A novel protein kinase involved in Na(+) exclusion revealed from positional cloning

AtCIPK20 regulates microtubule stability to mediate stomatal closure under drought stress in Arabidopsis

Drought stress is a common abiotic challenge that profoundly impacts plant growth and development. As sessile organisms, plants rely on various physiological and morphological adaptations to cope with drought conditions. The CIPK (calcineurin B-like protein-interacting protein kinase) family proteins play a pivotal role in mediating plant responses to abiotic stress through modulation of cellular membrane events via the CBL-CIPK complex. However, reports documenting the CIPKs' regulation of non-membrane events are scant. In this study, we discovered a novel subcellular localisation pattern of the AtCIPK20 protein of Arabidopsis, specifically to cortical microtubules (cMT), which is distinct from previously reported localisation patterns of plant CIPKs. AtCIPK20 regulates ABA-induced loss of cMT organisation in guard cells, thereby facilitating stomatal closure, mitigating leaf water loss, and protecting plants from drought stress in Arabidopsis. The C-terminal regulatory domain of AtCIPK20 governs its cMT targeting, whereas the interaction of AtCIPK20 with its CBL partners disrupts this localisation. Notably, the cMT targeting characteristic of AtCIPK20 is not exclusive, as several other CIPK members in Arabidopsis, maize, and rice exhibit similar localisation patterns. These findings broaden our current understanding of the role of plant CIPK members in abiotic stress resistance and suggest that future exploration of CIPK molecular functions should adopt a more comprehensive perspective.

The role of CBL-CIPK signaling in plant responses to biotic and abiotic stresses

Plants have a variety of regulatory mechanisms to perceive, transduce, and respond to biotic and abiotic stress. One such mechanism is the calcium-sensing CBL-CIPK system responsible for the sensing of specific stressors, such as drought or pathogens. CBLs perceive and bind Calcium (Ca2+) in response to stress and then interact with CIPKs to form an activated complex. This leads to the phosphorylation of downstream targets, including transporters and ion channels, and modulates transcription factor levels and the consequent levels of stress-associated genes. This review describes the mechanisms underlying the response of the CBL-CIPK pathway to biotic and abiotic stresses, including regulating ion transport channels, coordinating plant hormone signal transduction, and pathways related to ROS signaling. Investigation of the function of the CBL-CIPK pathway is important for understanding plant stress tolerance and provides a promising avenue for molecular breeding.

Investigating the genetic basis of salt-tolerance in common bean: a genome-wide association study at the early vegetative stage

Salinity poses a significant challenge to global crop productivity, affecting approximately 20% of cultivated and 33% of irrigated farmland, and this issue is on the rise. Negative impact of salinity on plant development and metabolism leads to physiological and morphological alterations mainly due to high ion concentration in tissues and the reduced water and nutrients uptake. Common bean (Phaseolus vulgaris L.), a staple food crop accounting for a substantial portion of consumed grain legumes worldwide, is highly susceptible to salt stress resulting in noticeable reduction in dry matter gain in roots and shoots even at low salt concentrations. In this study we screened a common bean panel of diversity encompassing 192 homozygous genotypes for salt tolerance at seedling stage. Phenotypic data were leveraged to identify genomic regions involved in salt stress tolerance in the species through GWAS. We detected seven significant associations between shoot dry weight and SNP markers. The candidate genes, in linkage with the regions associated to salt tolerance or harbouring the detected SNP, showed strong homology with genes known to be involved in salt tolerance in Arabidopsis. Our findings provide valuable insights onto the genetic control of salt tolerance in common bean and represent a first contribution to address the challenge of salinity-induced yield losses in this species and poses the ground to eventually breed salt tolerant common bean varieties.

Overexpression of CdtCIPK21 from triploid bermudagrass reduces salt and drought tolerance but increases chilling tolerance in transgenic rice

Calcineurin B-like-interacting protein kinase (CIPK) is a serine/threonine kinase, which transmits the Ca2+ signal sensed by CBL proteins. A CdtCIPK21 showing highly identical to OsCIPK21 in rice was isolated from triploid bermudagrass (Cynodon dactylon × Cynodon transvaalensis). CdtCIPK21 transcript could be detected in roots, rhizomes, stems, stolons, and leaves, with highest level in roots. It was induced by salinity, dehydration and chilling, but reduced by ABA treatment. Transgenic rice plants overexpressing CdtCIPK21 had decreased salt and drought tolerance as well as ABA sensitivity but increased chilling tolerance. Lower SOD and CAT activities was observed in transgenic lines under salinity and drought stress conditions, but higher levels under chilling stress. Similarly, lower levels of proline concentration and P5CS1 and P5CS2 transcripts were maintained in transgenic lines under salinity and drought stresses, and higher levels were maintained under chilling. In addition, transgenic lines had lower transcript levels of ABA-independent genes (OsDREB1A, OsDREB1B, and OsDREB2A) and ABA responsive genes (OsLEA3, OsLIP9, and OsRAB16A) under salinity and drought but higher levels under chilling compared with WT. The results suggest that CdtCIPK21 regulates salt and drought tolerance negatively and chilling tolerance positively, which are associated with the altered ABA sensitivity, antioxidants, proline accumulation and expression of ABA-dependent and ABA-independent stress responsive genes.

