Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoa Willd.) in response to photoperiod and plant development

Understanding the regulation of flowering time is crucial for adaptation of crops to new environment. In this study, we examined the timing of floral transition and analysed transcriptomes in leaf and shoot apical meristems of photoperiod-sensitive and -insensitive quinoa accessions. Histological analysis showed that floral transition in quinoa initiates 2-3 weeks after sowing. We found four groups of differentially expressed genes in quinoa genome that responded to plant development and floral transition: (i) 222 genes responsive to photoperiod in leaves, (ii) 1812 genes differentially expressed between accessions under long-day conditions in leaves, (iii) 57 genes responding to developmental changes under short-day conditions in leaves and (iv) 911 genes responding to floral transition within the shoot apical meristem. Interestingly, among numerous candidate genes, two putative FT orthologs together with other genes (e.g. SOC1, COL, AP1) were previously reported as key regulators of flowering time in other species. Additionally, we used coexpression networks to associate novel transcripts to a putative biological process based on the annotated genes within the same coexpression cluster. The candidate genes in this study would benefit quinoa breeding by identifying and integrating their beneficial haplotypes in crossing programs to develop adapted cultivars to diverse environmental conditions.

A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes

Quinoa (Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for four accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we use in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean accession PI 614886 (QQ74). The final assembly spans 1.326 Gb, of which 90.5% is assembled into 18 chromosome-scale scaffolds. The genome is annotated with 54,499 protein-coding genes, 96.9% of which are located on the 18 largest scaffolds. We also report an updated genome assembly for the B-genome diploid C. suecicum and use it, together with the A-genome diploid C. pallidicaule, to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.2%, 48.6%, and 57.9% of the quinoa, C. pallidicaule, and C. suecicum genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.

Salt-Tolerant Crops: Time to Deliver

Despite the numerous advances made in our understanding of the physiology and molecular genetics of salinity tolerance, there have been relatively few applications of these to improve the salt tolerance of crops. The most significant advances have historically utilized intraspecific variation, introgression of traits from close crop wild relatives, or, less frequently, introgression from more distant relatives. Advanced lines often fail due to difficulties in the introgression or tracking of traits or due to yield penalties associated with the alleles in nonsaline environments. However, the greatest limitation is that salinity is not a primary trait for breeders. We must close the gap between research and delivery, especially for farmers who have precious few alternatives. These efforts should include a reassessment of old techniques such as grafting current crops with salt-tolerant hybrid rootstocks. Alternatively, future crops can be produced via domestication of salt-tolerant wild species-an approach that is now feasible in our lifetime.

PlantACT! - how to tackle the climate crisis

Greenhouse gas (GHG) emissions have created a global climate crisis which requires immediate interventions to mitigate the negative effects on all aspects of life on this planet. As current agriculture and land use contributes up to 25% of total GHG emissions, plant scientists take center stage in finding possible solutions for a transition to sustainable agriculture and land use. In this article, the PlantACT! (Plants for climate ACTion!) initiative of plant scientists lays out a road map of how and in which areas plant scientists can contribute to finding immediate, mid-term, and long-term solutions, and what changes are necessary to implement these solutions at the personal, institutional, and funding levels.

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.

A comprehensive characterization of agronomic and end-use quality phenotypes across a quinoa world core collection

Quinoa (Chenopodium quinoa Willd.), a pseudocereal with high protein quality originating from the Andean region of South America, has broad genetic variation and adaptability to diverse agroecological conditions, contributing to the potential to serve as a global keystone protein crop in a changing climate. However, the germplasm resources currently available to facilitate quinoa expansion worldwide are restricted to a small portion of quinoa's total genetic diversity, in part because of day-length sensitivity and issues related to seed sovereignty. This study aimed to characterize phenotypic relationships and variation within a quinoa world core collection. The 360 accessions were planted in a randomized complete block design with four replicates in each of two greenhouses in Pullman, WA during the summer of 2018. Phenological stages, plant height, and inflorescence characteristics were recorded. Seed yield, composition, thousand seed weight, nutritional composition, shape, size, and color were measured using a high-throughput phenotyping pipeline. Considerable variation existed among the germplasm. Crude protein content ranged from 11.24% to 17.81% (fixed at 14% moisture). We found that protein content was negatively correlated with yield and positively correlated with total amino acid content and days to harvest. Mean essential amino acids values met adult daily requirements but not leucine and lysine infant requirements. Yield was positively correlated with thousand seed weight and seed area, and negatively correlated with ash content and days to harvest. The accessions clustered into four groups, with one-group representing useful accessions for long-day breeding programs. The results of this study establish a practical resource for plant breeders to leverage as they strategically develop germplasm in support of the global expansion of quinoa.

Physiological responses induced by phospholipase C isoform 5 upon heat stress in Arabidopsis thaliana

Plant's perception of heat stress involves several pathways and signaling molecules, such as phosphoinositide, which is derived from structural membrane lipids phosphatidylinositol. Phospholipase C (PLC) is a well-known signaling enzyme containing many isoforms in different organisms. In the present study, Phospholipase C Isoform 5 (PLC5) was investigated for its role in thermotolerance in Arabidopsis thaliana. Two over-expressing lines and one knock-down mutant of PLC5 were first treated at a moderate temperature (37 °C) and left for recovery. Then again exposed to a high temperature (45 °C) to check the seedling viability and chlorophyll contents. Root behavior and changes in ³²P_i labeled phospholipids were investigated after their exposure to high temperatures. Over-expression of PLC5 (PLC5 OE) exhibited quick and better phenotypic recovery with bigger and greener leaves followed by chlorophyll contents as compared to wild-type (Col-0) and PLC5 knock-down mutant in which seedling recovery was compromised. PLC5 knock-down mutant illustrated well-developed root architecture under controlled conditions but stunted secondary roots under heat stress as compared to over-expressing PLC5 lines. Around 2.3-fold increase in phosphatidylinositol 4,5-bisphosphate level was observed in PLC5 OE lines upon heat stress compared to wild-type and PLC5 knock-down mutant lines. A significant increase in phosphatidylglycerol was also observed in PLC5 OE lines as compared to Col-0 and PLC5 knock-down mutant lines. The results of the present study demonstrated that PLC5 over-expression contributes to heat stress tolerance while maintaining its photosynthetic activity and is also observed to be associated with primary and secondary root growth in Arabidopsis thaliana.

