Identification of metabolites associated with water stress responses in Solanum tuberosum L. clones

Optimizing saffron cormlet production through substrate composition nutrient concentration and irrigation management in soilless cultivation

A two-year study has been conducted to optimize saffron cormlet production in a soilless cultivation system. Variations in the concentration of phosphate, boron, and irrigation events were assessed in the first year. Subsequently, after optimizing the substrate composition, the effects of nutrient solution volume and the concentration of nitrate, iron, and boron were investigated on the yield and weight of cormlets and leaves, photosynthetic activities, and productivity of nutrient solutions in the second year. Irrigation events in the first year significantly influenced cormlet growth, while phosphate and boron had no substantial effects. Moisture characteristics indicated an optimal substrate composition of 15% cocopeat, 15% cocochips, and 70% perlite. In the second year, increasing nutrient solution volume (225 ml/pot/week) and nitrate concentration up to 9800 µM significantly increased the weight of the leaf, total photosynthesis rate, and large-sized cormlets (> 8 g) to nearly 50% of total cormlets. Conversely, increasing iron concentration notably decreased the weight of total and large-sized cormlets. Boron concentration again showed no significant effect on the parameters. The highest nutrient solution productivity was achieved with a 150 (ml/pot/week) nutrient solution containing 9800 µM nitrogen and 25 µM iron. These findings underscore the importance of effective irrigation and nutrition management in enhancing the quantity and quality of cormlet production, potentially boosting perennial saffron yield in the following years.

Carotenoid composition and sequestration in cassava (Manihot esculentum Crantz) roots

Cassava (Manihot esculentum Crantz) is a staple food source for many developing countries. Its edible roots are high in starch but lack micronutrients such as β-carotene. In the present study, analysis of pedigree breeding populations has led to the identification of cassava accessions with enhanced β-carotene contents up to 40 μg/g DW. This represents 0.2% of the Recommended Daily Allowance (RDA) for vitamin A. The β-branch of the carotenoid pathway predominates in cassava roots, with dominant levels of β-carotene followed by other minor epoxides of β-ring derived carotenoids. Metabolomic analysis revealed that steady state levels of intermediary metabolism were not altered by the formation of carotenoids, similar to starch and carbohydrate levels. Apocarotenoids appeared to be independent of their carotenoid precursors. Lipidomic analysis provided evidence of a significant positive correlation between carotenoid and lipid content, in particular plastid specific galactolipids. Proteomic analysis of isolated amyloplasts identified the majority of proteins associated with translation and carbohydrate/starch biosynthesis (e.g. glucose-1-phosphate adenylyltransferase). No carotenoid related proteins were detected even in the highest carotenoid containing lines. Carotenoids were associated with fractions typically annotated as plastoglobuli and plastid membranes (particularly the envelope). Proteomic analysis confirmed these structures apart from plastoglobuli, thus potentially amyloplast structures may not contain classical plastoglobuli structures.

Genetic architecture of tuber-bound free amino acids in potato and effect of growing environment on the amino acid content

Free amino acids in potato tubers contribute to their nutritional value and processing quality. Exploring the natural variation in their accumulation in tubers across diverse genetic backgrounds is critical to potato breeding programs aiming to enhance or partition their distribution effectively. This study assessed variation in the tuber-bound free amino acids in a diversity panel of tetraploid potato clones developed and maintained by the Texas A&M Potato Breeding Program to explore their genetic basis and to obtain genomic-estimated breeding values for applied breeding purposes. Free amino acids content was evaluated in tubers of 217 tetraploid potato clones collected from Dalhart, Texas in 2019 and 2020, and Springlake, Texas in 2020. Most tuber amino acids were not affected by growing location, except histidine and proline, which were significantly lower (- 59.0%) and higher (+ 129.0%), respectively, at Springlake, Texas (a location that regularly suffers from abiotic stresses, mainly high-temperature stress). Single nucleotide polymorphism markers were used for genome-wide association studies and genomic selection of clones based on amino acid content. Most amino acids showed significant variations among potato clones and moderate to high heritabilities. Principal component analysis separated fresh from processing potato market classes based on amino acids distribution patterns. Genome-wide association studies discovered 33 QTL associated with 13 free amino acids. Genomic-estimated breeding values were calculated and are recommended for practical potato breeding applications to select parents and advance clones with the desired free amino acid content.

