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Mohammad T, Ghogare R, Morton LB, Dhingra A, Potlakayala S, Rudrabhatla S, Dhir SK. Evaluation of Parameters Affecting Agrobacterium-Mediated Transient Gene Expression in Industrial Hemp ( Cannabis sativa L.). Plants (Basel) 2024; 13:664. [PMID: 38475511 DOI: 10.3390/plants13050664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Industrial hemp Cannabis sativa L. is an economically important crop mostly grown for its fiber, oil, and seeds. Due to its increasing applications in the pharmaceutical industry and a lack of knowledge of gene functions in cannabinoid biosynthesis pathways, developing an efficient transformation platform for the genetic engineering of industrial hemp has become necessary to enable functional genomic and industrial application studies. A critical step in the development of Agrobacterium tumefaciens-mediated transformation in the hemp genus is the establishment of optimal conditions for T-DNA gene delivery into different explants from which whole plantlets can be regenerated. As a first step in the development of a successful Agrobacterium tumefaciens-mediated transformation method for hemp gene editing, the factors influencing the successful T-DNA integration and expression (as measured by transient β-glucuronidase (GUS) and Green Florescent Protein (GFP) expression) were investigated. In this study, the parameters for an agroinfiltration system in hemp, which applies to the stable transformation method, were optimized. In the present study, we tested different explants, such as 1- to 3-week-old leaves, cotyledons, hypocotyls, root segments, nodal parts, and 2- to 3-week-old leaf-derived calli. We observed that the 3-week-old leaves were the best explant for transient gene expression. Fully expanded 2- to 3-week-old leaf explants, in combination with 30 min of immersion time, 60 µM silver nitrate, 0.5 µM calcium chloride, 150 µM natural phenolic compound acetosyringone, and a bacterial density of OD600nm = 0.4 resulted in the highest GUS and GFP expression. The improved method of genetic transformation established in the present study will be useful for the introduction of foreign genes of interest, using the latest technologies such as genome editing, and studying gene functions that regulate secondary metabolites in hemp.
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Affiliation(s)
- Tasnim Mohammad
- Center for Biotechnology, Department of Agricultural Sciences, Fort Valley State University, 113, Alva Tabor Building, Fort Valley, GA 31030, USA
| | - Rishikesh Ghogare
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Lauren B Morton
- Center for Biotechnology, Department of Agricultural Sciences, Fort Valley State University, 113, Alva Tabor Building, Fort Valley, GA 31030, USA
| | - Amit Dhingra
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Shobha Potlakayala
- The Central Pennsylvania Research and Teaching Laboratory for Biofuels, Penn State Harrisburg, Middletown, PA 17057, USA
| | - Sairam Rudrabhatla
- The Central Pennsylvania Research and Teaching Laboratory for Biofuels, Penn State Harrisburg, Middletown, PA 17057, USA
| | - Sarwan K Dhir
- Center for Biotechnology, Department of Agricultural Sciences, Fort Valley State University, 113, Alva Tabor Building, Fort Valley, GA 31030, USA
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Hewitt S, Hernández-Montes E, Dhingra A, Keller M. Impact of heat stress, water stress, and their combined effects on the metabolism and transcriptome of grape berries. Sci Rep 2023; 13:9907. [PMID: 37336951 DOI: 10.1038/s41598-023-36160-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023] Open
Abstract
Recurring heat and drought episodes present challenges to the sustainability of grape production worldwide. We investigated the impacts of heat and drought stress on transcriptomic and metabolic responses of berries from two wine grape varieties. Cabernet Sauvignon and Riesling grapevines were subjected to one of four treatments during early fruit ripening: (1) drought stress only, (2) heat stress only, (3) simultaneous drought and heat stress, (4) no drought or heat stress (control). Berry metabolites, especially organic acids, were analyzed, and time-course transcriptome analysis was performed on samples before, during, and after the stress episode. Both alone and in conjunction with water stress, heat stress had a much more significant impact on berry organic acid content, pH, and titratable acidity than water stress. This observation contrasts with previous reports for leaves, which responded more strongly to water stress, indicating that grape berries display a distinct, organ-specific response to environmental stresses. Consistent with the metabolic changes, the global transcriptomic analysis revealed that heat stress had a more significant impact on gene expression in grape berries than water stress in both varieties. The differentially expressed genes were those associated with the tricarboxylic acid cycle and glyoxylate cycle, mitochondrial electron transport and alternative respiration, glycolysis and gluconeogenesis, carbohydrate allocation, ascorbate metabolism, and abiotic stress signaling pathways. Knowledge regarding how environmental stresses, alone and in combination, impact the berry metabolism of different grape varieties will form the basis for developing recommendations for climate change mitigation strategies and genetic improvement.
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Affiliation(s)
- Seanna Hewitt
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Esther Hernández-Montes
- Department of Viticulture and Enology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
- Department of Agricultural Production, CEIGRAM, Universidad Politécnica de Madrid, Madrid, Spain
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA.
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA.
| | - Markus Keller
- Department of Horticulture, Washington State University, Pullman, WA, USA.
- Department of Viticulture and Enology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA.
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Christian R, Labbancz J, Usadel B, Dhingra A. Understanding protein import in diverse non-green plastids. Front Genet 2023; 14:969931. [PMID: 37007964 PMCID: PMC10063809 DOI: 10.3389/fgene.2023.969931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the plastid and the subsequent export of the ancestral cyanobacterial genome to the nuclear genome, and adaptation of the plants to all types of environments has resulted in the emergence of diverse and a highly orchestrated metabolism across the plant kingdom that is entirely reliant on a complex protein import and translocation system. The TOC and TIC translocons, critical for importing nuclear-encoded proteins into the plastid stroma, remain poorly resolved, especially in the case of TIC. From the stroma, three core pathways (cpTat, cpSec, and cpSRP) may localize imported proteins to the thylakoid. Non-canonical routes only utilizing TOC also exist for the insertion of many inner and outer membrane proteins, or in the case of some modified proteins, a vesicular import route. Understanding this complex protein import system is further compounded by the highly heterogeneous nature of transit peptides, and the varying transit peptide specificity of plastids depending on species and the developmental and trophic stage of the plant organs. Computational tools provide an increasingly sophisticated means of predicting protein import into highly diverse non-green plastids across higher plants, which need to be validated using proteomics and metabolic approaches. The myriad plastid functions enable higher plants to interact and respond to all kinds of environments. Unraveling the diversity of non-green plastid functions across the higher plants has the potential to provide knowledge that will help in developing climate resilient crops.
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Affiliation(s)
- Ryan Christian
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - June Labbancz
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | | | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Amit Dhingra,
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Duval H, Coindre E, Ramos-Onsins SE, Alexiou KG, Rubio-Cabetas MJ, Martínez-García PJ, Wirthensohn M, Dhingra A, Samarina A, Arús P. Development and Evaluation of an Axiom TM 60K SNP Array for Almond ( Prunus dulcis). Plants (Basel) 2023; 12:242. [PMID: 36678957 PMCID: PMC9866729 DOI: 10.3390/plants12020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.
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Affiliation(s)
- Henri Duval
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE (French National Research Institute for Agriculture, Food and Environment), 84143 Montfavet, France
| | - Eva Coindre
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE (French National Research Institute for Agriculture, Food and Environment), 84143 Montfavet, France
| | - Sebastian E. Ramos-Onsins
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Konstantinos G. Alexiou
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
- IRTA (Institute of Agrifood Research and Technology), Campus UAB, Edifici CRAG, Cerdanyola del Valles (Bellaterra), 08193 Barcelona, Spain
| | - Maria J. Rubio-Cabetas
- CITA (Agrifood Research and Technology Centre of Aragon), Department of Plant Science, Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Pedro J. Martínez-García
- CEBAS (Centro de Edafología y Biología Aplicada del Segura), CSIC, Department of Plant Breeding, Campus Universitario de Espinardo, 30100 Espinardo, Spain
| | - Michelle Wirthensohn
- Waite Research Institute, University of Adelaide, PMB 1 Glen, Osmond, SA 5064, Australia
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Anna Samarina
- Thermo Fisher Scientific, Frankfurter Str. 129B, 64293 Darmstadt, Germany
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
- IRTA (Institute of Agrifood Research and Technology), Campus UAB, Edifici CRAG, Cerdanyola del Valles (Bellaterra), 08193 Barcelona, Spain
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Sharpe RM, Killian B, Koepke T, Ghogare R, Oraguzie N, Whiting M, Meisel LA, Silva H, Dhingra A. Draft genome data of Prunus avium cv ‘Stella’. Data Brief 2022; 45:108611. [PMID: 36164303 PMCID: PMC9508403 DOI: 10.1016/j.dib.2022.108611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/29/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
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McCord P, Hewitt S, Dhingra A. Nanopore sequencing data and structural variants identified in Prunus avium seedlings derived through mutagenesis. Data Brief 2022; 43:108384. [PMID: 35799853 PMCID: PMC9253453 DOI: 10.1016/j.dib.2022.108384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/03/2022] [Accepted: 06/08/2022] [Indexed: 11/19/2022] Open
Abstract
DNA from four sweet cherry seedlings derived from gamma-irradiated female parents was sequenced via nanopore technology (Oxford Nanopore MinION). Total data yield was 8.07 Gb, ranging from 0.92 to 3.36 Gb per sample, with the average length of mapped reads ranging from 22 Kbp–24 Kbp. Sequence data was then analysed to identify and characterize variants using a published sweet cherry reference genome. Small and medium-sized indels (55–135 bp), as well as structural variants, including several large indels and complex variants were detected. Of these, 20 variants were localized within protein-coding gene sequences, including those encoding a putative F-box protein, an ADP-ribose glyxohydrolase protein, a predicted 26S protease regulatory subunit, an E3 ubiquitin protein ligase, a UDP-galactose/UDP-blucose transporter, an alpha/beta hydrolase domain-containing protein, a rhodanese-like domain-containing protein, a cytochrome p450 protein, phosphoinositide phosphatase, cysteine synthase-like, phosphoenolpyruvate carboxylase 4, and several uncharacterized proteins. These variations could have functional and phenotypic consequences that are useful in basic research and breeding.