Genetic networks underlying salinity tolerance in wheat uncovered with genome-wide analyses and selective sweeps

A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r²) ranged between 0.57 and 0.74. The r² values for flag leaf weight, days to flowering, biomass, and number of spikes per plant were all above 0.70, validating the phenotypic effects of the loci discovered in this study. Furthermore, the germplasm sets were compared to identify selection sweeps associated with salt tolerance loci in SYN-DERs. Six loci associated with salinity tolerance were found to be differentially selected in the SYN-DERs (12.4 Mb on chromosome (chr)1B, 7.1 Mb on chr2A, 11.2 Mb on chr2D, 200 Mb on chr3D, 600 Mb on chr6B, and 700.9 Mb on chr7B). A total of 228 reported markers and genes, including 17 well-characterized genes, were uncovered using GWAS and EigenGWAS. A linkage disequilibrium (LD) block on chr5A, including the Vrn-A1 gene at 575 Mb and its homeologs on chr5D, were strongly associated with multiple yield-related traits and flowering time under salinity stress conditions. The diversity panel was screened with more than 68 kompetitive allele-specific PCR (KASP) markers of functional genes in wheat, and the pleiotropic effects of superior alleles of Rht-1, TaGASR-A1, and TaCwi-A1 were revealed under salinity stress. To effectively utilize the extensive genetic information obtained from the GWAS analysis, a genetic interaction network was constructed to reveal correlations among the investigated traits. The genetic network data combined with GWAS, selective sweeps, and the functional gene survey provided a quantitative genetic framework for identifying differentially retained loci associated with salinity tolerance in wheat.

Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.9 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with F_ST divergence of 0.36 and LD decay of 6.5 and 49.8 Kb, respectively. A genome-wide association study using multi-year phenotyping trials uncovered 600 SNPs stably associated with 17 traits. Two candidate genes are associated with thousand seed weight, and a resistance gene analog is associated with downy mildew resistance. We also identified pleiotropically acting loci for four agronomic traits important for adaptation. This work demonstrates the use of re-sequencing data of an orphan crop, which is partially domesticated to rapidly identify marker-trait association and provides the underpinning elements for genomics-enabled quinoa breeding.

The diversity of quinoa morphological traits and seed metabolic composition

Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.

32Pi Labeled Transgenic Wheat Shows the Accumulation of Phosphatidylinositol 4,5-bisphosphate and Phosphatidic Acid Under Heat and Osmotic Stress

The ensuing heat stress drastically affects wheat plant growth and development, consequently compromising its grain yield. There are many thermoregulatory processes/mechanisms mediated by ion channels, lipids, and lipid-modifying enzymes that occur in the plasma membrane and the chloroplast. With the onset of abiotic or biotic stresses, phosphoinositide-specific phospholipase C (PI-PLC), as a signaling enzyme, hydrolyzes phosphatidylinositol 4,5-bisphosphate (PIP₂) to generate inositol 1,4,5-trisphosphate (IP₃) and diacylglycerol (DAG) which is further phosphorylated into phosphatidic acid (PA) as a secondary messenger and is involved in multiple processes. In the current study, a phospholipase C (PLC) signaling pathway was investigated in spring wheat (Triticum aestivum L.) and evaluated its four AtPLC5 overexpressed (OE)/transgenic lines under heat and osmotic stresses through ³²P_i radioactive labeling. Naturally, the wheat harbors only a small amount of PIP₂. However, with the sudden increase in temperature (40°C), PIP₂ levels start to rise within 7.5 min in a time-dependent manner in wild-type (Wt) wheat. While the Phosphatidic acid (PA) level also elevated up to 1.6-fold upon exposing wild-type wheat to heat stress (40°C). However, at the anthesis stage, a significant increase of ∼4.5-folds in PIP₂ level was observed within 30 min at 40°C in AtPLC5 over-expressed wheat lines. Significant differences in PIP₂ level were observed in Wt and AtPLC5-OE lines when treated with 1200 mM sorbitol solution. It is assumed that the phenomenon might be a result of the activation of PLC/DGK pathways. Together, these results indicate that heat stress and osmotic stress activate several lipid responses in wild-type and transgenic wheat and can explain heat and osmotic stress tolerance in the wheat plant.

Characterization of epidermal bladder cells in Chenopodium quinoa

Chenopodium quinoa (quinoa) is considered a superfood with its favourable nutrient composition and being gluten free. Quinoa has high tolerance to abiotic stresses, such as salinity, water deficit (drought) and cold. The tolerance mechanisms are yet to be elucidated. Quinoa has epidermal bladder cells (EBCs) that densely cover the shoot surface, particularly the younger parts of the plant. Here, we report on the EBC's primary and secondary metabolomes, as well as the lipidome in control conditions and in response to abiotic stresses. EBCs were isolated from plants after cold, heat, high-light, water deficit and salt treatments. We used untargeted gas chromatography-mass spectrometry (GC-MS) to analyse metabolites and untargeted and targeted liquid chromatography-MS (LC-MS) for lipids and secondary metabolite analyses. We identified 64 primary metabolites, including sugars, organic acids and amino acids, 19 secondary metabolites, including phenolic compounds, betanin and saponins and 240 lipids categorized in five groups including glycerolipids and phospholipids. We found only few changes in the metabolic composition of EBCs in response to abiotic stresses; these were metabolites related with heat, cold and high-light treatments but not salt stress. Na⁺ concentrations were low in EBCs with all treatments and approximately two orders of magnitude lower than K⁺ concentrations.

Quinoa Phenotyping Methodologies: An International Consensus

Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.