AtCIPK16, a CBL-interacting protein kinase gene, confers salinity tolerance in transgenic wheat

Globally, wheat is the major source of staple food, protein, and basic calories for most of the human population. Strategies must be adopted for sustainable wheat crop production to fill the ever-increasing food demand. Salinity is one of the major abiotic stresses involved in plant growth retardation and grain yield reduction. In plants, calcineurin-B-like proteins form a complicated network with the target kinase CBL-interacting protein kinases (CIPKs) in response to intracellular calcium signaling as a consequence of abiotic stresses. The AtCIPK16 gene has been identified in Arabidopsis thaliana and found to be significantly upregulated under salinity stress. In this study, the AtCIPK16 gene was cloned in two different plant expression vectors, i.e., pTOOL37 having a UBI1 promoter and pMDC32 having a 2XCaMV35S constitutive promoter transformed through the Agrobacterium-mediated transformation protocol, in the local wheat cultivar Faisalabad-2008. Based on their ability to tolerate different levels of salt stress (0, 50, 100, and 200 mM), the transgenic wheat lines OE1, OE2, and OE3 expressing AtCIPK16 under the UBI1 promoter and OE5, OE6, and OE7 expressing the same gene under the 2XCaMV35S promoter performed better at 100 mM of salinity stress as compared with the wild type. The AtCIPK16 overexpressing transgenic wheat lines were further investigated for their K⁺ retention ability in root tissues by utilizing the microelectrode ion flux estimation technique. It has been demonstrated that after 10 min of 100 mM NaCl application, more K⁺ ions were retained in the AtCIPK16 overexpressing transgenic wheat lines than in the wild type. Moreover, it could be concluded that AtCIPK16 functions as a positive elicitor in sequestering Na⁺ ions into the cell vacuole and retaining more cellular K⁺ under salt stress to maintain ionic homeostasis.

Photosynthesis and Salt Exclusion Are Key Physiological Processes Contributing to Salt Tolerance of Canola (Brassica napus L.): Evidence from Physiology and Transcriptome Analysis

Plant salt tolerance is controlled by various physiological processes such as water and ion homeostasis, photosynthesis, and cellular redox balance, which are in turn controlled by gene expression. In the present study, plants of six canola cultivars (DGL, Dunkled, Faisal Canola, Cyclone, Legend, and Oscar) were evaluated for salt tolerance by subjecting them to 0 or 200 mM NaCl stress. Based on growth, cultivars DGL, Dunkled, and Faisal Canola were ranked as salt tolerant, while cultivars Cyclone, Legend, and Oscar were ranked as salt-sensitive ones. Differential salt tolerance in these canola cultivars was found to be associated with a relatively lower accumulation of Na⁺ and greater accumulation of K⁺ in the leaves, lower oxidative damage (MDA), and better antioxidative defense system (Superoxide dismutase, SOD; peroxidase, POD, and catalase, CAT). Cultivar Oscar was the poorest to discriminate Na⁺ and K⁺ uptake and accumulation in leaves and had poor antioxidant potential to scavenge ROS. Salt stress did not affect the structural stability of photosystem-II (PSII) till three weeks, thereafter it caused a significant decrease. Salt stress increased the performance index (PI_ABS) by increasing the density of active reaction centers in Oscar. Salt stress decreased the antenna size thereby lowering the absorption and trapping energy flux, and maintaining the electron transport with an increase in heat dissipation. This may represent a potential mechanism to cope with salt stress. Transcriptome analysis of salt-sensitive cultivar Oscar further revealed that salt stress down-regulated DEGs related to hormonal signal transduction pathways, photosynthesis, and transcription factors, while DEGs related to the biosynthesis of amino acid and ion transport were up-regulated. In conclusion, salt tolerance in canola cultivars was associated with ion exclusion and maintenance of photosynthesis. Salt stress sensitivity in cultivar Oscar was mainly associated with poor control of ion homeostasis which caused oxidative stress and reduced photosynthetic efficiency.

Natural variation and domestication selection of ZmSULTR3;4 is associated with maize lateral root length in response to salt stress

Soil salinity is a major constraint that restricts crop productivity worldwide. Lateral roots (LRs) are important for water and nutrient acquisition, therefore understanding the genetic basis of natural variation in lateral root length (LRL) is of great agronomic relevance to improve salt tolerance in cultivated germplasms. Here, using a genome-wide association study, we showed that the genetic variation in ZmSULTR3;4, which encodes a plasma membrane-localized sulfate transporter, is associated with natural variation in maize LRL under salt stress. The transcript of ZmSULTR3;4 was found preferentially in the epidermal and vascular tissues of root and increased by salt stress, supporting its essential role in the LR formation under salt stress. Further candidate gene association analysis showed that DNA polymorphisms in the promoter region differentiate the expression of ZmSULTR3;4 among maize inbred lines that may contribute to the natural variation of LRL under salt stress. Nucleotide diversity and neutrality tests revealed that ZmSULTR3;4 has undergone selection during maize domestication and improvement. Overall, our results revealed a regulatory role of ZmSULTR3;4 in salt regulated LR growth and uncovered favorable alleles of ZmSULTR3;4, providing an important selection target for breeding salt-tolerant maize cultivar.

