought conditions in two loblolly pine (Pinus taeda L.) clones with contrasting tolerance to drought. Loblolly pine is the prevalent conifer in southeastern U.S. and a major commercial forestry species worldwide. Significant changes in gene expression levels were found in more than 4,000 transcripts [drought-related transcripts (DRTs)]. Genotype by environment (GxE) interactions were prevalent, suggesting that different cohorts of genes are influenced by drought conditions in the tolerant vs. sensitive genotypes. Functional annotation categories and metabolic pathways associated with DRTs showed higher levels of overlap between clones, with the notable exception of GO categories in upregulated DRTs. Conversely, both differentially expressed transcription factors (TFs) and TF families were largely different between clones. Our results indicate that the response of a drought-tolerant loblolly pine genotype vs. a sensitive genotype to water limitation is remarkably different on a gene-by-gene level, although it involves similar genetic networks. Upregulated transcripts under drought conditions represent the most diverging component between genotypes, which might depend on the activation and repression of substantially different groups of TFs.

Genetics and genomics of root system variation in adaptation to drought stress in cereal crops

Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant's root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.

Identification and characterization of differentially expressed genes in the rice root following exogenous application of spermidine during salt stress

Salinity is a major limiting factor in crop production. Exogenous spermidine (spd) effectively ameliorates salt injury, though the underlying molecular mechanism is poorly understood. We have used a suppression subtractive hybridization method to construct a cDNA library that has identified up-regulated genes from rice root under the treatment of spd and salt. Total 175 high-quality ESTs of about 100-500 bp in length with an average size of 200 bp are isolated, clustered and assembled into a collection of 62 unigenes. Gene ontology analysis using the KEGG pathway annotation database has classified the unigenes into 5 main functional categories and 13 subcategories. The transcripts abundance has been validated using Real-Time PCR. We have observed seven different types of post-translational modifications in the DEPs. 44 transmembrane helixes are predicted in 6 DEPs. This above information can be used as first-hand data for dissecting the administrative role of spd during salinity.

Transcriptional analyses reveal the molecular mechanism governing shade tolerance in the invasive plant Solidago canadensis

Solidago canadensis is an invasive plant that is capable of adapting to variable light conditions. To elucidate the shade tolerance mechanism in S. canadensis at the molecular level, transcriptome analyses were performed for leaves growing under natural light and three shade level conditions. Many differentially expressed genes (DEGs) were found in the comparative analysis, including those involved in photosynthesis, antioxidant, and secondary metabolism of phenol- and flavonoid-related pathways. Most genes encoding proteins involved in photosynthesis, such as photosystem I reaction center subunit (Psa), photosystem II core complex protein (Psb), and light-harvesting chlorophyll protein (Lhca and Lhcb), and reactive oxygen species (ROS) scavenging-related enzymes, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were upregulated with the shade levels. Furthermore, most of the DEGs related to secondary metabolite synthesis were also upregulated in the shade conditions. Our study indicates that S. canadensis can respond to shade stress by modulating the expression of several photosynthesis-related, free radical scavenging-related, and secondary metabolism-related genes; thus, this species has the ability to adapt to different light conditions.

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties.