Considering that maize (Zea mays L.) is a staple food for a large segment of the population worldwide, many attempts have been made to improve the nutritional value of its grain and at the same time to achieve sustainable cropping systems. The present study aimed to characterize the composition and nutritional value of maize grain as influenced by cropping system, genetic background (variety), and growing year using untargeted NMR metabolomics. The composition of both water- (sugars and polyols, organic acids, and amino acids) and liposoluble metabolites (free and esterified fatty acids, sterols, and lipids) extracted from the maize grain was determined. Multivariate statistical analyses (PCA and ANOVA) pointed to the growing year and the variety as the most important random and fixed factors, respectively, influencing the metabolite profile. The samples were separated along PC1 and PC3 according to the growing year and the variety, respectively. A higher content of citric acid and diunsaturated fatty acids and a lower content of tyrosine, trigonelline, and monounsaturated fatty acids was observed in the organic with respect to the conventional variety. The effect of the cropping system was overwhelmed by the random effect of the growing year. The results provide novel knowledge on the influence of agronomic practices on maize micronutrient contents.

Molecular regulation of fruit ripening is fundamental for sustainable production of quality fruits with desired traits. Ethylene and abscisic acid (ABA) are two of the most studied plant hormones during fruit development, onset, and progression of fruit ripening, while the abundance and role(s) of other phytohormones have remained elusive. Here, we used high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) to quantify endogenous concentrations of numerous plant hormones, namely cytokinins (CKs), auxins, gibberellins, jasmonates, ABA and salicylic acid (SA), as well as their pathway metabolites during tomato fruit development and ripening. Changes in the levels of 47 compounds including active phytohormones and their derivatives during fruit development (stages Dev1, Dev2 and Dev3) and ripening (stages mature green, breaker, breaker + 3 d and breaker + 8 days) of tomato fruit were identified. Quantitative multivariant analyses of the phytohormones and their related compounds involving the seven analyzed stages showed their differential accumulation during fruit development and ripening. Early developmental stage (Dev1) of cell number proliferation was associated with auxins (IAA-GE, IAA-Glu, OxIAA-GE, OxIAA, and OxIAA-Asp), trans-zeatin (tZ)-, dihydrozeatin (DZ)- and N6-(∆2-isopentenyl) adenine (iP)-type CKs (tZ7G, tZ9G, tZRMP, tZOG, DZOG, iP7G, iP9G), jasmonic acid (JA)-isoleucine, and gibberellin GA29. The cell expansion phase, Dev2, was found associated with auxins IAA-Asp and I3A, gibberellins GA19 and GA20, JA, SA and phenylacetic acid. Abundance of ABA and benzoic acid at the maturation phase (Dev3), mature green and breaker stages of fruit development were apparent. At the fruit ripening phase (BR + 3 and BR + 8) accumulation of iP-, cis-zeatin (cZ)-, tZ-, DZ-type CKs (iP, iPR, iPRMP, cZR, cZ7G, cZROG, cZRMP, tZR, tZROG, DZR, DZRMP) and CK methylthioderivatives (MeS-Z, MeS-ZR), auxin IAM, and jasmonates DiH-JA and JA-Me was apparent. Notably, the mevalonate CK pathway cZRMP→cZR→cZ was found to be the dominant pathway during fruit ripening, which contrasts with the known CK abundances in non-climacteric fruits. Taken together, these results provide a map of the differential accumulation of phytohormones and their metabolites during the development and ripening of fleshy tomato fruit.

Polyamines (PA) cellular levels are maintained through a balance between synthesis and catabolism, achieved by two classes of enzymes polyamine oxidases (PAOs) and copper amine oxidases (CuAO). Here we investigated the occurrence, molecular evolution and role(s) of PAOs and CuAO gene families in aquatic duckweed and their comparison with other aquatic plants -sea eelgrass, bladderwort, and Lotus. We identified eight bona fide PAO genes (SpPAO1–SpPAO8) and one SpCuAO1 in the greater duckweed genome from three genome assemblies. Interestingly, duckweed PAO genes increased their number through a tandem duplication event, while contrary to this CuAO genes were significantly lost to a single gene SpCuAO1. Phylogenetic analysis revealed that tandemly duplicated SpPAO2-7 share close similarity to well-known terminal catabolism (TC) pathway PAO genes while SpPAO1 and SpPAO8 seem to segregate along with back conversion (BC) participating known PAO genes, suggesting that all tandem duplicated PAOs are involved in TC pathway which is contrary to known trend in land plants where CuAOs are mainly involved in TC pathway. Comparative transcript abundance studies indicated that all eight PAOs and one CuAO gene respond to multiple stresses and principal component analysis identifies SpPAO4 as a highly active gene in response to multiple stresses. Results showed that oxidation of higher polyamines (SPD/SPM) through the TC pathway is diversified in duckweeds. Taken together this study reveals unique insights into the genomic losses and gains of polyamine metabolism possibly involved in achieving the structural and physiological adaptations required for aquatic lifestyle of duckweeds.