Physiological response and yield components under greenhouse drought stress conditions in potato

Due to the effects of climate change, conditions tend to be increasingly extreme, with water availability being one of the main limiting factors in potato production. The objective of this study was to analyze the differential response of physiological and yield components in six potato varieties under water deficit conditions. For this purpose, a greenhouse trial was carried out with the varieties Agata, Agria, Kennebec, Monalisa, Sante and Zorba. The drought stress was applied in stressed plants 36 days after planting (DAP) by withholding water for 25 days. All measurements were taken at four different times: before stress (T0), 17 days (T1) and 24 days (T2) after stress and five days after re-watering. The physiological parameters evaluated were chlorophyll content and fluorescence, relative leaf water content, stomatal conductance, electrolytic leakage and water potential. After the drought period, the aerial part of half of the plants was cut to evaluate the produced biomass. At the end of the cycle yield components were determined. Stomatal conductance and water potential were the parameters that showed the highest differences between the two hydric conditions, and Monalisa was the variety with the best response in tuber production under stress conditions. Indirect selection based on parameters associated with water stress can be a useful tool in potato breeding programs for the identification of more tolerant varieties.

Irrigation Management in Potato (Solanum tuberosum L.) Production: A Review

Limited water resources coupled with the increase of the human population calls for more efficient use of water in irrigated agriculture. Potato (Solanum tuberosum L.) is one of the most widely grown crops worldwide and is very sensitive to water stress due to its shallow rooting system. With the dilemma of potato sensitivity to drought and limited available water resources restricting crop production, researchers and crop growers have been investigating different approaches for optimizing potato yield and improving crop water use efficiency under different irrigation methods. While potato response to water is affected by other management practices such as fertilizer management, the present review is focused on the potato response to water under different environments and different irrigation methods and the impact on potato quality and potato diseases. Variable results obtained from research studies indicate the non-transferability of the results from one location to another as potato cultivars are not the same and potato breeders are still making effort to develop new high-yielding varieties to increase crop production and or develop new varieties for a specific trait to satisfy consumers exigence. This review is a valuable source of information for potato growers and scientists as it is not only focused on the impact of irrigation regimes on potato yield and water productivity as most reviews on water management, but it also presents the impact of irrigation regime on diseases in potatoes, tuber specific gravity, metabolite content of the tubers and the quality of the processed potato products.

Transcriptional and Metabolic Profiling of Potato Plants Expressing a Plastid-Targeted Electron Shuttle Reveal Modulation of Genes Associated to Drought Tolerance by Chloroplast Redox Poise

Water limitation represents the main environmental constraint affecting crop yield worldwide. Photosynthesis is a primary drought target, resulting in over-reduction of the photosynthetic electron transport chain and increased production of reactive oxygen species in plastids. Manipulation of chloroplast electron distribution by introducing alternative electron transport sinks has been shown to increase plant tolerance to multiple environmental challenges including hydric stress, suggesting that a similar strategy could be used to improve drought tolerance in crops. We show herein that the expression of the cyanobacterial electron shuttle flavodoxin in potato chloroplasts protected photosynthetic activities even at a pre-symptomatic stage of drought. Transcriptional and metabolic profiling revealed an attenuated response to the adverse condition in flavodoxin-expressing plants, correlating with their increased stress tolerance. Interestingly, 5-6% of leaf-expressed genes were affected by flavodoxin in the absence of drought, representing pathways modulated by chloroplast redox status during normal growth. About 300 of these genes potentially contribute to stress acclimation as their modulation by flavodoxin proceeds in the same direction as their drought response in wild-type plants. Tuber yield losses under chronic water limitation were mitigated in flavodoxin-expressing plants, indicating that the flavoprotein has the potential to improve major agronomic traits in potato.