Haplotype variations of major flowering time genes in quinoa unveil their role in the adaptation to different environmental conditions

Response to photoperiod is of major importance in crop production. It defines the adaptation of plants to local environments. Quinoa is a short-day plant which had been domesticated in the Andeans regions. We wanted to understand the adaptation to long-day conditions by studying orthologues of two major flowering time regulators of Arabidopsis, FLOWERING LOCUS T (FT) and CONSTANS (CO) in quinoa accessions with contrasting photoperiod response. By searching the quinoa reference genome sequence, we identified 24 FT and six CO homologs. CqFT genes displayed remarkably different expression patterns between long- and short-day conditions, whereas the influence of the photoperiod on CqCOL expressions was moderate. Cultivation of 276 quinoa accessions under short- and long-day conditions revealed great differences in photoperiod sensitivity. After sequencing their genomes, we identified large sequence variations in 12 flowering time genes. We found non-random distribution of haplotypes across accessions from different geographical origins, highlighting the role of CqFT and CqCOL genes in the adaptation to different day-length conditions. We identified five haplotypes causing early flowering under long days. This study provides assets for quinoa breeding because superior haplotypes can be assembled in a predictive breeding approach to produce well-adapted early flowering lines under long-day photoperiods.

Genetic mapping of the early responses to salt stress in Arabidopsis thaliana

Salt stress decreases plant growth prior to significant ion accumulation in the shoot. However, the processes underlying this rapid reduction in growth are still unknown. To understand the changes in salt stress responses through time and at multiple physiological levels, examining different plant processes within a single set-up is required. Recent advances in phenotyping has allowed the image-based estimation of plant growth, morphology, colour and photosynthetic activity. In this study, we examined the salt stress-induced responses of 191 Arabidopsis accessions from 1 h to 7 days after treatment using high-throughput phenotyping. Multivariate analyses and machine learning algorithms identified that quantum yield measured in the light-adapted state (F_v' /F_m' ) greatly affected growth maintenance in the early phase of salt stress, whereas the maximum quantum yield (QY_max ) was crucial at a later stage. In addition, our genome-wide association study (GWAS) identified 770 loci that were specific to salt stress, in which two loci associated with QY_max and F_v' /F_m' were selected for validation using T-DNA insertion lines. We characterized an unknown protein kinase found in the QY_max locus that reduced photosynthetic efficiency and growth maintenance under salt stress. Understanding the molecular context of the candidate genes identified will provide valuable insights into the early plant responses to salt stress. Furthermore, our work incorporates high-throughput phenotyping, multivariate analyses and GWAS, uncovering details of temporal stress responses and identifying associations across different traits and time points, which are likely to constitute the genetic components of salinity tolerance.

Early Growth Stage Characterization and the Biochemical Responses for Salinity Stress in Tomato

Salinity is one of the most significant environmental stresses for sustainable crop production in major arable lands of the globe. Thus, we conducted experiments with 27 tomato genotypes to screen for salinity tolerance at seedling stage, which were treated with non-salinized (S1) control (18.2 mM NaCl) and salinized (S2) (200 mM NaCl) irrigation water. In all genotypes, the elevated salinity treatment contributed to a major depression in morphological and physiological characteristics; however, a smaller decrease was found in certain tolerant genotypes. Principal component analyses (PCA) and clustering with percentage reduction in growth parameters and different salt tolerance indices classified the tomato accessions into five key clusters. In particular, the tolerant genotypes were assembled into one cluster. The growth and tolerance indices PCA also showed the order of salt-tolerance of the studied genotypes, where Saniora was the most tolerant genotype and P.Guyu was the most susceptible genotype. To investigate the possible biochemical basis for salt stress tolerance, we further characterized six tomato genotypes with varying levels of salinity tolerance. A higher increase in proline content, and antioxidants activities were observed for the salt-tolerant genotypes in comparison to the susceptible genotypes. Salt-tolerant genotypes identified in this work herald a promising source in the tomato improvement program or for grafting as scions with improved salinity tolerance in tomato.

Digital insights: bridging the phenotype-to-genotype divide

This article comments on:

Han R, Wong AJY, Tang Z, Truco MJ, Lavelle DO, Kozik A, Jin Y, Michelmore R. 2021. Drone phenotyping and machine learning enable discovery of loci regulating daily floral opening in lettuce. Journal of Experimental Botany 72,2979–2994.

The role of PQL genes in response to salinity tolerance in Arabidopsis and barley

While soil salinity is a global problem, how salt enters plant root cells from the soil solution remains underexplored. Non-selective cation channels (NSCCs) are suggested to be the major pathway for the entry of sodium ions (Na+), yet their genetic constituents remain unknown. Yeast PQ loop (PQL) proteins were previously proposed to encode NSCCs, but the role of PQLs in plants is unknown. The hypothesis tested in this research is that PQL proteins constitute NSCCs mediating some of the Na+ influx into the root, contributing to ion accumulation and the inhibition of growth in saline conditions. We identified plant PQL homologues, and studied the role of one clade of PQL genes in Arabidopsis and barley. Using heterologous expression of AtPQL1a and HvPQL1 in HEK293 cells allowed us to resolve sizable inwardly directed currents permeable to monovalent cations such as Na+, K+, or Li+ upon membrane hyperpolarization. We observed that GFP-tagged PQL proteins localized to intracellular membrane structures, both when transiently over-expressed in tobacco leaf epidermis and in stable Arabidopsis transformants. Expression of AtPQL1a, AtPQL1b, and AtPQL1c was increased by salt stress in the shoot tissue compared to non-stressed plants. Mutant lines with altered expression of AtPQL1a, AtPQL1b, and AtPQL1c developed larger rosettes in saline conditions, while altered levels of AtPQL1a severely reduced development of lateral roots in all conditions. This study provides the first step toward understanding the function of PQL proteins in plants and the role of NSCC in salinity tolerance.

Assessing Rice Salinity Tolerance: From Phenomics to Association Mapping

Rice is the most salt-sensitive cereal, suffering yield losses above 50% with soil salinity of 6 dS/m. Thus, understanding the mechanisms of rice salinity tolerance is key to address food security. In this chapter, we provide guidelines to assess rice salinity tolerance using a high-throughput phenotyping platform (HTP) with digital imaging at seedling/early tillering stage and suggest improved analysis methods using stress indices. The protocols described here also include computer scripts for users to improve their experimental design, run genome-wide association studies (GWAS), perform multi-testing corrections, and obtain the Manhattan plots, enabling the identification of loci associated with salinity tolerance. Notably, the computer scripts provided here can be used for any stress or GWAS experiment and independently of HTP.

Dissecting new genetic components of salinity tolerance in two-row spring barley at the vegetative and reproductive stages

Soil salinity imposes an agricultural and economic burden that may be alleviated by identifying the components of salinity tolerance in barley, a major crop and the most salt tolerant cereal. To improve our understanding of these components, we evaluated a diversity panel of 377 two-row spring barley cultivars during both the vegetative, in a controlled environment, and the reproductive stages, in the field. In the controlled environment, a high-throughput phenotyping platform was used to assess the growth-related traits under both control and saline conditions. In the field, the agronomic traits were measured from plots irrigated with either fresh or saline water. Association mapping for the different components of salinity tolerance enabled us to detect previously known associations, such as HvHKT1;5. Using an "interaction model", which took into account the interaction between treatment (control and salt) and genetic markers, we identified several loci associated with yield components related to salinity tolerance. We also observed that the two developmental stages did not share genetic regions associated with the components of salinity tolerance, suggesting that different mechanisms play distinct roles throughout the barley life cycle. Our association analysis revealed that genetically defined regions containing known flowering genes (Vrn-H3, Vrn-H1, and HvNAM-1) were responsive to salt stress. We identified a salt-responsive locus (7H, 128.35 cM) that was associated with grain number per ear, and suggest a gene encoding a vacuolar H+-translocating pyrophosphatase, HVP1, as a candidate. We also found a new QTL on chromosome 3H (139.22 cM), which was significant for ear number per plant, and a locus on chromosome 2H (141.87 cM), previously identified using a nested association mapping population, which associated with a yield component and interacted with salinity stress. Our study is the first to evaluate a barley diversity panel for salinity stress under both controlled and field conditions, allowing us to identify contributions from new components of salinity tolerance which could be used for marker-assisted selection when breeding for marginal and saline regions.

Emerging Technologies to Enable Sustainable Controlled Environment Agriculture in the Extreme Environments of Middle East-North Africa Coastal Regions

Despite global shifts in attitudes toward sustainability and increasing awareness of human impact on the environment, projected population growth and climate change require technological adaptations to ensure food and resource security at a global scale. Although desert areas have long been proposed as ideal sites for solar electricity generation, only recently have efforts shifted toward development of specialized and regionally focused agriculture in these extreme environments. In coastal regions of the Middle East and North Africa (MENA), the most abundant resources are consistent intense sunlight and saline sea water. MENA coastal regions hold incredible untapped potential for agriculture driven by the combination of key emerging technologies in future greenhouse concepts: transparent infrared collecting solar panels and low energy salt water cooling. These technologies can be combined to create greenhouses that drive regionally relevant agriculture in this extreme environment, especially when the target crops are salt-tolerant plants and algal biomass. Future controlled environment agriculture concepts will not compete for municipal fresh water and can be readily integrated into local human/livestock/fisheries food chains. With strategic technological implementation, marginal lands in these environments could participate in production of biomass, sustainable energy generation, and the circular carbon economy. The goal of this perspective is to reframe the idea of these environments as extreme, to having incredible untapped development potential.

Energy costs of salt tolerance in crop plants

Agriculture is expanding into regions that are affected by salinity. This review considers the energetic costs of salinity tolerance in crop plants and provides a framework for a quantitative assessment of costs. Different sources of energy, and modifications of root system architecture that would maximize water vs ion uptake are addressed. Energy requirements for transport of salt (NaCl) to leaf vacuoles for osmotic adjustment could be small if there are no substantial leaks back across plasma membrane and tonoplast in root and leaf. The coupling ratio of the H⁺ -ATPase also is a critical component. One proposed leak, that of Na⁺ influx across the plasma membrane through certain aquaporin channels, might be coupled to water flow, thus conserving energy. For the tonoplast, control of two types of cation channels is required for energy efficiency. Transporters controlling the Na⁺ and Cl^- concentrations in mitochondria and chloroplasts are largely unknown and could be a major energy cost. The complexity of the system will require a sophisticated modelling approach to identify critical transporters, apoplastic barriers and root structures. This modelling approach will inform experimentation and allow a quantitative assessment of the energy costs of NaCl tolerance to guide breeding and engineering of molecular components.

Diverse Traits Contribute to Salinity Tolerance of Wild Tomato Seedlings from the Galapagos Islands

Traits of modern crops have been heavily selected in agriculture, leaving commercial lines often more susceptible to harsh conditions compared with their wild relatives. Understanding the mechanisms of stress tolerance in wild relatives can enhance crop performance under stress conditions such as high salinity. In this study, we investigated salinity tolerance of two species of wild tomato endemic to the Galapagos Islands, Solanum cheesmaniae and Solanum galapagense Since these tomatoes grow well despite being constantly splashed with seawater, they represent a valuable genetic resource for improving salinity tolerance in commercial tomatoes. To explore their potential, we recorded over 20 traits reflecting plant growth, physiology, and ion content in 67 accessions and two commercial tomato lines of Solanum lycopersicum. Salt treatments were applied for 10 d using supported hydroponics. The Galapagos tomatoes displayed greater tolerance to salt stress than the commercial lines and showed substantial natural variation in their responses. The accessions LA0317, LA1449, and LA1403 showed particularly high salinity tolerance based on growth under salinity stress. Therefore, Galapagos tomatoes should be further explored to identify the genes underlying their high tolerance and be used as a resource for increasing the salinity tolerance of commercial tomatoes. The generated data, along with useful analysis tools, have been packaged and made publicly available via an interactive online application (https://mmjulkowska.shinyapps.io/La_isla_de_tomato/) to facilitate trait selection and the use of Galapagos tomatoes for the development of salt-tolerant commercial tomatoes.

