Comparative transcriptome and translatome analysis in contrasting rice genotypes reveals differential mRNA translation in salt-tolerant Pokkali under salt stress

Alternative splicing as a driver of natural variation in abscisic acid response

Abscisic acid (ABA) is a crucial player in plant responses to the environment. It accumulates under stress, activating downstream signaling to implement molecular responses that restore homeostasis. Natural variance in ABA sensitivity remains barely understood, and the ABA pathway has been mainly studied at the transcriptional level, despite evidence that posttranscriptional regulation, namely, via alternative splicing, contributes to plant stress tolerance. Here, we identified the Arabidopsis accession Kn-0 as less sensitive to ABA than the reference Col-0, as shown by reduced effects of the hormone on seedling establishment, root branching, and stomatal closure, as well as by decreased induction of ABA marker genes. An in-depth comparative transcriptome analysis of the ABA response in the two variants revealed lower expression changes and fewer genes affected for the least ABA-sensitive ecotype. Notably, Kn-0 exhibited reduced levels of the ABA-signaling SnRK2 protein kinases and lower basal expression of ABA-reactivation genes, consistent with our finding that Kn-0 contains less endogenous ABA than Col-0. ABA also markedly affected alternative splicing, primarily intron retention, with Kn-0 being less responsive regarding both the number and magnitude of alternative splicing events, particularly exon skipping. We find that alternative splicing introduces a more ecotype-specific layer of ABA regulation and identify ABA-responsive splicing changes in key ABA pathway regulators that provide a functional and mechanistic link to the differential sensitivity of the two ecotypes. Our results offer new insight into the natural variation of ABA responses and corroborate a key role for alternative splicing in implementing ABA-mediated stress responses.

RNA N6-Methyladenosine Affects Copper-Induced Oxidative Stress Response in Arabidopsis thaliana

Recently, post-transcriptional regulation of mRNA mediated by N6-methyladenosine (m6A) has been found to have profound effects on transcriptome regulation during plant responses to various abiotic stresses. However, whether this RNA modification can affect an oxidative stress response in plants has not been studied. To assess the role of m6A modifications during copper-induced oxidative stress responses, m6A-IP-seq was performed in Arabidopsis seedlings exposed to high levels of copper sulfate. This analysis revealed large-scale shifts in this modification on the transcripts most relevant for oxidative stress. This altered epitranscriptomic mark is known to influence transcript abundance and translation; therefore we scrutinized these possibilities. We found an increased abundance of copper-enriched m6A-containing transcripts. Similarly, we also found increased ribosome occupancy of copper-enriched m6A-containing transcripts, specifically those encoding proteins involved with stress responses relevant to oxidative stressors. Furthermore, the significance of the m6A epitranscriptome on plant oxidative stress tolerance was uncovered by assessing germination and seedling development of the mta (N6-methyladenosine RNA methyltransferase A mutant complemented with ABI3:MTA) mutant exposed to high copper treatment. These analyses suggested hypersensitivity of the mta mutant compared to the wild-type plants in response to copper-induced oxidative stress. Overall, our findings suggest an important role for m6A in the oxidative stress response of Arabidopsis.

Integrative analyses of transcriptomes and metabolomes provide insight into salinity adaption in Bangia (Rhodaphyta)

The salinity of the external environment poses a serious threat to most land plants. Although seaweeds can adapt to this, intertidal species are subject to wide fluctuations in salinity, including hypo- and hyper-saline conditions. The red algal genus Bangiales is a typical example; it is one of the oldest eukaryotes with sexual reproduction and has successfully adapted to both marine and freshwater environments. However, there is a dearth of research focused on elucidating the mechanism by which marine Bangia (Bangia fuscopurpurea) adapts to hypo-salinity, as well as the mechanism by which freshwater Bangia (Bangia atropurpurea) adapts to hyper-salinity. The objective of this study is to employ third-generation full-length transcriptome data and untargeted metabolome data, to provide insights into the salinity adaptation mechanism of as well as the evolutionary relationship between both Bangia species. B. fuscopurpurea and B. atropurpurea exhibited 9112 and 8772 differentially expressed genes (DEGs), respectively, during various periods of hyper-saline condition. These genes were primarily enriched in secondary metabolites and energy-related metabolic pathways. Additionally, B. fuscopurpurea displayed 16,285 DEGs during different periods of hypo-saline condition, which were mainly enriched in metabolic pathways related to ion transport and membrane proteins. In the hyper- and hypo-saline adapt response processes of B. fuscopurpurea, a total of 303 transcription factors were identified, which belonged to 26 families. Among these, 85 and 142 differential transcription factors were identified, respectively, mainly belonging to the C2H2 and MYB family. Similarly, in the response process of B. atropurpurea to hyper-saline condition, a total of 317 transcription factors were identified, mainly belonging to 17 families. Among these, 121 differential transcription factors were identified, mainly belonging to the C2H2 and bZIP family. Furthermore, a correlation analysis was conducted to examine the relationship between the transcriptional and metabolic levels of both species under saline adaptation. The findings demonstrated that Bangia exhibits intricate adaptations to salinity, which involve swift regulation of its photosynthetic processes, alternations in membrane contents, and a robust anti-oxidation system to mitigate the effects of excess redox energy during exposure to varying salinity. Notably, the unsaturated fat and glutathione metabolic pathways were found to be significantly enriched in this context.

The comparative transcriptome analysis of two green super rice genotypes with varying tolerance to salt stress

BACKGROUND

Salinity is one of the main abiotic factors that restrict plant growth, physiology, and crop productivity is salt stress. About 33% of the total irrigated land suffers from severe salinity because of intensive underground water extraction and irrigation with brackish water. Thus, it is important to understand the genetic mechanism and identify the novel genes involved in salt tolerance for the development of climate-resilient rice cultivars.

METHODS AND RESULTS

In this study, two rice genotypes with varying tolerance to salt stress were used to investigate the differential expressed genes and molecular pathways to adapt under saline soil by comparative RNA sequencing at 42 days of the seedling stage. Salt-susceptible (S3) and -tolerant (S13) genotypes revealed 3982 and 3463 differentially expressed genes in S3 and S13 genotypes. The up-regulated genes in both genotypes were substantially enriched in different metabolic processes and binding activities. Biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and plant signal transduction mechanisms were highly enriched. Salt-susceptible and -tolerant genotypes shared the same salt adaptability mechanism with no significant quantitative differences at the transcriptome level. Moreover, bHLH, ERF, NAC, WRKY, and MYB transcription factors were substantially up-regulated under salt stress. 391 out of 1806 identified novel genes involved in signal transduction mechanisms. Expression profiling of six novel genes further validated the findings from RNA-seq data.

