Jorge Freire da Silva Ferreira
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Research Subjects
Research Interests
Jorge Freire da Silva Ferreira has a total of 228 co-authors. Here are the top co-authors by number of shared publications:
- Devinder Sandhu
U.S. Salinity Laboratory (USDA-ARS), 450 W Big Springs Road, Riverside, California 92507, United States
13 shared publications - Claudivan Feitosa de Lacerda
Universidade Federal do Ceará, Brazil
12 shared publications - Ana Carolina de Souza Chagas
Embrapa Pecuária Sudeste, São Carlos, SP, Brazil
5 shared publications - Adriana Cruz de Oliveira
Universidade Federal do Ceará, Brazil
4 shared publications - Alessandro Francisco Talamini Amarante
Department of Biodiversity and Biostatistics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil
4 shared publications - Hans Raj Gheyi
Academic Unit of Agricultural Engineering, Federal University of Campina Grande, Campina Grande 58430-380, PB, Brazil
4 shared publications
Latest Publications
- Open Access
- 29 November 2025
- Published by Springer Nature in Communications Biology
- Vol. 8 (1)
Spinach (Spinacia oleracea) has epidermal bladder cells and exhibits characteristics of a facultative halophyte
While epidermal bladder cells (EBCs) have been well documented in quinoa, their presence in spinach has not been previously reported. Spinach is traditionally classified as a glycophyte but our previous and current results strongly suggest otherwise. In this study, we compared two quinoa with two spinach cultivars grown under low (2 dS m⁻¹) and high (25 dS m⁻¹) irrigation-water salinities. Using Scanning Electron Microscopy coupled with Energy-Dispersive X-ray Spectroscopy (SEM-EDS), we demonstrated that spinach has EBCs that accumulate mostly Cl, followed by K, and to a lesser extent Na, while quinoa EBCs showed no detectable Na signal. Morphologically, quinoa EBCs have single-celled stalks while spinach EBCs have multicellular stalks; both feature globular heads approximately 150 µm in diameter. Spinach displayed higher expression of Na- and Cl-transporter genes in EBCs than in EBC-free leaf tissue. Under identical salinity levels (2-24 dS m⁻¹), both spinach and quinoa exhibited comparable reductions in biomass and plant height. Despite higher Na and Cl accumulation, spinach exhibited no visible signs of salt toxicity. The presence of EBCs and apparent tissue-level salt tolerance provide new insights into spinach anatomy and ion partitioning under salinity stress, suggesting that spinach may be more accurately classified as a facultative halophyte.
- 29 November 2025
- Published by Springer Nature in Communications Biology
- Vol. 8 (1)
Open AccessSpinach (Spinacia oleracea) has epidermal bladder cells and exhibits characteristics of a facultative halophyte
While epidermal bladder cells (EBCs) have been well documented in quinoa, their presence in spinach has not been previously reported. Spinach is traditionally classified as a glycophyte but our previous and current results strongly suggest otherwise. In this study, we compared two quinoa with two spinach cultivars grown under low (2 dS m⁻¹) and high (25 dS m⁻¹) irrigation-water salinities. Using Scanning Electron Microscopy coupled with Energy-Dispersive X-ray Spectroscopy (SEM-EDS), we demonstrated that spinach has EBCs that accumulate mostly Cl, followed by K, and to a lesser extent Na, while quinoa EBCs showed no detectable Na signal. Morphologically, quinoa EBCs have single-celled stalks while spinach EBCs have multicellular stalks; both feature globular heads approximately 150 µm in diameter. Spinach displayed higher expression of Na- and Cl-transporter genes in EBCs than in EBC-free leaf tissue. Under identical salinity levels (2-24 dS m⁻¹), both spinach and quinoa exhibited comparable reductions in biomass and plant height. Despite higher Na and Cl accumulation, spinach exhibited no visible signs of salt toxicity. The presence of EBCs and apparent tissue-level salt tolerance provide new insights into spinach anatomy and ion partitioning under salinity stress, suggesting that spinach may be more accurately classified as a facultative halophyte.
- Open Access
- 23 September 2025
- Published by Wiley in The Plant Genome
- Vol. 18 (3) , e70102
Untargeted metabolomics reveals key metabolites and genes underlying salinity tolerance mechanisms in maize
Understanding the physiological, metabolic, and genetic mechanisms underlying salt tolerance is essential for improving crop resilience and productivity, yet their complex interactions remain poorly defined. We compared physiological and metabolic responses to salinity between two contrasting maize ( Zea mays L.) inbred lines: the salt‐sensitive C68 and the salt‐tolerant NC326. The sensitivity of C68 was characterized by reduced shoot and root dry weights and plant height, high tissue accumulation of Na and Cl but low K, and lower leaf proline accumulation compared to the salt‐tolerant NC326. Untargeted metabolomics identified 56 metabolites categorized as constitutively upregulated or salt‐responsive. In NC326, constitutive accumulation of flavonoids, including schaftoside, tricin, and kaempferol‐related compounds in leaves, suggests adaptive priming against oxidative stress, while constitutively higher lipids and fatty acids in roots may enhance membrane stability. Salt‐responsive metabolites, notably antioxidants and lanosterol, highlighted inducible oxidative‐stress mitigation and membrane‐stabilization strategies. By integrating metabolomic and genetic analyses, we identified 10 candidate genes involved in the biosynthesis of key metabolites. These findings establish a comprehensive platform for functional validation of metabolites and candidate genes for developing maize varieties with improved resilience to soil salinity through targeted breeding or biotechnological strategies.
- 23 September 2025
- Published by Wiley in The Plant Genome
- Vol. 18 (3) , e70102
Open AccessUntargeted metabolomics reveals key metabolites and genes underlying salinity tolerance mechanisms in maize
Understanding the physiological, metabolic, and genetic mechanisms underlying salt tolerance is essential for improving crop resilience and productivity, yet their complex interactions remain poorly defined. We compared physiological and metabolic responses to salinity between two contrasting maize ( Zea mays L.) inbred lines: the salt‐sensitive C68 and the salt‐tolerant NC326. The sensitivity of C68 was characterized by reduced shoot and root dry weights and plant height, high tissue accumulation of Na and Cl but low K, and lower leaf proline accumulation compared to the salt‐tolerant NC326. Untargeted metabolomics identified 56 metabolites categorized as constitutively upregulated or salt‐responsive. In NC326, constitutive accumulation of flavonoids, including schaftoside, tricin, and kaempferol‐related compounds in leaves, suggests adaptive priming against oxidative stress, while constitutively higher lipids and fatty acids in roots may enhance membrane stability. Salt‐responsive metabolites, notably antioxidants and lanosterol, highlighted inducible oxidative‐stress mitigation and membrane‐stabilization strategies. By integrating metabolomic and genetic analyses, we identified 10 candidate genes involved in the biosynthesis of key metabolites. These findings establish a comprehensive platform for functional validation of metabolites and candidate genes for developing maize varieties with improved resilience to soil salinity through targeted breeding or biotechnological strategies.
- 8 August 2025
- Published by American Chemical Society (ACS) in ACS Agricultural Science & Technology
- Vol. 5 (9) , 1817-1826
Decoding the Genetic Basis of Salinity Tolerance in Tomatoes through Ion Transport and Stress Regulation
- 8 August 2025
- Published by American Chemical Society (ACS) in ACS Agricultural Science & Technology
- Vol. 5 (9) , 1817-1826
Decoding the Genetic Basis of Salinity Tolerance in Tomatoes through Ion Transport and Stress Regulation
- Open Access
Cilantro Photosynthetic Parameters in Response to Different Flows of Nutrient Solutions Prepared with Brackish Waters Dominant in Na+, Cl−, or Ca2+
Although the NFT (nutrient film technique) solution application rate for cilantro is known for fresh water, the application rate is still debatable when using brackish water. The application rate alone influences flow velocity dynamics, which, when associated with nutrient solution salinity, can impact plant development when saline water is used. Knowledge of how to best combine solution salinity and application rates will help decide if brackish water can be used to produce cilantro under hydroponic conditions. Thus, two trials were conducted in sequence from November 2019 to February 2020 under a protected environment. Cilantro cv. Verdão was submitted to four levels of electrical conductivity of nutrient solutions (ECns of 1.7, 3.0, 4.5, and 6.0 dS m−1) combined with four flow rates (1.0, 2.0, 3.0, and 4.0 L min−1). Because Na+ and Ca2+ are predominant ions in brackish waters in the crystalline and sedimentary regions in the Brazilian Semiarid region, the first study used brackish waters dominated by NaCl and the second study used waters dominated by CaCl2. We measured gas exchange and other photosynthetic parameters in plants cultivated with nutrient solutions high in Cl− and prevalent in Na+ or Ca2+, each combined with different application rates. We concluded that the increment in salinity decreased the gas exchange of cilantro plants, especially when the brackish waters were dominant in Ca2+ and Cl−. Up to an ECns of 4.5 dS m−1, plants maintained their leaf chlorophyll concentrations, although with reduced gas exchange. Salt stress compromised chlorophyll a fluorescence, affecting important parameters such as initial, maximum, and variable fluorescence. Besides the effects of salinity on chlorophyll a and b concentrations, the quantum and maximum yields of photosystem II remained stable, indicating that photosystem II may have adapted to the saline conditions applied in this study. The variation in application rates was unable to attenuate the deleterious effects of salinity, regardless of the ionic prevalence. We conclude that cilantro plants can be cultivated under hydroponic conditions, using currently accepted flow rates, with nutrient solutions of up to 3.0 dS m−1 without severe damage to plant photosynthetic parameters.
Open AccessCilantro Photosynthetic Parameters in Response to Different Flows of Nutrient Solutions Prepared with Brackish Waters Dominant in Na+, Cl−, or Ca2+
Although the NFT (nutrient film technique) solution application rate for cilantro is known for fresh water, the application rate is still debatable when using brackish water. The application rate alone influences flow velocity dynamics, which, when associated with nutrient solution salinity, can impact plant development when saline water is used. Knowledge of how to best combine solution salinity and application rates will help decide if brackish water can be used to produce cilantro under hydroponic conditions. Thus, two trials were conducted in sequence from November 2019 to February 2020 under a protected environment. Cilantro cv. Verdão was submitted to four levels of electrical conductivity of nutrient solutions (ECns of 1.7, 3.0, 4.5, and 6.0 dS m−1) combined with four flow rates (1.0, 2.0, 3.0, and 4.0 L min−1). Because Na+ and Ca2+ are predominant ions in brackish waters in the crystalline and sedimentary regions in the Brazilian Semiarid region, the first study used brackish waters dominated by NaCl and the second study used waters dominated by CaCl2. We measured gas exchange and other photosynthetic parameters in plants cultivated with nutrient solutions high in Cl− and prevalent in Na+ or Ca2+, each combined with different application rates. We concluded that the increment in salinity decreased the gas exchange of cilantro plants, especially when the brackish waters were dominant in Ca2+ and Cl−. Up to an ECns of 4.5 dS m−1, plants maintained their leaf chlorophyll concentrations, although with reduced gas exchange. Salt stress compromised chlorophyll a fluorescence, affecting important parameters such as initial, maximum, and variable fluorescence. Besides the effects of salinity on chlorophyll a and b concentrations, the quantum and maximum yields of photosystem II remained stable, indicating that photosystem II may have adapted to the saline conditions applied in this study. The variation in application rates was unable to attenuate the deleterious effects of salinity, regardless of the ionic prevalence. We conclude that cilantro plants can be cultivated under hydroponic conditions, using currently accepted flow rates, with nutrient solutions of up to 3.0 dS m−1 without severe damage to plant photosynthetic parameters.
- Open Access
Saturated Hydraulic Conductivity of Nine Soils According to Water Quality, Soil Texture, and Clay Mineralogy
Water quality affects soils by promoting their degradation by the accumulation of salts that will lead to salinization and sodification. However, the magnitude of these processes varies with soil attributes. Saturated hydraulic conductivity (Ksat) is the rate at which water passes through saturated soil, which is fundamental to determining water movement through the soil profile. The Ksat may differ from soil to soil according to the sodium adsorption ratio (SAR), water electrical conductivity (ECw), soil texture, and clay mineralogical assemblage. In this study, an experiment with vertical columns and constant-load permeameters was conducted to evaluate changes in soil Ksat with waters comprising five ECw values (128, 718, 1709, 2865, and 4671 µS cm−1) and five SAR values [0, 5, 12, 20, and 30 (mmolc L−1)0.5] in combination. Horizons from nine northeastern Brazilian soils (ranging from tropical to semiarid) were selected according to their texture and clay mineralogical composition. The data obtained were fit with multiple regression equations for Ksat as a function of ECw and SAR. This study also determined the null SAR at each ECw level, using Ksat = 0 on each equation, to predict the SAR needed to achieve zero drainage on each soil for each ECw level and the threshold electrolyte concentration (CTH) that would lead to a 20% reduction of maximum Ksat. Neither the ECw nor SAR of the applied waters affected the Ksat of soils with a mineralogical assemblage of oxides and kaolinite such as Ferralsol, Nitisol, and Lixisol, with an average Ksat of 2.75, 6.06, and 3.33 cm h−1, respectively. In smectite- and illite-rich soils, the Ksat increased with higher ECw levels and decreased with higher SAR levels, especially comparing the soil’s estimated Ksat for water with low ECw and high SAR in combination (ECw of 128 µS cm−1 and SAR 30) and water with high ECw and low SAR in combination (ECw of 4671 µS cm−1 and SAR 0) such as Regosol (4.95 to 10.94 cm h−1); Vertisol (0.28 to 2.04 cm h−1); Planosol (0 to 0.29 cm h−1); Luvisol (0.46 to 2.12 cm h−1); Cambisol (0 to 0.23 cm h−1); and Fluvisol (1.87 to 3.34 cm h−1). The CTH was easily reached in soils with high concentrations of highly active clays such as smectites. In sandy soils, the target CTH was only reached under extremely high SAR values, indicating a greater resistance of these soils to salinization/sodification. Due to their mineralogical assemblage, soils from tropical sub-humid/hot and semiarid climates were more affected by treatments than soils from tropical humid/hot climates, indicating serious risks of physical and chemical degradation. The results showed the importance of monitoring water quality for irrigation, mainly in less weathered, more clayey soils, with high clay activity to minimize the rate of salt accumulation in soils of the Brazilian semiarid region. Our study also proved that clay mineralogy had more influence on the Ksat than clay concentration, mainly in soils irrigated with saline and sodic waters, and that soils with highly active smectite are more prone to degradation than soils with high concentrations of kaolinite.
Open AccessSaturated Hydraulic Conductivity of Nine Soils According to Water Quality, Soil Texture, and Clay Mineralogy
Water quality affects soils by promoting their degradation by the accumulation of salts that will lead to salinization and sodification. However, the magnitude of these processes varies with soil attributes. Saturated hydraulic conductivity (Ksat) is the rate at which water passes through saturated soil, which is fundamental to determining water movement through the soil profile. The Ksat may differ from soil to soil according to the sodium adsorption ratio (SAR), water electrical conductivity (ECw), soil texture, and clay mineralogical assemblage. In this study, an experiment with vertical columns and constant-load permeameters was conducted to evaluate changes in soil Ksat with waters comprising five ECw values (128, 718, 1709, 2865, and 4671 µS cm−1) and five SAR values [0, 5, 12, 20, and 30 (mmolc L−1)0.5] in combination. Horizons from nine northeastern Brazilian soils (ranging from tropical to semiarid) were selected according to their texture and clay mineralogical composition. The data obtained were fit with multiple regression equations for Ksat as a function of ECw and SAR. This study also determined the null SAR at each ECw level, using Ksat = 0 on each equation, to predict the SAR needed to achieve zero drainage on each soil for each ECw level and the threshold electrolyte concentration (CTH) that would lead to a 20% reduction of maximum Ksat. Neither the ECw nor SAR of the applied waters affected the Ksat of soils with a mineralogical assemblage of oxides and kaolinite such as Ferralsol, Nitisol, and Lixisol, with an average Ksat of 2.75, 6.06, and 3.33 cm h−1, respectively. In smectite- and illite-rich soils, the Ksat increased with higher ECw levels and decreased with higher SAR levels, especially comparing the soil’s estimated Ksat for water with low ECw and high SAR in combination (ECw of 128 µS cm−1 and SAR 30) and water with high ECw and low SAR in combination (ECw of 4671 µS cm−1 and SAR 0) such as Regosol (4.95 to 10.94 cm h−1); Vertisol (0.28 to 2.04 cm h−1); Planosol (0 to 0.29 cm h−1); Luvisol (0.46 to 2.12 cm h−1); Cambisol (0 to 0.23 cm h−1); and Fluvisol (1.87 to 3.34 cm h−1). The CTH was easily reached in soils with high concentrations of highly active clays such as smectites. In sandy soils, the target CTH was only reached under extremely high SAR values, indicating a greater resistance of these soils to salinization/sodification. Due to their mineralogical assemblage, soils from tropical sub-humid/hot and semiarid climates were more affected by treatments than soils from tropical humid/hot climates, indicating serious risks of physical and chemical degradation. The results showed the importance of monitoring water quality for irrigation, mainly in less weathered, more clayey soils, with high clay activity to minimize the rate of salt accumulation in soils of the Brazilian semiarid region. Our study also proved that clay mineralogy had more influence on the Ksat than clay concentration, mainly in soils irrigated with saline and sodic waters, and that soils with highly active smectite are more prone to degradation than soils with high concentrations of kaolinite.
- Open Access
- 1 May 2024
- Published by FapUNIFESP (SciELO) in Revista Brasileira de Engenharia Agrícola E Ambiental
- Vol. 28 (5) , e276677
Salt tolerance and foliar spectral responses in seedlings of four ornamental herbaceous species
Studies on using brackish water for the irrigation of ornamental species are still scarce, mainly considering qualitative aspects of the plants. Therefore, the present study aimed to identify salt tolerance and characterize leaf spectral responses of herbaceous ornamental species at the stage of commercial seedling production. The research was carried out from December 2020 to February 2021, under greenhouse conditions, in Fortaleza - Ceará, Brazil. The experiment was conducted in a randomized block design with split plots, with main plots consisting of irrigation-water salinity levels (0.5, 2.0, 4.0, 6.0, and 8.0 dS m-1), and subplots by the species Catharanthus roseus, Celosia cristata, Celosia plumosa, and Chrysanthemum coronarium, with four replications. The evaluation parameters were dry mass production, visual sensory analysis, salt tolerance, and leaf spectral responses. Plant visual quality was maintained up to 2.0 dS m-1 for Chrysanthemum coronarium and 4.0 dS m-1 for Celosia cristata, Celosia plumosa, and Catharanthus roseus, which were classified as moderately tolerant at those respective salinity levels. Salinity caused noticeable changes in leaf spectral responses, especially in the visible region.
- 1 May 2024
- Published by FapUNIFESP (SciELO) in Revista Brasileira de Engenharia Agrícola E Ambiental
- Vol. 28 (5) , e276677
Open AccessSalt tolerance and foliar spectral responses in seedlings of four ornamental herbaceous species
Studies on using brackish water for the irrigation of ornamental species are still scarce, mainly considering qualitative aspects of the plants. Therefore, the present study aimed to identify salt tolerance and characterize leaf spectral responses of herbaceous ornamental species at the stage of commercial seedling production. The research was carried out from December 2020 to February 2021, under greenhouse conditions, in Fortaleza - Ceará, Brazil. The experiment was conducted in a randomized block design with split plots, with main plots consisting of irrigation-water salinity levels (0.5, 2.0, 4.0, 6.0, and 8.0 dS m-1), and subplots by the species Catharanthus roseus, Celosia cristata, Celosia plumosa, and Chrysanthemum coronarium, with four replications. The evaluation parameters were dry mass production, visual sensory analysis, salt tolerance, and leaf spectral responses. Plant visual quality was maintained up to 2.0 dS m-1 for Chrysanthemum coronarium and 4.0 dS m-1 for Celosia cristata, Celosia plumosa, and Catharanthus roseus, which were classified as moderately tolerant at those respective salinity levels. Salinity caused noticeable changes in leaf spectral responses, especially in the visible region.