Emerging roles of protein phosphorylation in plant iron homeostasis

Remarkable progress has been made in dissecting the molecular mechanisms involved in iron (Fe) homeostasis in plants, especially the identification of key transporter and transcriptional regulatory networks. But how the protein activity of these master players is regulated by Fe status remains underexplored. Recent studies show that major players toggle switch their properties by protein phosphorylation under different Fe conditions and consequently control the signaling cascade and metabolic adjustment. Moreover, Fe deficiency causes changes of multiple kinases and phosphatases. Here, we discuss how these findings highlight the emergence of the protein phosphorylation-dependent regulation for rapid and precise responses to Fe status to attain Fe homeostasis. Further studies will be needed to fully understand the regulation of these intricate networks.

Salt stress proteins in plants: An overview

Salinity stress is considered the most devastating abiotic stress for crop productivity. Accumulating different types of soluble proteins has evolved as a vital strategy that plays a central regulatory role in the growth and development of plants subjected to salt stress. In the last two decades, efforts have been undertaken to critically examine the genome structure and functions of the transcriptome in plants subjected to salinity stress. Although genomics and transcriptomics studies indicate physiological and biochemical alterations in plants, it do not reflect changes in the amount and type of proteins corresponding to gene expression at the transcriptome level. In addition, proteins are a more reliable determinant of salt tolerance than simple gene expression as they play major roles in shaping physiological traits in salt-tolerant phenotypes. However, little information is available on salt stress-responsive proteins and their possible modes of action in conferring salinity stress tolerance. In addition, a complete proteome profile under normal or stress conditions has not been established yet for any model plant species. Similarly, a complete set of low abundant and key stress regulatory proteins in plants has not been identified. Furthermore, insufficient information on post-translational modifications in salt stress regulatory proteins is available. Therefore, in recent past, studies focused on exploring changes in protein expression under salt stress, which will complement genomic, transcriptomic, and physiological studies in understanding mechanism of salt tolerance in plants. This review focused on recent studies on proteome profiling in plants subjected to salinity stress, and provide synthesis of updated literature about how salinity regulates various salt stress proteins involved in the plant salt tolerance mechanism. This review also highlights the recent reports on regulation of salt stress proteins using transgenic approaches with enhanced salt stress tolerance in crops.

Progress in understanding salt stress response in plants using biotechnological tools

Salinization is a worldwide environmental problem, which is negatively impacting crop yield and thus posing a threat to the world's food security. Considering the rising threat of salinity, it is need of time, to understand the salt tolerant mechanism in plants and find avenues for the development of salinity resistant plants. Several plants tolerate salinity in a different manner, thereby halophytes and glycophytes evolved altered mechanisms to counter the stress. Therefore, in this review article, physiological, metabolic, and molecular aspects of the plant adaptation to salt stress have been discussed. The conventional breeding techniques for developing salt tolerant plants has not been much successful, due to its multigenic trait. The inflow of data from plant sequencing projects and annotation of genes led to the identification of many putative genes having a role in salt stress. The bioinformatics tools provided preliminary information and were helpful for making salt stress-specific databases. The microRNA identification and characterization led to unraveling the finer intricacies of the network. The transgenic approach finally paved a way for overexpressing some important genes viz. DREB, MYB, COMT, SOS, PKE, NHX, etc. conferred salt stress tolerance. In this review, we tried to show the effect of salinity on plants, considering ion homeostasis, antioxidant defense response, proteins involved, possible utilization of transgenic plants, and bioinformatics for coping with this stress factor. An overview of previous studies related to salt stress is presented in order to assist researchers in providing a potential solution for this increasing environmental threat.

Functions and structure of roots and their contributions to salinity tolerance in plants

Soil salinity is an increasing threat to the productivity of glycophytic crops worldwide. The root plays vital roles under various stress conditions, including salinity, as well as has diverse functions in non-stress soil environments. In this review, we focus on the essential functions of roots such as in ion homeostasis mediated by several different membrane transporters and signaling molecules under salinity stress and describe recent advances in the impacts of quantitative trait loci (QTLs) or genetic loci (and their causal genes, if applicable) on salinity tolerance. Furthermore, we introduce important literature for the development of barriers against the apoplastic flow of ions, including Na⁺, as well as for understanding the functions and components of the barrier structure under salinity stress.

Physiological and molecular responses for long term salinity stress in common fig (Ficus carica L.)