CONCLUSION

These findings suggest that the differentially expressed genes and molecular mechanisms involved in salt stress adaptation are conserved in both salt-susceptible and salt-tolerant rice genotypes. Further molecular characterization of novel genes will help to understand the genetic mechanism underlying salt tolerance in rice.

Transcriptomic and metabolomic analyses reveal that ABA increases the salt tolerance of rice significantly correlated with jasmonic acid biosynthesis and flavonoid biosynthesis

Abscisic acid (ABA) has been shown to mitigate the deleterious effects of abiotic stresses and to regulate plant growth and development. Salinity is one of the important abiotic stresses affecting plant cell metabolism and physiology, which causes serious damages to crops. In this study, we investigated the protective role of exogenous ABA on leaves in response to salinity stress using rice seedlings (two leaf-one heart) subjected to three treatments: ZCK (control), ZS (50 mM NaCl), and ZSA (5 mg L-1 ABA + 50 mM NaCl). We carried out transcriptomic and metabolomic analyses to identify the molecular mechanisms by which ABA protects plants against salt stress. Results showed that 1159 differentially expressed genes (DEGs) (916 up-regulated, 243 down-regulated) and 63 differentially accumulated metabolites (DAMs) (42 up-regulated, 21 down-regulated) were identified between the ZS and ZSA treatments, respectively. In addition, ABA pretreatment regulated the expression pattern of genes responsible for oxidation redox, starch and sucrose metabolism, and phenylpropanoid biosynthesis. The combined transcriptomic and metabolomic analysis revealed that 16 DEGs and 2 DAMs were involved in Flavonoid biosynthesis and 8 DEGs and 2 DAMs were involved alpha-Linolenic acid metabolism which are responsible for salinity stress tolerance through induced by exogenous ABA. Overall, ABA could enhance rice leaves growth and development mainly by regulating flavonoid biosynthesis and linoleic acid metabolism pathway.

Microbe-Responsive Proteomes During Plant-Microbe Interactions Between Rice Genotypes and the Multifunctional Methylobacterium oryzae CBMB20

BACKGROUND

Rice is colonized by plant growth promoting bacteria such as Methylobacterium leading to mutually beneficial plant-microbe interactions. As modulators of the rice developmental process, Methylobacterium influences seed germination, growth, health, and development. However, little is known about the complex molecular responsive mechanisms modulating microbe-driven rice development. The application of proteomics to rice-microbe interactions helps us elucidate dynamic proteomic responses mediating this association.

RESULTS

In this study, a total of 3908 proteins were detected across all treatments of which the non-inoculated IR29 and FL478 share up to 88% similar proteins. However, intrinsic differences appear in IR29 and FL478 as evident in the differentially abundant proteins (DAPs) and their associated gene ontology terms (GO). Successful colonization of M. oryzae CBMB20 in rice resulted to dynamic shifts in proteomes of both IR29 and FL478. The GO terms of DAPs for biological process in IR29 shifts in abundance from response to stimulus, cellular amino acid metabolic process, regulation of biological process and translation to cofactor metabolic process (6.31%), translation (5.41%) and photosynthesis (5.41%). FL478 showed a different shift from translation-related to response to stimulus (9%) and organic acid metabolic acid (8%). Both rice genotypes also showed a diversification of GO terms due to the inoculation of M. oryzae CBMB20. Specific proteins such as peptidyl-prolyl cis-trans isomerase (A2WJU9), thiamine thiazole synthase (A2YM28), and alanine-tRNA ligase (B8B4H5) upregulated in IR29 and FL478 indicate key mechanisms of M. oryzae CBMB20 mediated plant growth promotion in rice.

CONCLUSIONS

Interaction of Methylobacterium oryzae CBMB20 to rice results in a dynamic, similar, and plant genotype-specific proteomic changes supporting associated growth and development. The multifaceted CBMB20 expands the gene ontology terms and increases the abundance of proteins associated with photosynthesis, diverse metabolic processes, protein synthesis and cell differentiation and fate potentially attributed to the growth and development of the host plant. The specific proteins and their functional relevance help us understand how CBMB20 mediate growth and development in their host under normal conditions and potentially link subsequent responses when the host plants are exposed to biotic and abiotic stresses.

Comparative transcriptomic and metabolomic analyses provide insights into the responses to NaCl and Cd stress in Tamarix hispida

Salinity and heavy metal pollution seriously affect plant growth. Tamarix hispida (T. hispida) has the potential to remediate soil saline-alkali and heavy metal pollution. In this study, the response mechanisms of T. hispida under NaCl, CdCl₂ (Cd) and combined CdCl₂ and NaCl (Cd-NaCl) stresses were explored. Overall, the antioxidant system showed changes under the three stresses. The addition of NaCl inhibited the absorption of Cd²⁺. However, there were obvious differences in the transcripts and metabolites identified among the three stress responses. Interestingly, the number of DEGs was greatest under NaCl stress (929), but the number of differentially expressed metabolites (DEMs) was lowest (48), with 143 and 187 DEMs identified under Cd and Cd-NaCl stress, respectively. It is worth noting that both DEGs and DEMs were enriched in the linoleic acid metabolism pathway under Cd stress. In particular, the content of lipids changed significantly under Cd and Cd-NaCl stress, suggesting that maintaining normal lipid synthesis and metabolism may be an important way to improve the Cd tolerance of T. hispida. Flavonoids may also play an important role in the response to NaCl and Cd stress. These results provide a theoretical basis for cultivating plants with improved salt and cadmium repair abilities.