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Affiliation(s)
- Per McCord
- Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, WA 99350, USA
- Corresponding author.
| | - Seanna Hewitt
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77845, USA
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Peng H, Phung J, Stowe EC, Dhingra A, Neff MM. The NAC transcription factor ATAF2 promotes ethylene biosynthesis and response in Arabidopsis thaliana seedlings. FEBS Lett 2022; 596:1586-1599. [PMID: 35170054 DOI: 10.1002/1873-3468.14317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/10/2022]
Abstract
Arabidopsis thaliana ACTIVATING FACTOR 2 (ATAF2) plays extensive regulatory roles in pathogenesis, seedling development, and stress responses. Here, we performed transcriptome analysis on ATAF2 loss- and gain-of-function mutants to identify differentially expressed genes (DEGs). Gene ontology analyses on DEGs reveal that ATAF2 enhances seedling responses to multiple hormone and stress signals. In particular, our transcriptome analysis suggests that ATAF2 promotes ethylene biosynthesis and responses via activating relevant genes. This novel role of ATAF2 was further demonstrated by using multiple ATAF2 null and overexpression lines for reverse transcription quantitative PCR verification, ethylene production measurements, and assays of seedlings growth responses to the ethylene immediate biosynthetic precursor 1-aminocyclopropane-1-carboxylic acid (ACC). ACC suppresses ATAF2 expression to form a negative feedback regulation loop.
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Affiliation(s)
- Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.,Chemical and Hop Laboratory, Department of Agriculture, Washington State, Yakima, WA, 98902, USA
| | - Jessica Phung
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Evan C Stowe
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA.,Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Michael M Neff
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
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Williamson-Benavides BA, Sharpe RM, Nelson G, Bodah ET, Porter LD, Dhingra A. Identification of Root Rot Resistance QTLs in Pea Using Fusarium solani f. sp. pisi-Responsive Differentially Expressed Genes. Front Genet 2021; 12:629267. [PMID: 34421980 PMCID: PMC8375389 DOI: 10.3389/fgene.2021.629267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 07/06/2021] [Indexed: 12/02/2022] Open
Abstract
Pisum sativum (pea) yields in the United States have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome 5 explained 14.8% of the variance with a confidence interval of 10.4 cM. The other four QTLs located on chromosomes 2, 3, and 5, explained 5.3-8.1% of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.
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Affiliation(s)
| | - Richard M. Sharpe
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Grant Nelson
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
| | - Eliane T. Bodah
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Lyndon D. Porter
- USDA-ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA, United States
| | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
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Lobato-Gómez M, Hewitt S, Capell T, Christou P, Dhingra A, Girón-Calva PS. Transgenic and genome-edited fruits: background, constraints, benefits, and commercial opportunities. Hortic Res 2021; 8:166. [PMID: 34274949 PMCID: PMC8286259 DOI: 10.1038/s41438-021-00601-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/14/2021] [Accepted: 05/20/2021] [Indexed: 05/14/2023]
Abstract
Breeding has been used successfully for many years in the fruit industry, giving rise to most of today's commercial fruit cultivars. More recently, new molecular breeding techniques have addressed some of the constraints of conventional breeding. However, the development and commercial introduction of such novel fruits has been slow and limited with only five genetically engineered fruits currently produced as commercial varieties-virus-resistant papaya and squash were commercialized 25 years ago, whereas insect-resistant eggplant, non-browning apple, and pink-fleshed pineapple have been approved for commercialization within the last 6 years and production continues to increase every year. Advances in molecular genetics, particularly the new wave of genome editing technologies, provide opportunities to develop new fruit cultivars more rapidly. Our review, emphasizes the socioeconomic impact of current commercial fruit cultivars developed by genetic engineering and the potential impact of genome editing on the development of improved cultivars at an accelerated rate.
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Affiliation(s)
- Maria Lobato-Gómez
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain
| | - Seanna Hewitt
- Department of Horticulture, Washington State University, PO Box, 646414, Pullman, WA, USA
| | - Teresa Capell
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain
| | - Paul Christou
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, 08010, Barcelona, Spain
| | - Amit Dhingra
- Department of Horticulture, Washington State University, PO Box, 646414, Pullman, WA, USA
| | - Patricia Sarai Girón-Calva
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain.
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Alvarez D, Cerda-Bennasser P, Stowe E, Ramirez-Torres F, Capell T, Dhingra A, Christou P. Fruit crops in the era of genome editing: closing the regulatory gap. Plant Cell Rep 2021; 40:915-930. [PMID: 33515309 DOI: 10.1007/s00299-021-02664-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 05/27/2023]
Abstract
The conventional breeding of fruits and fruit trees has led to the improvement of consumer-driven traits such as fruit size, yield, nutritional properties, aroma and taste, as well as the introduction of agronomic properties such as disease resistance. However, even with the assistance of modern molecular approaches such as marker-assisted selection, the improvement of fruit varieties by conventional breeding takes considerable time and effort. The advent of genetic engineering led to the rapid development of new varieties by allowing the direct introduction of genes into elite lines. In this review article, we discuss three such case studies: the Arctic® apple, the Pinkglow pineapple and the SunUp/Rainbow papaya. We consider these events in the light of global regulations for the commercialization of genetically modified organisms (GMOs), focusing on the differences between product-related systems (the USA/Canada comparative safety assessment) and process-related systems (the EU "precautionary principle" model). More recently, genome editing has provided an efficient way to introduce precise mutations in plants, including fruits and fruit trees, replicating conventional breeding outcomes without the extensive backcrossing and selection typically necessary to introgress new traits. Some jurisdictions have reacted by amending the regulations governing GMOs to provide exemptions for crops that would be indistinguishable from conventional varieties based on product comparison. This has revealed the deficiencies of current process-related regulatory frameworks, particularly in the EU, which now stands against the rest of the world as a unique example of inflexible and dogmatic governance based on political expediency and activism rather than rigorous scientific evidence.
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Affiliation(s)
- Derry Alvarez
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Pedro Cerda-Bennasser
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Evan Stowe
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, 99164, USA
| | - Fabiola Ramirez-Torres
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, 99164, USA
| | - Teresa Capell
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA.
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, 99164, USA.
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
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Kalra S, Dhingra A, Sharma SK, Bhattacharya S. Sheehan's syndrome as a mimic of premature ovarian insufficiency: need for advocacy. Climacteric 2021; 24:526. [PMID: 33830850 DOI: 10.1080/13697137.2021.1905626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- S Kalra
- Department of Endocrinology, Bharti Hospital, Karnal, India
| | - A Dhingra
- Department of Endocrinology, Gangaram Bansal Hospital, Sri Ganganagar, India
| | - S K Sharma
- Department of Endocrinology, Dr. SK Sharma's Diabetes, Thyroid and Endocrine Centre, Jaipur, India
| | - S Bhattacharya
- Department of Endocrinology, Max Superspeciality Hospital, New Delhi, India
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Kalra S, A K D, Md F, K S, P S, A A R, M J, S S, A O, M R S, Selim S, M P B, Gangopadhyay KK, Y A L, T N, D D, S D T, V D, Dutta D, H K, R M, S D, A D, A B, G P, S C, Dhingra A, N P, A AA, M M. Glucodynamics and glucocracy in type 2 diabetes mellitus: clinical evidence and practice-based opinion on modern sulfonylurea use, from an International Expert Group (South Asia, Middle East & Africa) via modified Delphi method. Curr Med Res Opin 2021; 37:403-409. [PMID: 33319626 DOI: 10.1080/03007995.2020.1864309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is a global epidemic. According to international guidelines, the management protocol of T2DM includes lowering of blood glucose, along with preventing disease-related complications and maintaining optimal quality of life. Further, the guidelines recommend the use of a patient-centric approaches for the management of T2DM; however, Asian population is underrepresented in landmark cardiovascular outcome trials (CVOTs). There are several guidelines available today for the diagnosis and management of T2DM, and hence there is much confusion among practitioners about which guidelines to follow. A group of thirty international clinical experts comprising of endocrinologists, diabetologists and cardiologist from South Asia, Middle East and Africa met at New Delhi, India on February 8 and 9, 2020 and developed an international expert opinion statements via a structured modified Delphi method on the glucodynamic properties of OADs and the glucocratic treatment approach for the management of T2DM. In this modified Delphi consensus report, we document the glucodynamic properties of Modern SUs in terms of glucoconfidence, glucosafety, and gluconomics. According to glucodynamics theory, an ideal antidiabetic drug should be efficacious, safe, and affordable. Modern SUs as a class of OADs that have demonstrated optimal glucodynamics in terms of glucoconfidence, glucosafety, and gluconomics. Hence, modern SUs are most suitable second line drug after metformin for developing countries. Based on the current evidence, we recommend a glucocratic approach for the treatment of T2DM, where an individualized treatment plan with phenotype, lifestyle, environmental, social, and cultural factors should be considered for persons with T2DM in the South Asian, Middle Eastern and African regions.
