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Diane M. Beckles
Department of Plant Sciences, University of California, Davis, CA, 95616, USA

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Journal article
Published: 14 March 2021 in Scientia Horticulturae
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Postharvest handling of tomato (Solanum lycopersicum L.), specifically low-temperature storage and early harvest, are used to extend shelf life but often reduce fruit quality. Recent work suggests that DNA methylation dynamics influences fruit ripening through the demethylase SlDML2 gene. However, the influence of postharvest handling on DNA methylation in relation to fruit quality is unclear. This work aimed to clarify these issues by analyzing DNA methylation using methyl-sensitive amplification polymorphism (MSAP), semi-quantitative transcriptional analysis of marker genes for fruit quality (RIN; RIPENING INHIBITOR) and DNA methylation (SlDML2; Solanum lycopersicum L. DNA demethylase 2), and, fruit biochemical quality biomarkers. Multivariate analysis of these data suggested that fruit DNA methylation state was associated with different postharvest handling techniques. Chilled postharvest fruit were distinct in their DNA methylation state and quality characteristics, which implied that these three phenomena i.e., chilling, methylation, and quality are highly connected. In addition, different postharvest handling methods modulated SlDML2 transcript levels but had little effect on the level of RIN transcripts in fruit that reached the Turning stage after early harvest, and cold storage. Although not a comprehensive global assessment, these data collectively helped to advance our interpretation of tomato fruit ripening. In conclusion, our findings revealed that postharvest-induced variation in fruit quality is in relation to DNA methylation. Long-term this work will help better connect physiological changes in tomato fruit to events happening at the molecular level.

ACS Style

Jiaqi Zhou; Bixuan Chen; Karin Albornoz; Diane M. Beckles. Postharvest handling induces changes in fruit DNA methylation status and is associated with alterations in fruit quality in tomato (Solanum lycopersicum L.). Scientia Horticulturae 2021, 283, 110090 .

AMA Style

Jiaqi Zhou, Bixuan Chen, Karin Albornoz, Diane M. Beckles. Postharvest handling induces changes in fruit DNA methylation status and is associated with alterations in fruit quality in tomato (Solanum lycopersicum L.). Scientia Horticulturae. 2021; 283 ():110090.

Chicago/Turabian Style

Jiaqi Zhou; Bixuan Chen; Karin Albornoz; Diane M. Beckles. 2021. "Postharvest handling induces changes in fruit DNA methylation status and is associated with alterations in fruit quality in tomato (Solanum lycopersicum L.)." Scientia Horticulturae 283, no. : 110090.

Research article
Published: 17 February 2021 in PLOS ONE
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Coffee (Coffea spp.) is one of the most popular refreshing beverages globally. Coffee lipid diversity has untapped potential for improving coffee marketability because lipids contribute significantly to both the health benefits and cup quality of coffee. However, in spite of its potential importance, there have not been extensive studies of lipids among C. canephora genotypes. In this study, ultra-performance liquid chromatography coupled with mass spectrometry (UPLC–MS) profiling of lipid molecules was performed for 30 genotypes consisting of 15 cultivated and 15 conserved genotypes of C. canephora in Southwestern Nigeria. We identified nine classes of lipids in the 30 genotypes which belong to the ‘Niaouli’, ‘Kouillou’ and ‘Java Robusta’ group: among these, the most abundant lipid class was the triacylglycerols, followed by the fatty acyls group. Although ‘Niaouli’ diverged from the ‘Kouillou’ and ‘Java Robusta’ genotypes when their lipid profiles were compared, there was greater similarity in their lipid composition by multivariate analysis, compared to that observed when their primary metabolites and especially their secondary metabolite profiles were examined. However, distinctions could be made among genotypes. Members of the fatty acyls group had the greatest power to discriminate among genotypes, however, lipids that were low in abundance e.g. a cholesterol ester (20:3), and phosphotidylethanolamine (34:0) were also helpful to understand the relationships among C. canephora genotypes. The divergent lipid profiles identified among the C. canephora genotypes, correlated with their Single Nucleotide Polymorphism grouping as assessed by genotype-by-sequencing, and will be exploited to improve coffee cup quality.

ACS Style

Chinyere F. Anagbogu; Jiaqi Zhou; Festus O. Olasupo; Mohammed Baba Nitsa; Diane M. Beckles. Lipidomic and metabolomic profiles of Coffea canephora L. beans cultivated in Southwestern Nigeria. PLOS ONE 2021, 16, e0234758 .

AMA Style

Chinyere F. Anagbogu, Jiaqi Zhou, Festus O. Olasupo, Mohammed Baba Nitsa, Diane M. Beckles. Lipidomic and metabolomic profiles of Coffea canephora L. beans cultivated in Southwestern Nigeria. PLOS ONE. 2021; 16 (2):e0234758.

Chicago/Turabian Style

Chinyere F. Anagbogu; Jiaqi Zhou; Festus O. Olasupo; Mohammed Baba Nitsa; Diane M. Beckles. 2021. "Lipidomic and metabolomic profiles of Coffea canephora L. beans cultivated in Southwestern Nigeria." PLOS ONE 16, no. 2: e0234758.

Review article
Published: 01 January 2021 in Horticulture Research
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Postharvest waste and loss of horticultural crops exacerbates the agricultural problems facing humankind and will continue to do so in the next decade. Fruits and vegetables provide us with a vast spectrum of healthful nutrients, and along with ornamentals, enrich our lives with a wide array of pleasant sensory experiences. These commodities are, however, highly perishable. Approximately 33% of the produce that is harvested is never consumed since these products naturally have a short shelf-life, which leads to postharvest loss and waste. This loss, however, could be reduced by breeding new crops that retain desirable traits and accrue less damage over the course of long supply chains. New gene-editing tools promise the rapid and inexpensive production of new varieties of crops with enhanced traits more easily than was previously possible. Our aim in this review is to critically evaluate gene editing as a tool to modify the biological pathways that determine fruit, vegetable, and ornamental quality, especially after storage. We provide brief and accessible overviews of both the CRISPR–Cas9 method and the produce supply chain. Next, we survey the literature of the last 30 years, to catalog genes that control or regulate quality or senescence traits that are “ripe” for gene editing. Finally, we discuss barriers to implementing gene editing for postharvest, from the limitations of experimental methods to international policy. We conclude that in spite of the hurdles that remain, gene editing of produce and ornamentals will likely have a measurable impact on reducing postharvest loss and waste in the next 5–10 years.

ACS Style

Emma N. Shipman; Jingwei Yu; Jiaqi Zhou; Karin Albornoz; Diane M. Beckles. Can gene editing reduce postharvest waste and loss of fruit, vegetables, and ornamentals? Horticulture Research 2021, 8, 1 -21.

AMA Style

Emma N. Shipman, Jingwei Yu, Jiaqi Zhou, Karin Albornoz, Diane M. Beckles. Can gene editing reduce postharvest waste and loss of fruit, vegetables, and ornamentals? Horticulture Research. 2021; 8 (1):1-21.

Chicago/Turabian Style

Emma N. Shipman; Jingwei Yu; Jiaqi Zhou; Karin Albornoz; Diane M. Beckles. 2021. "Can gene editing reduce postharvest waste and loss of fruit, vegetables, and ornamentals?" Horticulture Research 8, no. 1: 1-21.

Journal article
Published: 21 December 2020 in Horticulturae
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The GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) proteins are a family of plant-specific transcription factors that regulate plant growth, development, and stress response. Currently, the role of GRAS transcription factors in various abiotic stress responses has not been systematically studied in cucumber (Cucumis sativus L.), a popular vegetable crop. Here, we provide a comprehensive bioinformatics analysis of the 35 GRAS genes identified in the cucumber genome. In this study, cucumber genotypes, i.e., “CG104”, which is stress-tolerant, and genotype “CG37”, which is stress-sensitive, were examined to provide insight on potential differences in the GRAS-regulated abiotic stress pathways. Transcriptional analysis by RNA-seq or qRT-PCR of these two genotypes revealed common and divergent functions of CsGRAS genes regulated by low and high temperatures, salinity, and by exposure to the phytohormones gibberellin (GA) and abscisic acid (ABA). Notably, CsGRAS2 (DELLA) and CsGRAS26 (LISCL) were regulated by all abiotic stresses and hormone treatments, suggesting that they may function in the biological cross-talk between multiple signaling pathways. This study provides candidate genes for improving cucumber tolerance to various environmental stresses.

ACS Style

Caixia Li; Shaoyun Dong; Xiaoping Liu; Kailiang Bo; Han Miao; Diane M. Beckles; Shengping Zhang; Xingfang Gu. Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses. Horticulturae 2020, 6, 110 .

AMA Style

Caixia Li, Shaoyun Dong, Xiaoping Liu, Kailiang Bo, Han Miao, Diane M. Beckles, Shengping Zhang, Xingfang Gu. Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses. Horticulturae. 2020; 6 (4):110.

Chicago/Turabian Style

Caixia Li; Shaoyun Dong; Xiaoping Liu; Kailiang Bo; Han Miao; Diane M. Beckles; Shengping Zhang; Xingfang Gu. 2020. "Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses." Horticulturae 6, no. 4: 110.

Preprint content
Published: 09 October 2020
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Postharvest handling of tomato (Solanum lycopersicum L.), specifically low-temperature storage and early harvest are used to extend shelf life, but often reduce fruit quality. Recent work suggests that DNA methylation dynamics influences fruit ripening through the demethylase SlDML2 gene. However, the influence of postharvest handling on DNA methylation in relation to fruit quality is unclear. This work aimed to clarify these issues by analyzing DNA methylation using methyl-sensitive amplification polymorphism (MSAP), semi-quantitative transcriptional analysis of marker genes for fruit quality, (RIN; RIPENING INHIBITOR) and DNA methylation (SlDML2; Solanum lycopersicum L. DNA demethylase 2), and, fruit biochemical quality biomarkers. Multivariate analysis of these data supported the view that DNA methylation of fruit was influenced more by postharvest handling than ripening stage, however, fruit quality was influenced mainly by ripening. Fruit chilled postharvest were distinct in their DNA methylation state and quality characteristics, which implied that these three phenomena i.e., chilling, methylation, and quality are highly connected. In addition, different postharvest handling methods modulated SlDML2 transcript levels but had little effect on the level of RIN transcripts in fruit that reached the Turning stage after early harvest, and cold storage. These data collectively helped to advance our interpretation of tomato fruit ripening. In conclusion, our findings revealed that postharvest-induced variation in fruit quality is in relation to DNA methylation. Long-term this work will help better connect physiological changes in tomato fruit to events happening at the molecular level.

ACS Style

Jiaqi Zhou; Bixuan Chen; Karin Albornoz; Diane Maria Beckles. Postharvest handling induces changes in fruit DNA methylation status and is associated with alterations in fruit quality in tomato (Solanum lycopersicum L.). 2020, 1 .

AMA Style

Jiaqi Zhou, Bixuan Chen, Karin Albornoz, Diane Maria Beckles. Postharvest handling induces changes in fruit DNA methylation status and is associated with alterations in fruit quality in tomato (Solanum lycopersicum L.). . 2020; ():1.

Chicago/Turabian Style

Jiaqi Zhou; Bixuan Chen; Karin Albornoz; Diane Maria Beckles. 2020. "Postharvest handling induces changes in fruit DNA methylation status and is associated with alterations in fruit quality in tomato (Solanum lycopersicum L.)." , no. : 1.

Preprint content
Published: 03 June 2020
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Coffee (Coffea spp.) is one of the most popular refreshments globally. Coffee lipid diversity has untapped potential for improving coffee marketability because lipids contribute significantly to both the health benefits and cup quality of coffee. However, there have not been extensive studies of lipids of C. canephora genotypes. In this study, Ultra-performance liquid chromatography coupled with mass spectrometry (UPLC–MS) profiling of lipid molecules was performed for 30 genotypes consisting of 15 cultivated and 15 conserved genotypes of C. canephora in Southwestern Nigeria. We identified nine classes of lipids in the 30 genotypes which belong to the ‘Niaouli’, ‘Kouillou’ and ‘Java Robusta’ group: among these, the most abundant lipid class was the triacylglycerols, followed by the fatty acyls group. Although ‘Niaouli’ diverged from the ‘Kouillou’ and ‘Java Robusta’ genotypes when their lipid profiles were compared, there was greater similarity in their lipid composition by multivariate analysis, compared to that observed when their primary metabolites and especially their secondary metabolite profiles were examined. However, distinctions could be made among genotypes. Members of the fatty acyls group had the greatest power to discriminate among genotypes, however, lipids that were low in abundance e.g. a cholesterol ester (20:3), and phosphotidylethanolamine (34:0) were also helpful to understand the relationships among C. canephora genotypes. The lipid diversity identified among the C. canephora genotypes examined correlated with their overall Single Nucleotide Polymorphism diversity assessed by genotype-by-sequencing, supporting the relevance of this study to coffee cup quality improvement.

ACS Style

Chinyere F. Anagbogu; Jiaqi Zhou; Festus O. Olasupo; Mohammed Baba-Nitsa; Diane Maria Beckles. Lipidomic and metabolomic profiles of Coffea canephora L. beans cultivated in South-western Nigeria. 2020, 1 .

AMA Style

Chinyere F. Anagbogu, Jiaqi Zhou, Festus O. Olasupo, Mohammed Baba-Nitsa, Diane Maria Beckles. Lipidomic and metabolomic profiles of Coffea canephora L. beans cultivated in South-western Nigeria. . 2020; ():1.

Chicago/Turabian Style

Chinyere F. Anagbogu; Jiaqi Zhou; Festus O. Olasupo; Mohammed Baba-Nitsa; Diane Maria Beckles. 2020. "Lipidomic and metabolomic profiles of Coffea canephora L. beans cultivated in South-western Nigeria." , no. : 1.

Journal article
Published: 01 April 2020 in Acta Horticulturae
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ACS Style

Karin Albornoz; B. Chen; M. McCarthy; L. Zhang; M. Cantwell; Diane Beckles. Investigating postharvest chilling injury in tomato (Solanum lycopersicum L.) fruit using magnetic resonance imaging and 5-azacytidine, a hypomethylation agent. Acta Horticulturae 2020, 243 -252.

AMA Style

Karin Albornoz, B. Chen, M. McCarthy, L. Zhang, M. Cantwell, Diane Beckles. Investigating postharvest chilling injury in tomato (Solanum lycopersicum L.) fruit using magnetic resonance imaging and 5-azacytidine, a hypomethylation agent. Acta Horticulturae. 2020; (1278):243-252.

Chicago/Turabian Style

Karin Albornoz; B. Chen; M. McCarthy; L. Zhang; M. Cantwell; Diane Beckles. 2020. "Investigating postharvest chilling injury in tomato (Solanum lycopersicum L.) fruit using magnetic resonance imaging and 5-azacytidine, a hypomethylation agent." Acta Horticulturae , no. 1278: 243-252.

Journal article
Published: 02 January 2020 in Plants
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Starch provides plants with carbon and energy during stressful periods; however, relatively few regulators of starch metabolism under stress-induced carbon starvation have been discovered. We studied a protein kinase Ser/Thr/Tyr (STY) 46, identified by gene co-expression network analysis as a potential regulator of the starch starvation response in Arabidopsis thaliana. We showed that STY46 was induced by (1) abscisic acid and prolonged darkness, (2) by abiotic stressors, including salinity and osmotic stress, and (3) by conditions associated with carbon starvation. Characterization of STY46 T-DNA knockout mutants indicated that there was functional redundancy among the STY gene family, as these genotypes did not show strong phenotypes. However, Arabidopsis with high levels of STY46 transcripts (OE-25) grew faster at the early seedling stage, had higher photosynthetic rates, and more carbon was stored as protein in the seeds under control conditions. Further, OE-25 source leaf accumulated more sugars under 100 mM NaCl stress, and salinity also accelerated root growth, which is consistent with an adaptive response. Salt-stressed OE-25 partitioned 14C towards sugars and amino acids, and away from starch and protein in source leaves. Together, these findings suggested that STY46 may be part of the salinity stress response pathway that utilizes starch during early plant growth.

ACS Style

Shaoyun Dong; Fenglan Zhang; Diane M. Beckles. A Cytosolic Protein Kinase STY46 in Arabidopsis thaliana Is Involved in Plant Growth and Abiotic Stress Response. Plants 2020, 9, 57 .

AMA Style

Shaoyun Dong, Fenglan Zhang, Diane M. Beckles. A Cytosolic Protein Kinase STY46 in Arabidopsis thaliana Is Involved in Plant Growth and Abiotic Stress Response. Plants. 2020; 9 (1):57.

Chicago/Turabian Style

Shaoyun Dong; Fenglan Zhang; Diane M. Beckles. 2020. "A Cytosolic Protein Kinase STY46 in Arabidopsis thaliana Is Involved in Plant Growth and Abiotic Stress Response." Plants 9, no. 1: 57.

Journal article
Published: 18 October 2019 in Plants
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The flavor and health benefits of coffee (Coffea spp.) are derived from the metabolites that accumulate in the mature bean. However, the chemical profiles of many C. canephora genotypes remain unknown, even as the production of these coffee types increases globally. Therefore, we used Gas Chromatography-Mass Spectrophotometry to determine the chemical composition of C. canephora genotypes in Nigeria-those conserved in germplasm repositories and those cultivated by farmers. GC-MS revealed 340 metabolites in the ripe beans, with 66 metabolites differing (p-value < 0.05) across the represented group. Univariate and multivariate approaches showed that the 'Niaouli' genotypes could be clearly distinguished from 'Kouillou' and 'Java' genotypes, while there was almost no distinction between 'Kouillou' and 'Java,'. Varietal genotyping based on bean metabolite profiling was synchronous with that based on genome-wide Single Nucleotide Polymorphism analysis. Across genotypes, the sucrose-to-caffeine ratio was low, a characteristic indicative of low cup quality. The sucrose-to-caffeine ratio was also highly correlated, indicative of common mechanisms regulating the accumulation of these compounds. Nevertheless, this strong correlative link was broken within the 'Niaouli' group, as caffeine and sucrose content were highly variable among these genotypes. These 'Niaouli' genotypes could therefore serve as useful germplasm for starting a Nigerian C. canephora quality improvement breeding program.

ACS Style

Chinyere F. Anagbogu; Christopher O. Ilori; Ranjana Bhattacharjee; Olufemi O. Olaniyi; Diane M. Beckles. Gas Chromatography-Mass Spectrometry and Single Nucleotide Polymorphism-Genotype-By-Sequencing Analyses Reveal the Bean Chemical Profiles and Relatedness of Coffea canephora Genotypes in Nigeria. Plants 2019, 8, 425 .

AMA Style

Chinyere F. Anagbogu, Christopher O. Ilori, Ranjana Bhattacharjee, Olufemi O. Olaniyi, Diane M. Beckles. Gas Chromatography-Mass Spectrometry and Single Nucleotide Polymorphism-Genotype-By-Sequencing Analyses Reveal the Bean Chemical Profiles and Relatedness of Coffea canephora Genotypes in Nigeria. Plants. 2019; 8 (10):425.

Chicago/Turabian Style

Chinyere F. Anagbogu; Christopher O. Ilori; Ranjana Bhattacharjee; Olufemi O. Olaniyi; Diane M. Beckles. 2019. "Gas Chromatography-Mass Spectrometry and Single Nucleotide Polymorphism-Genotype-By-Sequencing Analyses Reveal the Bean Chemical Profiles and Relatedness of Coffea canephora Genotypes in Nigeria." Plants 8, no. 10: 425.

Original article
Published: 02 April 2019 in International Journal of Fruit Science
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One problem with the pink pulp color of the ‘Thong Dee’ (TD) pummelo (Citrus maxima [Burm.] Merr.) is that it becomes pale during some harvesting periods. The cause of the pale pulp is not known. Therefore, the aim of this study was to determine the effect of growing temperature and rainfall on carotenoid contents and pulp color in the TD fruit. The experiments were conducted in 11 harvesting periods over two years from four orchards. The pale pink pulp coincided with low lycopene and was observed when the average daily minimum temperature two months before harvest was less than 20°C. Lycopene content and a*, which indicates pulp ‘redness’, positively correlated with the average daily minimum temperature two months before harvest (r = 0.6644 and r= 0.6013, respectively). In addition, TD pulp mineral nutrients, which include N, P, K, Ca, Mg, Zn, Cu, Fe, B, Mn, and Na, were not significantly related to the lycopene levels or the pale pink color in the pulp (P> .05). It is possible to conclude that the pale pulp of pummelo fruit is caused by the growing temperature during fruit development. This is the first study that comprehensively addresses the effects of environmental conditions on the pulp color of pummelo fruit. Abbreviations : TD: ‘Thong Dee’; MAP: Months after pollination; ABA: Abscisic acid; GAs: Gibberellic acids; MEP: 2-C-methyl-D-erythritol 4-phosphate; TSS: Total soluble solids; TA: Titratable acidity; HPLC: High performance liquid chromatography; N: Nitrogen; P: Phosphorus; K: Potassium; Ca: Calcium; Mg: Magnesium; Cu: Copper; Zn: Zinc; B: Boron; Fe: Iron; Mn: Manganese; Na: Sodium

ACS Style

Parichat Buaban; Diane M. Beckles; Orarat Mongkolporn; Kietsuda Luengwilai. Lycopene Accumulation in Pummelo (Citrus Maxima [Burm.] Merr.) Is Influenced by Growing Temperature. International Journal of Fruit Science 2019, 20, 149 -163.

AMA Style

Parichat Buaban, Diane M. Beckles, Orarat Mongkolporn, Kietsuda Luengwilai. Lycopene Accumulation in Pummelo (Citrus Maxima [Burm.] Merr.) Is Influenced by Growing Temperature. International Journal of Fruit Science. 2019; 20 (2):149-163.

Chicago/Turabian Style

Parichat Buaban; Diane M. Beckles; Orarat Mongkolporn; Kietsuda Luengwilai. 2019. "Lycopene Accumulation in Pummelo (Citrus Maxima [Burm.] Merr.) Is Influenced by Growing Temperature." International Journal of Fruit Science 20, no. 2: 149-163.

Journal article
Published: 23 March 2019 in Scientia Horticulturae
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Seedlings have been used as an experimental model to understand plant response to chilling-stress. In this study, we investigated if the occurrence or severity of chilling injury correlated with genomic methylation state in cucumber radicles, using Methylation-Sensitive Amplification Polymorphism (MSAP) analysis. Radicles were chilled or treated with a methylation inhibitor, 5-azacytidine (AZA), or a combination thereof. Chilling cucumber radicles at 2.5 °C was marked by an immediate cessation in elongation and higher levels of genomic methylation. Rewarming was associated with a partial reversal of the methylation caused by chilling-stress, a decrease in genomic methylation to the same level as that before chilling, and to a resumption in radicle growth, but only to 18.6% of that without chilling. This cessation and recovery of elongation during and after chilling was also observed when radicles were treated with AZA. Under normal and rewarming conditions, 60% and 74% suppression of elongation were detected in AZA-treated radicles, respectively. Growth rate of the radicles was slowest in AZA-treated radicles after exposure to chilling-stress, suggesting a “double” suppressive effect due to the treatment combination. This was paralleled by methylation modifications at novel sites, with no change in the global methylation level, although the latter was expected to decrease as an effect of AZA. This work showed that DNA methylation is associated with, and may partially regulate, radicle elongation rate under chilling-stress, through a dynamic alteration of methylation pattern.

ACS Style

Bixuan Chen; Mikal E. Saltveit; Diane M. Beckles. Chilling-stress modifies DNA methylation level in cucumber (Cucumis sativus L.) seedling radicle to regulate elongation rate. Scientia Horticulturae 2019, 252, 14 -19.

AMA Style

Bixuan Chen, Mikal E. Saltveit, Diane M. Beckles. Chilling-stress modifies DNA methylation level in cucumber (Cucumis sativus L.) seedling radicle to regulate elongation rate. Scientia Horticulturae. 2019; 252 ():14-19.

Chicago/Turabian Style

Bixuan Chen; Mikal E. Saltveit; Diane M. Beckles. 2019. "Chilling-stress modifies DNA methylation level in cucumber (Cucumis sativus L.) seedling radicle to regulate elongation rate." Scientia Horticulturae 252, no. : 14-19.

Journal article
Published: 26 February 2019 in Scientific Reports
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Postharvest chilling injury (PCI) reduces fruit quality and shelf-life in tomato (Solanum lycopersicum L.). PCI has been traditionally studied in the pericarp, however its development is likely heterogeneous in different fruit tissues. To gain insight into PCI’s spatio-temporal development, we used postharvest biomarkers e.g. respiration and ethylene rates, ion leakage etc., to confirm the occurrence of PCI, and compared these data with molecular (gene expression), biophysical (MRI data) and biochemical parameters (Malondialdehyde (MDA) and starch content) from the pericarp or columella. Tissues were stored at control (12.5 °C) or PCI-inducing temperatures (2.5 or 5 °C) followed by rewarming at 20 °C. MRI and ion leakage revealed that cold irreversibly impairs ripening-associated membrane liquefaction; MRI also showed that the internal and external fruit tissues responded differently to cold. MDA and especially starch contents, were affected by chilling in a tissue-specific manner. The expression of the six genes studied: ACO1 and ACS2 (ripening), CBF1 (cold response), DHN, AOX1a and LoxB (stress-related) showed non-overlapping temporal and spatially-specific responses. Overall, the data highlighted the interconnectedness of fruit cold response and ripening, and showed how cold stress reconfigures the latter. They further underscored that multidimensional spatial and temporal biological studies are needed to develop effective solutions to PCI.

ACS Style

Karin Albornoz; Marita I. Cantwell; Lu Zhang; Diane M. Beckles. Integrative analysis of postharvest chilling injury in cherry tomato fruit reveals contrapuntal spatio-temporal responses to ripening and cold stress. Scientific Reports 2019, 9, 1 -14.