Transcriptome Landscapes of Salt-Susceptible Rice Cultivar IR29 Associated with a Plant Growth Promoting Endophytic Streptomyces

Plant growth-promoting endophytic (PGPE) actinomycetes have been known to enhance plant growth and mitigate plant from abiotic stresses via their PGP-traits. In this study, PGPE Streptomyces sp. GKU 895 promoted growth and alleviated salt tolerance of salt-susceptible rice cultivar IR29 by augmentation of plant weight and declined ROS after irrigation with 150 mM NaCl in a pot experiment. Transcriptome analysis of IR29 exposed to the combination of strain GKU 895 and salinity demonstrated up and downregulated differentially expressed genes (DEGs) classified by gene ontology and plant reactome. Streptomyces sp. GKU 895 induced changes in expression of rice genes including transcription factors under salt treatment which involved in growth and development, photosynthesis, plant hormones, ROS scavenging, ion transport and homeostasis, and plant-microbe interactions regarding pathogenesis- and symbiosis-related proteins. Taken together, these data demonstrate that PGPE Streptomyces sp. GKU 895 colonized and enhanced growth of rice IR29 and triggered salt tolerance phenotype. Our findings suggest that utilisation of beneficial endophytes in the saline fields could allow for the use of such marginal soils for growing rice and possibly other crops.

New Insights into rice pyrimidine catabolic enzymes

INTRODUCTION

Rice is a primary global food source, and its production is affected by abiotic stress, caused by climate change and other factors. Recently, the pyrimidine reductive catabolic pathway, catalyzed by dihydropyrimidine dehydrogenase (DHPD), dihydropyrimidinase (DHP) and β-ureidopropionase (β-UP), has emerged as a potential participant in the abiotic stress response of rice.

METHODS

The rice enzymes were produced as recombinant proteins, and two were kinetically characterized. Rice dihydroorotate dehydrogenase (DHODH), an enzyme of pyrimidine biosynthesis often confused with DHPD, was also characterized. Salt-sensitive and salt-resistant rice seedlings were subjected to salt stress (24 h) and metabolites in leaves were determined by mass spectrometry.

RESULTS

The OsDHPD sequence was homologous to the C-terminal half of mammalian DHPD, conserving FMN and uracil binding sites, but lacked sites for Fe/S clusters, FAD, and NADPH. OsDHPD, truncated to eliminate the chloroplast targeting peptide, was soluble, but inactive. Database searches for polypeptides homologous to the N-terminal half of mammalian DHPD, that could act as co-reductants, were unsuccessful. OsDHODH exhibited kinetic parameters similar to those of other plant DHODHs. OsDHP, truncated to remove a signal sequence, exhibited a kcat/Km = 3.6 x 103 s-1M-1. Osb-UP exhibited a kcat/Km = 1.8 x 104 s-1M-1. Short-term salt exposure caused insignificant differences in the levels of the ureide intermediates dihydrouracil and ureidopropionate in leaves of salt-sensitive and salt-resistant plants. Allantoin, a ureide metabolite of purine catabolism, was found to be significantly higher in the resistant cultivar compared to one of the sensitive cultivars.

DISCUSSION

OsDHP, the first plant enzyme to be characterized, showed low kinetic efficiency, but its activity may have been affected by truncation. Osb-UP exhibited kinetic parameters in the range of enzymes of secondary metabolism. Levels of two pathway metabolites were similar in sensitive and resistant cultivars and appeared to be unaffected by short-term salt exposure."

Marker-Assisted Introgression of the Salinity Tolerance Locus Saltol in Temperate Japonica Rice

BACKGROUND

Rice is one of the most salt sensitive crops at seedling, early vegetative and reproductive stages. Varieties with salinity tolerance at seedling stage promote an efficient growth at early stages in salt affected soils, leading to healthy vegetative growth that protects crop yield. Saltol major QTL confers capacity to young rice plants growing under salt condition by maintaining a low Na⁺/K⁺ molar ratio in the shoots.

RESULTS

Marker-assisted backcross (MABC) procedure was adopted to transfer Saltol locus conferring salt tolerance at seedling stage from donor indica IR64-Saltol to two temperate japonica varieties, Vialone Nano and Onice. Forward and background selections were accomplished using polymorphic KASP markers and a final evaluation of genetic background recovery of the selected lines was conducted using 15,580 SNP markers obtained from Genotyping by Sequencing. Three MABC generations followed by two selfing, allowed the identification of introgression lines achieving a recovery of the recurrent parent (RP) genome up to 100% (based on KASP markers) or 98.97% (based on GBS). Lines with highest RP genome recovery (RPGR) were evaluated for agronomical-phenological traits in field under non-salinized conditions. VN1, VN4, O1 lines were selected considering the agronomic evaluations and the RPGR% results as the most interesting for commercial exploitation. A physiological characterization was conducted by evaluating salt tolerance under hydroponic conditions. The selected lines showed lower standard evaluation system (SES) scores: 62% of VN4, and 57% of O1 plants reaching SES 3 or SES 5 respectively, while only 40% of Vialone Nano and 25% of Onice plants recorded scores from 3 to 5, respectively. VN1, VN4 and O1 showed a reduced electrolyte leakage values, and limited negative effects on relative water content and shoot/root fresh weight ratio.

CONCLUSION

The Saltol locus was successfully transferred to two elite varieties by MABC in a time frame of three years. The application of background selection until BC₃F₃ allowed the selection of lines with a RPGR up to 98.97%. Physiological evaluations for the selected lines indicate an improved salinity tolerance at seedling stage. The results supported the effectiveness of the Saltol locus in temperate japonica and of the MABC procedure for recovering of the RP favorable traits.

The PPR-Domain Protein SOAR1 Regulates Salt Tolerance in Rice

Previous studies in Arabidopsis reported that the PPR protein SOAR1 plays critical roles in plant response to salt stress. In this study, we reported that expression of the Arabidopsis SOAR1 (AtSOAR1) in rice significantly enhanced salt tolerance at seedling growth stage and promoted grain productivity under salt stress without affecting plant productivity under non-stressful conditions. The transgenic rice lines expressing AtSOAR1 exhibited increased ABA sensitivity in ABA-induced inhibition of seedling growth, and showed altered transcription and splicing of numerous genes associated with salt stress, which may explain salt tolerance of the transgenic plants. Further, we overexpressed the homologous gene of SOAR1 in rice, OsSOAR1, and showed that transgenic plants overexpressing OsSOAR1 enhanced salt tolerance at seedling growth stage. Five salt- and other abiotic stress-induced SOAR1-like PPRs were also identified. These data showed that the SOAR1-like PPR proteins are positively involved in plant response to salt stress and may be used for crop improvement in rice under salinity conditions through transgenic manipulation.