Nitrogen (N) is a critical element for plant growth and development. Hence, improving nitrogen use efficiency (NUE) is vital for reducing costs and the environmental impact of agricultural practices. Understanding the genetic control of N metabolism is crucial to improve NUE, especially in agronomically important plants, such as barley (Hordeum vulgare).Using bioinformatics and functional genomics tools, we identified and characterized sixteen barley nitrogen metabolism-related gene families (HvNMGs) on a genome-wide scale, analysing gene features and evolution. These genes, located on six of seven barley chromosomes, are highly conserved in plants (including barley, rice, and Arabidopsis), as shown by phylogenetic analysis. We further explored the evolutionary relationships of NMGs through a genome-to-genome synteny analysis, which indicated higher conservation of NMGs between barley and other monocots, suggesting that these orthologous pairs predate species divergence. Protein-protein interaction analyses revealed that all of the HvNMGs show interactions, mainly with each other. The H. vulgare miRNAs target sites (hvu-miR) prediction identified six hvu-miR in 4 HvNMGs (HvGABA-T2, HvALDH10-1, HvALDH10-2 and HvARGAH), indicating their potential involvement in stress responses. The expression patterns analysis of publicly available RNA-seq data revealed that HvNMGs are expressed in all developmental stages of barley, and they respond to different stress conditions, indicating their essential role in plant growth, development and stress response. The organ-specific expression analysis, conducted using qPCR, of HvNMGs revealed higher expression of HvNiR and HvNRs in the leaf and significantly higher expression of HvARGAH and HvALDH10 in the spike than in other tissues, showing that some of the genes may be particularly important in some tissues than others. This data provides a foundation for understanding HvNMG function and could be used to improve barley yield by enhancing NUE — an important goal for both crop productivity and environmental sustainability.

Genetic improvements of solanaceous crops for quality and stress responsive traits are needed because of the central role vegetables and fruits have in providing nutrients to human diets. Copper amine oxidase (CuAO) encoding genes involved in metabolism of primary/di-amine nitrogenous compounds, play a role in balancing internal nitrogen (N) pools especially when external N supply fluctuates during growth, development and environmental stresses. In the present study, we investigated the occurrence, molecular evolution and possible role(s) of these unknown genes in tomato crops. Multiple genome-wide bioinformatics approaches led to the identification of eight bona fide CuAO genes (SlCuAO1-SlCuAO8) in the tomato genome with gene numbers like those in Arabidopsis and rice indicating their conserved functional relevance with a tandemly duplicated SlCuAO6-SlCuAO7 pair at chr.9. A conserved intron-exon size and phase distribution for SlCuAO2, 3, 4 pairs are similar to a recently identified single duckweed SpCuAO1 orthologue gene indicating its evolutionary conservation. Synteny analysis showed their closest association to Arabidopsis and but not with rice. Transcriptome data indicated that gene expression for about six genes (SlCuAO1, 2, 3, 4, 6, 7) is root specific, fruit specific for SlCuAO5 and flower specific for SlCuAO8 thus indicating amine oxidation is variable across tissues with a prominance in the root tissue. The majority of CuAO genes are negatively regulated by methyl jasmonate. Positive regulation, however, involves CuAO3/8. Transcript analysis of the ethylene-deficient transgenic lines indicated that ethylene is required for activation of SlCuAO4. CuAO4 and CuAO5 exhibited most significant tissues-independent gene expression responses across various nitrogen regimes. Drought, heat and N stress identified CuAO5 as an overlapping highly expressed gene that corroborates with putrescine accumulation for free and conjugated forms with an opposite abundance of bound forms. Taken together our study highlights new insights into the roles of copper amine oxidation genes and identifies CuAO5 as a multiple stress induced gene that can be used in genetic improvement programs for combining heat, drought and nitrogen use efficiency related traits.

Main conclusion Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. Abstract The circadian clock senses light and temperature in day–night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis . Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional–translational feedback loops involving morning ( CCA1 , LHY ), mid-day ( PRR9 , PRR7 , PRR5 ), and evening ( TOC1 , ELF3 , ELF4 , LUX ) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis , maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.

Polyamines (PAs) are important molecules that determine cell longevity or death. Studies have shown that nutritional supplementation with spermidine can reduce age-related pathology and increase life span in a number of organisms, including humans. In addition, applying PAs to plants prevents their senescence. This review aims to provide an integrated understanding of the regulation of PA metabolism and its effect(s) on cell homeostasis. PA metabolism is universal for plants and animals. Research has shown that increased levels of PA synthesizing enzymes are associated with cell proliferation, whereas activation of the PA catabolic pathway increases oxidative stress and leads to aging/senescence due to cellular damage. Intracellular PA levels are regulated at the transcriptional and translational levels of the PA metabolic genes. The cis-acting regulatory elements and transcription factors determine the tissue-, developmental stage-, and stress-specific expression of a gene. At the translational level, it is regulated by miRNAs targeting mRNAs for cleavage or translational suppression. The byproducts of PA metabolism, such as hypusine and acrolein, are important for cell survival or death. PAs and their metabolic enzymes play several other important roles in plant and animal physiology via their effects on chromatin condensation, histone acetylation, histone deacetylation, transmethylation, and protein-protein interactions. This review focuses on the role(s) of PAs as universal bioregulators in processes across kingdoms, with specific reference to regulation of cellular longevity and death.

The non-climacteric octoploid strawberry (Fragaria x ananassa Duchesne ex Rozier) was used as a model to study its regulation during fruit ripening. High performance liquid chromatography electrospray tandem-mass spec-trometry (HPLC-ESI-MS/MS) was employed to profile 28 different endogenous phytohormones in strawberry. These include auxins, cytokinins (CKs), abscisic acid (ABA), ethylene precursor 1-aminocyclopropane-1-carbox-ylic acid (ACC), jasmonates, and phenolic compounds salicylic acid (SA), benzoic acid (BzA) and phenylacetic acid (PAA) together with their various metabolic forms that have remained largely unexplored thus far. ABA, ACC and CK N6-(A2-isopentenyl)adenine (iP) were found to be associated with ripening while ABA catabolites 9-hydroxy-ABA and phaseic acid mimicked the pattern of climacteric decline at the turning phase of strawberry ripening. The content of other CK forms except iP decreased as fruit ripened, as also that of auxins indole-3-acetic acid (IAA) and oxo-IAA, and of jasmonates. Data presented here also suggest that both the transition and pro -gression of strawberry fruit ripening are associated with N6-(A2-isopentenyl)adenosine-5 '-monophosphate (iPRMP)-* N6-(A2-isopentenyl)adenosine (iPR)-* iP as the preferred CK metabolic pathway. In contrast, the ethylene precursor ACC was present at higher levels, with its abundance increasing from the onset of ripening to the red ripe stage. Further investigation of ripening-specific ACC accumulation revealed the presence of a large ACC synthase (ACS) encoding gene family in octoploid strawberry that was previously unknown. Seventeen ACS genes were found differentially expressed in fruit tissues, while six of them showed induced expression during strawberry fruit ripening. These data suggest a possible role(s) of ACC, ABA, and iP in strawberry fruit ripening. These data add new dimension to the existing knowledge of the interplay of different endogenous phytohor-mones in octoploid strawberry, paving the way for further investigation of their individual role(s) in fruit ripening.

Tomato (Solanum lycopersicon) is one of the most traded vegetables in the world. Fertilizer application is essential to sustain high tomato yields. While there is often a strong emphasis on increasing yield, less attention has been given to the effect of fertilizers on tomato quality and plant characteristics. Here, our meta-analysis explored 313 published studies consisting of 9752 organic fertilizers and 5915 organic-inorganic fertilizer combinations from 353 sites globally. These studies indicated that organic fertilizers significantly improve tomato quality compared to inorganic fertilizers. These improvements included increases in sugars (0.38–12.0 %), aromatic volatiles (72.1 %), and brighter color (1.64 %) along with decreases in organic acids (−6.76 %), nitrates (−16.9 %), and disease incidence (−73.0 % to −45.3 %). However, there were also some undesirable outcomes, including decreases in fruit firmness (−2.99 %) and tomato yield (−5.50 %). Interestingly, relative to inorganic fertilizers, the organic-inorganic fertilizer combinations significantly improved tomato yield (12.4 %) and morphological characteristics, including titratable acid (3.52 %), mean fruit weight (7.28 %), number of fruits per plant (5.58 %), fruit diameter (2.74 %), plant height (52.4 %), and plant dry weight (41.6 %). Our study also shows that greenhouse cultivation enhances tomato quality compared to field cultivation. We also highlight the importance of increasing the utilization of organic resources to achieve reduced fertilizer usage, cost savings, and improved agronomic efficiency.

Agriculture is an important link to many issues that challenge society today, including adaptation to and mitigation of climate change, food security, and communicable and non-communicable diseases in animals and humans. Transformation of agriculture and food systems has become a priority for a range of federal agencies and global organizations. It is imperative that food and agricultural researchers effectively harness the global convergence of priorities to overcome research "silos" through deep and sustained systemic change. Herein, we identify intersections in federal and global initiatives encompassing climate adaptation and mitigation; human health and nutrition; animal health and welfare; food safety and security; and equity and inclusion. Many agencies and organizations share these priorities, but efforts to address them remain uncoordinated and opportunities for collaboration untapped. Based on the interconnectedness of the identified priority areas, we present a research framework to catalyze agricultural transformation, beginning with the research enterprise. We propose that transformation in agricultural research should incorporate (1) innovation, (2) integration, (3) implementation, and (4) evaluation. This framework provides approaches for food and agricultural research to contribute to sustainable, flexible, and coordinated transformation in the agricultural sector.

Maize is important to global food security, being one of the predominant cereals in human and domesticated livestock diets worldwide. Due to the increasing human population, it will be important to not only design cropping systems to increase maize yield and sustainability but also to improve the nutritional quality of maize edible tissues. To determine cropping system impacts on maize grain nutritional content, we sampled grain from conventional and organic maize varieties grown for three growing seasons using five cropping systems. We analyzed the grain using metabolic fingerprinting of methanol extracts with ultra-high performance liquid chromatography (UHPLC) coupled with mass spectrometry (MS), adopting both non-targeted and targeted approaches. The cropping systems are part of a long-term study at the Beltsville Agricultural Research Center in Beltsville, Maryland, and were a three-year conventional no-till rotation (NT), a three-year conventional chisel-till rotation (CT), a two-year organic rotation (Org2), a three-year organic rotation (Org3), and a six-year organic rotation (Org6). Each cropping system had been in place for at least 10 years, allowing specific cropping-system-induced alterations of soil edaphic and microbial properties. Non-targeted metabolic fingerprinting detected a total of 90 compounds, the majority of which were phenolics. Metabolic profiling was further targeted toward 15 phenolics, 1 phytohormone, 7 carbohydrates and 7 organic acids, which were quantified in the maize grain originating from the five cropping systems. Statistical analysis of this subset of quantitative data determined that cropping system can significantly influence levels of certain maize grain metabolites. However, natural impacts (growing year) were substantially greater than cropping system impacts, likely masking or over-riding some cropping system impacts. Additionally, maize cultivar genetics had greater impact than cropping system on the maize grain metabolome and was the greatest “managed” impact on the metabolite profiles. Results indicate that until natural environmental impacts on maize grain metabolite levels are understood and managed, the best approach to reliably increase maize grain nutritional quality is through development of maize cultivars with enhanced nutritional content that are robust to natural environmental influence.

L-Ascorbic acid (AsA), a strong antioxidant, serves as an enzyme cofactor and redox status marker, modulating a plethora of biological processes. As tomato commercial varieties and hybrids possess relatively low amounts of AsA, the improvement of fruit AsA represents a strategic goal for enhanced human health. Previously, we have suggested that GDP-L-Galactose phosphorylase (GGP) and L-galactose-1-phosphate phosphatase (GPP) can serve as possible targets for AsA manipulation in tomato (Solanum lycopersicon L.) fruit. To this end, we produced and evaluated T3 transgenic tomato plants carrying these two genes under the control of CaMV-35S and two fruit specific promoters, PPC2 and PG-GGPI. The transgenic lines had elevated levels of AsA, with the PG-GGP1 line containing 3-fold more AsA than WT, without affecting fruit characteristics. Following RNA-Seq analysis, 164 and 13 DEGs were up- or down-regulated, respectively, between PG-GGP1 and WT pink fruits. PG-GGP1 fruit had a distinct number of up-regulated transcripts associated with cell wall modification, ethylene biosynthesis and signaling, pollen fertility and carotenoid metabolism. The elevated AsA accumulation resulted in the up regulation of AsA associated transcripts and alternative biosynthetic pathways suggesting that the entire metabolic pathway was influenced, probably via master regulation. We show here that AsA-fortification of tomato ripe fruit via GGP1 overexpression under the action of a fruit specific promoter PG affects fruit development and ripening, reduces ethylene production, and increased the levels of sugars, and carotenoids, supporting a robust database to further explore the role of AsA induced genes for agronomically important traits, breeding programs and precision gene editing approaches.

Malnutrition, unhealthy diets, and lifestyle changes have become major risk factors for non-communicable diseases while adversely impacting economic growth and sustainable development. Anthocyanins, a group of flavonoids that are rich in fruits and vegetables, contribute positively to human health. This review focuses on genetic variation harnessed through crossbreeding and biotechnology-led approaches for developing anthocyanins-rich fruit and vegetable crops. Significant progress has been made in identifying genes involved in anthocyanin biosynthesis in various crops. Thus, the use of genetics has led to the development and release of anthocyanin-rich potato and sweet potato cultivars in Europe and the USA. The purple potato 'Kufri Neelkanth' has been released for cultivation in northern India. In Europe, the anthocyanin-rich tomato cultivar 'Sun Black' developed via the introgression of Aft and atv genes has been released. The development of anthocyanin-rich food crops without any significant yield penalty has been due to the use of genetic engineering involving specific transcription factors or gene editing. Anthocyanin-rich food ingredients have the potential of being more nutritious than those devoid of anthocyanins. The inclusion of anthocyanins as a target characteristic in breeding programs can ensure the development of cultivars to meet the nutritional needs for human consumption in the developing world.

The photosystem II (PSII) reaction centre is the critical supramolecular pigment–protein complex in the chloroplast which catalyses the light-induced transfer of electrons from water to plastoquinone. Structural studies have demonstrated the existence of an oligomeric PSII. We carried out radiation inactivation target analysis (RTA), together with sucrose gradient ultracentrifugation (SGU) of PSII, to study the functional size of PSII in diverse plant species under physiological and stress conditions. Two PSII populations, made of dimeric and monomeric core particles, were revealed in Pisum sativum, Spinacea oleracea, Phaseulus vulgaris, Medicago sativa, Zea mais and Triticum durum. However, this core pattern was not ubiquitous in the higher plants since we found one monomeric core population in Vicia faba and a dimeric core in the Triticum durum yellow-green strain, respectively. The PSII functional sizes measured in the plant seedlings in vivo, as a decay of the maximum quantum yield of PSII for primary photochemistry, were in the range of 75–101 ± 18 kDa, 2 to 3 times lower than those determined in vitro. Two abiotic stresses, heat and drought, imposed individually on Pisum sativum, increased the content of the dimeric core in SGU and the minimum functional size determined by RTA in vivo. These data suggest that PSII can also function as a monomer in vivo, while under heat and drought stress conditions, the dimeric PSII structure is predominant.