Salinity stress in increasingly becoming a major challenge in current and expanding agricultural ecosystems. Unlike temporal abiotic stresses, plants are usually exposed to salinity stress for an entire lifespan. Therefore, a long term effect (10 weeks) of continuous salinity exposure was investigated for three common fig landraces (Zraki, Mwazi, and Khdari). Both relative water content and chlorophyll content decreased with elevated salinity stress, while stem length barely changed. The most prominent decline was observed in root biomass. The data would align common fig to moderately tolerant threshold slop with a C₅₀ range of 100 to 150 mM NaCl. A high and significant correlation was evident between root biomass and chlorophyll content (85%). Concurrently, differential expression of putative salinity responsive genes in common fig were determined; signal peptide peptidase-like 2B (FcSPPL2B), dehydration responsive element binding protein (FcDREB), calcineurin B-like protein (CBL)-CBL-interacting serine/threonine-protein kinase 11 (FcCIPK11), sorbitol dehydrogenase (FcSORD) and dehydrin (FcDHN). The data were discussed for each gene in respect of its potential role in salinity stress mitigation. The combined physiological and molecular data would conclude Zraki as the most salinity tolerant genotype. The major implication of the data emphasizes the tremendous genotype by environment (salinity stress) interaction in common fig.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at (10.1007/s12298-020-00921-z).

A CBL-interacting protein kinase AdCIPK5 confers salt and osmotic stress tolerance in transgenic tobacco

CBL interacting protein kinases play important roles in adaptation to stress conditions. In the present study, we isolated a CBL-interacting protein kinase homolog (AdCIPK5) from a wild peanut (Arachis diogoi) with similarity to AtCIPK5 of Arabidopsis. Expression analyses in leaves of the wild peanut showed AdCIPK5 induction by exogenous signaling molecules including salicylic acid, abscisic acid and ethylene or abiotic stress factors like salt, PEG and sorbitol. The recombinant AdCIPK5-GFP protein was found to be localized to the nucleus, plasma membrane and cytoplasm. We overexpressed AdCIPK5 in tobacco plants and checked their level of tolerance to biotic and abiotic stresses. While wild type and transgenic plants displayed no significant differences to the treatment with the phytopathogen, Phytophthora parasitica pv nicotianae, the expression of AdCIPK5 increased salt and osmotic tolerance in transgenic plants. Analysis of different physiological parameters revealed that the transgenic plants maintained higher chlorophyll content and catalase activity with lower levels of H2O2 and MDA content during the abiotic stress conditions. AdCIPK5 overexpression also contributed to the maintenance of a higher the K+/Na+ ratio under salt stress. The enhanced tolerance of transgenic plants was associated with elevated expression of stress-related marker genes; NtERD10C, NtERD10D, NtNCED1, NtSus1, NtCAT and NtSOS1. Taken together, these results indicate that AdCIPK5 is a positive regulator of salt and osmotic stress tolerance.

Basic-leucine zipper 17 and Hmg-CoA reductase degradation 3A are involved in salt acclimation memory in Arabidopsis

Salt acclimation, which is induced by previous salt exposure, increases the resistance of plants to future exposure to salt stress. However, little is known about the underlying mechanism, particularly how plants store the "memory" of salt exposure. In this study, we established a system to study salt acclimation in Arabidopsis thaliana. Following treatment with a low concentration of salt, seedlings were allowed to recover to allow transitory salt responses to subside while maintaining the sustainable effects of salt acclimation. We performed transcriptome profiling analysis of these seedlings to identify genes related to salt acclimation memory. Notably, the expression of Basic-leucine zipper 17 (bZIP17) and Hmg-CoA reductase degradation 3A (HRD3A), which are important in the unfolded protein response (UPR) and endoplasmic reticulum-associated degradation (ERAD), respectively, increased following treatment with a low concentration of salt and remained at stably high levels after the stimulus was removed, a treatment which improved plant tolerance to future high-salinity challenge. Our findings suggest that the upregulated expression of important genes involved in the UPR and ERAD represents a "memory" of the history of salt exposure and enables more potent responses to future exposure to salt stress, providing new insights into the mechanisms underlying salt acclimation in plants.

The Complex Fine-Tuning of K⁺ Fluxes in Plants in Relation to Osmotic and Ionic Abiotic Stresses

As the main cation in plant cells, potassium plays an essential role in adaptive responses, especially through its involvement in osmotic pressure and membrane potential adjustments. K⁺ homeostasis must, therefore, be finely controlled. As a result of different abiotic stresses, especially those resulting from global warming, K⁺ fluxes and plant distribution of this ion are disturbed. The hormone abscisic acid (ABA) is a key player in responses to these climate stresses. It triggers signaling cascades that ultimately lead to modulation of the activities of K⁺ channels and transporters. After a brief overview of transcriptional changes induced by abiotic stresses, this review deals with the post-translational molecular mechanisms in different plant organs, in Arabidopsis and species of agronomical interest, triggering changes in K⁺ uptake from the soil, K⁺ transport and accumulation throughout the plant, and stomatal regulation. These modifications involve phosphorylation/dephosphorylation mechanisms, modifications of targeting, and interactions with regulatory partner proteins. Interestingly, many signaling pathways are common to K⁺ and Cl^-/NO3^- counter-ion transport systems. These cross-talks are also addressed.

Expressing Arabidopsis thaliana V-ATPase subunit C in barley (Hordeum vulgare) improves plant performance under saline condition by enabling better osmotic adjustment

Salinity is a global problem affecting agriculture that results in an estimated US$27 billion loss in revenue per year. Overexpression of vacuolar ATPase subunits has been shown to be beneficial in improving plant performance under saline conditions. Most studies, however, have not shown whether overexpression of genes encoding ATPase subunits results in improvements in grain yield, and have not investigated the physiological mechanisms behind the improvement in plant growth. In this study, we constitutively expressed Arabidopsis Vacuolar ATPase subunit C (AtVHA-C) in barley. Transgenic plants were assessed for agronomical and physiological characteristics, such as fresh and dry biomass, leaf pigment content, stomatal conductance, grain yield, and leaf Na+ and K+ concentration, when grown in either 0 or 300mM NaCl. When compared with non-transformed barley, AtVHA-C expressing barley lines had a smaller reduction in both biomass and grain yield under salinity stress. The transgenic lines accumulated Na+ and K+ in leaves for osmotic adjustment. This in turn saves energy consumed in the synthesis of organic osmolytes that otherwise would be needed for osmotic adjustment.

The endophytic fungus Piriformospora indica enhances Arabidopsis thaliana growth and modulates Na+/K+ homeostasis under salt stress conditions

The mutualistic, endophytic fungus Piriformospora indica has been shown to confer biotic and abiotic stress tolerance to host plants. In this study, we investigated the impact of P. indica on the growth of Arabidopsis plants under normal and salt stress conditions. Our results demonstrate that P. indica colonization increases plant biomass, lateral roots density, and chlorophyll content under both conditions. Colonization with P. indica under salt stress was accompanied by a lower Na⁺/K⁺ ratio and less pronounced accumulation of anthocyanin, compared to control plants. Moreover, P. indica colonized roots under salt stress showed enhanced transcript levels of the genes encoding the high Affinity Potassium Transporter 1 (HKT1) and the inward-rectifying K⁺ channels KAT1 and KAT2, which play key roles in regulating Na⁺ and K⁺ homeostasis. The effect of P. indica colonization on AtHKT1;1 expression was also confirmed in the Arabidopsis line gl1-HKT:AtHKT1;1 that expresses an additional AtHKT1;1 copy driven by the native promoter. Colonization of the gl1-HKT:AtHKT1;1 by P. indica also increased lateral roots density and led to a better Na⁺/K⁺ ratio, which may be attributed to the observed increase in KAT1 and KAT2 transcript levels. Our findings demonstrate that P. indica colonization promotes Arabidopsis growth under salt stress conditions and that this effect is likely caused by modulation of the expression levels of the major Na⁺ and K⁺ ion channels, which allows establishing a balanced ion homeostasis of Na⁺/K⁺ under salt stress conditions.

Translating knowledge about abiotic stress tolerance to breeding programmes

Plant breeding and improvements in agronomic practice are making a consistent contribution to increasing global crop production year upon year. However, the rate of yield improvement currently lags behind the targets set to produce enough food to meet the demands of the predicted global population in 2050. Furthermore, crops that are exposed to harmful abiotic environmental factors (abiotic stresses, e.g. water limitation, salinity, extreme temperature) are prone to reduced yields. Here, we briefly describe the processes undertaken in conventional breeding programmes, which are usually designed to improve yields in near-optimal conditions rather than specifically breeding for improved crop yield stability under stressed conditions. While there is extensive fundamental research activity that examines mechanisms of plant stress tolerance, there are few examples that apply this research to improving commercial crop yields. There are notable exceptions, and we highlight some of these to demonstrate the magnitude of yield gains that could be made by translating agronomic, phenological and genetic solutions focused on improving or mitigating the effect of abiotic stress in the field; in particular, we focus on improvements in crop water-use efficiency and salinity tolerance. We speculate upon the reasons for the disconnect between research and research translation. We conclude that to realise untapped rapid gains towards food security targets new funding structures need to be embraced. Such funding needs to serve both the core and collaborative activities of the fundamental, pre-breeding and breeding research communities in order to expedite the translation of innovative research into the fields of primary producers.

Genomics, Physiology, and Molecular Breeding Approaches for Improving Salt Tolerance

Salt stress reduces land and water productivity and contributes to poverty and food insecurity. Increased salinization caused by human practices and climate change is progressively reducing agriculture productivity despite escalating calls for more food. Plant responses to salt stress are well understood, involving numerous critical processes that are each controlled by multiple genes. Knowledge of the critical mechanisms controlling salt uptake and exclusion from functioning tissues, signaling of salt stress, and the arsenal of protective metabolites is advancing. However, little progress has been made in developing salt-tolerant varieties of crop species using standard (but slow) breeding approaches. The genetic diversity available within cultivated crops and their wild relatives provides rich sources for trait and gene discovery that has yet to be sufficiently utilized. Transforming this knowledge into modern approaches using genomics and molecular tools for precision breeding will accelerate the development of tolerant cultivars and help sustain food production.

Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses

Chenopodium quinoa (quinoa) is an emerging crop that produces nutritious grains with the potential to contribute to global food security. Quinoa can also grow on marginal lands, such as soils affected by high salinity. To identify candidate salt tolerance genes in the recently sequenced quinoa genome, we used a multifaceted approach integrating RNAseq analyses with comparative genomics and topology prediction. We identified 219 candidate genes by selecting those that were differentially expressed in response to salinity, were specific to or overrepresented in quinoa relative to other Amaranthaceae species, and had more than one predicted transmembrane domain. To determine whether these genes might underlie variation in salinity tolerance in quinoa and its close relatives, we compared the response to salinity stress in a panel of 21 Chenopodium accessions (14 C. quinoa, 5 C. berlandieri, and 2 C. hircinum). We found large variation in salinity tolerance, with one C. hircinum displaying the highest salinity tolerance. Using genome re-sequencing data from these accessions, we investigated single nucleotide polymorphisms and copy number variation (CNV) in the 219 candidate genes in accessions of contrasting salinity tolerance, and identified 15 genes that could contribute to the differences in salinity tolerance of these Chenopodium accessions.

Using Phenomic Analysis of Photosynthetic Function for Abiotic Stress Response Gene Discovery

Monitoring the photosynthetic performance of plants is a major key to understanding how plants adapt to their growth conditions. Stress tolerance traits have a high genetic complexity as plants are constantly, and unavoidably, exposed to numerous stress factors, which limits their growth rates in the natural environment. Arabidopsis thaliana, with its broad genetic diversity and wide climatic range, has been shown to successfully adapt to stressful conditions to ensure the completion of its life cycle. As a result, A. thaliana has become a robust and renowned plant model system for studying natural variation and conducting gene discovery studies. Genome wide association studies (GWAS) in restructured populations combining natural and recombinant lines is a particularly effective way to identify the genetic basis of complex traits. As most abiotic stresses affect photosynthetic activity, chlorophyll fluorescence measurements are a potential phenotyping technique for monitoring plant performance under stress conditions. This review focuses on the use of chlorophyll fluorescence as a tool to study genetic variation underlying the stress tolerance responses to abiotic stress in A. thaliana.

Natural variation in rosette size under salt stress conditions corresponds to developmental differences between Arabidopsis accessions and allelic variation in the LRR-KISS gene

Natural variation among Arabidopsis accessions is an important genetic resource to identify mechanisms underlying plant development and stress tolerance. To evaluate the natural variation in salinity stress tolerance, two large-scale experiments were performed on two populations consisting of 160 Arabidopsis accessions each. Multiple traits, including projected rosette area, and fresh and dry weight were collected as an estimate for salinity tolerance. Our results reveal a correlation between rosette size under salt stress conditions and developmental differences between the accessions grown in control conditions, suggesting that in general larger plants were more salt tolerant. This correlation was less pronounced when plants were grown under severe salt stress conditions. Subsequent genome wide association study (GWAS) revealed associations with novel candidate genes for salinity tolerance such as LRR-KISS (At4g08850),flowering locus KH-domain containing protein and a DUF1639-containing protein Accessions with high LRR-KISS expression developed larger rosettes under salt stress conditions. Further characterization of allelic variation in candidate genes identified in this study will provide more insight into mechanisms of salt stress tolerance due to enhanced shoot growth.

Transcriptome Profiling of Beach Morning Glory (Ipomoea imperati) under Salinity and Its Comparative Analysis with Sweetpotato

The response and adaption to salt remains poorly understood for beach morning glory [Ipomoea imperati (Vahl) Griseb], one of a few relatives of sweetpotato, known to thrive under salty and extreme drought conditions. In order to understand the genetic mechanisms underlying salt tolerance of a Convolvulaceae member, a genome-wide transcriptome study was carried out in beach morning glory by 454 pyrosequencing. A total of 286,584 filtered reads from both salt stressed and unstressed (control) root and shoot tissues were assembled into 95,790 unigenes with an average length of 667 base pairs (bp) and N50 of 706 bp. Putative differentially expressed genes (DEGs) were identified as transcripts overrepresented under salt stressed tissues compared to the control, and were placed into metabolic pathways. Most of these DEGs were involved in stress response, membrane transport, signal transduction, transcription activity and other cellular and molecular processes. We further analyzed the gene expression of 14 candidate genes of interest for salt tolerance through quantitative reverse transcription PCR (qRT-PCR) and confirmed their differential expression under salt stress in both beach morning glory and sweetpotato. The results comparing transcripts of I. imperati against the transcriptome of other Ipomoea species, including sweetpotato are also presented in this study. In addition, 6,233 SSR markers were identified, and an in silico analysis predicted that 434 primer pairs out of 4,897 target an identifiable homologous sequence in other Ipomoea transcriptomes, including sweetpotato. The data generated in this study will help in understanding the basics of salt tolerance of beach morning glory and the SSR resources generated will be useful for comparative genomics studies and further enhance the path to the marker-assisted breeding of sweetpotato for salt tolerance.