AMA Style

Karin Albornoz, Marita I. Cantwell, Lu Zhang, Diane M. Beckles. Integrative analysis of postharvest chilling injury in cherry tomato fruit reveals contrapuntal spatio-temporal responses to ripening and cold stress. Scientific Reports. 2019; 9 (1):1-14.

Chicago/Turabian Style

Karin Albornoz; Marita I. Cantwell; Lu Zhang; Diane M. Beckles. 2019. "Integrative analysis of postharvest chilling injury in cherry tomato fruit reveals contrapuntal spatio-temporal responses to ripening and cold stress." Scientific Reports 9, no. 1: 1-14.

Research article
Published: 07 February 2019 in Genetic Resources and Crop Evolution
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Coffea canephora is an important economic crop in Nigeria, however, little is known about the diversity inherent within, and the genetic relationship among coffee grown and conserved in the country. We examined the genetic diversity and relatedness among 48 Coffea genotypes which included: (a) C. arabica, C. abeokutae, C. liberica, and C. stenophylla, (b) 14 C. canephora accessions conserved in the germplasm of Cocoa Research Institute of Nigeria (CRIN), and (c) 30 farmer-cultivated genotypes collected from South-Western Nigeria. By analyzing 433048 single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing we discovered that previous characterizations of C. canephora based on morphological data were inconclusive. Here, we established the correct number of C. canephora varieties present in the CRIN genebank which was four and not six as previously described based on morphological characters. We found three distinct diversity structures within the C. canephora genepool that were dominated by a single genetic group determined from passport descriptors to most likely be of Congolese (Democratic Republic of Congo) origin. High uniformity was also found among the farmer-cultivated accessions with 99% of them representing C. canephora var. Niaouli as their ancestral background. The analysis showed that the genetic base of coffee germplasm in Nigeria is narrow compared to the large genetic diversity of C. canephora. Therefore, broadening this genetic base through future acquisition and hybridization is imperative. However, the relatively high genetic differentiation (FST estimate = 0.3037) identified between Java Robusta and Niaouli will be used as a starting point for our breeding program.

ACS Style

Chinyere F. Anagbogu; Ranjana Bhattacharjee; Christopher Ilori; Pumipat Tongyoo; Keji E. Dada; Anna A. Muyiwa; Paul Gepts; Diane M. Beckles. Genetic diversity and re-classification of coffee (Coffea canephora Pierre ex A. Froehner) from South Western Nigeria through genotyping-by-sequencing-single nucleotide polymorphism analysis. Genetic Resources and Crop Evolution 2019, 66, 685 -696.

AMA Style

Chinyere F. Anagbogu, Ranjana Bhattacharjee, Christopher Ilori, Pumipat Tongyoo, Keji E. Dada, Anna A. Muyiwa, Paul Gepts, Diane M. Beckles. Genetic diversity and re-classification of coffee (Coffea canephora Pierre ex A. Froehner) from South Western Nigeria through genotyping-by-sequencing-single nucleotide polymorphism analysis. Genetic Resources and Crop Evolution. 2019; 66 (3):685-696.

Chicago/Turabian Style

Chinyere F. Anagbogu; Ranjana Bhattacharjee; Christopher Ilori; Pumipat Tongyoo; Keji E. Dada; Anna A. Muyiwa; Paul Gepts; Diane M. Beckles. 2019. "Genetic diversity and re-classification of coffee (Coffea canephora Pierre ex A. Froehner) from South Western Nigeria through genotyping-by-sequencing-single nucleotide polymorphism analysis." Genetic Resources and Crop Evolution 66, no. 3: 685-696.

Journal article
Published: 01 February 2019 in African Journal of Food, Agriculture, Nutrition and Development
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ACS Style

Mk Mtunguja; Diane Beckles; Hs Laswai; Jc Ndunguru; Nj Sinha. Opportunities to Commercialize Cassava Production for Poverty Alleviation and Improved Food Security in Tanzania. African Journal of Food, Agriculture, Nutrition and Development 2019, 19, 13928 -13946.

AMA Style

Mk Mtunguja, Diane Beckles, Hs Laswai, Jc Ndunguru, Nj Sinha. Opportunities to Commercialize Cassava Production for Poverty Alleviation and Improved Food Security in Tanzania. African Journal of Food, Agriculture, Nutrition and Development. 2019; 19 (1):13928-13946.

Chicago/Turabian Style

Mk Mtunguja; Diane Beckles; Hs Laswai; Jc Ndunguru; Nj Sinha. 2019. "Opportunities to Commercialize Cassava Production for Poverty Alleviation and Improved Food Security in Tanzania." African Journal of Food, Agriculture, Nutrition and Development 19, no. 1: 13928-13946.

Review article
Published: 14 January 2019 in Journal of Plant Physiology
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Starch is a significant store of sugars, and the starch-sugar interconversion in source and sink tissues plays a profound physiological role in all plants. In this review, we discuss how changes in starch metabolism can facilitate adaptive changes in source-sink carbon allocation, for protection against environmental stresses. The stress-related roles of starch are described, and published mechanisms by which starch metabolism responds to short- or long-term water deficit, salinity, or extreme temperatures are discussed. Numerous examples of starch metabolism as a stress response are also provided, focusing on studies where carbohydrates and cognate enzymes were assayed in source, sink, or both. We develop a model that integrates these findings with the theoretical and known roles of sugars and starch in various species, tissues, and developmental stages. In this model, localized starch degradation into sugars is vital to the plant cold stress response, with the sugars produced providing osmoprotection. In contrast, high starch accumulation is prominent under salinity stress, and associated with higher assimilate allocation from source to sink. Our model explains how starch-sugar interconversion can be a convergent point for regulating carbon use in stress tolerance at the whole-plant level.

ACS Style

Shaoyun Dong; Diane M. Beckles. Dynamic changes in the starch-sugar interconversion within plant source and sink tissues promote a better abiotic stress response. Journal of Plant Physiology 2019, 234-235, 80 -93.

AMA Style

Shaoyun Dong, Diane M. Beckles. Dynamic changes in the starch-sugar interconversion within plant source and sink tissues promote a better abiotic stress response. Journal of Plant Physiology. 2019; 234-235 ():80-93.

Chicago/Turabian Style

Shaoyun Dong; Diane M. Beckles. 2019. "Dynamic changes in the starch-sugar interconversion within plant source and sink tissues promote a better abiotic stress response." Journal of Plant Physiology 234-235, no. : 80-93.

Journal article
Published: 18 June 2018 in Scientific Reports
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Plant carbon status is optimized for normal growth but is affected by abiotic stress. Here, we used 14C-labeling to provide the first holistic picture of carbon use changes during short-term osmotic, salinity, and cold stress in Arabidopsis thaliana. This could inform on the early mechanisms plants use to survive adverse environment, which is important for efficient agricultural production. We found that carbon allocation from source to sinks, and partitioning into major metabolite pools in the source leaf, sink leaves and roots showed both conserved and divergent responses to the stresses examined. Carbohydrates changed under all abiotic stresses applied; plants re-partitioned 14C to maintain sugar levels under stress, primarily by reducing 14C into the storage compounds in the source leaf, and decreasing 14C into the pools used for growth processes in the roots. Salinity and cold increased 14C-flux into protein, but as the stress progressed, protein degradation increased to produce amino acids, presumably for osmoprotection. Our work also emphasized that stress regulated the carbon channeled into starch, and its metabolic turnover. These stress-induced changes in starch metabolism and sugar export in the source were partly accompanied by transcriptional alteration in the T6P/SnRK1 regulatory pathway that are normally activated by carbon starvation.

ACS Style

Shaoyun Dong; Joshua Zhang; Diane M. Beckles. A pivotal role for starch in the reconfiguration of 14C-partitioning and allocation in Arabidopsis thaliana under short-term abiotic stress. Scientific Reports 2018, 8, 9314 .

AMA Style

Shaoyun Dong, Joshua Zhang, Diane M. Beckles. A pivotal role for starch in the reconfiguration of 14C-partitioning and allocation in Arabidopsis thaliana under short-term abiotic stress. Scientific Reports. 2018; 8 (1):9314.

Chicago/Turabian Style

Shaoyun Dong; Joshua Zhang; Diane M. Beckles. 2018. "A pivotal role for starch in the reconfiguration of 14C-partitioning and allocation in Arabidopsis thaliana under short-term abiotic stress." Scientific Reports 8, no. 1: 9314.

Journal article
Published: 01 March 2018 in Postharvest Biology and Technology
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ACS Style

Kietsuda Luengwilai; Diane M. Beckles; Ute Roessner; Daniel A. Dias; Veronica Lui; Jingtair Siriphanich. Identification of physiological changes and key metabolites coincident with postharvest internal browning of pineapple ( Ananas comosus L.) fruit. Postharvest Biology and Technology 2018, 137, 56 -65.

AMA Style

Kietsuda Luengwilai, Diane M. Beckles, Ute Roessner, Daniel A. Dias, Veronica Lui, Jingtair Siriphanich. Identification of physiological changes and key metabolites coincident with postharvest internal browning of pineapple ( Ananas comosus L.) fruit. Postharvest Biology and Technology. 2018; 137 ():56-65.

Chicago/Turabian Style

Kietsuda Luengwilai; Diane M. Beckles; Ute Roessner; Daniel A. Dias; Veronica Lui; Jingtair Siriphanich. 2018. "Identification of physiological changes and key metabolites coincident with postharvest internal browning of pineapple ( Ananas comosus L.) fruit." Postharvest Biology and Technology 137, no. : 56-65.

Article addendum
Published: 02 December 2017 in Plant Signaling & Behavior
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We have previously shown that overexpression of GSK3-like kinase 5 in rice (OsGSK5) was associated with higher starch accumulation and better growth under severe salinity stress. Short-term 14CO2 feeding experiments suggested that OsGSK5 promoted higher flux to starch accumulation in the roots under this condition and that this mechanism may help to underscore the better growth characteristics observed. Here, we expand upon this hypothesis and consider (1) how OsGSK5 action could fit into a signaling model that integrates salinity stress to changes in starch metabolism, and (2) how this would facilitate whole plant physiological adaptations in source-to-sink partitioning. We also discuss additional functions of OsGSK5, necessary to support this adaptive mechanism.