- Open Access
- 1 April 2024
- Published by FapUNIFESP (SciELO) in Revista Brasileira de Engenharia Agrícola E Ambiental
- Vol. 28 (4) , e278645
Algae biostimulant improves salt tolerance and visual quality of tropical ornamental herbaceous species
The use of biostimulants may mitigate the deleterious effects of salt stress on plant growth and physiological variables. Thus, the present study aimed to evaluate the growth, physiology, organic solutes, and visual characteristics of two tropical ornamental species (Celosia argentea and Catharanthus roseus) cultivated with brackish waters and treated with Ascophyllum nodosum extract. The experiment was performed in greenhouse conditions. The experimental design was a complete randomized block arranged in a split-plot scheme. The plots comprised three levels of electrical conductivity of the irrigation water (ECw - 0.5, 2.5, and 4.5 dS m-1), the subplots four concentrations of algae extract (0, 400, 800, and 1200 mg L-1), and the sub-subplots two tropical ornamental herbaceous species [C. argentea and C. roseus]. The salinity of the irrigation water negatively affects the morphological and physiological characteristics of the two species studied, mainly C. roseus. Irrigation with water up to 2.5 dS m-1 favored visual quality and increased the purchasing preference for C. argentea. The use of intermediate concentrations (400 mg L-1) of algae extract (A. nodosum) promoted partial mitigation of the effects of salt stress on biomass production and leaf gas exchange, especially for C. argentea, but these positive responses decreased or disappeared with the intensification of salt stress and the increase in algae extract concentration.
- 1 April 2024
- Published by FapUNIFESP (SciELO) in Revista Brasileira de Engenharia Agrícola E Ambiental
- Vol. 28 (4) , e278645
Open AccessAlgae biostimulant improves salt tolerance and visual quality of tropical ornamental herbaceous species
The use of biostimulants may mitigate the deleterious effects of salt stress on plant growth and physiological variables. Thus, the present study aimed to evaluate the growth, physiology, organic solutes, and visual characteristics of two tropical ornamental species (Celosia argentea and Catharanthus roseus) cultivated with brackish waters and treated with Ascophyllum nodosum extract. The experiment was performed in greenhouse conditions. The experimental design was a complete randomized block arranged in a split-plot scheme. The plots comprised three levels of electrical conductivity of the irrigation water (ECw - 0.5, 2.5, and 4.5 dS m-1), the subplots four concentrations of algae extract (0, 400, 800, and 1200 mg L-1), and the sub-subplots two tropical ornamental herbaceous species [C. argentea and C. roseus]. The salinity of the irrigation water negatively affects the morphological and physiological characteristics of the two species studied, mainly C. roseus. Irrigation with water up to 2.5 dS m-1 favored visual quality and increased the purchasing preference for C. argentea. The use of intermediate concentrations (400 mg L-1) of algae extract (A. nodosum) promoted partial mitigation of the effects of salt stress on biomass production and leaf gas exchange, especially for C. argentea, but these positive responses decreased or disappeared with the intensification of salt stress and the increase in algae extract concentration.
- Open Access
Best Morpho-Physiological Parameters to Characterize Seed-Potato Plant Growth under Aeroponics: A Pilot Study
Although plant characterization under the International Potato Center’s (CIP’s) aeroponic system requires many morpho-physiological parameters to evaluate a cultivar, there is no method to evaluate the best parameters or the most suitable cultivation time. Thus, several morpho-physiological parameters were compared under a modified aeroponic system, using different statistical tools, to determine the best parameters and most efficient time to characterize seed-potato plants. We evaluated 21 parameters for cv. Agata under a randomized complete block design with weekly harvests for 9 weeks. The best parameters for growth characterization were selected based on multivariate statistical approaches involving correlation plots, similarity clusters (dendrograms), and principal component analysis. The best parameters for seed potato characterization were as follows, in order of importance: main stem diameter, leaf number, the length of the fourth leaf, leaf area, number of mini-tubers, mini-tuber fresh weight, root dry weight, and total dry weight. The days after transplanting (DAT) significantly affected the morpho-physiological parameters, with 45 DAT being the best cultivation time to estimate mini-tuber yield, and the data for bi-weekly harvests were as reliable as for weekly harvests. Our results, applied to either the CIP or to our modified aeroponics method, will be valuable in streamlining the characterization of other seed potato cultivars used by certified producers.
Open AccessBest Morpho-Physiological Parameters to Characterize Seed-Potato Plant Growth under Aeroponics: A Pilot Study
Although plant characterization under the International Potato Center’s (CIP’s) aeroponic system requires many morpho-physiological parameters to evaluate a cultivar, there is no method to evaluate the best parameters or the most suitable cultivation time. Thus, several morpho-physiological parameters were compared under a modified aeroponic system, using different statistical tools, to determine the best parameters and most efficient time to characterize seed-potato plants. We evaluated 21 parameters for cv. Agata under a randomized complete block design with weekly harvests for 9 weeks. The best parameters for growth characterization were selected based on multivariate statistical approaches involving correlation plots, similarity clusters (dendrograms), and principal component analysis. The best parameters for seed potato characterization were as follows, in order of importance: main stem diameter, leaf number, the length of the fourth leaf, leaf area, number of mini-tubers, mini-tuber fresh weight, root dry weight, and total dry weight. The days after transplanting (DAT) significantly affected the morpho-physiological parameters, with 45 DAT being the best cultivation time to estimate mini-tuber yield, and the data for bi-weekly harvests were as reliable as for weekly harvests. Our results, applied to either the CIP or to our modified aeroponics method, will be valuable in streamlining the characterization of other seed potato cultivars used by certified producers.
- Open Access
- 5 May 2023
- Published by Oxford University Press (OUP) in The Plant Cell
- Vol. 35 (8) , 2750-2772
Plant phase extraction: A method for enhanced discovery of the RNA-binding proteome and its dynamics in plants
RNA-binding proteins (RBPs) play critical roles in posttranscriptional gene regulation. Current methods of systematically profiling RBPs in plants have been predominantly limited to proteins interacting with polyadenylated (poly(A)) RNAs. We developed a method called plant phase extraction (PPE), which yielded a highly comprehensive RNA-binding proteome (RBPome), uncovering 2,517 RBPs from Arabidopsis (Arabidopsis thaliana) leaf and root samples with a highly diverse array of RNA-binding domains. We identified traditional RBPs that participate in various aspects of RNA metabolism and a plethora of nonclassical proteins moonlighting as RBPs. We uncovered constitutive and tissue-specific RBPs essential for normal development and, more importantly, revealed RBPs crucial for salinity stress responses from a RBP–RNA dynamics perspective. Remarkably, 40% of the RBPs are non-poly(A) RBPs that were not previously annotated as RBPs, signifying the advantage of PPE in unbiasedly retrieving RBPs. We propose that intrinsically disordered regions contribute to their nonclassical binding and provide evidence that enzymatic domains from metabolic enzymes have additional roles in RNA binding. Taken together, our findings demonstrate that PPE is an impactful approach for identifying RBPs from complex plant tissues and pave the way for investigating RBP functions under different physiological and stress conditions at the posttranscriptional level.
- 5 May 2023
- Published by Oxford University Press (OUP) in The Plant Cell
- Vol. 35 (8) , 2750-2772
Open AccessPlant phase extraction: A method for enhanced discovery of the RNA-binding proteome and its dynamics in plants
RNA-binding proteins (RBPs) play critical roles in posttranscriptional gene regulation. Current methods of systematically profiling RBPs in plants have been predominantly limited to proteins interacting with polyadenylated (poly(A)) RNAs. We developed a method called plant phase extraction (PPE), which yielded a highly comprehensive RNA-binding proteome (RBPome), uncovering 2,517 RBPs from Arabidopsis (Arabidopsis thaliana) leaf and root samples with a highly diverse array of RNA-binding domains. We identified traditional RBPs that participate in various aspects of RNA metabolism and a plethora of nonclassical proteins moonlighting as RBPs. We uncovered constitutive and tissue-specific RBPs essential for normal development and, more importantly, revealed RBPs crucial for salinity stress responses from a RBP–RNA dynamics perspective. Remarkably, 40% of the RBPs are non-poly(A) RBPs that were not previously annotated as RBPs, signifying the advantage of PPE in unbiasedly retrieving RBPs. We propose that intrinsically disordered regions contribute to their nonclassical binding and provide evidence that enzymatic domains from metabolic enzymes have additional roles in RNA binding. Taken together, our findings demonstrate that PPE is an impactful approach for identifying RBPs from complex plant tissues and pave the way for investigating RBP functions under different physiological and stress conditions at the posttranscriptional level.
- 19 January 2023
- Published by Wiley in Crop Science
- Vol. 63 (2) , 585-597
Salinity responses in 24 guar genotypes are linked to multigenic regulation explaining the complexity of tolerance mechanisms in planta
Guar (Cyamopsis tetragonoloba (L.) Taub.) is an economically important, drought‐tolerant legume crop affected by moderate to high salinity. Guar has various industrial applications, including gum extracted from seeds that is widely used in the oil and natural gas industries. In this investigation, we evaluated the salinity tolerance of different guar genotypes and their relation to genetic mechanisms regulating guar responses to salinity stress. We screened 24 guar genotypes in a greenhouse lysimeter system under control (electrical conductivity (EC) = 1.46 dS m−1) and high salinity (EC = 13.65 dS m−1) treatments. Both length and biomass of shoots were significantly affected by salinity compared to roots, indicating higher shoot than root sensitivity to salinity. Twenty‐four genotypes were classified based on salt tolerance index for each trait. Tissue ion analysis revealed that roots accumulated over 10‐fold higher Na than leaves, demonstrating that guar effectively regulated the root‐to‐shoot movement of Na+. However, higher Cl concentrations in leaves than roots indicated less regulatory control of Cl− movement. Based on the morphological traits and tissue ion analysis, six genotypes (PI 164486, PI 253186, PI 26152, PI 158125, PI 179926, and PI 263698) with different responses to salinity were selected for gene expression analysis. Expression patterns of different genes showed that a complex network of component traits, including Na+ exclusion, Cl− exclusion, and tissue tolerance, regulate salinity tolerance in guar. Hence, the genetic information about different component traits will benefit guar breeders in developing new varieties that are more tolerant to salinity than current ones.
- 19 January 2023
- Published by Wiley in Crop Science
- Vol. 63 (2) , 585-597
Salinity responses in 24 guar genotypes are linked to multigenic regulation explaining the complexity of tolerance mechanisms in planta
Guar (Cyamopsis tetragonoloba (L.) Taub.) is an economically important, drought‐tolerant legume crop affected by moderate to high salinity. Guar has various industrial applications, including gum extracted from seeds that is widely used in the oil and natural gas industries. In this investigation, we evaluated the salinity tolerance of different guar genotypes and their relation to genetic mechanisms regulating guar responses to salinity stress. We screened 24 guar genotypes in a greenhouse lysimeter system under control (electrical conductivity (EC) = 1.46 dS m−1) and high salinity (EC = 13.65 dS m−1) treatments. Both length and biomass of shoots were significantly affected by salinity compared to roots, indicating higher shoot than root sensitivity to salinity. Twenty‐four genotypes were classified based on salt tolerance index for each trait. Tissue ion analysis revealed that roots accumulated over 10‐fold higher Na than leaves, demonstrating that guar effectively regulated the root‐to‐shoot movement of Na+. However, higher Cl concentrations in leaves than roots indicated less regulatory control of Cl− movement. Based on the morphological traits and tissue ion analysis, six genotypes (PI 164486, PI 253186, PI 26152, PI 158125, PI 179926, and PI 263698) with different responses to salinity were selected for gene expression analysis. Expression patterns of different genes showed that a complex network of component traits, including Na+ exclusion, Cl− exclusion, and tissue tolerance, regulate salinity tolerance in guar. Hence, the genetic information about different component traits will benefit guar breeders in developing new varieties that are more tolerant to salinity than current ones.