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Affiliation(s)
- Sanjay Kalra
- Department of Endocrinology, Bharti Hospital, Karnal, Haryana, India
| | - Das A K
- Department of Endocrinology & Medicine, Pondicherry Institute of Medical Sciences, Puducherry, India
| | - Fariduddin Md
- Department of Endocrinology, Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shaikh K
- Department of Diabetes, Faculty of Internal Medicine, Royal Oman Police Hospital, Muscat, Oman
| | - Shah P
- Department of Endocrinology and Diabetes, Gujarat Endocrine Centre, Ahmedabad, India
| | - Rehim A A
- Department of Endocrinology & Medicine, Alexandria University, Alexandria, Egypt
| | - John M
- Department of Endocrinology, Providence Endocrine & Diabetes Specialty Centre, Thiruvananthapuram, India
| | - Shaikh S
- Department of Endocrinology & Diabetes, Prince Aly Khan Hospital, Mumbai, India
| | - Orabi A
- Department of Internal Medicine, Zagazig University, Zagazig, Egypt
| | - Saraswati M R
- Department of Endocrinology and Metabolism, Udayana University/Sanglah Hospital, Bali, Indonesia
| | - Shahjada Selim
- Department of Endocrinology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Baruah M P
- Department of Endocrinology, Excelcare Hospital, Guwahati, India
| | | | - Langi Y A
- Department of Endocrinology and Metabolic, R. D. Kandou Hospital, Manado, Indonesia
| | - Nair T
- Department of Cardiology, PRS Hospital, Trivandrum, Kerala, India
| | - Dhanwal D
- Department of Endocrinology, Diabetology and Metabolic Disorders, NMC Specialty Hospital, Abu Dhabi, UAE
| | - Thapa S D
- Department of Endocrinology and Metabolism, Grande International Hospital, Kathmandu, Nepal
| | - Deshmukh V
- Department of Endocrinology, Deshmukh Clinic and Research Centre, Pune, Maharashtra, India
| | - D Dutta
- Department of Endocrinology, Center for Endocrinology Diabetes Arthritis & Rheumatology (CEDAR), Superspeciality Clinic, New Delhi, India
| | - Khalfan H
- Department of Endocrinology, Metabolism, and Diabetes, King Hamad University Hospital, Al Sayh, Bahrain
| | - Maskey R
- Department of Internal Medicine, B. P. Koirala Institute of Health Sciences, Dharan, Nepal
| | - Das S
- Department of Endocrinology, Apollo Hospitals in Bhubaneswar, Bhubaneswar, India
| | - Dasgupta A
- Department of Endocrinology, Rudraksh Superspeciality Care, Siliguri, India
| | - Bajaj A
- Department of Diabetes & Endocrinology, Al Seef Hospital, Salmiya, Kuwait
| | - Priya G
- Department of Endocrinology, Fortis Hospital, Chandigarh, Punjab, India
| | - Chandrasekaran S
- Department of Endocrinology & Diabetes, Dr. Rela Institute of Medical Science, Chennai, Tamil Nadu, India
| | - A Dhingra
- Department of Endocrinology, Gangaram Bansal Hospital, Ganganagar, Rajasthan, India
| | - Pandey N
- Department of Endocrinology, Max Hospital, Gurgaon, India
| | - Al Ani A
- Department of Internal Medicine, Hamad General Hospital, Doha, Qatar
| | - Moosa M
- Department of Internal Medicine, Indira Gandhi Memorial Hospital, Male, Maldives
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Dhingra A, Götting J, Varanasi PR, Steinbrueck L, Camiolo S, Zischke J, Heim A, Schulz TF, Weissinger EM, Kay-Fedorov PC, Davison AJ, Suárez NM, Ganzenmueller T. Human cytomegalovirus multiple-strain infections and viral population diversity in haematopoietic stem cell transplant recipients analysed by high-throughput sequencing. Med Microbiol Immunol 2021; 210:291-304. [PMID: 34611744 PMCID: PMC8541999 DOI: 10.1007/s00430-021-00722-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/21/2021] [Indexed: 01/22/2023]
Abstract
Human cytomegalovirus (HCMV) is an important opportunistic pathogen in allogeneic haematopoietic stem cell transplant (HSCT) recipients. High-throughput sequencing of target-enriched libraries was performed to characterise the diversity of HCMV strains present in this high-risk group. Forty-four HCMV-DNA-positive plasma specimens (median viral input load 321 IU per library) collected at defined time points from 23 HSCT recipients within 80 days of transplantation were sequenced. The genotype distribution for 12 hypervariable HCMV genes and the number of HCMV strains present (i.e. single- vs. multiple-strain infection) were determined for 29 samples from 16 recipients. Multiple-strain infection was observed in seven of these 16 recipients, and five of these seven recipients had the donor (D)/recipient (R) HCMV-serostatus combination D + R + . A very broad range of genotypes was detected, with an intrahost composition that was generally stable over time. Multiple-strain infection was not associated with particular virological or clinical features, such as altered levels or duration of antigenaemia, development of acute graft-versus-host disease or increased mortality. In conclusion, despite relatively low viral plasma loads, a high frequency of multiple-strain HCMV infection and a high strain complexity were demonstrated in systematically collected clinical samples from this cohort early after HSCT. However, robust evaluation of the pathogenic role of intrahost viral diversity and multiple-strain infection will require studies enrolling larger numbers of recipients.
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Affiliation(s)
- A. Dhingra
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - J. Götting
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - P. R. Varanasi
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany ,Department of Haematology, Haemostasis and Oncology, Hannover Medical School, Hannover, Germany ,Present Address: National Centre for Biological Sciences, Bangalore, India
| | - L. Steinbrueck
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - S. Camiolo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - J. Zischke
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - A. Heim
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - T. F. Schulz
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - E. M. Weissinger
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany ,Department of Haematology, Haemostasis and Oncology, Hannover Medical School, Hannover, Germany
| | - P. C. Kay-Fedorov
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - A. J. Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - N. M. Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - T. Ganzenmueller
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany ,Institute for Medical Virology and Epidemiology, University Hospital Tuebingen, Elfriede-Aulhorn-Str. 6, 72076 Tuebingen, Germany
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Hewitt S, Dhingra A. Beyond Ethylene: New Insights Regarding the Role of Alternative Oxidase in the Respiratory Climacteric. Front Plant Sci 2020; 11:543958. [PMID: 33193478 PMCID: PMC7652990 DOI: 10.3389/fpls.2020.543958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Climacteric fruits are characterized by a dramatic increase in autocatalytic ethylene production that is accompanied by a spike in respiration at the onset of ripening. The change in the mode of ethylene production from autoinhibitory to autostimulatory is known as the System 1 (S1) to System 2 (S2) transition. Existing physiological models explain the basic and overarching genetic, hormonal, and transcriptional regulatory mechanisms governing the S1 to S2 transition of climacteric fruit. However, the links between ethylene and respiration, the two main factors that characterize the respiratory climacteric, have not been examined in detail at the molecular level. Results of recent studies indicate that the alternative oxidase (AOX) respiratory pathway may play an essential role in mediating cross-talk between ethylene response, carbon metabolism, ATP production, and ROS signaling during climacteric ripening. New genomic, metabolic, and epigenetic information sheds light on the interconnectedness of ripening metabolic pathways, necessitating an expansion of the current, ethylene-centric physiological models. Understanding points at which ripening responses can be manipulated may reveal key, species- and cultivar-specific targets for regulation of ripening, enabling superior strategies for reducing postharvest wastage.
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Affiliation(s)
- Seanna Hewitt
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Amit Dhingra
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
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Sharpe RM, Williamson-Benavides B, Edwards GE, Dhingra A. Methods of analysis of chloroplast genomes of C 3, Kranz type C 4 and Single Cell C 4 photosynthetic members of Chenopodiaceae. Plant Methods 2020; 16:119. [PMID: 32874195 PMCID: PMC7457496 DOI: 10.1186/s13007-020-00662-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Chloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C3 photosynthesis, and variations of C4 photosynthesis in which photorespiration is reduced by concentrating CO2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C4 species, and greatest structural and biochemical diversity in forms of C4 including the canonical dual-cell Kranz anatomy, and the recently identified single cell C4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family. RESULTS Methodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C3, Kranz type C4 and single cell C4 (SSC4) photosynthesis six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera, and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae. CONCLUSIONS This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.
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Affiliation(s)
- Richard M. Sharpe
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Bruce Williamson-Benavides
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
- Molecular Plants Sciences, Washington State University, Pullman, WA 99164 USA
| | - Gerald E. Edwards
- Molecular Plants Sciences, Washington State University, Pullman, WA 99164 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
- Molecular Plants Sciences, Washington State University, Pullman, WA 99164 USA
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16
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Christian RW, Hewitt SL, Nelson G, Roalson EH, Dhingra A. Plastid transit peptides-where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution. PeerJ 2020; 8:e9772. [PMID: 32913678 PMCID: PMC7456531 DOI: 10.7717/peerj.9772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/30/2020] [Indexed: 01/22/2023] Open
Abstract
Subcellular relocalization of proteins determines an organism's metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.