ACS Style

Maysaya Thitisaksakul; Shaoyun Dong; Diane M. Beckles. How rice Glycogen Synthase Kinase-like 5 (OsGSK5) integrates salinity stress response to source-sink adaptation: A proposed model. Plant Signaling & Behavior 2017, 12, e1403708 .

AMA Style

Maysaya Thitisaksakul, Shaoyun Dong, Diane M. Beckles. How rice Glycogen Synthase Kinase-like 5 (OsGSK5) integrates salinity stress response to source-sink adaptation: A proposed model. Plant Signaling & Behavior. 2017; 12 (12):e1403708.

Chicago/Turabian Style

Maysaya Thitisaksakul; Shaoyun Dong; Diane M. Beckles. 2017. "How rice Glycogen Synthase Kinase-like 5 (OsGSK5) integrates salinity stress response to source-sink adaptation: A proposed model." Plant Signaling & Behavior 12, no. 12: e1403708.

Journal article
Published: 01 January 2017 in Functional Plant Biology
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Rice (Oryza sativa L.) is very sensitive to soil salinity. To identify endogenous mechanisms that may help rice to better survive salt stress, we studied a rice GSK3-like isoform (OsGSK5), an orthologue of a Medicago GSK3 previously shown to enhance salinity tolerance in Arabidopsis by altering carbohydrate metabolism. We wanted to determine whether OsGSK5 functions similarly in rice. OsGSK5 was cloned and sequence, expression, evolutionary and functional analyses were conducted. OsGSK5 was expressed highest in rice seedling roots and was both salt and sugar starvation inducible in this tissue. A short-term salt-shock (150 mM) activated OsGSK5, whereas moderate (50 mM) salinity over the same period repressed the transcript. OsGSK5 response to salinity was due to an ionic effect since it was unaffected by polyethylene glycol. We engineered a rice line with 3.5-fold higher OsGSK5 transcript, which better tolerated cultivation on saline soils (EC = 8 and 10 dS m–2). This line produced more panicles and leaves, and a higher shoot biomass under high salt stress than the control genotypes. Whole-plant 14C-tracing and correlative analysis of OsGSK5 transcript with eco-physiological assessments pointed to the accelerated allocation of carbon to the root and its deposition as starch, as part of the tolerance mechanism.

ACS Style

Maysaya Thitisaksakul; Maria C. Arias; Shaoyun Dong; Diane M. Beckles. Overexpression of GSK3-like Kinase 5 (OsGSK5) in rice (Oryza sativa) enhances salinity tolerance in part via preferential carbon allocation to root starch. Functional Plant Biology 2017, 44, 705 .

AMA Style

Maysaya Thitisaksakul, Maria C. Arias, Shaoyun Dong, Diane M. Beckles. Overexpression of GSK3-like Kinase 5 (OsGSK5) in rice (Oryza sativa) enhances salinity tolerance in part via preferential carbon allocation to root starch. Functional Plant Biology. 2017; 44 (7):705.

Chicago/Turabian Style

Maysaya Thitisaksakul; Maria C. Arias; Shaoyun Dong; Diane M. Beckles. 2017. "Overexpression of GSK3-like Kinase 5 (OsGSK5) in rice (Oryza sativa) enhances salinity tolerance in part via preferential carbon allocation to root starch." Functional Plant Biology 44, no. 7: 705.

Journal article
Published: 01 September 2016 in Journal of Plant Physiology
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A typical symptom of postharvest chilling injury (PCI) in pineapple fruit (Ananas comosus (L.) Merr.) is internal browning (IB) near the fruit core. Since vascular bundles (VBs) are localized to this region, it was hypothesized that the VBs might be the site of IB. To test this, the anatomy and histochemistry of VBs during chilling stress in four pineapple cultivars with different levels of sensitivity to PCI were examined. Fruit were stored at 10°C for up to three weeks to stimulate translucency symptoms (TS; the initiation of IB). After three weeks of chilling exposure, the cultivars 'MD2' showed 0%, 'Pattavia' and 'Savee' showed 10-16%, and 'Trad Sri Thong' showed 100% TS and IB symptom. Scanning electron microscopy and in situ histochemical staining techniques that detect enzymes and substrates commonly associated with IB initiation were used in parallel. The TS of pineapple fruit coincided with the collapse of the phloem tissue. The VBs in the tissue where IB was initiated (i.e., the flesh adjacent to the core or F/C) had the highest activity of polyphenol oxidase, hydrogen peroxide, and phenolic compounds. The IB-resistant 'MD2' genotype had fewer VBs, but a greater proportion of sclerenchyma fibers (P<0.05) than did the susceptible 'Trad Sri Thong'. Based on these data, the first report of pineapple IB occurrence in the phloem was proposed.

ACS Style

Kietsuda Luengwilai; Diane M. Beckles; Jingtair Siriphanich. Postharvest internal browning of pineapple fruit originates at the phloem. Journal of Plant Physiology 2016, 202, 121 -133.

AMA Style

Kietsuda Luengwilai, Diane M. Beckles, Jingtair Siriphanich. Postharvest internal browning of pineapple fruit originates at the phloem. Journal of Plant Physiology. 2016; 202 ():121-133.

Chicago/Turabian Style

Kietsuda Luengwilai; Diane M. Beckles; Jingtair Siriphanich. 2016. "Postharvest internal browning of pineapple fruit originates at the phloem." Journal of Plant Physiology 202, no. : 121-133.