Engineering drought and salinity tolerance traits in crops through CRISPR-mediated genome editing: Targets, tools, challenges, and perspectives

Prolonged periods of drought triggered by climate change hamper plant growth and cause substantial agricultural yield losses every year. In addition to drought, salinity is one of the major abiotic stresses that severely affect crop health and agricultural production. Plant responses to drought and salinity involve multiple processes that operate in a spatiotemporal manner, such as stress sensing, perception, epigenetic modifications, transcription, post-transcriptional processing, translation, and post-translational changes. Consequently, drought and salinity stress tolerance are polygenic traits influenced by genome-environment interactions. One of the ideal solutions to these challenges is the development of high-yielding crop varieties with enhanced stress tolerance, together with improved agricultural practices. Recently, genome-editing technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR) tools, have been effectively applied to elucidate how plants deal with drought and saline environments. In this work, we aim to portray that the combined use of CRISPR-based genome engineering tools and modern genomic-assisted breeding approaches are gaining momentum in identifying genetic determinants of complex traits for crop improvement. This review provides a synopsis of plant responses to drought and salinity stresses at the morphological, physiological, and molecular levels. We also highlight recent advances in CRISPR-based tools and their use in understanding the multi-level nature of plant adaptations to drought and salinity stress. Integrating CRISPR tools with modern breeding approaches is ideal for identifying genetic factors that regulate plant stress-response pathways and for the introgression of beneficial traits to develop stress-resilient crops.

mRNA N6 -methyladenosine is critical for cold tolerance in Arabidopsis

Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post-transcriptional level, these cold stress-responsive transcripts undergo alternative splicing, microRNA-mediated regulation and alternative polyadenylation, amongst others. Recently, m⁶ A, m⁵ C and other mRNA modifications that can affect the regulation and stability of RNA were discovered, thus revealing another layer of post-transcriptional regulation that plays an important role in modulating gene expression. The importance of m⁶ A in plant growth and development has been appreciated, although its significance under stress conditions is still underexplored. To assess the role of m⁶ A modifications during cold stress responses, methylated RNA immunoprecipitation sequencing was performed in Arabidopsis seedlings esposed to low temperature stress (4°C) for 24 h. This transcriptome-wide m⁶ A analysis revealed large-scale shifts in this modification in response to low temperature stress. Because m⁶ A is known to affect transcript stability/degradation and translation, we investigated these possibilities. Interestingly, we found that cold-enriched m⁶ A-containing transcripts demonstrated the largest increases in transcript abundance coupled with increased ribosome occupancy under cold stress. The significance of the m⁶ A epitranscriptome on plant cold tolerance was further assessed using the mta mutant in which the major m⁶ A methyltransferase gene was mutated. Compared to the wild-type, along with the differences in CBFs and COR gene expression levels, the mta mutant exhibited hypersensitivity to cold treatment as determined by primary root growth, biomass, and reactive oxygen species accumulation. Furthermore, and most importantly, both non-acclimated and cold-acclimated mta mutant demonstrated hypersensitivity to freezing tolerance. Taken together, these findings suggest a critical role for the epitranscriptome in cold tolerance of Arabidopsis.

The molecular basis of cereal grain proteostasis

Storage proteins deposited in the endosperm of cereal grains are both a nitrogen reserve for seed germination and seedling growth and a primary protein source for human nutrition. Detailed surveys of the patterns of storage protein accumulation in cereal grains during grain development have been undertaken, but an in-depth understanding of the molecular mechanisms that regulate these patterns is still lacking. Accumulation of storage proteins in cereal grains involves a series of subcellular compartments, a set of energy-dependent events that compete with other cellular processes, and a balance of protein synthesis and protein degradation rates at different times during the developmental process. In this review, we focus on the importance of rates in cereal grain storage protein accumulation during grain development and outline the potential implications and applications of this information to accelerate modern agriculture breeding programmes and optimize energy use efficiency in proteostasis.

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

Integrated Multi-Omics Perspective to Strengthen the Understanding of Salt Tolerance in Rice

Salt stress is one of the major constraints to rice cultivation worldwide. Thus, the development of salt-tolerant rice cultivars becomes a hotspot of current rice breeding. Achieving this goal depends in part on understanding how rice responds to salt stress and uncovering the molecular mechanism underlying this trait. Over the past decade, great efforts have been made to understand the mechanism of salt tolerance in rice through genomics, transcriptomics, proteomics, metabolomics, and epigenetics. However, there are few reviews on this aspect. Therefore, we review the research progress of omics related to salt tolerance in rice and discuss how these advances will promote the innovations of salt-tolerant rice breeding. In the future, we expect that the integration of multi-omics salt tolerance data can accelerate the solution of the response mechanism of rice to salt stress, and lay a molecular foundation for precise breeding of salt tolerance.

Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines

Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress, which is currently worsened due to climate change. This study reports the development of salt tolerant introgression lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol quantitative trait loci (QTL), and the salt-sensitive japonica elite cultivar OLESA. Genotyping-by-sequencing (GBS) and Kompetitive allele specific PCR (KASPar) genotyping, in combination with step-wise phenotypic selection in hydroponic culture, were used for the identification of salt-tolerant ILs. Transcriptome-based genotyping allowed the fine mapping of indica genetic introgressions in the best performing IL (IL22). A total of 1,595 genes were identified in indica regions of IL22, which mainly located in large introgressions at Chromosomes 1 and 3. In addition to OsHKT1;5, an important number of genes were identified in the introgressed indica segments of IL22 whose expression was confirmed [e.g., genes involved in ion transport, callose synthesis, transcriptional regulation of gene expression, hormone signaling and reactive oxygen species (ROS) accumulation]. These genes might well contribute to salt stress tolerance in IL22 plants. Furthermore, comparative transcript profiling revealed that indica introgressions caused important alterations in the background gene expression of IL22 plants (japonica cultivar) compared with its salt-sensitive parent, both under non-stress and salt-stress conditions. In response to salt treatment, only 8.6% of the salt-responsive genes were found to be commonly up- or down-regulated in IL22 and OLESA plants, supporting massive transcriptional reprogramming of gene expression caused by indica introgressions into the recipient genome. Interactions among indica and japonica genes might provide novel regulatory networks contributing to salt stress tolerance in introgression rice lines. Collectively, this study illustrates the usefulness of transcriptomics in the characterization of new rice lines obtained in breeding programs in rice.