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Affiliation(s)
- Ryan W. Christian
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Seanna L. Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Grant Nelson
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Eric H. Roalson
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
- Department of Horticulture, Washington State University, Pullman, WA, USA
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17
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Williamson-Benavides BA, Sharpe RM, Nelson G, Bodah ET, Porter LD, Dhingra A. Identification of Fusarium solani f. sp. pisi ( Fsp) Responsive Genes in Pisum sativum. Front Genet 2020; 11:950. [PMID: 33014017 PMCID: PMC7461991 DOI: 10.3389/fgene.2020.00950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022] Open
Abstract
Pisum sativum (pea) is rapidly emerging as an inexpensive and significant contributor to the plant-derived protein market. Due to its nitrogen-fixation capability, short life cycle, and low water usage, pea is a useful cover-and-break crop that requires minimal external inputs. It is critical for sustainable agriculture and indispensable for future food security. Root rot in pea, caused by the fungal pathogen Fusarium solani f. sp. pisi (Fsp), can result in a 15-60% reduction in yield. It is urgent to understand the molecular basis of Fsp interaction in pea to develop root rot tolerant cultivars. A complementary genetics and gene expression approach was undertaken in this study to identify Fsp-responsive genes in four tolerant and four susceptible pea genotypes. Time course RNAseq was performed on both sets of genotypes after the Fsp challenge. Analysis of the transcriptome data resulted in the identification of 42,905 differentially expressed contigs (DECs). Interestingly, the vast majority of DECs were overexpressed in the susceptible genotypes at all sampling time points, rather than in the tolerant genotypes. Gene expression and GO enrichment analyses revealed genes coding for receptor-mediated endocytosis, sugar transporters, salicylic acid synthesis, and signaling, and cell death were overexpressed in the susceptible genotypes. In the tolerant genotypes, genes involved in exocytosis, and secretion by cell, the anthocyanin synthesis pathway, as well as the DRR230 gene, a pathogenesis-related (PR) gene, were overexpressed. The complementary genetic and RNAseq approach has yielded a set of potential genes that could be targeted for improved tolerance against root rot in P. sativum. Fsp challenge produced a futile transcriptomic response in the susceptible genotypes. This type of response is hypothesized to be related to the speed at which the pathogen infestation advances in the susceptible genotypes and the preexisting level of disease-preparedness in the tolerant genotypes.
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Affiliation(s)
| | - Richard M Sharpe
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Grant Nelson
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
| | - Eliane T Bodah
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Lyndon D Porter
- USDA-ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA, United States
| | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
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18
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Kaiser N, Douches D, Dhingra A, Glenn KC, Herzig PR, Stowe EC, Swarup S. The role of conventional plant breeding in ensuring safe levels of naturally occurring toxins in food crops. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.03.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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19
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Hewitt SL, Hendrickson CA, Dhingra A. Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in 'D'Anjou' and 'Bartlett' Pear Fruit. Sci Rep 2020; 10:8478. [PMID: 32439928 PMCID: PMC7242362 DOI: 10.1038/s41598-020-65275-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/30/2020] [Indexed: 11/24/2022] Open
Abstract
European pear (Pyrus communis L.) cultivars require a genetically pre-determined duration of cold-temperature exposure to induce autocatalytic system 2 ethylene biosynthesis and subsequent fruit ripening. The physiological responses of pear to cold-temperature-induced ripening have been well characterized, but the molecular mechanisms underlying this phenomenon continue to be elucidated. This study employed previously established cold temperature conditioning treatments for ripening of two pear cultivars, 'D'Anjou' and 'Bartlett'. Using a time-course transcriptomics approach, global gene expression responses of each cultivar were assessed at four stages of developmental during the cold conditioning process. Differential expression, functional annotation, and gene ontology enrichment analyses were performed. Interestingly, evidence for the involvement of cold-induced, vernalization-related genes and repressors of endodormancy release was found. These genes have not previously been described to play a role in fruit during the ripening transition. The resulting data provide insight into cultivar-specific mechanisms of cold-induced transcriptional regulation of ripening in European pear, as well as a unique comparative analysis of the two cultivars with very different cold conditioning requirements.
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Affiliation(s)
- Seanna L Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, Washington, USA
- Department of Horticulture, Washington State University, Pullman, Washington, USA
| | | | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, Washington, USA.
- Department of Horticulture, Washington State University, Pullman, Washington, USA.
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20
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Christian RW, Hewitt SL, Roalson EH, Dhingra A. Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. Sci Rep 2020; 10:8281. [PMID: 32427841 PMCID: PMC7237471 DOI: 10.1038/s41598-020-64670-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
Plastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at a genome-wide scale using experimental methods. A bioinformatics workflow was developed and evaluated using a combination of fast and user-friendly subcellular prediction programs to maximize performance and accuracy for chloroplast transit peptides and demonstrate this technique on the predicted proteomes of 15 sequenced plant genomes. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. A total of 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted protein-coding gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on a genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to influence plastid morphology and biochemistry.
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Affiliation(s)
- Ryan W Christian
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA
| | - Seanna L Hewitt
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA
| | - Eric H Roalson
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA.
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA.
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21
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Hewitt SL, Ghogare R, Dhingra A. Glyoxylic acid overcomes 1-MCP-induced blockage of fruit ripening in Pyrus communis L. var. 'D'Anjou'. Sci Rep 2020; 10:7084. [PMID: 32341384 PMCID: PMC7184741 DOI: 10.1038/s41598-020-63642-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/17/2020] [Indexed: 11/09/2022] Open
Abstract
1-methylcyclopropene (1-MCP) in an ethylene receptor antagonist that blocks ethylene perception and downstream ripening responses in climacteric fruit imparting a longer shelf life. However, in European pear, the application of 1-MCP irreversibly obstructs the onset of system 2 ethylene production resulting in perpetually unripe fruit with undesirable quality. Application of exogenous ethylene, carbon dioxide and treatment to high temperatures is not able to reverse the blockage in ripening. We recently reported that during cold conditioning, activation of alternative oxidase (AOX) occurs pre-climacterically. In this study, we report that activation of AOX via exposure of 1-MCP treated 'D'Anjou' pear fruit to glyoxylic acid triggers an accelerated ripening response. Time course physiological analysis revealed that ripening is evident from decreased fruit firmness and increased internal ethylene. Transcriptomic and functional enrichment analyses revealed genes and ontologies implicated in glyoxylic acid-mediated ripening, including AOX, TCA cycle, fatty acid metabolism, amino acid metabolism, organic acid metabolism, and ethylene-responsive pathways. These observations implicate the glyoxylate cycle as a biochemical hub linking multiple metabolic pathways to stimulate ripening through an alternate mechanism. The results provide information regarding how blockage caused by 1-MCP may be circumvented at the metabolic level, thus opening avenues for consistent ripening in pear and possibly other fruit.
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Affiliation(s)
- Seanna L Hewitt
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, USA
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Rishikesh Ghogare
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, USA.
- Department of Horticulture, Washington State University, Pullman, WA, USA.
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Sharpe RM, Gustafson L, Hewitt S, Kilian B, Crabb J, Hendrickson C, Jiwan D, Andrews P, Dhingra A. Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer. PLoS One 2020; 15:e0227429. [PMID: 31931517 PMCID: PMC6957345 DOI: 10.1371/journal.pone.0227429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/18/2019] [Indexed: 12/01/2022] Open
Abstract
Enhanced levels of antioxidants, phenolic compounds, carotenoids and vitamin C have been reported for several crops grown under organic fertilizer, albeit with yield penalties. As organic agricultural practices continue to grow and find favor it is critical to gain an understanding of the molecular underpinnings of the factors that limit the yields in organically farmed crops. Concomitant phytochemical and transcriptomic analysis was performed on mature fruit and leaf tissues derived from Solanum lycopersicum L. ‘Oregon Spring’ grown under organic and conventional fertilizer conditions to evaluate the following hypotheses. 1. Organic soil fertilizer management results in greater allocation of photosynthetically derived resources to the synthesis of secondary metabolites than to plant growth, and 2. Genes involved in changes in the accumulation of phytonutrients under organic fertilizer regime will exhibit differential expression, and that the growth under different fertilizer treatments will elicit a differential response from the tomato genome. Both these hypotheses were supported, suggesting an adjustment of the metabolic and genomic activity of the plant in response to different fertilizers. Organic fertilizer treatment showed an activation of photoinhibitory processes through differential activation of nitrogen transport and assimilation genes resulting in higher accumulation of phytonutrients. This information can be used to identify alleles for breeding crops that allow for efficient utilization of organic inputs.
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Affiliation(s)
- Richard M. Sharpe
- Department of Horticulture, Washington State University,Pullman, WA, United States of America
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, United States of America
| | - Luke Gustafson
- Department of Horticulture, Washington State University,Pullman, WA, United States of America
| | - Seanna Hewitt
- Department of Horticulture, Washington State University,Pullman, WA, United States of America
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, United States of America
| | - Benjamin Kilian
- Department of Horticulture, Washington State University,Pullman, WA, United States of America
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, United States of America
| | - James Crabb
- Department of Horticulture, Washington State University,Pullman, WA, United States of America
| | - Christopher Hendrickson
- Department of Horticulture, Washington State University,Pullman, WA, United States of America
| | - Derick Jiwan
- Department of Horticulture, Washington State University,Pullman, WA, United States of America
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, United States of America
| | - Preston Andrews
- Department of Horticulture, Washington State University,Pullman, WA, United States of America
| | - Amit Dhingra
- Department of Horticulture, Washington State University,Pullman, WA, United States of America
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, United States of America
- * E-mail:
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23
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Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fernández i Martí Á, Frias L, Galán B, García JL, Howad W, Gómez‐Garrido J, Gut M, Julca I, Morata J, Puigdomènech P, Ribeca P, Rubio Cabetas MJ, Vlasova A, Wirthensohn M, Garcia‐Mas J, Gabaldón T, Casacuberta JM, Arús P. Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. Plant J 2020; 101:455-472. [PMID: 31529539 PMCID: PMC7004133 DOI: 10.1111/tpj.14538] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/19/2023]
Abstract
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.