Phosphorus relieves aluminum toxicity in oil tea seedlings by regulating the metabolic profiling in the roots

Oil tea (Camellia oleifera Abel.) is an important edible oil tree mainly grown in acidic soils, whose growth and yield can be severely limited due to soil aluminum (Al) toxicity and phosphorus (P) deficiency. In this study, we investigated the physiological and metabolic responses of oil tea to Al and P treatment for an 8-week duration. Al reduced root length, root volume, and plant biomass, while P addition alleviated the effects of Al toxicity. P addition increased P content and reduced Al accumulation in roots. The profiles of 58 metabolites were significantly changed in roots of oil tea seedlings. Al toxicity increased various amino acids, but decreased many kinds of organic acids and carbohydrates. Interestingly, P addition reduced the amino acids accumulation which were induced by Al toxicity, while only a few organic acids changed under P supply. Most carbohydrates, including sucrose and glucose, significantly increased with P addition under Al toxicity. Results indicated that Al toxicity increased the accumulation of amino acids and reduced the accumulation of organic acids and carbohydrates, while the addition of P promoted root growth by alleviating the inhibition of protein synthesis and increasing carbohydrates content. However, P addition did not increase the organic acids content in roots.

Metabolite database for root, tuber, and banana crops to facilitate modern breeding in understudied crops

Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the available diversity due to lack of efficient germplasm characterization and structure. In recent years large-scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics-based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on-going genomic and phenotypic studies will enhance 'omics-wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization.

Physiological, Biochemical, and Transcriptional Responses to Single and Combined Abiotic Stress in Stress-Tolerant and Stress-Sensitive Potato Genotypes

Potato production is often constrained by abiotic stresses such as drought and high temperatures which are often present in combination. In the present work, we aimed to identify key mechanisms and processes underlying single and combined abiotic stress tolerance by comparative analysis of tolerant and susceptible cultivars. Physiological data indicated that the cultivars Desiree and Unica were stress tolerant while Agria and Russett Burbank were stress susceptible. Abiotic stress caused a greater reduction of photosynthetic carbon assimilation in the susceptible cultivars which was associated with a lower leaf transpiration rate. Oxidative stress, as estimated by the accumulation of malondialdehyde was not induced by stress treatments in any of the genotypes with the exception of drought stress in Russett Burbank. Stress treatment resulted in increases in ascorbate peroxidase activity in all cultivars except Agria which increased catalase activity in response to stress. Transcript profiling highlighted a decrease in the abundance of transcripts encoding proteins associated with PSII light harvesting complex in stress tolerant cultivars. Furthermore, stress tolerant cultivars accumulated fewer transcripts encoding a type-1 metacaspase implicated in programmed cell death. Stress tolerant cultivars exhibited stronger expression of genes associated with plant growth and development, hormone metabolism and primary and secondary metabolism than stress susceptible cultivars. Metabolite profiling revealed accumulation of proline in all genotypes following drought stress that was partially suppressed in combined heat and drought. On the contrary, the sugar alcohols inositol and mannitol were strongly accumulated under heat and combined heat and drought stress while galactinol was most strongly accumulated under drought. Combined heat and drought also resulted in the accumulation of Valine, isoleucine, and lysine in all genotypes. These data indicate that single and multiple abiotic stress tolerance in potato is associated with a maintenance of CO₂ assimilation and protection of PSII by a reduction of light harvesting capacity. The data further suggests that stress tolerant cultivars suppress cell death and maintain growth and development via fine tuning of hormone signaling, and primary and secondary metabolism. This study highlights potential targets for the development of stress tolerant potato cultivars.

Metabolite profiling characterises chemotypes of Musa diploids and triploids at juvenile and pre-flowering growth stages

Bananas (Musa spp.) are consumed worldwide as dessert and cooking types. Edible banana varieties are for the most part seedless and sterile and therefore vegetatively propagated. This confers difficulties for breeding approaches against pressing biotic and abiotic threats and for the nutritional enhancement of banana pulp. A panel of banana accessions, representative of the diversity of wild and cultivated bananas, was analysed to assess the range of chemotypes available globally. The focus of this assessment was banana leaves at two growth stages (juvenile and pre-flowering), to see when during the plant growth metabolic differences can be established. The metabolic data corresponded to genomic trends reported in previous studies and demonstrated a link between metabolites/pathways and the genomes of M. acuminata and M. balbisiana. Furthermore, the vigour and resistance traits of M. balbisiana was connected to the phenolic composition and showed differences with the number of B genes in the hybrid accessions. Differences in the juvenile and pre-flowering data led to low correlation between the growth stages for prediction purposes.

Metabolic diversity in sweet potato (Ipomoea batatas, Lam.) leaves and storage roots

Sweet potato (Ipomoea batatas, Lam.) is an important root vegetable in developing countries. After its domestication in Neotropical America, human migration led to the distribution of the sweet potato plant throughout the world. Both leaf and storage root are high in compounds of nutritional value. Yet, the storage roots are of particular value due to their significant content of provitamin A (β-carotene). The breeding effort for elite sweet potato lines led to the reduction of genetic diversity and the potential to improve other traits. The focus of the present study was to assess the metabolic diversity of 27 sweet potato cultivars including landraces and improved varieties. A metabolite profiling approach was optimised for sweet potato leaf and storage root tissue and 130 metabolites identified with three different analysis platforms. The data highlighted a lack of correlation between storage root phenotype and leaf metabolism. Furthermore, the metabolic diversity of storage roots was based on the secondary metabolism, including phenylpropanoids and carotenoids. Three cultivars of three different flesh colouration (yellow, orange and purple) showed a significant difference of the primary metabolism. This data demonstrates the value of metabolite profiling to breeding programs as a means of identifying differences in phenotypes/chemotypes and characterising parental material for future pre-breeding resources.

Simultaneous untargeted and targeted metabolomics profiling of underivatized primary metabolites in sulfur-deficient barley by ultra-high performance liquid chromatography-quadrupole/time-of-flight mass spectrometry

BACKGROUND

Metabolomics based on mass spectrometry analysis are increasingly applied in diverse scientific domains, notably agronomy and plant biology, in order to understand plants' behaviors under different stress conditions. In fact, these stress conditions are able to disrupt many biosynthetic pathways that include mainly primary metabolites. Profiling and quantifying primary metabolites remain a challenging task because they are poorly retained in reverse phase columns, due to their high polarity and acid-base properties. The aim of this work is to develop a simultaneous untargeted/targeted profiling of amino acids, organic acids, sulfur metabolites, and other several metabolites. This method will be applied on sulfur depleted barley, in order to study this type of stress, which is difficult to detect at early stage. Also, this method aims to explore the impact of this stress on barley's metabolome.

RESULTS

Ultra-high performance liquid chromatography-high resolution mass spectrometry-based method was successfully applied to real samples allowing to discriminate, detect, and quantify primary metabolites in short-runs without any additional sampling step such as derivatization or ion pairing. The retention of polar metabolites was successfully achieved using modified C18 columns with high reproducibility (relative standard deviation below 10%). The quantification method showed a high sensitivity and robustness. Furthermore, high resolution mass spectrometry detection provided reliable quantification based on exact mass, eliminating potential interferences, and allowing the simultaneous untargeted metabolomics analysis. The untargeted data analysis was conducted using Progenesis QI software, performing alignment, peak picking, normalization and multivariate analysis. The simultaneous analysis provided cumulative information allowing to discriminate between two plant batches. Thus, discriminant biomarkers were identified and validated. Simultaneously, quantification confirmed coherently the relative abundance of these biomarkers.

CONCLUSIONS

A fast and innovated simultaneous untargeted/targeted method has successfully been developed and applied to sulfur deficiency on barley. This work opens interesting perspectives in both fundamental and applied research. Biomarker discovery give precious indication to understand plant behavior during a nutritional deficiency. Thus, direct or indirect measurement of these compounds allows a real time fertilization management and encounter the challenges of sustainable agriculture.