Root System Architecture and Abiotic Stress Tolerance: Current Knowledge in Root and Tuber Crops

The challenge to produce more food for a rising global population on diminishing agricultural land is complicated by the effects of climate change on agricultural productivity. Although great progress has been made in crop improvement, so far most efforts have targeted above-ground traits. Roots are essential for plant adaptation and productivity, but are less studied due to the difficulty of observing them during the plant life cycle. Root system architecture (RSA), made up of structural features like root length, spread, number, and length of lateral roots, among others, exhibits great plasticity in response to environmental changes, and could be critical to developing crops with more efficient roots. Much of the research on root traits has thus far focused on the most common cereal crops and model plants. As cereal yields have reached their yield potential in some regions, understanding their root system may help overcome these plateaus. However, root and tuber crops (RTCs) such as potato, sweetpotato, cassava, and yam may hold more potential for providing food security in the future, and knowledge of their root system additionally focuses directly on the edible portion. Root-trait modeling for multiple stress scenarios, together with high-throughput phenotyping and genotyping techniques, robust databases, and data analytical pipelines, may provide a valuable base for a truly inclusive 'green revolution.' In the current review, we discuss RSA with special reference to RTCs, and how knowledge on genetics of RSA can be manipulated to improve their tolerance to abiotic stresses.

AtNPF2.5 Modulates Chloride (Cl-) Efflux from Roots of Arabidopsis thaliana

The accumulation of high concentrations of chloride (Cl^-) in leaves can adversely affect plant growth. When comparing different varieties of the same Cl^- sensitive plant species those that exclude relatively more Cl^- from their shoots tend to perform better under saline conditions; however, the molecular mechanisms involved in maintaining low shoot Cl^- remain largely undefined. Recently, it was shown that the NRT1/PTR Family 2.4 protein (NPF2.4) loads Cl^- into the root xylem, which affects the accumulation of Cl^- in Arabidopsis shoots. Here we characterize NPF2.5, which is the closest homolog to NPF2.4 sharing 83.2% identity at the amino acid level. NPF2.5 is predominantly expressed in root cortical cells and its transcription is induced by salt. Functional characterisation of NPF2.5 via its heterologous expression in yeast (Saccharomyces cerevisiae) and Xenopus laevis oocytes indicated that NPF2.5 is likely to encode a Cl^- permeable transporter. Arabidopsis npf2.5 T-DNA knockout mutant plants exhibited a significantly lower Cl^- efflux from roots, and a greater Cl^- accumulation in shoots compared to salt-treated Col-0 wild-type plants. At the same time, [Formula: see text] content in the shoot remained unaffected. Accumulation of Cl^- in the shoot increased following (1) amiRNA-induced knockdown of NPF2.5 transcript abundance in the root, and (2) constitutive over-expression of NPF2.5. We suggest that both these findings are consistent with a role for NPF2.5 in modulating Cl^- transport. Based on these results, we propose that NPF2.5 functions as a pathway for Cl^- efflux from the root, contributing to exclusion of Cl^- from the shoot of Arabidopsis.

Target Enrichment Improves Mapping of Complex Traits by Deep Sequencing

Complex traits such as crop performance and human diseases are controlled by multiple genetic loci, many of which have small effects and often go undetected by traditional quantitative trait locus (QTL) mapping. Recently, bulked segregant analysis with large F2 pools and genome-level markers (named extreme-QTL or X-QTL mapping) has been used to identify many QTL. To estimate parameters impacting QTL detection for X-QTL mapping, we simulated the effects of population size, marker density, and sequencing depth of markers on QTL detectability for traits with differing heritabilities. These simulations indicate that a high (>90%) chance of detecting QTL with at least 5% effect requires 5000× sequencing depth for a trait with heritability of 0.4-0.7. For most eukaryotic organisms, whole-genome sequencing at this depth is not economically feasible. Therefore, we tested and confirmed the feasibility of applying deep sequencing of target-enriched markers for X-QTL mapping. We used two traits in Arabidopsis thaliana with different heritabilities: seed size (H(2) = 0.61) and seedling greening in response to salt (H(2) = 0.94). We used a modified G test to identify QTL regions and developed a model-based statistical framework to resolve individual peaks by incorporating recombination rates. Multiple QTL were identified for both traits, including previously undiscovered QTL. We call our method target-enriched X-QTL (TEX-QTL) mapping; this mapping approach is not limited by the genome size or the availability of recombinant inbred populations and should be applicable to many organisms and traits.

Salinity tolerance of crops - what is the cost?

Soil salinity reduces crop yield. The extent and severity of salt-affected agricultural land is predicted to worsen as a result of inadequate drainage of irrigated land, rising water tables and global warming. The growth and yield of most plant species are adversely affected by soil salinity, but varied adaptations can allow some crop cultivars to continue to grow and produce a harvestable yield under moderate soil salinity. Significant costs are associated with saline soils: the economic costs to the farming community and the energy costs of plant adaptations. We briefly consider mechanisms of adaptation and highlight recent research examples through a lens of their applicability to improving the energy efficiency of crops under saline field conditions.

Genome-wide gene phylogeny of CIPK family in cassava and expression analysis of partial drought-induced genes

Cassava is an important food and potential biofuel crop that is tolerant to multiple abiotic stressors. The mechanisms underlying these tolerances are currently less known. CBL-interacting protein kinases (CIPKs) have been shown to play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to abiotic stress. However, no data is currently available about the CPK family in cassava. In this study, a total of 25 CIPK genes were identified from cassava genome based on our previous genome sequencing data. Phylogenetic analysis suggested that 25 MeCIPKs could be classified into four subfamilies, which was supported by exon-intron organizations and the architectures of conserved protein motifs. Transcriptomic analysis of a wild subspecies and two cultivated varieties showed that most MeCIPKs had different expression patterns between wild subspecies and cultivatars in different tissues or in response to drought stress. Some orthologous genes involved in CIPK interaction networks were identified between Arabidopsis and cassava. The interaction networks and co-expression patterns of these orthologous genes revealed that the crucial pathways controlled by CIPK networks may be involved in the differential response to drought stress in different accessions of cassava. Nine MeCIPK genes were selected to investigate their transcriptional response to various stimuli and the results showed the comprehensive response of the tested MeCIPK genes to osmotic, salt, cold, oxidative stressors, and ABA signaling. The identification and expression analysis of CIPK family suggested that CIPK genes are important components of development and multiple signal transduction pathways in cassava. The findings of this study will help lay a foundation for the functional characterization of the CIPK gene family and provide an improved understanding of abiotic stress responses and signaling transduction in cassava.

Capturing Arabidopsis root architecture dynamics with ROOT-FIT reveals diversity in responses to salinity

The plant root is the first organ to encounter salinity stress, but the effect of salinity on root system architecture (RSA) remains elusive. Both the reduction in main root (MR) elongation and the redistribution of the root mass between MRs and lateral roots (LRs) are likely to play crucial roles in water extraction efficiency and ion exclusion. To establish which RSA parameters are responsive to salt stress, we performed a detailed time course experiment in which Arabidopsis (Arabidopsis thaliana) seedlings were grown on agar plates under different salt stress conditions. We captured RSA dynamics with quadratic growth functions (root-fit) and summarized the salt-induced differences in RSA dynamics in three growth parameters: MR elongation, average LR elongation, and increase in number of LRs. In the ecotype Columbia-0 accession of Arabidopsis, salt stress affected MR elongation more severely than LR elongation and an increase in LRs, leading to a significantly altered RSA. By quantifying RSA dynamics of 31 different Arabidopsis accessions in control and mild salt stress conditions, different strategies for regulation of MR and LR meristems and root branching were revealed. Different RSA strategies partially correlated with natural variation in abscisic acid sensitivity and different Na(+)/K(+) ratios in shoots of seedlings grown under mild salt stress. Applying root-fit to describe the dynamics of RSA allowed us to uncover the natural diversity in root morphology and cluster it into four response types that otherwise would have been overlooked.

Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis

cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.

Evaluating contribution of ionic, osmotic and oxidative stress components towards salinity tolerance in barley

BACKGROUND

Salinity tolerance is a physiologically multi-faceted trait attributed to multiple mechanisms. Three barley (Hordeum vulgare) varieties contrasting in their salinity tolerance were used to assess the relative contribution of ionic, osmotic and oxidative stress components towards overall salinity stress tolerance in this species, both at the whole-plant and cellular levels. In addition, transcriptional changes in the gene expression profile were studied for key genes mediating plant ionic and oxidative homeostasis (NHX; RBOH; SOD; AHA and GORK), to compare a contribution of transcriptional and post-translational factors towards the specific components of salinity tolerance.

RESULTS

Our major findings are two-fold. First, plant tissue tolerance was a dominating component that has determined the overall plant responses to salinity, with root K(+) retention ability and reduced sensitivity to stress-induced hydroxyl radical production being the main contributing tolerance mechanisms. Second, it was not possible to infer which cultivars were salinity tolerant based solely on expression profiling of candidate genes at one specific time point. For the genes studied and the time point selected that transcriptional changes in the expression of these specific genes had a small role for barley's adaptive responses to salinity.

CONCLUSIONS

For better tissue tolerance, sodium sequestration, K(+) retention and resistance to oxidative stress all appeared to be crucial. Because these traits are highly interrelated, it is suggested that a major progress in crop breeding for salinity tolerance can be achieved only if these complementary traits are targeted at the same time. This study also highlights the essentiality of post translational modifications in plant adaptive responses to salinity.

Calcium and reactive oxygen species rule the waves of signaling

Calcium signaling and reactive oxygen species signaling are directly connected, and both contribute to cell-to-cell signal propagation in plants.

Transgenic barley: a prospective tool for biotechnology and agriculture

Barley (Hordeum vulgare L.) is one of the founder crops of agriculture, and today it is the fourth most important cereal grain worldwide. Barley is used as malt in brewing and distilling industry, as an additive for animal feed, and as a component of various food and bread for human consumption. Progress in stable genetic transformation of barley ensures a potential for improvement of its agronomic performance or use of barley in various biotechnological and industrial applications. Recently, barley grain has been successfully used in molecular farming as a promising bioreactor adapted for production of human therapeutic proteins or animal vaccines. In addition to development of reliable transformation technologies, an extensive amount of various barley genetic resources and tools such as sequence data, microarrays, genetic maps, and databases has been generated. Current status on barley transformation technologies including gene transfer techniques, targets, and progeny stabilization, recent trials for improvement of agricultural traits and performance of barley, especially in relation to increased biotic and abiotic stress tolerance, and potential use of barley grain as a protein production platform have been reviewed in this study. Overall, barley represents a promising tool for both agricultural and biotechnological transgenic approaches, and is considered an ancient but rediscovered crop as a model industrial platform for molecular farming.