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Affiliation(s)
- Tyler Alioto
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Konstantinos G. Alexiou
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fabio Barteri
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fernando Cruz
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Amit Dhingra
- Department of HorticultureWashington State University99164-6414PullmanWAUSA
| | - Henri Duval
- INRA, UR1052Unité de Génétique et Amélioration des Fruits et Légumes (GAFL)Domaine St. Maurice CS 6009484143Montfavet CedexFrance
| | - Ángel Fernández i Martí
- Department of Environmental Science Policy and ManagementUniversity of CaliforniaBerkeley94720CAUSA
- Innovative Genomics Institute (IGI)94720BerkeleyCAUSA
| | - Leonor Frias
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Beatriz Galán
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - José L. García
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - Werner Howad
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Jèssica Gómez‐Garrido
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Marta Gut
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Irene Julca
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Jordi Morata
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Puigdomènech
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Paolo Ribeca
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- The Pirbright InstituteWokingSurreyGU24 0NFUK
| | - María J. Rubio Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)Unidad de HortofruticulturaGobierno de Aragón, Avda. Montañana 93050059ZaragozaSpain
- Instituto Agroalimentario de Aragón – IA2 (CITA‐Universidad de Zaragoza)Calle Miguel Servet 17750013ZaragozaSpain
| | - Anna Vlasova
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Michelle Wirthensohn
- University of AdelaideWaite Research InstituteSchool of Agriculture, Food and WinePMB 1Glen OsmondSA5064Australia
| | - Jordi Garcia‐Mas
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Toni Gabaldón
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Pg Lluís Companys 2308010BarcelonaSpain
| | - Josep M. Casacuberta
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Arús
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
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24
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Hendrickson C, Hewitt S, Swanson ME, Einhorn T, Dhingra A. Evidence for pre-climacteric activation of AOX transcription during cold-induced conditioning to ripen in European pear (Pyrus communis L.). PLoS One 2019; 14:e0225886. [PMID: 31800597 PMCID: PMC6892529 DOI: 10.1371/journal.pone.0225886] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/14/2019] [Indexed: 11/28/2022] Open
Abstract
European pears (Pyrus communis L.) require a range of cold-temperature exposure to induce ethylene biosynthesis and fruit ripening. Physiological and hormonal responses to cold temperature storage in pear have been well characterized, but the molecular underpinnings of these phenomena remain unclear. An established low-temperature conditioning model was used to induce ripening of 'D'Anjou' and 'Bartlett' pear cultivars and quantify the expression of key genes representing ripening-related metabolic pathways in comparison to non-conditioned fruit. Physiological indicators of pear ripening were recorded, and fruit peel tissue sampled in parallel, during the cold-conditioning and ripening time-course experiment to correlate gene expression to ontogeny. Two complementary approaches, Nonparametric Multi-Dimensional Scaling and efficiency-corrected 2-(ΔΔCt), were used to identify genes exhibiting the most variability in expression. Interestingly, the enhanced alternative oxidase (AOX) transcript abundance at the pre-climacteric stage in 'Bartlett' and 'D'Anjou' at the peak of the conditioning treatments suggests that AOX may play a key and a novel role in the achievement of ripening competency. There were indications that cold-sensing and signaling elements from ABA and auxin pathways modulate the S1-S2 ethylene transition in European pears, and that the S1-S2 ethylene biosynthesis transition is more pronounced in 'Bartlett' as compared to 'D'Anjou' pear. This information has implications in preventing post-harvest losses of this important crop.
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Affiliation(s)
- Christopher Hendrickson
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
| | - Seanna Hewitt
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, United States of America
| | - Mark E. Swanson
- School of the Environment, Washington State University, Pullman, WA, United States of America
| | - Todd Einhorn
- Department of Horticulture, Michigan State University, East Lansing, MI, United States of America
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, United States of America
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25
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Ghogare R, Williamson-Benavides B, Ramírez-Torres F, Dhingra A. CRISPR-associated nucleases: the Dawn of a new age of efficient crop improvement. Transgenic Res 2019; 29:1-35. [PMID: 31677059 DOI: 10.1007/s11248-019-00181-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/23/2019] [Indexed: 12/26/2022]
Abstract
The world stands at a new threshold today. As a planet, we face various challenges, and the key one is how to continue to produce enough food, feed, fiber, and fuel to support the burgeoning population. In the past, plant breeding and the ability to genetically engineer crops contributed to increasing food production. However, both approaches rely on random mixing or integration of genes, and the process can be unpredictable and time-consuming. Given the challenge of limited availability of natural resources and changing environmental conditions, the need to rapidly and precisely improve crops has become urgent. The discovery of CRISPR-associated endonucleases offers a precise yet versatile platform for rapid crop improvement. This review summarizes a brief history of the discovery of CRISPR-associated nucleases and their application in genome editing of various plant species. Also provided is an overview of several new endonucleases reported recently, which can be utilized for editing of specific genes in plants through various forms of DNA sequence alteration. Genome editing, with its ever-expanding toolset, increased efficiency, and its potential integration with the emerging synthetic biology approaches hold promise for efficient crop improvement to meet the challenge of supporting the needs of future generations.
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26
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Dhingra A, Suárez N, Varanasi P, Zischke J, Heim A, Mischak-Weissinger E, Schulz T, Davison A, Kay-Fedorov P, Ganzenmueller T. A42 Next-generation sequencing to analyze multiple-strain infections, genotype distribution, and antiviral resistance in hematopoietic stem cell transplantation recipients with human cytomegalovirus infection. Virus Evol 2019. [PMCID: PMC6735887 DOI: 10.1093/ve/vez002.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Next-generation sequencing (NGS) produces comprehensive insights across the entire genome of the human cytomegalovirus (HCMV), which is an important opportunistic pathogen following hematopoietic stem cell transplantation (HSCT). To assess the clinical impact of HCMV diversity, genotype distribution, and resistance mutations, we performed NGS directly on plasma specimens from HSCT recipients with HCMV reactivation. Twenty-nine HCMV-positive plasma samples (median viral load 1.7 × 103 IU/ml) collected from a prospective allogenic HSCT recipient cohort (n = 16) between 21 and 80 days after transplantation were sequenced on an Illumina MiSeq after preparation of target-enriched sequencing libraries. Consensus HCMV genome sequences were assembled for 24 samples. The presence of multiple-strain infections and antiviral resistance mutations in genes UL54 and UL97 was determined by variant analysis. Genotype distribution was determined by specific marker analysis of several hypervariable genes (RL5A, RL6, RL12, RL13, UL1, UL9, UL11, UL73, UL74, UL120, UL146, and UL139). Associations between genomic and clinical features (e.g. graft-versus-host disease (GvHD), donor/recipient HCMV serostatus, dynamics of HCMV antigenemia, survival) were explored. Multiple infections involving up to 3 HCMV strains were detected in seven out of sixteen patients, with one patient analyzed at > 2 time points, showing a switch of the dominant HCMV population. No known antiviral resistance mutations were detected, which may be expected due to sample collection early after HSCT from patients without antiviral prophylaxis. Multiple-strain infection was associated with an earlier peak of HCMV-antigenemia (P = 0.054), but not with duration of viremia, antigenemia peak values, donor/recipient HCMV serostatus, T-cell depletion, acute or chronic GvHD, disease relapse, or reduced survival. Genotype distribution analysis revealed a potential link of one genotype of the immunomodulatory gene UL11 with GvHD incidence after HCMV reactivation. NGS of HCMV diversity directly from plasma samples, even with low viral loads, enables the acquisition of data of potential clinical interest. To identify reliable associations between clinical features and HCMV diversity, further patient cohorts with suitable sample sizes are required.
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Affiliation(s)
- A Dhingra
- Hannover Medical School, Institute of Virology, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Germany
| | - N Suárez
- MRC-University of Glasgow, Centre for Virus Research, Glasgow, UK
| | - P Varanasi
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Germany
- Department of Haematology, Haemostasis and Oncology, Hannover Medical School, Hannover, Germany
| | - J Zischke
- Hannover Medical School, Institute of Virology, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Germany
| | - A Heim
- Hannover Medical School, Institute of Virology, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Germany
| | - E Mischak-Weissinger
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Germany
- Department of Haematology, Haemostasis and Oncology, Hannover Medical School, Hannover, Germany
| | - T Schulz
- Hannover Medical School, Institute of Virology, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Germany
| | - A Davison
- MRC-University of Glasgow, Centre for Virus Research, Glasgow, UK
| | - P Kay-Fedorov
- Hannover Medical School, Institute of Virology, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Germany
| | - T Ganzenmueller
- Hannover Medical School, Institute of Virology, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Germany
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27
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Garczynski SF, Hendrickson CA, Harper A, Unruh TR, Dhingra A, Ahn SJ, Choi MY. Neuropeptides and peptide hormones identified in codling moth, Cydia pomonella (Lepidoptera: Tortricidae). Arch Insect Biochem Physiol 2019; 101:e21587. [PMID: 31271487 DOI: 10.1002/arch.21587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/19/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
The codling moth, Cydia pomonella, is a worldwide pest of pome fruits. Neuropeptides regulate most physiological functions in insects and represent new targets for the development of control agents. The only neuropeptides reported from the codling moth to date are the allatostatin A family peptides. To identify other neuropeptides and peptide hormones from codling moth, we analyzed head transcriptomes, identified 50 transcripts, and predicted 120 prepropeptides for the codling moth neuropeptides and peptide hormones. All transcripts were amplified, and these sequences were verified. One of the notable findings in this study is that diapause hormones (DHs) reported from Tortricid moths, including the codling moth, do not have the WFGPRL sequence in C-terminal ends in the pban genes. The C-terminal motif is critical to characterize insect DH peptides, and always conserved in pban/dh genes in Lepidoptera and many insect orders. Interestingly, the WFGPRL sequence was produced only from the capa gene in the codling moth. The allatostatin A-family encoding transcript predicted nine peptides, seven of which, as expected, are identical to those previously isolated from the moth. We also identified new codling moth orthologs of insect neuropeptides including CCHamides, allatostatin CC, RYamides, and natalisins. The information provided in this study will benefit future codling moth investigations using peptidoproteomics to determine peptide presence and functions.
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Affiliation(s)
| | | | - Artemus Harper
- Department of Horticulture, Washington State University, Pullman, Washington
| | - Thomas R Unruh
- Yakima Agricultural Research Laboratory, USDA-ARS, Wapato, Washington
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, Washington
| | - Seung-Joon Ahn
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon
- Horticultural Crops Research Unit, USDA-ARS, Corvallis, Oregon
| | - Man-Yeon Choi
- Horticultural Crops Research Unit, USDA-ARS, Corvallis, Oregon
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28
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Montanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB. Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization. BMC Genomics 2019; 20:331. [PMID: 31046664 PMCID: PMC6498479 DOI: 10.1186/s12864-019-5712-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
Background Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies. Results By applying a two-step design process, which consisted of the construction of a first ‘draft’ array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping. Conclusions The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus. Electronic supplementary material The online version of this article (10.1186/s12864-019-5712-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Montanari
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Nahla V Bassil
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Joseph Postman
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Mareike Knäbel
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Biff Kitson
- Motueka Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Motueka, New Zealand
| | - Cecilia H Deng
- Auckland Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Kate Evans
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, USA
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29
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Maldonado J, Dhingra A, Carrasco B, Meisel L, Silva H. Transcriptome datasets from leaves and fruits of the sweet cherry cultivars ‘Bing’, ‘Lapins’ and ‘Rainier’. Data Brief 2019; 23:103696. [PMID: 30788404 PMCID: PMC6369327 DOI: 10.1016/j.dib.2019.01.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/08/2019] [Accepted: 01/18/2019] [Indexed: 11/05/2022] Open
Abstract
Sweet cherry fruits from different cultivars have different pre- and post-harvest qualities. Here we present the transcriptome profile datasets of leaves and mature fruits of three sweet cherry cultivars (‘Bing’, ‘Lapin’ and ‘Rainier’). Using 454 GS-FLX technology (454 Life Sciences, Roche), transcriptomes of leaves and mature fruits were obtained from these cultivars. These transcriptome data sets are reported here.
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30
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Bielsa B, Hewitt S, Reyes-Chin-Wo S, Dhingra A, Rubio-Cabetas MJ. Identification of water use efficiency related genes in 'Garnem' almond-peach rootstock using time-course transcriptome analysis. PLoS One 2018; 13:e0205493. [PMID: 30308016 PMCID: PMC6181374 DOI: 10.1371/journal.pone.0205493] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/26/2018] [Indexed: 11/19/2022] Open
Abstract
Drought is one of the main abiotic stresses with far-reaching ecological and socioeconomic impacts, especially in perennial food crops such as Prunus. There is an urgent need to identify drought resilient rootstocks that can adapt to changes in water availability. In this study, we tested the hypothesis that PEG-induced water limitation stress will simulate drought conditions and drought-related genes, including transcription factors (TFs), will be differentially expressed in response to this stress. 'Garnem' genotype, an almond × peach hybrid [P. amygdalus Batsch, syn P. dulcis (Mill.) x P. persica (L.) Batsch] was exposed to PEG-6000 solution, and a time-course transcriptome analysis of drought-stressed roots was performed at 0, 2 and 24 h time points post-stress. Transcriptome analysis resulted in the identification of 12,693 unique differentially expressed contigs (DECs) at the 2 h time point, and 7,705 unique DECs at the 24 h time point after initiation of the drought treatment. Interestingly, three drought-induced genes, directly related to water use efficiency (WUE) namely, ERF023 TF; LRR receptor-like serine/threonine-kinase ERECTA; and NF-YB3 TF, were found induced under stress. The RNAseq results were validated with quantitative RT-PCR analysis of eighteen randomly selected differentially expressed contigs (DECs). Pathway analysis in the present study provides valuable information regarding metabolic events that occur during stress-induced signalling in 'Garnem' roots. This information is expected to be useful in understanding the potential mechanisms underlying drought stress responses and drought adaptation strategies in Prunus species.
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Affiliation(s)
- Beatriz Bielsa
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
| | - Seanna Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | | | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - María José Rubio-Cabetas
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
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31
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Ikiz D, Gallardo RK, Dhingra A, Hewitt S. Assessing consumers' preferences and willingness to pay for novel sliced packed fresh pears: A latent class approach. Agribusiness (N Y N Y) 2017; 34:321-337. [PMID: 31354182 PMCID: PMC6660009 DOI: 10.1002/agr.21532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The North American fresh pear industry faces marketing challenges that could jeopardize its' long-term economic profitability. The production of sliced fresh pears is a promising alternative to overcome the lack of supplying consistently a product with superior quality with added convenience, potentially able to increase domestic consumption. In this paper, we used sensory evaluation and a Vickrey experimental auction to elicit consumers' preferences and willingness to pay for sliced packed fresh pears treated with SmartFresh™ (1-methylcyclopropene)and subsequently with a ripening compound (RC) in the form of glyoxylic acid at different concentration levels (1%, 2%, 3%, and control). Panelists were willing to pay a price premium equivalent to $0.119/2 oz packet for the 2% RC sample, $0.055/2 oz packet for the 3% RC sample, and $0.025/2 oz packet for the 1% RC sample compared to the control sample. Results from a market segmentation analyses indicate the presence of two groups in the panelist sample. The group that liked sliced pears assigned higher importance to locally grown fruit and price, shopped at conventional retailer grocery stores, had fewer children in the household, and were younger compared to the group that disliked sliced pears.
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Affiliation(s)
- Dila Ikiz
- School of Economic Sciences,Washington State University, PO Box 646210, Pullman,WA99164, USA
| | - R. Karina Gallardo
- School of Economic Sciences and the Puyallup Research and Extension Center and the Center for Precision and Automated Agricultural Systems, Washington State University, 2606 W. Pioneer, Puyallup,WA98371,USA
| | - Amit Dhingra
- Department of Horticulture,Washington State University, PO Box 646414, Pullman,WA99164, USA
| | - Seanna Hewitt
- Molecular PlantSciences,Washington State University, PO Box 646414, Pullman,WA99164, USA
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32
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Lawrence NC, Hauvermale AL, Dhingra A, Burke IC. Population structure and genetic diversity of Bromus tectorum within the small grain production region of the Pacific Northwest. Ecol Evol 2017; 7:8316-8328. [PMID: 29075451 PMCID: PMC5648657 DOI: 10.1002/ece3.3386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 07/22/2017] [Accepted: 07/26/2017] [Indexed: 11/06/2022] Open
Abstract
Bromus tectorum L. is an invasive winter annual grass naturalized across the United States. Numerous studies have investigated B. tectorum population structure and genetics in the context of B. tectorum as an ecological invader of natural areas and rangeland. Despite the wealth of information regarding B. tectorum, previous studies have not focused on, or made comparisons to, B. tectorum as it persists in individual agroecosystems. The objectives of this study were to assess the genetic diversity and structure, the occurrence of generalist and specialist genotypes, and the influence of climate on distribution of B. tectorum sourced exclusively from within small grain production regions of the Pacific Northwest. Genetic diversity of B. tectorum sourced from agronomic fields was found to be similar to what has been observed from other land use histories. Six distinct genetic clusters of B. tectorum were identified, with no evidence to indicate that any of the genetic clusters were better adapted to a particular geographical area or climate within the region. Given the apparent random spatial distribution of B. tectorum genetic clusters at the spatial scale of this analysis, unique genotypes may be well mixed within region, similar to what was reported for other inbreeding weedy grass species.
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Affiliation(s)
- Nevin C. Lawrence
- Department of Crop and Soil SciencesWashington State UniversityPullmanWAUSA
- University of Nebraska‐LincolnScottsbluffNEUSA
| | | | - Amit Dhingra
- Department of HorticultureWashington State UniversityPullmanWAUSA
| | - Ian C. Burke
- Department of Crop and Soil SciencesWashington State UniversityPullmanWAUSA
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Schaeffer SM, Christian R, Castro-Velasquez N, Hyden B, Lynch-Holm V, Dhingra A. Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development. Plant Cell Rep 2017; 36:1627-1640. [PMID: 28698906 PMCID: PMC5693628 DOI: 10.1007/s00299-017-2179-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/03/2017] [Indexed: 05/02/2023]
Abstract
Comparative ultrastructural developmental time-course analysis has identified discrete stages at which the fruit plastids undergo structural and consequently functional transitions to facilitate subsequent development-guided understanding of the complex plastid biology. Plastids are the defining organelle for a plant cell and are critical for myriad metabolic functions. The role of leaf plastid, chloroplast, is extensively documented; however, fruit plastids-chromoplasts-are poorly understood, especially in the context of the diverse metabolic processes operating in these diverse plant organs. Recently, in a comparative study of the predicted plastid-targeted proteomes across seven plant species, we reported that each plant species is predicted to harbor a unique set of plastid-targeted proteins. However, the temporal and developmental context of these processes remains unknown. In this study, an ultrastructural analysis approach was used to characterize fruit plastids in the epidermal and collenchymal cell layers at 11 developmental timepoints in three genotypes of apple (Malus × domestica Borkh.): chlorophyll-predominant 'Granny Smith', carotenoid-predominant 'Golden Delicious', and anthocyanin-predominant 'Top Red Delicious'. Plastids transitioned from a proplastid-like plastid to a chromoplast-like plastid in epidermis cells, while in the collenchyma cells, they transitioned from a chloroplast-like plastid to a chloro-chromo-amyloplast plastid. Plastids in the collenchyma cells of the three genotypes demonstrated a diverse array of structures and features. This study enabled the identification of discrete developmental stages during which specific functions are most likely being performed by the plastids as indicated by accumulation of plastoglobuli, starch granules, and other sub-organeller structures. Information regarding the metabolically active developmental stages is expected to facilitate biologically relevant omics studies to unravel the complex biochemistry of plastids in perennial non-model systems.
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Affiliation(s)
- Scott M Schaeffer
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Science Graduate Program, Washington State University, Pullman, WA, USA
- Indigo Agriculture, 500 Rutherford Ave, Suite 201, Charlestown, MA, 02129, USA
| | - Ryan Christian
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Science Graduate Program, Washington State University, Pullman, WA, USA
| | | | - Brennan Hyden
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Valerie Lynch-Holm
- Franchesci Microscopy and Imaging Center, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA.
- Molecular Plant Science Graduate Program, Washington State University, Pullman, WA, USA.
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34
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Hewitt S, Kilian B, Hari R, Koepke T, Sharpe R, Dhingra A. Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry ( Prunus avium L.). Comput Struct Biotechnol J 2017; 15:290-298. [PMID: 28392892 PMCID: PMC5376269 DOI: 10.1016/j.csbj.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species. For the identification of polymorphisms in five closely related genotypes of sweet cherry, a gel-based approach (TRAP), reduced representation sequencing (TRAPseq), a 6k cherry SNParray, and whole genome sequencing (WGS) approaches were evaluated in the identification of genome-wide polymorphisms in sweet cherry cultivars. All platforms facilitated detection of polymorphisms among the genotypes with variable efficiency. In assessing multiple SNP detection platforms, this study has demonstrated that a combination of appropriate approaches is necessary for efficient polymorphism identification, especially between closely related cultivars of a species. The information generated in this study provides a valuable resource for future genetic and genomic studies in sweet cherry, and the insights gained from the evaluation of multiple approaches can be utilized for other closely related species with limited genetic diversity in the breeding germplasm.
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Affiliation(s)
- Seanna Hewitt
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Benjamin Kilian
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Ramyya Hari
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Tyson Koepke
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Richard Sharpe
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Amit Dhingra
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
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Garg S, Mittal M, Swami A, Khosla V, Dhingra A. Our experience with multi-drug resistant acinetobacter meningitis. Journal of Neuroanaesthesiology and Critical Care 2017. [DOI: 10.1055/s-0038-1646218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- S. Garg
- Department of Anaesthesia, Fortis Hospital, Mohali, India
| | - M. Mittal
- Department of Anaesthesia, Fortis Hospital, Mohali, India
| | - A. Swami
- Department of Anaesthesia, Fortis Hospital, Mohali, India
| | - V. Khosla
- Department of Neurosurgery, Fortis Hospital, Mohali, India
| | - A. Dhingra
- Department of Neurosurgery, Fortis Hospital, Mohali, India
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Kohzuma K, Froehlich JE, Davis GA, Temple JA, Minhas D, Dhingra A, Cruz JA, Kramer DM. The Role of Light-Dark Regulation of the Chloroplast ATP Synthase. Front Plant Sci 2017; 8:1248. [PMID: 28791032 PMCID: PMC5522872 DOI: 10.3389/fpls.2017.01248] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/03/2017] [Indexed: 05/18/2023]
Abstract
The chloroplast ATP synthase catalyzes the light-driven synthesis of ATP and is activated in the light and inactivated in the dark by redox-modulation through the thioredoxin system. It has been proposed that this down-regulation is important for preventing wasteful hydrolysis of ATP in the dark. To test this proposal, we compared the effects of extended dark exposure in Arabidopsis lines expressing the wild-type and mutant forms of ATP synthase that are redox regulated or constitutively active. In contrast to the predictions of the model, we observed that plants with wild-type redox regulation lost photosynthetic capacity rapidly in darkness, whereas those expressing redox-insensitive form were far more stable. To explain these results, we propose that in wild-type plants, down-regulation of ATP synthase inhibits ATP hydrolysis, leading to dissipation of thylakoid proton motive force (pmf) and subsequent inhibition of protein transport across the thylakoid through the twin arginine transporter (Tat)-dependent and Sec-dependent import pathways, resulting in the selective loss of specific protein complexes. By contrast, in mutants with a redox-insensitive ATP synthase, pmf is maintained by ATP hydrolysis, thus allowing protein transport to maintain photosynthetic activities for extended periods in the dark. Hence, a basal level of Tat-dependent, as well as, Sec-dependent import activity, in the dark helps replenishes certain components of the photosynthetic complexes and thereby aids in maintaining overall complex activity. However, the influence of a dark pmf on thylakoid protein import, by itself, could not explain all the effects we observed in this study. For example, we also observed in wild type plants a large transient buildup of thylakoid pmf and nonphotochemical exciton quenching upon sudden illumination of dark adapted plants. Therefore, we conclude that down-regulation of the ATP synthase is probably not related to preventing loss of ATP per se. Instead, ATP synthase redox regulation may be impacting a number of cellular processes such as (1) the accumulation of chloroplast proteins and/or ions or (2) the responses of photosynthesis to rapid changes in light intensity. A model highlighting the complex interplay between ATP synthase regulation and pmf in maintaining various chloroplast functions in the dark is presented. Significance Statement: We uncover an unexpected role for thioredoxin modulation of the chloroplast ATP synthase in regulating the dark-stability of the photosynthetic apparatus, most likely by controlling thylakoid membrane transport of proteins and ions.
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Affiliation(s)
- Kaori Kohzuma
- Department of Energy Plant Research Laboratory, Michigan State University, East LansingMI, United States
| | - John E. Froehlich
- Department of Energy Plant Research Laboratory, Michigan State University, East LansingMI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
- *Correspondence: John E. Froehlich,
| | - Geoffry A. Davis
- Department of Energy Plant Research Laboratory, Michigan State University, East LansingMI, United States
- Department of Cell and Molecular Biology, Michigan State University, East LansingMI, United States
| | - Joshua A. Temple
- Department of Energy Plant Research Laboratory, Michigan State University, East LansingMI, United States
| | - Deepika Minhas
- Department of Horticulture and Landscape Architecture, Washington State University, WashingtonDC, United States
| | - Amit Dhingra
- Department of Horticulture and Landscape Architecture, Washington State University, WashingtonDC, United States
| | - Jeffrey A. Cruz
- Department of Energy Plant Research Laboratory, Michigan State University, East LansingMI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
| | - David M. Kramer
- Department of Energy Plant Research Laboratory, Michigan State University, East LansingMI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East LansingMI, United States
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Abstract
There is increasing evidence documenting the critical role played by autophagic and autophagy-associated processes in maintaining cell homeostasis and overall systemic health. Autophagy is considered a degradative as well as a recycling pathway that relies on encapsulated intracellular components trafficking to and fusing with degradative compartments, including lysosomes. In this chapter, we describe the use of DQ™-BSA to study autophagosome-lysosome fusion as well as a means by which to analyze hybrid autophagic pathways. Such noncanonical pathways include LC3-associated phagocytosis, better known as LAP. Both autophagosomes and LAPosomes (LC3-associated phagosomes) deliver cargo for degradation. The use of fluorescent DQ™-BSA in conjugation with autophagic makers and biomarkers of hybrid autophagy offers a reliable technique to monitor the formation of autolysosomes and LAPo-lysosomes in both fixed- and live-cell studies. This technique relies on cleavage of the self-quenched DQ™ Green- or DQ™ Red BSA protease substrates in an acidic compartment to generate a highly fluorescent product.
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Affiliation(s)
- L S Frost
- SDM, University of Pennsylvania, Philadelphia, PA, United States
| | - A Dhingra
- SDM, University of Pennsylvania, Philadelphia, PA, United States
| | - J Reyes-Reveles
- SDM, University of Pennsylvania, Philadelphia, PA, United States
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38
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Davis GA, Kanazawa A, Schöttler MA, Kohzuma K, Froehlich JE, Rutherford AW, Satoh-Cruz M, Minhas D, Tietz S, Dhingra A, Kramer DM. Limitations to photosynthesis by proton motive force-induced photosystem II photodamage. eLife 2016. [PMID: 27697149 DOI: 10.7554/elife.16921.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
The thylakoid proton motive force (pmf) generated during photosynthesis is the essential driving force for ATP production; it is also a central regulator of light capture and electron transfer. We investigated the effects of elevated pmf on photosynthesis in a library of Arabidopsis thaliana mutants with altered rates of thylakoid lumen proton efflux, leading to a range of steady-state pmf extents. We observed the expected pmf-dependent alterations in photosynthetic regulation, but also strong effects on the rate of photosystem II (PSII) photodamage. Detailed analyses indicate this effect is related to an elevated electric field (Δψ) component of the pmf, rather than lumen acidification, which in vivo increased PSII charge recombination rates, producing singlet oxygen and subsequent photodamage. The effects are seen even in wild type plants, especially under fluctuating illumination, suggesting that Δψ-induced photodamage represents a previously unrecognized limiting factor for plant productivity under dynamic environmental conditions seen in the field.
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Affiliation(s)
- Geoffry A Davis
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
- Graduate Program of Cell and Molecular Biology, Michigan State University, East Lansing, United States
| | - Atsuko Kanazawa
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
- Department of Chemistry, Michigan State University, East Lansing, United States
| | | | - Kaori Kohzuma
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - John E Froehlich
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
| | | | - Mio Satoh-Cruz
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Deepika Minhas
- Department of Horticulture, Washington State University, Pullman, United States
| | - Stefanie Tietz
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, United States
| | - David M Kramer
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
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39
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Davis GA, Kanazawa A, Schöttler MA, Kohzuma K, Froehlich JE, Rutherford AW, Satoh-Cruz M, Minhas D, Tietz S, Dhingra A, Kramer DM. Limitations to photosynthesis by proton motive force-induced photosystem II photodamage. eLife 2016; 5. [PMID: 27697149 PMCID: PMC5050024 DOI: 10.7554/elife.16921] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/08/2016] [Indexed: 12/20/2022] Open
Abstract
The thylakoid proton motive force (pmf) generated during photosynthesis is the essential driving force for ATP production; it is also a central regulator of light capture and electron transfer. We investigated the effects of elevated pmf on photosynthesis in a library of Arabidopsis thaliana mutants with altered rates of thylakoid lumen proton efflux, leading to a range of steady-state pmf extents. We observed the expected pmf-dependent alterations in photosynthetic regulation, but also strong effects on the rate of photosystem II (PSII) photodamage. Detailed analyses indicate this effect is related to an elevated electric field (Δψ) component of the pmf, rather than lumen acidification, which in vivo increased PSII charge recombination rates, producing singlet oxygen and subsequent photodamage. The effects are seen even in wild type plants, especially under fluctuating illumination, suggesting that Δψ-induced photodamage represents a previously unrecognized limiting factor for plant productivity under dynamic environmental conditions seen in the field. DOI:http://dx.doi.org/10.7554/eLife.16921.001
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Affiliation(s)
- Geoffry A Davis
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States.,Graduate Program of Cell and Molecular Biology, Michigan State University, East Lansing, United States
| | - Atsuko Kanazawa
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States.,Department of Chemistry, Michigan State University, East Lansing, United States
| | | | - Kaori Kohzuma
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - John E Froehlich
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
| | | | - Mio Satoh-Cruz
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Deepika Minhas
- Department of Horticulture, Washington State University, Pullman, United States
| | - Stefanie Tietz
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, United States
| | - David M Kramer
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, United States.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
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Sharpe RM, Koepke T, Harper A, Grimes J, Galli M, Satoh-Cruz M, Kalyanaraman A, Evans K, Kramer D, Dhingra A. CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites. PLoS One 2016; 11:e0152404. [PMID: 27071032 PMCID: PMC4829253 DOI: 10.1371/journal.pone.0152404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 03/14/2016] [Indexed: 11/30/2022] Open
Abstract
High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.
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Affiliation(s)
- Richard M. Sharpe
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, Washington, United States of America
- School of Biological Sciences, Washington State University, Pullman, WA, Washington, United States of America
| | - Tyson Koepke
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - Artemus Harper
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - John Grimes
- Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, United States of America
| | - Marco Galli
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - Mio Satoh-Cruz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Ananth Kalyanaraman
- Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, United States of America
| | - Katherine Evans
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - David Kramer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Amit Dhingra
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Strand DD, Livingston AK, Satoh-Cruz M, Koepke T, Enlow HM, Fisher N, Froehlich JE, Cruz JA, Minhas D, Hixson KK, Kohzuma K, Lipton M, Dhingra A, Kramer DM. Defects in the Expression of Chloroplast Proteins Leads to H 2O 2 Accumulation and Activation of Cyclic Electron Flow around Photosystem I. Front Plant Sci 2016; 7:2073. [PMID: 28133462 PMCID: PMC5233679 DOI: 10.3389/fpls.2016.02073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/28/2016] [Indexed: 05/02/2023]
Abstract
We describe a new member of the class of mutants in Arabidopsis exhibiting high rates of cyclic electron flow around photosystem I (CEF), a light-driven process that produces ATP but not NADPH. High cyclic electron flow 2 (hcef2) shows strongly increased CEF activity through the NADPH dehydrogenase complex (NDH), accompanied by increases in thylakoid proton motive force (pmf), activation of the photoprotective qE response, and the accumulation of H2O2. Surprisingly, hcef2 was mapped to a non-sense mutation in the TADA1 (tRNA adenosine deaminase arginine) locus, coding for a plastid targeted tRNA editing enzyme required for efficient codon recognition. Comparison of protein content from representative thylakoid complexes, the cytochrome bf complex, and the ATP synthase, suggests that inefficient translation of hcef2 leads to compromised complex assembly or stability leading to alterations in stoichiometries of major thylakoid complexes as well as their constituent subunits. Altered subunit stoichiometries for photosystem I, ratios and properties of cytochrome bf hemes, and the decay kinetics of the flash-induced thylakoid electric field suggest that these defect lead to accumulation of H2O2 in hcef2, which we have previously shown leads to activation of NDH-related CEF. We observed similar increases in CEF, as well as increases in H2O2 accumulation, in other translation defective mutants. This suggests that loss of coordination in plastid protein levels lead to imbalances in photosynthetic energy balance that leads to an increase in CEF. These results taken together with a large body of previous observations, support a general model in which processes that lead to imbalances in chloroplast energetics result in the production of H2O2, which in turn activates CEF. This activation could be from either H2O2 acting as a redox signal, or by a secondary effect from H2O2 inducing a deficit in ATP.
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Affiliation(s)
- Deserah D. Strand
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA
- DOE-Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
| | - Aaron K. Livingston
- Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - Mio Satoh-Cruz
- DOE-Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
| | - Tyson Koepke
- Department of Horticulture, Washington State UniversityPullman, WA, USA
| | - Heather M. Enlow
- Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - Nicholas Fisher
- DOE-Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
| | - John E. Froehlich
- DOE-Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Jeffrey A. Cruz
- DOE-Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
| | - Deepika Minhas
- Department of Horticulture, Washington State UniversityPullman, WA, USA
| | - Kim K. Hixson
- Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Kaori Kohzuma
- DOE-Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
| | - Mary Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State UniversityPullman, WA, USA
| | - David M. Kramer
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA
- DOE-Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
- *Correspondence: David M. Kramer
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Blasi I, Korostoff J, Dhingra A, Reyes-Reveles J, Shenker BJ, Shahabuddin N, Alexander D, Lally ET, Bragin A, Boesze-Battaglia K. Variants of Porphyromonas gingivalis lipopolysaccharide alter lipidation of autophagic protein, microtubule-associated protein 1 light chain 3, LC3. Mol Oral Microbiol 2015; 31:486-500. [PMID: 26452236 DOI: 10.1111/omi.12141] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2015] [Indexed: 01/13/2023]
Abstract
Porphyromonas gingivalis often subverts host cell autophagic processes for its own survival. Our previous studies document the association of the cargo sorting protein, melanoregulin (MREG), with its binding partner, the autophagic protein, microtubule-associated protein 1 light chain 3 (LC3) in macrophages incubated with P. gingivalis (strain 33277). Differences in the lipid A moiety of lipopolysaccharide (LPS) affect the virulence of P. gingivalis; penta-acylated LPS1690 is a weak Toll-like receptor 4 agonist compared with Escherichia coli LPS, whereas tetra-acylated LPS1435/1449 acts as an LPS1690 antagonist. To determine how P. gingivalis LPS1690 affects autophagy we assessed LC3-dependent and MREG-dependent processes in green fluorescent protein (GFP)-LC3-expressing Saos-2 cells. LPS1690 stimulated the formation of very large LC3-positive vacuoles and MREG puncta. This LPS1690 -mediated LC3 lipidation decreased in the presence of LPS1435/1449 . When Saos-2 cells were incubated with P. gingivalis the bacteria internalized but did not traffic to GFP-LC3-positive structures. Nevertheless, increases in LC3 lipidation and MREG puncta were observed. Collectively, these results suggest that P. gingivalis internalization is not necessary for LC3 lipidation. Primary human gingival epithelial cells isolated from patients with periodontitis showed both LC3II and MREG puncta whereas cells from disease-free individuals exhibited little co-localization of these two proteins. These results suggest that the prevalence of a particular LPS moiety may modulate the degradative capacity of host cells, so influencing bacterial survival.
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Affiliation(s)
- I Blasi
- Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Orthodontics, School of Dentistry, International University of Catalonia, Barcelona, Spain
| | - J Korostoff
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - A Dhingra
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Reyes-Reveles
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - B J Shenker
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N Shahabuddin
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - D Alexander
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E T Lally
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - A Bragin
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - K Boesze-Battaglia
- Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Balashova N, Dhingra A, Boesze-Battaglia K, Lally ET. Aggregatibacter actinomycetemcomitans leukotoxin induces cytosol acidification in LFA-1 expressing immune cells. Mol Oral Microbiol 2015; 31:106-14. [PMID: 26361372 DOI: 10.1111/omi.12136] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 01/18/2023]
Abstract
Studies have suggested that Aggregatibacter actinomycetemcomitans leukotoxin (LtxA) kills human lymphocyte function-associated antigen 1 (LFA-1; CD11a/CD18)-bearing immune cells through a lysosomal-mediated mechanism. Lysosomes are membrane-bound cellular organelles that contain an array of acid hydrolases that are capable of breaking down biomolecules. The lysosomal membrane bilayer confines the pH-sensitive enzymes within an optimal acidic (pH 4.8) environment thereby protecting the slightly basic cytosol (pH 6.8-7.5). In the current study, we have probed the effect of LtxA-induced cytolysis on lysosomal integrity in two different K562 erythroleukemia cell lines. K562-puro/LFA-1 cells were stably transfected with CD11a and CD18 cDNA to express LFA-1 on the cell surface while K562-puro, which does not express LFA-1, served as a control. Following treatment with 100 ng ml(-1) LtxA cells were analyzed by live cell imaging in conjunction with time-lapse confocal microscopy and by flow cytometry. Using a pH-sensitive indicator (pHrodo(®)) we demonstrated that the toxin causes a decrease in the intracellular pH in K562-puro/LFA-1 cells that is noticeable within the first 15 min of treatment. This process correlated with the disappearance of lysosomes in the cytosol as determined by both acridine orange and LysoTracker(®) Red DND-99 staining. These changes were not observed in K562-puro cells or when heat inactivated toxin was added to K562-puro/LFA-1. