Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds

Nunes Nesi, Adriano. Universidade Federal de Viçosa. Departamento de Biologia Vegetal. Viçosa, Minas Gerais, Brazil.Alseekh, Saleh. Max - Planck- Institute of Molecular Plant Physiology. Potsdam, Germany.Oliveira Silva, Franklin Magnum de. Universidade Federal de Viçosa. Departamento de Biologia Vegetal. Viçosa, Minas Gerais, Brazil.Omranian, Nooshin. Max - Planck- Institute of Molecular Plant Physiology. Potsdam, Germany.Lichtenstein, Gabriel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología. Castelar, Buenos Aires, Argentina.Mirnezhad, Mohammad. Leiden University. Plant Ecology, Institute of Biology. The Netherlands.Romero González, Roman R. Leiden University. Plant Ecology. Institute of Biology. The Netherlands.Carrari, Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología. Castelar, Buenos Aires, Argentina.1-13Introduction To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Methods The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. Results Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. Conclusions Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits

Integrative analyses of photosynthesis, plant growth, metabolite levels and enzyme activities in an introgression line population of Solanum pennellii

To identify genomic regions involved in the regulation of fundamental physiological processes such as photosynthesis, respiration and underlying traits, a population of 71 Solanum pennellii introgression lines (ILs) in the genetic background of S. lycopersicum (M82) was analyzed. We determined IL phenotypes physiological, metabolic and growth related traits, ranging from gas- exchange parameters (e.g. CO 2 assimilation rates and stomatal conductance), chlorophyll fluorescence parameters (e.g. electron transport rate and photochemical quenching) as well as growth related traits (e.g. relative growth rate, shoot and root dry matter accumulation). In parallel, we also analyzed by robotized platform the major metabolic intermediates (e.g. sugars and starch), and the activities of nine representative enzymes from central C and N metabolism. We aimed: (1) combine information about enzyme activities and metabolite levels from stem, petiole and leaf with biomass and fruit yield; (2) by studying these three interconnected organs, examine how much connectivity exists between enzyme activities and metabolite levels; (3) provide predictive information about differences in C partitioning and inorganic N assimilation; (4) investigate the natural genetic diversity and identify QTL controlling variation of enzyme activities and metabolite levels in stem, petiole and leaf. Data analyses allowed identification of 67 physiological and metabolic QTL. Additionally, a comprehensive and detailed annotation of these regions allowed to point out a total of 87 candidate genes that might control the investigated traits. Out of those, 70 genes showed allelic variants related to differentially transposable element insertions pattern between both parental genotypes. Furthermore, the results revealed high frequency of positive correlations between enzyme activities, moderate frequency of correlations between related metabolites, and few correlations between enzyme activities and metabolite levels. Taken together, we present the largest study of photosynthetic and growth parameters in tomato plants to date. Our results allowed the identification of candidate genes that might be involved in the regulation of photosynthesis, primary metabolismo and plant growth, and provide an valuable genetic resource to understanding of the biochemical mechanisms involved in the regulation of primary metabolism in tomato plants.Para identificar regiões genômicas envolvidas na regulação de processos fisiológicos fundamentais, como fotossíntese, respiração e aqueles relacionados, uma população de ILs de Solanum pennellii em fundo genético de S. lycopersicum (M82) foi analisada. Foram estudados parâmetros fisiológicos, metabólicos e de crescimento, que vão desde troca gasosa (por exemplo, taxa de assimilação de CO 2 e condutância estomática), fluorescência da clorofila (por exemplo, taxa de transporte de elétrons e de extinção fotoquímica), bem como parâmetros de crescimento (por exemplo, taxa de crescimento relativo, matéria seca da raiz e parte aérea). Em paralelo, nós também analisamos, por meio de uma plataforma robotizada, os principais intermediários metabólicos (por exemplo, açúcares, amido, nitrato, aminoácidos e proteínas), e a atividade de nove enzimas representativas do metabolismo central do C e N. O objetivo do estudo foi: (1) combinar informações sobre as atividades enzimáticas e os níveis de metabólitos de caule, pecíolo e folha com a biomassa e rendimento de frutos; (2) através do estudo desses três órgãos interligados, examinar o quanto há de conectividade entre a atividade das enzimas e os níveis de metabólitos; (3) fornecer informações preditivas sobre as diferenças de particionamento do C e assimilação N inorgânico; (4) investigar a diversidade genética natural e identificar QTLs relacionados ao metabolimo central e a atividade enzimática no caule, pecíolo e folha. As análises dos dados permitiram a identificação de 67 QTL relacionados à parametros fisiológicos e metabólicos. Além disso, uma anotação abrangente e detalhada destas regiões permitiu apontar um total de 87 genes candidatos que possam controlar as características investigadas. Desses, 70 genes apresentou variantes alélicas relacionadas inserções de elementos transponíveis entre os dois genótipos parentais. As análises metabólicas e enzimática revelaram alta frequência de correlações positivas entre as enzymas, frequência moderada de correlações entre metabólitos relacionados, e baixa correlações entre a atividade das enzimas e os níveis de metabólitos. Tomados em conjunto, vapresentamos o maior estudo de parâmetros de fotossíntese e crescimento em plantas de tomate até à data. Os resultados permitiram a identificação de genes candidatos que podem estar envolvidos na regulação da fotossíntese, metabolismo primário e crescimento da planta, e fornece um recurso genético valioso para a compreensão dos mecanismos bioquímicos envolvidos na regulação do metabolismo primário em tomateiro.Fundação de Amparo à Pesquisa do Estado de MInas Gerai

Identification of genetic factors involved in the control of respiration and optimization of photosynthesis in tomato leaf

Para identificar regiões genômicas envolvidas na regulação de importantes parâmetros fisiológicos como fotossíntese, respiração e processos relacionados. Sessenta e seis linhagens introgredidas de S. pennellii em fundo genético de S. lycopersicum, foram cultivadas em condições semicontroladas até o estádio vegetativo. Nesse estudo, examinaram-se os parâmetros de trocas gasosas e florescência da clorofila a, acúmulo de biomassa e o conteúdo de alguns metabólitos relacionados com o metabolismo do carbono e do nitrogênio. 23 ILs apresentaram taxas fotossintéticas superiores ao parental M82. Essa maior assimilação líquida de CO 2 foi fortemente correlacionada com condutância estomática. Em adição, uma correlação positiva entre a fotossíntese e os parâmetros de fluorescência sugere que maior taxa fotossintética pode estar associada a alterações nos parâmetros de fluorescência. Quanto ao metabolismo do carbono, verificou-se uma alta correlação negativa entre a produção de biomassa e o acúmulo de amido indicando que amido também pode atuar como um importante metabólito integrador na regulação do crescimento vegetativo. Em relação ao metabolismo do nitrogênio, constatou-se que a maior eficiência na incorporação do N inorgânico esteve fortemente relacionada ao acúmulo de amido. Por meio de análises multivariadas, foi possível identificar 21 ILs que diferiram da espécie parental S. lycopersicum. Dentre estas, a IL 7-5 diferiu de modo mais relevantes das demais ILs e do M82. Em virtude de estudos anteriores relatarem um alto rendimento de frutos por parte desta IL, esta região cromossômica torna-se promissora na identificação de fatores genéticos envolvidos no controle da respiração e potencialização da fotossíntese em folhas de tomate.To identify genomic regions involved in the regulation of important physiological parameters such as photosynthesis, respiration and related processes. Sixty-six introgression line (ILs) of S. pennellii in genetic background of S. lycopersicum were cultivated in partially controlled conditions to the vegetative stage. In this study, we examined the parameters of gas exchange and chlorophyll a flowering, biomass accumulation and content of some metabolites related to the metabolism of carbon and nitrogen. 23 ILs showed photosynthetic rates higher than the parental M82. This increased net CO2 assimilation was strongly correlated with stomatal conductance. In addition, a positive correlation between photosynthesis and fluorescence parameters suggests that higher photosynthetic rate may be associated with changes in fluorescence parameters. The metabolism of carbon, there was a high negative correlation between biomass production and accumulation of starch indicating that starch can also act as an important metabolite in the regulation of integrating vegetative growth. In relation to nitrogen metabolism, it was found that the more efficient incorporation of inorganic N was strongly related to the accumulation of starch. Through multivariate analyzes, we identified 21 ILs that differ from the parental species S. lycopersicum. Among these, IL 7-5 differed in more relevant to other ILs and M82. Because previous studies have reported a high yield of fruit from this IL, this chromosomal region becomes promising in identifying genetic factors involved in the control of the potentiation of respiration and photosynthesis in tomato leaves.Coordenação de Aperfeiçoamento de Pessoal de Nível Superio

Eucalypts and low phosphorus availability: between responsiveness and efficiency

Background and aims Twenty-four species of eucalypts were studied regarding their ability to grow under low P and their responsiveness to P inputs. Methods Growth and photosynthesis-related parameters were evaluated. Results Growth of all species was influenced by low P availability. No significant correlation was found between leaf P concentration and biomass, indicating that P concentrations in leaves cannot be solely considered an indication of the responsiveness to P in eucalypts. Species responsive to P-input (high agronomic P efficiency values, APE) were those with low P use efficiency - PUE (here assessed as relative efficiency of P-use, REP) and low P uptake efficiency (PUpE). But, non-responsive species were related to higher P-efficiency under low soil P-availability. Eucalyptus tereticornis, E. cladocalyx, E. globulus and E. camaldulensis were efficient under low-P availability. Whereas, E. crebra and E acmenoides were the most responsive species, with high APE, suggesting that for these species P-inputs are needed to guarantee plant growth. The root:shoot ratio remained constant at different P availabilities, suggesting that biomass allocation towards the root in response to P and greater investment in roots were not correlated with greater PUE. Under limited P, E. robusta and E. botryoides exhibited low foliar P contents and higher root:shoot ratios than those of other species with higher P contents, indicating that greater root investment does not necessarily result in greater PUE. Conclusion The results suggest that the divergence among species is probably related to different mechanisms, which may improve P-use efficiency44543862349368CAPES - Coordenação de Aperfeiçoamento de Pessoal e Nível SuperiorCNPQ - Conselho Nacional de Desenvolvimento Científico e TecnológicoFAPESP – Fundação de Amparo à Pesquisa Do Estado De São Paulosem informação2018/09624-02016/25498-0; 2017/21738-

Natural genetic variation for morphological and molecular determinants of plant growth and yield

The rates of increase in yield of the main commercial crops have been steadily falling in many areas worldwide. This generates concerns because there is a growing demand for plant biomass due to the increasing population. Plant yield should thus be improved in the context of climate change and decreasing natural resources. It is a major challenge which could be tackled by improving and/or altering light-use efficiency, CO2 uptake and fixation, primary metabolism, plant architecture and leaf morphology, and developmental plant processes. In this review, we discuss some of the traits which could lead to yield increase, with a focus on how natural genetic variation could be harnessed. Moreover, we provide insights for advancing our understanding of the molecular aspects governing plant growth and yield, and propose future avenues for improvement of crop yield. We also suggest that knowledge accumulated over the last decade in the field of molecular physiology should be integrated into new ideotypes

Natural genetic variation for morphological and molecular determinants of plant growth and yield

Although a yield ceiling has been reached for several major crops, enhancements are required to keep up with the demands of the increasing population. Here, traits which could help tackle this issue are discussed.The rates of increase in yield of the main commercial crops have been steadily falling in many areas worldwide. This generates concerns because there is a growing demand for plant biomass due to the increasing population. Plant yield should thus be improved in the context of climate change and decreasing natural resources. It is a major challenge which could be tackled by improving and/or altering light-use efficiency, CO2 uptake and fixation, primary metabolism, plant architecture and leaf morphology, and developmental plant processes. In this review, we discuss some of the traits which could lead to yield increase, with a focus on how natural genetic variation could be harnessed. Moreover, we provide insights for advancing our understanding of the molecular aspects governing plant growth and yield, and propose future avenues for improvement of crop yield. We also suggest that knowledge accumulated over the last decade in the field of molecular physiology should be integrated into new ideotypes

Different levels of UV-B resistance in Vaccinium corymbosum cultivars reveal distinct backgrounds of phenylpropanoid metabolites

UV-B radiation induces several physiological and biochemical effects that can influence regulatory plant processes. Vaccinium corymbosum responds differently to UV-B radiation depending on the UV-B resistance of cultivars, according to their physiological and biochemical features. In this work, the effect of two levels of UV-B radiation during long-term exposure on the phenylpropanoid biosynthesis, and the expression of genes associated with flavonoid biosynthesis as well as the absolute quantification of secondary metabolites were studied in two contrasting UV-B-resistant cultivars (Legacy, resistant and Bluegold, sensitive). Multivariate analyses were performed to understand the role of phenylpropanoids in UV-B defense mechanisms. The amount of phenylpropanoid compounds was generally higher in Legacy than in Bluegold. Different expression levels of flavonoid biosynthetic genes for both cultivars were transiently induced, showing that even in longer period of UV-B exposure; plants are still adjusting their phenylpropanoids at the transcription levels. Multivariate analysis in Legacy indicated no significant correlation between gene expression and the levels of the flavonoids and phenolic acids. By contrast, in the Bluegold cultivar higher number of correlations between secondary metabolite and transcript levels was found. Taken together, the results indicated different adjustments between the cultivars for a successful UV-B acclimation. While the sensitive cultivar depends on metabolite adjustments to respond to UV-B exposure, the resistant cultivar also possesses an intrinsically higher antioxidant and UV-B screening capacity. Thus, we conclude that UV-B resistance involves not only metabolite level adjustments during the acclimation period, but also depends on the intrinsic metabolic status of the plant and metabolic features of the phenylpropanoid compounds

Metabolic responses of Vaccinium corymbosum L. cultivars to Al3+ toxicity and gypsum amendment