We explored the polyamine (PA) metabolic pathway genes in barley (Hv) to understand plant development and stress adaptation in Gramineae crops with emphasis on leaf senescence. Bioinformatics and functional genomics tools were utilized for genome-wide identification, comprehensive gene features, evolution, development and stress effects on the expression of the polyamine metabolic pathway gene families (PMGs). Three S-adenosylmethionine decarboxylases (HvSAMDCs), two ornithine decarboxylases (HvODCs), one arginine decarboxylase (HvADC), one spermidine synthase (HvSPDS), two spermine synthases (HvSPMSs), five copper amine oxidases (HvCuAOs) and seven polyamine oxidases (HvPAOs) members of PMGs were identified and characterized in barley. All the HvPMG genes were found to be distributed on all chromosomes of barley. The phylogenetic and comparative assessment revealed that PA metabolic pathway is highly conserved in plants and the prediction of nine H. vulgare miRNAs (hvu-miR) target sites, 18 protein-protein interactions and 961 putative CREs in the promoter region were discerned. Gene expression of HvSAMDC3, HvCuAO7, HvPAO4 and HvSPMS1 was apparent at every developmental stage. SPDS/SPMS gene family was found to be the most responsive to induced leaf senescence. This study provides a reference for the functional investigation of the molecular mechanism(s) that regulate polyamine metabolism in plants as a tool for future breeding decision management systems.

Peroxynitrite fine-tunes the nitro-oxidative environment during dark-induced leaf senescence in Arabidopsis for selective nitrative modification of bio-targets, including proteins containing tryptophan and tyrosine, and nucleic acids. Nitric oxide (NO) is a critical molecule that links plant development with stress responses. Herein, new insights into the role of NO metabolism during leaf senescence in Arabidopsis are presented. A gradual decrease in NO emission accompanied dark-induced leaf senescence (DILS), and a transient wave of peroxynitrite (ONOO-) formation was detected by day 3 of DILS. The boosted ONOO- did not promote tryptophan (Trp) nitration, while the pool of 6-nitroTrp-containing proteins was depleted as senescence progressed. Immunoprecipitation combined with mass spectrometry was used to identify 63 and 4 characteristic 6-nitroTrp-containing proteins in control and individually darkened leaves, respectively. The potential in vivo targets of Trp nitration were mainly related to protein biosynthesis and carbohydrate metabolism. In contrast, nitration of tyrosine-containing proteins was intensified 2-fold on day 3 of DILS. Also, nitrative modification of RNA and DNA increased significantly on days 3 and 7 of DILS, respectively. Taken together, ONOO- can be considered a novel pro-senescence regulator that fine-tunes the redox environment for selective bio-target nitration. Thus, DILS-triggered nitrative changes at RNA and protein levels promote developmental shifts during the plant's lifespan and temporal adjustment in plant metabolism under suboptimal environmental conditions.

Polyamines have been implicated in ameliorating the detrimental effects of drought and saline conditions on plant growth and development. The independent impact of these two abiotic stresses on polyamine (PA) biosynthesis, catabolism, and homeostasis, as well as on their transcript abundance in tomato leaves, is presented here. We show that the total levels of putrescine (PUT), spermidine (SPD), and spermine (SPM) increase up to 72 h during drought and up to 48 h during salinity stress before their precipitable drop thereafter. Thus, tomato plants maintain survivability to drought as well as salinity stress for up to 3 and 2 days, respectively. Independent multivariant analyses of drought and salinity stress kinetic data separately showed a closer association with levels of free, conjugated, and bound forms of SPD and SPM, but not with free or bound PUT. However, combined multivariant analyses showed a closer association of free SPD, conjugated SPD, and bound SPD with both stresses; SPD-bound and SPM conjugated with drought; and free SPM and conjugated PUT with salinity stress, respectively. PA biosynthesis genes, ARG1, SPDS1, and SAMDc3, segregated with drought and SPDS2 with salinity stress. PA catabolic genes CuAO4-like and PAO4 were associated with drought and salinity stresses, respectively, suggesting differential involvement of PA biosynthesis and catabolic genes in drought and salinity stresses. Pearson correlation indicated mostly positive correlations between the levels of free, conjugated, and bound forms of PUT, SPD, and SPM under drought and salinity stress. However, negative correlations were mostly seen between the levels of various forms of the PAs and their biosynthesis/catabolic genes. Levels of different PA forms had a twofold higher negative correlation during drought as compared to salinity stress (66 vs. 32) and with transcript levels of PA biosynthesis and catabolic genes. Transcripts of light-harvesting chlorophyll a/b-binding genes were generally positively associated with different forms of PAs but negatively to carbon flow genes. Most of the PA biosynthesis genes were coordinately regulated under both stresses. Collectively, these results indicate that PAs are distinctly regulated under drought and salinity stress with different but specific homologs of PA biosynthesis and catabolic genes contributing to the accumulation of free, conjugated, and bound forms of PAs.