Quantile function modeling with application to salinity tolerance analysis of plant data

BACKGROUND

In plant science, the study of salinity tolerance is crucial to improving plant growth and productivity under saline conditions. Since quantile regression is a more robust, comprehensive and flexible method of statistical analysis than the commonly used mean regression methods, we applied a set of quantile analysis methods to barley field data. We use univariate and bivariate quantile analysis methods to study the effect of plant traits on yield and salinity tolerance at different quantiles.

RESULTS

We evaluate the performance of barley accessions under fresh and saline water using quantile regression with covariates such as flowering time, ear number per plant, and grain number per ear. We identify the traits affecting the accessions with high yields, such as late flowering time has a negative impact on yield. Salinity tolerance indices evaluate plant performance under saline conditions relative to control conditions, so we identify the traits affecting the accessions with high values of indices using quantile regression. It was observed that an increase in ear number per plant and grain number per ear in saline conditions increases the salinity tolerance of plants. In the case of grain number per ear, the rate of increase being higher for plants with high yield than plants with average yield. Bivariate quantile analysis methods were used to link the salinity tolerance index with plant traits, and it was observed that the index remains stable for earlier flowering times but declines as the flowering time decreases.

CONCLUSIONS

This analysis has revealed new dimensions of plant responses to salinity that could be relevant to salinity tolerance. Use of univariate quantile analyses for quantifying yield under both conditions facilitates the identification of traits affecting salinity tolerance and is more informative than mean regression. The bivariate quantile analyses allow linking plant traits to salinity tolerance index directly by predicting the joint distribution of yield and it also allows a nonlinear relationship between the yield and plant traits.

MVApp-Multivariate Analysis Application for Streamlined Data Analysis and Curation

Modern phenotyping techniques yield vast amounts of data that are challenging to manage and analyze. When thoroughly examined, this type of data can reveal genotype-to-phenotype relationships and meaningful connections among individual traits. However, efficient data mining is challenging for experimental biologists with limited training in curating, integrating, and exploring complex datasets. Additionally, data transparency, accessibility, and reproducibility are important considerations for scientific publication. The need for a streamlined, user-friendly pipeline for advanced phenotypic data analysis is pressing. In this article we present an open-source, online platform for multivariate analysis (MVApp), which serves as an interactive pipeline for data curation, in-depth analysis, and customized visualization. MVApp builds on the available R-packages and adds extra functionalities to enhance the interpretability of the results. The modular design of the MVApp allows for flexible analysis of various data structures and includes tools underexplored in phenotypic data analysis, such as clustering and quantile regression. MVApp aims to enhance findable, accessible, interoperable, and reproducible data transparency, streamline data curation and analysis, and increase statistical literacy among the scientific community.

Overexpression of the NAC transcription factor JUNGBRUNNEN1 (JUB1) increases salinity tolerance in tomato

Soil salinity is a major abiotic stress affecting plant growth and yield, due to both osmotic and ionic stresses. JUBGBRUNNEN1 (JUB1) is a NAC family transcription factor that has been shown to be involved in responses to abiotic stresses, such as water deficit, osmotic, salinity, heat and oxidative stress. In Arabidopsis thaliana (Arabidopsis), JUB1 has been shown to improve plant stress tolerance by regulating H₂O₂ levels. In the horticultural crop, Solanum lycopersicum cv. Moneymaker (tomato), overexpression of AtJUB1 has been shown to partially alleviate water deficit stress at the vegetative stage. In this study, we investigated the effect of Arabidopsis JUB1 overexpression in salinity tolerance in tomato. In hydroponically grown tomato seedlings, AtJUB1 overexpression results in higher prolines levels and improves the maintenance of water content in the plant under salinity stress. The transgenic tomato plants are more tolerant to salinity stress compared to control lines based on plant biomass. However, at the reproductive stage, we found that overexpression of AtJUB1 only provided marginal improvements in yield-related parameters, in the conditions used for the current work. The combination of improved water deficit and salinity stress tolerance conferred by AtJUB1 overexpression may be beneficial when tomato plants are grown in the field under marginal environments.

Breeding crops to feed 10 billion

Crop improvements can help us to meet the challenge of feeding a population of 10 billion, but can we breed better varieties fast enough? Technologies such as genotyping, marker-assisted selection, high-throughput phenotyping, genome editing, genomic selection and de novo domestication could be galvanized by using speed breeding to enable plant breeders to keep pace with a changing environment and ever-increasing human population.

High-throughput 3D modelling to dissect the genetic control of leaf elongation in barley (Hordeum vulgare)

To optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi-parental barley mapping population under low and high soil salinity. We detected quantitative trait loci (QTL) related to shoot growth per se, using both simple 2D total shoot measurements and our approach of measuring individual leaves. In addition, we detected QTL specific to leaf elongation and not to total shoot size. Of particular importance was the detection of a QTL on chromosome 3H specific to the early responses of leaf elongation to salt stress, a locus that could not be detected without the computer vision tools developed in this study.

Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues

Since the dawn of agriculture, crop yield has always been impaired through abiotic stresses. In a field trial across five locations worldwide, we tested three abiotic stresses, nitrogen deficiency, drought and salinity, using HEB-YIELD, a selected subset of the wild barley nested association mapping population HEB-25. We show that barley flowering time genes Ppd-H1, Sdw1, Vrn-H1 and Vrn-H3 exert pleiotropic effects on plant development and grain yield. Under field conditions, these effects are strongly influenced by environmental cues like day length and temperature. For example, in Al-Karak, Jordan, the day length-sensitive wild barley allele of Ppd-H1 was associated with an increase of grain yield by up to 30% compared to the insensitive elite barley allele. The observed yield increase is accompanied by pleiotropic effects of Ppd-H1 resulting in shorter life cycle, extended grain filling period and increased grain size. Our study indicates that the adequate timing of plant development is crucial to maximize yield formation under harsh environmental conditions. We provide evidence that wild barley alleles, introgressed into elite barley cultivars, can be utilized to support grain yield formation. The presented knowledge may be transferred to related crop species like wheat and rice securing the rising global food demand for cereals.

Mitochondrial and chloroplast genomes provide insights into the evolutionary origins of quinoa (Chenopodium quinoa Willd.)

Quinoa has recently gained international attention because of its nutritious seeds, prompting the expansion of its cultivation into new areas in which it was not originally selected as a crop. Improving quinoa production in these areas will benefit from the introduction of advantageous traits from free-living relatives that are native to these, or similar, environments. As part of an ongoing effort to characterize the primary and secondary germplasm pools for quinoa, we report the complete mitochondrial and chloroplast genome sequences of quinoa accession PI 614886 and the identification of sequence variants in additional accessions from quinoa and related species. This is the first reported mitochondrial genome assembly in the genus Chenopodium. Inference of phylogenetic relationships among Chenopodium species based on mitochondrial and chloroplast variants supports the hypotheses that 1) the A-genome ancestor was the cytoplasmic donor in the original tetraploidization event, and 2) highland and coastal quinoas were independently domesticated.

Salt stress under the scalpel - dissecting the genetics of salt tolerance

Salt stress limits the productivity of crops grown under saline conditions, leading to substantial losses of yield in saline soils and under brackish and saline irrigation. Salt tolerant crops could alleviate these losses while both increasing irrigation opportunities and reducing agricultural demands on dwindling freshwater resources. However, despite significant efforts, progress towards this goal has been limited, largely because of the genetic complexity of salt tolerance for agronomically important yield-related traits. Consequently, the focus is shifting to the study of traits that contribute to overall tolerance, thus breaking down salt tolerance into components that are more genetically tractable. Greater consideration of the plasticity of salt tolerance mechanisms throughout development and across environmental conditions furthers this dissection. The demand for more sophisticated and comprehensive methodologies is being met by parallel advances in high-throughput phenotyping and sequencing technologies that are enabling the multivariate characterisation of vast germplasm resources. Alongside steady improvements in statistical genetics models, forward genetics approaches for elucidating salt tolerance mechanisms are gaining momentum. Subsequent quantitative trait locus and gene validation has also become more accessible, most recently through advanced techniques in molecular biology and genomic analysis, facilitating the translation of findings to the field. Besides fuelling the improvement of established crop species, this progress also facilitates the domestication of naturally salt tolerant orphan crops. Taken together, these advances herald a promising era of discovery for research into the genetics of salt tolerance in plants.

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

'Speed breeding' (SB) shortens the breeding cycle and accelerates crop research through rapid generation advancement. SB can be carried out in numerous ways, one of which involves extending the duration of plants' daily exposure to light, combined with early seed harvest, to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. In this protocol, we present glasshouse and growth chamber-based SB approaches with supporting data from experimentation with several crops. We describe the conditions that promote the rapid growth of bread wheat, durum wheat, barley, oat, various Brassica species, chickpea, pea, grass pea, quinoa and Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale up plant numbers for single-seed descent (SSD). In addition, instructions are provided on how to perform SB on a small scale in a benchtop growth cabinet, enabling optimization of parameters at a low cost.

The Arabidopsis thaliana K+-Uptake Permease 5 (AtKUP5) Contains a Functional Cytosolic Adenylate Cyclase Essential for K+ Transport

Potassium (K⁺) is the most abundant cation in plants, and its uptake and transport are key to growth, development and responses to the environment. Here, we report that Arabidopsis thaliana K⁺ uptake permease 5 (AtKUP5) contains an adenylate cyclase (AC) catalytic center embedded in its N-terminal cytosolic domain. The purified recombinant AC domain generates cAMP in vitro; and when expressed in Escherichia coli, increases cAMP levels in vivo. Both the AC domain and full length AtKUP5 rescue an AC-deficient E. coli mutant, cyaA, and together these data provide evidence that AtKUP5 functions as an AC. Furthermore, full length AtKUP5 complements the Saccharomyces cerevisiae K⁺ transport impaired mutant, trk1 trk2, demonstrating its function as a K⁺ transporter. Surprisingly, a point mutation in the AC center that impairs AC activity, also abolishes complementation of trk1 trk2, suggesting that a functional catalytic AC domain is essential for K⁺ uptake. AtKUP5-mediated K⁺ uptake is not affected by cAMP, the catalytic product of the AC, but, interestingly, causes cytosolic cAMP accumulation. These findings are consistent with a role for AtKUP5 as K⁺ flux sensor, where the flux-dependent cAMP increases modulate downstream components essential for K⁺ homeostasis, such as cyclic nucleotide gated channels.

The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance

Solanum pimpinellifolium, a wild relative of cultivated tomato, offers a wealth of breeding potential for desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome assembly and annotation of S. pimpinellifolium 'LA0480.' Moreover, we present phenotypic data from one field experiment that demonstrate a greater salinity tolerance for fruit- and yield-related traits in S. pimpinellifolium compared with cultivated tomato. The 'LA0480' genome assembly size (811 Mb) and the number of annotated genes (25,970) are within the range observed for other sequenced tomato species. We developed and utilized the Dragon Eukaryotic Analyses Platform (DEAP) to functionally annotate the 'LA0480' protein-coding genes. Additionally, we used DEAP to compare protein function between S. pimpinellifolium and cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses. To understand the genomic basis for these differences in S. pimpinellifolium and S. lycopersicum, we analyzed 15 genes that have previously been shown to mediate salinity tolerance in plants. We show that S. pimpinellifolium has a higher copy number of the inositol-3-phosphate synthase and phosphatase genes, which are both key enzymes in the production of inositol and its derivatives. Moreover, our analysis indicates that changes occurring in the inositol phosphate pathway may contribute to the observed higher salinity tolerance in 'LA0480.' Altogether, our work provides essential resources to understand and unlock the genetic and breeding potential of S. pimpinellifolium, and to discover the genomic basis underlying its environmental robustness.

Mapping of novel salt tolerance QTL in an Excalibur × Kukri doubled haploid wheat population

KEY MESSAGE

Novel QTL for salinity tolerance traits have been detected using non-destructive and destructive phenotyping in bread wheat and were shown to be linked to improvements in yield in saline fields. Soil salinity is a major limitation to cereal production. Breeding new salt-tolerant cultivars has the potential to improve cereal crop yields. In this study, a doubled haploid bread wheat mapping population, derived from the bi-parental cross of Excalibur × Kukri, was grown in a glasshouse under control and salinity treatments and evaluated using high-throughput non-destructive imaging technology. Quantitative trait locus (QTL) analysis of this population detected multiple QTL under salt and control treatments. Of these, six QTL were detected in the salt treatment including one for maintenance of shoot growth under salinity (QG(1-5).asl-7A), one for leaf Na+ exclusion (QNa.asl-7A) and four for leaf K+ accumulation (QK.asl-2B.1, QK.asl-2B.2, QK.asl-5A and QK:Na.asl-6A). The beneficial allele for QG(1-5).asl-7A (the maintenance of shoot growth under salinity) was present in six out of 44 mainly Australian bread and durum wheat cultivars. The effect of each QTL allele on grain yield was tested in a range of salinity concentrations at three field sites across 2 years. In six out of nine field trials with different levels of salinity stress, lines with alleles for Na+ exclusion and/or K+ maintenance at three QTL (QNa.asl-7A, QK.asl-2B.2 and QK:Na.asl-6A) excluded more Na+ or accumulated more K+ compared to lines without these alleles. Importantly, the QK.asl-2B.2 allele for higher K+ accumulation was found to be associated with higher grain yield at all field sites. Several alleles at other QTL were associated with higher grain yields at selected field sites.

A donor-specific QTL, exhibiting allelic variation for leaf sheath hairiness in a nested association mapping population, is located on barley chromosome 4H

Leaf sheath hairiness is a morphological trait associated with various advantages, including tolerance to both abiotic and biotic stresses, thereby increasing yield. Understanding the genetic basis of this trait in barley can therefore improve the agronomic performance of this economically important crop. We scored leaf sheath hairiness in a two-year field trial in 1,420 BC₁S₃ lines from the wild barley nested association mapping (NAM) population HEB-25. Leaf sheath hairiness segregated in six out of 25 families with the reference parent Barke being glabrous. We detected the major hairy leaf sheath locus Hs (syn. Hsh) on chromosome 4H (111.3 cM) with high precision. The effects of the locus varied across the six different wild barley donors, with donor of HEB family 11 conferring the highest score of leaf sheath hairiness. Due to the high mapping resolution present in HEB-25, we were able to discuss physically linked pentatricopeptide repeat genes and subtilisin-like proteases as potential candidate genes underlying this locus. In this study, we proved that HEB-25 provides an appropriate tool to further understand the genetic control of leaf sheath hairiness in barley. Furthermore, our work represents a perfect starting position to clone the gene responsible for the 4H locus observed.

Genetics of Na+ exclusion and salinity tolerance in Afghani durum wheat landraces

BACKGROUND

Selecting for low concentration of Na+ in the shoot provides one approach for tackling salinity stress that adversely affects crop production. Novel alleles for Na+ exclusion can be identified and then introduced into elite crop cultivars.

RESULTS

We have identified loci associated with lower Na+ concentration in leaves of durum wheat landraces originating from Afghanistan. Seedlings of two F2 populations derived from crossings between Australian durum wheat (Jandaroi) and two Afghani landraces (AUS-14740 and AUS-14752) were grown hydroponically and evaluated for Na+ and K+ concentration in the third leaf. High heritability was found for both third leaf Na+ concentration and the K+/Na+ ratio in both populations. Further work focussed on line AUS-14740. Bulk segregant analysis using 9 K SNP markers identified two loci significantly associated with third leaf Na+ concentration. Marker regression analysis showed a strong association between all traits studied and a favourable allele originating from AUS-14740 located on the long arm of chromosome 4B.

CONCLUSIONS

The candidate gene in the relevant region of chromosome 4B is likely to be the high affinity K+ transporter B1 (HKT1;5-B1). A second locus associated with third leaf Na+ concentration was located on chromosome 3BL, with the favourable allele originating from Jandaroi; however, no candidate gene can be identified.

Variation in shoot tolerance mechanisms not related to ion toxicity in barley

Soil salinity can severely reduce crop growth and yield. Many studies have investigated salinity tolerance mechanisms in cereals using phenotypes that are relatively easy to measure. The majority of these studies measured the accumulation of shoot Na+ and the effect this has on plant growth. However, plant growth is reduced immediately after exposure to NaCl before Na+ accumulates to toxic concentrations in the shoot. In this study, nondestructive and destructive measurements are used to evaluate the responses of 24 predominately Australian barley (Hordeum vulgare L.) lines at 0, 150 and 250mM NaCl. Considerable variation for shoot tolerance mechanisms not related to ion toxicity (shoot ion-independent tolerance) was found, with some lines being able to maintain substantial growth rates under salt stress, whereas others stopped growing. Hordeum vulgare spp. spontaneum accessions and barley landraces predominantly had the best shoot ion independent tolerance, although two commercial cultivars, Fathom and Skiff, also had high tolerance. The tolerance of cv. Fathom may be caused by a recent introgression from H. vulgare L. spp. spontaneum. This study shows that the most salt-tolerant barley lines are those that contain both shoot ion-independent tolerance and the ability to exclude Na+ from the shoot (and thus maintain high K+:Na+ ratios).

DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species

Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published literature. We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms. To illustrate the utility of DES-TOMATO, we provide several examples how one can efficiently use this KB to retrieve known or potentially novel information. DES-TOMATO is free for academic and nonprofit users and can be accessed at http://cbrc.kaust.edu.sa/des_tomato/, using any of the mainstream web browsers, including Firefox, Safari and Chrome.

Transition from a maternal to external nitrogen source in maize seedlings

Maximizing NO₃^- uptake during seedling development is important as it has a major influence on plant growth and yield. However, little is known about the processes leading to, and involved in, the initiation of root NO₃^- uptake capacity in developing seedlings. This study examines the physiological processes involved in root NO₃^- uptake and metabolism, to gain an understanding of how the NO₃^- uptake system responds to meet demand as maize seedlings transition from seed N use to external N capture. The concentrations of seed-derived free amino acids within root and shoot tissues are initially high, but decrease rapidly until stabilizing eight days after imbibition (DAI). Similarly, shoot N% decreases, but does not stabilize until 12-13 DAI. Following the decrease in free amino acid concentrations, root NO₃^- uptake capacity increases until shoot N% stabilizes. The increase in root NO₃^- uptake capacity corresponds with a rapid rise in transcript levels of putative NO₃^- transporters, ZmNRT2.1 and ZmNRT2.2. The processes underlying the increase in root NO₃^- uptake capacity to meet N demand provide an insight into the processes controlling N uptake.

Growth curve registration for evaluating salinity tolerance in barley

BACKGROUND

Smarthouses capable of non-destructive, high-throughput plant phenotyping collect large amounts of data that can be used to understand plant growth and productivity in extreme environments. The challenge is to apply the statistical tool that best analyzes the data to study plant traits, such as salinity tolerance, or plant-growth-related traits.

RESULTS

We derive family-wise salinity sensitivity (FSS) growth curves and use registration techniques to summarize growth patterns of HEB-25 barley families and the commercial variety, Navigator. We account for the spatial variation in smarthouse microclimates and in temporal variation across phenotyping runs using a functional ANOVA model to derive corrected FSS curves. From FSS, we derive corrected values for family-wise salinity tolerance, which are strongly negatively correlated with Na but not significantly with K, indicating that Na content is an important factor affecting salinity tolerance in these families, at least for plants of this age and grown in these conditions.

CONCLUSIONS

Our family-wise methodology is suitable for analyzing the growth curves of a large number of plants from multiple families. The corrected curves accurately account for the spatial and temporal variations among plants that are inherent to high-throughput experiments.

Chloride on the Move

Chloride (Cl^-) is an essential plant nutrient but under saline conditions it can accumulate to toxic levels in leaves; limiting this accumulation improves the salt tolerance of some crops. The rate-limiting step for this process - the transfer of Cl^- from root symplast to xylem apoplast, which can antagonize delivery of the macronutrient nitrate (NO₃^-) to shoots - is regulated by abscisic acid (ABA) and is multigenic. Until recently the molecular mechanisms underpinning this salt-tolerance trait were poorly defined. We discuss here how recent advances highlight the role of newly identified transport proteins, some that directly transfer Cl^- into the xylem, and others that act on endomembranes in 'gatekeeper' cell types in the root stele to control root-to-shoot delivery of Cl^-.

The genome of Chenopodium quinoa

Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

AVP1: One Protein, Many Roles

Constitutive expression of the Arabidopsis vacuolar proton-pumping pyrophosphatase (H⁺-PPase) gene (AVP1) increases plant growth under various abiotic stress conditions and, importantly, under nonstressed conditions. Many interpretations have been proposed to explain these phenotypes, including greater vacuolar ion sequestration, increased auxin transport, enhanced heterotrophic growth, and increased transport of sucrose from source to sink tissues. In this review, we evaluate all the roles proposed for AVP1, using findings published to date from mutant plants lacking functional AVP1 and transgenic plants expressing AVP1. It is clear that AVP1 is one protein with many roles, and that one or more of these roles act to enhance plant growth. The complexity suggests that a systems biology approach to evaluate biological networks is required to investigate these intertwined roles.

Evaluating physiological responses of plants to salinity stress

BACKGROUND

Because soil salinity is a major abiotic constraint affecting crop yield, much research has been conducted to develop plants with improved salinity tolerance. Salinity stress impacts many aspects of a plant's physiology, making it difficult to study in toto Instead, it is more tractable to dissect the plant's response into traits that are hypothesized to be involved in the overall tolerance of the plant to salinity.

SCOPE AND CONCLUSIONS

We discuss how to quantify the impact of salinity on different traits, such as relative growth rate, water relations, transpiration, transpiration use efficiency, ionic relations, photosynthesis, senescence, yield and yield components. We also suggest some guidelines to assist with the selection of appropriate experimental systems, imposition of salinity stress, and obtaining and analysing relevant physiological data using appropriate indices. We illustrate how these indices can be used to identify relationships amongst the proposed traits to identify which traits are the most important contributors to salinity tolerance. Salinity tolerance is complex and involves many genes, but progress has been made in studying the mechanisms underlying a plant's response to salinity. Nevertheless, several previous studies on salinity tolerance could have benefited from improved experimental design. We hope that this paper will provide pertinent information to researchers on performing proficient assays and interpreting results from salinity tolerance experiments.

Evaluating physiological responses of plants to salinity stress

BACKGROUND

Because soil salinity is a major abiotic constraint affecting crop yield, much research has been conducted to develop plants with improved salinity tolerance. Salinity stress impacts many aspects of a plant's physiology, making it difficult to study in toto Instead, it is more tractable to dissect the plant's response into traits that are hypothesized to be involved in the overall tolerance of the plant to salinity.

SCOPE AND CONCLUSIONS

We discuss how to quantify the impact of salinity on different traits, such as relative growth rate, water relations, transpiration, transpiration use efficiency, ionic relations, photosynthesis, senescence, yield and yield components. We also suggest some guidelines to assist with the selection of appropriate experimental systems, imposition of salinity stress, and obtaining and analysing relevant physiological data using appropriate indices. We illustrate how these indices can be used to identify relationships amongst the proposed traits to identify which traits are the most important contributors to salinity tolerance. Salinity tolerance is complex and involves many genes, but progress has been made in studying the mechanisms underlying a plant's response to salinity. Nevertheless, several previous studies on salinity tolerance could have benefited from improved experimental design. We hope that this paper will provide pertinent information to researchers on performing proficient assays and interpreting results from salinity tolerance experiments.