Highbush blueberry (Vaccinium corymbosum L.) is an important crop well adapted to acid soils, but sensitive to Al3+ toxicity. Gypsum amendments are frequently used to reduce Al3+ toxicity in V. corymbosum. However, little is known about the physiological and metabolic responses to gypsum application in plants growing in the presence of Al3+ toxicity. Thus, we evaluated the mechanisms displayed by gypsum application at the metabolite levels in V. corymbosum cultivars growing under Al3+ toxicity. We characterized three cultivars (Brigitta, Legacy, and Bluegold) with different response mechanisms to Al3+ toxicity. Furthermore, four treatments were applied: (i) Acid substrate without Al (Control), (ii) Acid substrate + 1.4 g CaSO4 kg(-1), (iii) Acid substrate + 0.9 g AlCl3 kg(-1) and (iv) Acid substrate + 0.9 g AlCl3 kg(-1) + 1.4 g CaSO4 kg(-1). After ten days of treatment exposition, leaves, and roots were harvested for metabolite profiling analyses. Starch and amino acid concentrations in leaves and roots decreased in all cultivars growing under toxic Al3+ levels. However, gypsum amendment reduced Al concentration in leaves and roots, as well as increased Ca concentrations in leaves, and recovered amino acid and starch levels. In addition, metabolite profiling and multivariate analyses indicated that in roots, gamma-aminobutyric acid (GABA) might be a metabolite related to Al3+ toxicity. Taken together that gypsum amendment ameliorates the Al3+ toxicity, mainly in the cultivar Al-sensitive, Bluegold. The two Al-resistant cultivars (Legacy and Brigitta) showed distinct Al mechanisms (tolerance and exclusion, respectively)

Table_4_Low phosphorus induces differential metabolic responses in eucalyptus species improving nutrient use efficiency.xlsx

Phosphorus (P) is a vital nutrient for plant growth. P availability is generally low in soils, and plant responses to low P availability need to be better understood. In a previous study, we studied the growth and physiological responses of 24 species to low P availability in the soil and verified of eucalypts, five (Eucalyptus acmenoides, E. grandis, E. globulus, E. tereticornis, and Corymbia maculata) contrasted regarding their efficiency and responsiveness to soil P availability. Here, we obtained the metabolomic and lipidomic profile of leaves, stems, and roots from these species growing under low (4.5 mg dm–3) and sufficient (10.8 mg dm–3) P in the soil. Disregarding the level of P in the soils, P allocation was always higher in the stems. However, when grown in the P-sufficient soil, the stems steadily were the largest compartment of the total plant P. Under low P, the relative contents of primary metabolites, such as amino acids, TCA cycle intermediates, organic acids and carbohydrates, changed differently depending on the species. Additionally, phosphorylated metabolites showed enhanced turnover or reductions. While photosynthetic efficiencies were not related to higher biomass production, A/Ci curves showed that reduced P availability increased the eucalypt species’ Vcmax, Jmax and photosynthetic P-use efficiency. Plants of E. acmenoides increased galactolipids and sulfolipids in leaves more than other eucalypt species, suggesting that lipid remodelling can be a strategy to cope with the P shortage in this species. Our findings offer insights to understand genotypic efficiency among eucalypt species to accommodate primary metabolism under low soil P availability and eventually be used as biochemical markers for breeding programs.</p

Eucalypt plants are physiologically and metabolically affected by infection with Ceratocystis fimbriata

Ceratocystis wilt, caused by Ceratocystis fimbriata, is currently one of the most important disease in eucalypt plantations. Plants infected by C. fimbriata have lower volumetric growth, lower pulp yields and reduced timber values. The physiological bases of infection induced by this pathogen in eucalypt plant are not known. Therefore, this study aims to assess the physiological and metabolic changes in eucalypt clones that are resistant and susceptible to C. fimbriata. Once, we evaluated in detail their leaf gas exchange, chlorophyll a fluorescence, water potential, metabolite profiling and growth-related parameters. When inoculated, the susceptible clone displayed reduced water potential, CO2 assimilation rate, stomatal conductance, transpiration rate, photochemical quenching coefficient, electron transport rate, and root biomass. Inoculated resistant and susceptible clones both presented higher respiration rates than healthy plants. Many compounds of primary and secondary metabolism were significantly altered after fungal infection in both clones. These results suggest that, C. fimbriata interferes in the primary and secondary metabolism of plants that may be linked to the induction of defense mechanisms and that, due to water restrictions caused by the fungus in susceptible plants, there is a partial closure of the stomata to prevent water loss and a consequent reduction in photosynthesis and the transpiration rate, which in turn, leads to a decrease in the plant's growth-related. These results combined, allowed for a better understanding of the physiological and metabolic changes following the infectious process of C. fimbriata, which limit eucalypt plant growth