Identification of Key Genes in 'Luang Pratahn', Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks

Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of 'Luang Pratahn' rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.

Identification of differentially expressed genes and pathways in isonuclear kenaf genotypes under salt stress

Salinity is a potential abiotic stress and globally threatens crop productivity. However, the molecular mechanisms underlying salt stress tolerance with respect to cytoplasmic effect, gene expression, and metabolism pathway under salt stress have not yet been reported in isonuclear kenaf genotypes. To fill this knowledge gap, growth, physiological, biochemical, transcriptome, and cytoplasm changes in kenaf cytoplasmic male sterile (CMS) line (P3A) and its iso-nuclear maintainer line (P3B) under 200 mM sodium chloride (NaCl) stress and control conditions were analyzed. Salt stress significantly reduced leaf soluble protein, soluble sugars, proline, chlorophyll content, antioxidant enzymatic activity, and induced oxidative damage in terms of higher MDA contents in both genotypes. The reduction of these parameters resulted in a reduced plant growth compared with control. However, P3A was relatively more tolerant to salt stress than P3B. This tolerance of P3A was further confirmed by improved physio-biochemical traits under salt stress conditions. Transcriptome analysis showed that 4256 differentially expressed genes (DEGs) between the two genotypes under salt stress were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that photosynthesis, photosynthesis antenna-protein, and plant hormone signal transduction pathways might be associated with the improved NaCl stress tolerance in P3A. Conclusively, P3A cytoplasmic male sterile could be a potential salt-tolerant material for future breeding program of kenaf and can be used for phytoremediation of salt-affected soils. These data provide a valuable resource on the cytoplasmic effect of salt-responsive genes in kenaf and salt stress tolerance in kenaf.

How do rice seedlings of landrace Pokkali survive in saline fields after transplantation? Physiology, biochemistry, and photosynthesis

Rice, one of the most important staple food crops in the world, is highly sensitive to soil salinity at the seedling stage. The ultimate yield of this crop is a function of the number of seedlings surviving after transplantation in saline water. Oryza sativa cv. IR64 is a high-yielding salinity-sensitive variety, while Pokkali is a landrace traditionally cultivated by the local farmers in the coastal regions in India. However, the machinery responsible for the seedling-stage tolerance in Pokkali is not understood. To bridge this gap, we subjected young seedlings of these contrasting genotypes to salinity and performed detailed investigations about their growth parameters, ion homeostasis, biochemical composition, and photosynthetic parameters after every 24 h of salinity for three days. Taken together, all the physiological and biochemical indicators, such as proline accumulation, K⁺/Na⁺ ratio, lipid peroxidation, and electrolyte leakage, clearly revealed significant differences between IR64 and Pokkali under salinity, establishing their contrasting nature at this stage. In response to salinity, the F_v/F_m ratio (maximum quantum efficiency of Photosystem II as inferred from Chl a fluorescence) and the energy conserved for the electron transport after the reduction of Q_A (the primary electron acceptor of PSII), to Q_A^-, and reduction of the end electron acceptor molecules towards the PSI (Photosystem I) electron acceptor side was higher in Pokkali than IR64 plants. These observations reflect a direct contribution of photosynthesis towards seedling-stage salinity tolerance in rice. These findings will help to breed high-yielding crops for salinity prone agricultural lands.

Gene Mapping, Cloning and Association Analysis for Salt Tolerance in Rice

Soil salinization caused by the accumulation of sodium can decrease rice yield and quality. Identification of rice salt tolerance genes and their molecular mechanisms could help breeders genetically improve salt tolerance. We studied QTL mapping of populations for rice salt tolerance, period and method of salt tolerance identification, salt tolerance evaluation parameters, identification of salt tolerance QTLs, and fine-mapping and map cloning of salt tolerance QTLs. We discuss our findings as they relate to other genetic studies of salt tolerance association.

Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice

BACKGROUND

Soil salinization represents a serious threat to global rice production. Although significant research has been conducted to understand salt stress at the genomic, transcriptomic and proteomic levels, few studies have focused on the translatomic responses to this stress. Recent studies have suggested that transcriptional and translational responses to salt stress can often operate independently.

RESULTS

We sequenced RNA and ribosome-protected fragments (RPFs) from the salt-sensitive rice (O. sativa L.) cultivar 'Nipponbare' (NB) and the salt-tolerant cultivar 'Sea Rice 86' (SR86) under normal and salt stress conditions. A large discordance between salt-induced transcriptomic and translatomic alterations was found in both cultivars, with more translationally regulated genes being observed in SR86 in comparison to NB. A biased ribosome occupancy, wherein RPF depth gradually increased from the 5' ends to the 3' ends of coding regions, was revealed in NB and SR86. This pattern was strengthened by salt stress, particularly in SR86. On the contrary, the strength of ribosome stalling was accelerated in salt-stressed NB but decreased in SR86.

CONCLUSIONS

This study revealed that translational reprogramming represents an important layer of salt stress responses in rice, and the salt-tolerant cultivar SR86 adopts a more flexible translationally adaptive strategy to cope with salt stress compared to the salt susceptible cultivar NB. The differences in translational dynamics between NB and SR86 may derive from their differing levels of ribosome stalling under salt stress.

Heat stress response mechanisms in pollen development

Being rooted in place, plants are faced with the challenge of responding to unfavourable local conditions. One such condition, heat stress, contributes massively to crop losses globally. Heatwaves are predicted to increase, and it is of vital importance to generate crops that are tolerant to not only heat stress but also to several other abiotic stresses (e.g. drought stress, salinity stress) to ensure that global food security is protected. A better understanding of the molecular mechanisms that underlie the temperature stress response in pollen will be a significant step towards developing effective breeding strategies for high and stable production in crop plants. While most studies have focused on the vegetative phase of plant growth to understand heat stress tolerance, it is the reproductive phase that requires more attention as it is more sensitive to elevated temperatures. Every phase of reproductive development is affected by environmental challenges, including pollen and ovule development, pollen tube growth, male-female cross-talk, fertilization, and embryo development. In this review we summarize how pollen is affected by heat stress and the molecular mechanisms employed during the stress period, as revealed by classical and -omics experiments.

Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance

Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.

Improving rice salt tolerance by precision breeding in a new era

Rice is a premier staple food that constitutes the bulk of the daily diet of the majority of people in Asia. Agricultural productivity must be boosted to support this huge demand for rice. However, production is jeopardized by soil salinity. Advances in whole-genome sequencing, marker-assisted breeding strategies, and targeted mutagenesis have substantially improved the toolbox of today's breeders. Given that salinity has a major influence on rice at both the seedling and reproductive stages, understanding and manipulating this trait will have an enormous impact on sustainable production. This article summarizes recent developments in the understanding of the mechanisms of salt tolerance and how state-of-the-art tools such as RNA guided CRISPR endonuclease technology including targeted mutagenesis or base and prime editing can help in gene discovery and functional analysis as well as in transferring favorable alleles into elite breeding material to speed the breeding of salt-tolerant rice cultivars.

Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions

The reprogramming of gene expression is one of the key responses to environmental stimuli, whereas changes in mRNA do not necessarily bring forth corresponding changes of the protein, which seems partially due to the stress-induced selective translation. To address this issue, we systematically compared the transcriptome and translatome using self-produced and publicly available datasets to decipher how and to what extent the coordination and discordance between transcription and translation came to be in response to wounding (self-produced), dark to light transition, heat, hypoxia, Pi starvation and the pathogen-associated molecular pattern (elf18) in Arabidopsis. We found that changes in total mRNAs (transcriptome) and ribosome-protected fragments (translatome) are highly correlated upon dark to light transition or heat stress. However, this close correlation was generally lost under other four stresses analyzed in this study, especially during immune response, which suggests that transcription and translation are differentially coordinated under distinct stress conditions. Moreover, Gene Ontology (GO) enrichment analysis showed that typical stress responsive genes were upregulated at both transcriptional and translational levels, while non-stress-specific responsive genes were changed solely at either level or downregulated at both levels. Taking wounding responsive genes for example, typical stress responsive genes are generally involved in functional categories related to dealing with the deleterious effects caused by the imposed wounding stress, such as response to wounding, response to water deprivation and response to jasmonic acid, whereas non-stress-specific responsive genes are often enriched in functional categories like S-glycoside biosynthetic process, photosynthesis and DNA-templated transcription. Collectively, our results revealed the differential as well as targeted coordination between transcriptome and translatome in response to diverse stresses, thus suggesting a potential model wherein preferential ribosome loading onto the stress-upregulated mRNA pool could be a pacing factor for selective translation.

WinRoots: A High-Throughput Cultivation and Phenotyping System for Plant Phenomics Studies Under Soil Stress

Soil stress, such as salinity, is a primary cause of global crop yield reduction. Existing crop phenotyping platforms cannot fully meet the specific needs of phenomics studies of plant response to soil stress in terms of throughput, environmental controllability, or root phenotypic acquisition. Here, we report the WinRoots, a low-cost and high-throughput plant soil cultivation and phenotyping system that can provide uniform, controlled soil stress conditions and accurately quantify the whole-plant phenome, including roots. Using soybean seedlings exposed to salt stress as an example, we demonstrate the uniformity and controllability of the soil environment in this system. A high-throughput multiple-phenotypic assay among 178 soybean cultivars reveals that the cotyledon character can serve as a non-destructive indicator of the whole-seedling salt tolerance. Our results demonstrate that WinRoots is an effective tool for high-throughput plant cultivation and soil stress phenomics studies.

Gene Expression Dynamics in Rice Peduncles at the Heading Stage

Improving grain yield in the staple food crop rice has been long sought goal of plant biotechnology. One of the traits with significant impact on rice breeding programs is peduncle elongation at the time of heading failing which leads to significant reduction in grain yield due to incomplete panicle exsertion. To decipher transcriptional dynamics and molecular players underlying peduncle elongation, we performed RNA sequencing analysis of elongating and non-elongating peduncles in two Indian cultivars, Swarna and Pokkali, at the time of heading. Along with genes associated with cell division and cell wall biosynthesis, we observed significant enrichment of genes associated with auxins, gibberellins, and brassinosteroid biosynthesis/signaling in the elongating peduncles before heading in both the genotypes. Similarly, genes associated with carbohydrate metabolism and mobilization, abiotic stress response along with cytokinin, abscisic acid, jasmonic acid, and ethylene biosynthesis/signaling were enriched in non-elongating peduncles post heading. Significant enrichment of genes belonging to key transcription factor families highlights their specialized roles in peduncle elongation and grain filling before and after heading, respectively. A comparison with anther/pollen development-related genes provided 76 candidates with overlapping roles in anther/pollen development and peduncle elongation. Some of these are important for carbohydrate remobilization to the developing grains. These can be engineered to combat with incomplete panicle exsertion in male sterile lines and manipulate carbohydrate dynamics in grasses. Overall, this study provides baseline information about potential target genes for engineering peduncle elongation with implications on plant height, biomass composition and grain yields in rice.

De novo RNA-Seq analysis in sensitive rice cultivar and comparative transcript profiling in contrasting genotypes reveal genetic biomarkers for fluoride-stress response

The fluoride-sensitive indica rice cultivar, IR-64 was subjected to NaF-treatment for 25 days, following which RNA-Seq analysis identified significant up and down regulation of 1,303 and 93 transcripts respectively. Gene ontology (GO) enrichment analysis classified transcripts into groups related to 'cellular part', 'membrane', 'catalytic activity', 'transporter activity', 'binding', 'metabolic processes' and 'cellular processes'. Analysis of differentially expressed genes (DEGs) revealed fluoride-mediated suppression of abscisic acid (ABA) biosynthesis and signaling. Instead, the gibberellin-dependent pathway and signaling via ABA-independent transcription factors (TFs) was activated. Comparative profiling of selected DEGs in IR-64 and fluoride-tolerant variety, Khitish revealed significant cytoskeletal and nucleosomal remodelling, accompanied with escalated levels of autophagy in stressed IR-64 (unlike that in stressed Khitish). Genes associated with ion, solute and xenobiotic transport were strongly up regulated in stressed IR-64, indicating potential fluoride entry through these channels. On the contrary, genes associated with xenobiotic mobility were suppressed in the tolerant cultivar, which restricted bioaccumulation and translocation of fluoride. Pairwise expression profile analysis between stressed IR-64 and Khitish, supported by extensive statistical modelling predicted that fluoride susceptibility was associated with high expression of genes like amino acid transporter, ABC transporter2, CLCd, MFS monosaccharide transporter, SulfT2.1 and PotT2 while fluoride tolerance with high expression of Sweet11.

Transcriptome Analysis Reveals Complex Defensive Mechanisms in Salt-Tolerant and Salt-Sensitive Shrub Willow Genotypes under Salinity Stress

Salinity stress is one of the most devastating abiotic stresses limiting plant growth and productivity. As a moderately salt-tolerant crop, shrub willow (Salix spp.) is widely distributed over the world and can provide multiple bioenergy product and environmental benefits. To delve into the salt tolerance mechanism and screen out salt-tolerant genes, two shrub willow cultivars (a salt-sensitive genotype JW9-6 and a salt-tolerant genotype JW2372) at three time points (0, 2, and 12 h) after NaCl treatments were used for RNA sequencing. A comparative analysis between genotypes and time points showed 1,706 differentially expressed genes (DEGs), of which 1,029 and 431 DEGs were only found in the JW9-6 and JW2372, respectively. Gene Ontology (GO) and MapMan annotations suggested that many DEGs were involved in various defense-related biological pathways, including cell wall integrity, hormone signaling, antioxidant system, heat shock proteins, and transcription factors. Compared to JW9-6, JW2372 contained more DEGs involved in the maintenance of the cell wall integrity, ABA, and ethylene signal transduction pathways. In addition, more DEGs encoding heat shock proteins were found in JW2372. Instead, transcription factors including ERF, MYB, NAC, and WRKY were found to be more differentially expressed in JW9-6 under salinity stress. Furthermore, expressions of nine randomly selected DEGs were verified by qRT-PCR analysis. This study contributes in new perspicacity into underlying the salt tolerance mechanism of a shrub willow at the transcriptome level and also provides numerous salt-tolerant genes for further genetic engineering and breeding purposes in the future.

Identification and expression analysis of miRNAs and elucidation of their role in salt tolerance in rice varieties susceptible and tolerant to salinity

Soil salinization is a serious problem for cultivation of rice, as among cereals rice is the most salt sensitive crop, and more than 40% of the total agricultural land amounting to approximately 80 million ha the world over is salt affected. Salinity affects a plant in a varieties of ways, including ion toxicity, osmotic stress and oxidative damage. Since miRNAs occupy the top place in biochemical events determining a trait, understanding their role in salt tolerance is highly desirable, which may allow introduction of the trait in the rice cultivars of choice through biotechnological interventions. High throughput sequencing of sRNAs in the root and shoot tissues of the seedlings of the control and NaCl treated Pokkali, a salt-tolerant rice variety, identified 75 conserved miRNAs and mapped 200 sRNAs to the rice genome as novel miRNAs. Expression of nine novel miRNAs and two conserved miRNAs were confirmed by Northern blotting. Several of both conserved and novel miRNAs that expressed differentially in root and/or shoot tissues targeted transcription factors like AP2/EREBP domain protein, ARF, NAC, MYB, NF-YA, HD-Zip III, TCP and SBP reported to be involved in salt tolerance or in abiotic stress tolerance in general. Most of the novel miRNAs expressed in the salt tolerant wild rice Oryza coarctata, suggesting conservation of miRNAs in taxonomically related species. One of the novel miRNAs, osa-miR12477, also targeted L-ascorbate oxidase (LAO), indicating build-up of oxidative stress in the plant upon salt treatment, which was confirmed by DAB staining. Thus, salt tolerance might involve miRNA-mediated regulation of 1) cellular abundance of the hormone signaling components like EREBP and ARF, 2) synthesis of abiotic stress related transcription factors, and 3) antioxidative component like LAO for mitigation of oxidative damage. The study clearly indicated importance of osa-miR12477 regulated expression of LAO in salt tolerance in the plant.

Translational regulation contributes to the elevated CO2 response in two Solanum species

Understanding the impact of elevated CO2 (eCO2 ) in global agriculture is important given climate change projections. Breeding climate-resilient crops depends on genetic variation within naturally varying populations. The effect of genetic variation in response to eCO2 is poorly understood, especially in crop species. We describe the different ways in which Solanum lycopersicum and its wild relative S. pennellii respond to eCO2 , from cell anatomy, to the transcriptome, and metabolome. We further validate the importance of translational regulation as a potential mechanism for plants to adaptively respond to rising levels of atmospheric CO2 .

Mapping the Salt Stress-Induced Changes in the Root miRNome in Pokkali Rice

A plant's response to stress conditions is governed by intricately coordinated gene expression. The microRNAs (miRs) have emerged as relatively new players in the genetic network, regulating gene expression at the transcriptional and post-transcriptional level. In this study, we performed comprehensive profiling of miRs in roots of the naturally salt-tolerant Pokkali rice variety to understand their role in regulating plant physiology in the presence of salt. For comparisons, root miR profiles of the salt-sensitive rice variety Pusa Basmati were generated. It was seen that the expression levels of 65 miRs were similar for roots of Pokkali grown in the absence of salt (PKNR) and Pusa Basmati grown in the presence of salt (PBSR). The salt-induced dis-regulations in expression profiles of miRs showed controlled changes in the roots of Pokkali (PKSR) as compared to larger variations seen in the roots of Pusa Basmati. Target analysis of salt-deregulated miRs identified key transcription factors, ion-transporters, and signaling molecules that act to maintain cellular Ca2+ homeostasis and limit ROS production. These miR:mRNA nodes were mapped to the Quantitative trait loci (QTLs) to identify the correlated root traits for understanding their significance in plant physiology. The results obtained indicate that the adaptability of Pokkali to excess salt may be due to the genetic regulation of different cellular components by a variety of miRs.

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

Endophytes, both of bacterial and fungal origin, are ubiquitously present in all plants. While their origin and evolution are enigmatic, there is burgeoning literature on their role in promoting growth and stress responses in their hosts. We demonstrate that a salt-tolerant endophyte isolated from salt-adapted Pokkali rice, a Fusarium sp., colonizes the salt-sensitive rice variety IR-64, promotes its growth under salt stress and confers salinity stress tolerance to its host. Physiological parameters, such as assimilation rate and chlorophyll stability index were higher in the colonized plants. Comparative transcriptome analysis revealed 1348 up-regulated and 1078 down-regulated genes in plants colonized by the endophyte. Analysis of the regulated genes by MapMan and interaction network programs showed that they are involved in both abiotic and biotic stress tolerance, and code for proteins involved in signal perception (leucine-rich repeat proteins, receptor-like kinases) and transduction (Ca2+ and calmodulin-binding proteins), transcription factors, secondary metabolism and oxidative stress scavenging. For nine genes, the data were validated by qPCR analysis in both roots and shoots. Taken together, these results show that salt-adapted Pokkali rice varieties are powerful sources for the identification of novel endophytes, which can be used to confer salinity tolerance to agriculturally important, but salt-sensitive rice varieties.

Comparative Transcriptome and Proteome Analysis of Salt-Tolerant and Salt-Sensitive Sweet Potato and Overexpression of IbNAC7 Confers Salt Tolerance in Arabidopsis

Salt stress is one of the major devastating factors affecting the growth and yield of almost all crops, including the crucial staple food crop sweet potato. To understand their molecular responses to salt stress, comparative transcriptome and proteome analysis of salt-tolerant cultivar Xushu 22 and salt-sensitive cultivar Xushu 32 were investigated. The results showed the two genotypes had distinct differences at the transcription level and translation level even without salt stress, while inconsistent expression between the transcriptome and proteome data was observed. A total of 16,396 differentially expressed genes (DEGs) and 727 differentially expressed proteins (DEPs) were identified. Wherein, 1,764 DEGs and 93 DEPs were specifically expressed in the tolerant genotype. Furthermore, the results revealed that the significantly upregulated genes were mainly related to the regulation of ion accumulation, stress signaling, transcriptional regulation, redox reactions, plant hormone signal transduction, and secondary metabolite accumulation, which may be involved in the response of sweet potato to salt stress and/or may determine the salt tolerance difference between the two genotypes. In addition, 1,618 differentially expressed regulatory genes were identified, including bZIP, bHLH, ERF, MYB, NAC, and WRKY. Strikingly, transgenic Arabidopsis overexpressing IbNAC7 displayed enhanced salt tolerance compared to WT plants, and higher catalase (CAT) activity, chlorophyll and proline contents, and lower malondialdehyde (MDA) content and reactive oxygen species (ROS) accumulation were detected in transgenic plants compared with that of WT under salt stress. Furthermore, RNA-seq and qRT-PCR analysis displayed that the expression of many stress-related genes was upregulated in transgenic plants. Collectively, these findings provide revealing insights into sweet potato molecular response to salt stress and underlie the complex salt tolerance mechanisms between genotypes, and IbNAC7 was shown as a promising candidate gene to enhance salt tolerance of sweet potato.

A Meta-Analysis of Comparative Transcriptomic Data Reveals a Set of Key Genes Involved in the Tolerance to Abiotic Stresses in Rice

Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the "Drought and Salt Tolerance" TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.

Identification of Superior Alleles for Seedling Stage Salt Tolerance in the USDA Rice Mini-Core Collection

Salt stress is a major constraint to rice acreage and production worldwide. The purpose of this study was to evaluate the natural genetic variation available in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) for early vigor traits under salt stress and identify quantitative trait loci (QTLs) for seedling-stage salt tolerance via a genome-wide association study (GWAS). Using a hydroponic system, the seedlings of 162 accessions were subjected to electrical conductivity (EC) 6.0 dS m⁻¹ salt stress at the three-to-four leaf stage. After completion of the study, 59.4% of the accessions were identified as sensitive, 23.9% were identified as moderately tolerant, and 16.7% were identified as highly tolerant. Pokkali was the most tolerant variety, while Nerica-6 was the most sensitive. Adapting standard International Rice Research Institute (IRRI) protocols, eight variables associated with salt tolerance were determined. The GWAS of the URMC, using over three million single-nucleotide polymorphisms (SNPs), identified nine genomic regions associated with salt tolerance that were mapped to five different chromosomes. Of these, none were in the known Saltol QTL region, suggesting different probable genes and mechanisms responsible for salt tolerance in the URMC. The study uncovered genetic loci that explained a large portion of the variation in salt tolerance at the seedling stage. Fourteen highly salt-tolerant accessions, six novel loci, and 16 candidate genes in their vicinity were identified that may be useful in breeding for salt stress tolerance. Identified QTLs can be targeted for fine mapping, candidate gene verification, and marker-assisted breeding in future studies.

Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii)

The buff-throated partridge (Tetraophasis szechenyii) is a hypoxia-tolerant bird living in an extremely inhospitable high-altitude environment, which has high ultraviolet (UV) radiation as well as a low oxygen supply when compared with low-altitude areas. To further understand the molecular genetic mechanisms of the high-altitude adaptation of the buff-throated partridges, we de novo assembled the complete genome of the buff-throated partridge. Comparative genomics revealed that positively selected hypoxia-related genes in the buff-throated partridge were distributed in the HIF-1 signaling pathway (map04066), response to hypoxia (GO:0001666), response to oxygen-containing compound (GO:1901700), ATP binding (GO:0005524), and angiogenesis (GO:0001525). Of these positively selected hypoxia-related genes, one positively selected gene (LONP1) had one buff-throated partridge-specific missense mutation which was classified as deleterious by PolyPhen-2. Moreover, positively selected genes in the buff-throated partridge were enriched in cellular response to DNA damage stimulus (corrected P value: 0.028006) and DNA repair (corrected P value: 0.044549), which was related to the increased exposure of the buff-throated partridge to UV radiation. Compared with other avian genomes, the buff-throated partridge showed expansion in genes associated with steroid hormone receptor activity and contractions in genes related to immune and olfactory perception. Furthermore, comparisons between the buff-throated partridge genome and red junglefowl genome revealed a conserved genome structure and provided strong evidence of the sibling relationship between Tetraophasis and Lophophorus. Our data and analysis contributed to the study of Phasianidae evolutionary history and provided new insights into the potential adaptation mechanisms to the high altitude employed by the buff-throated partridge.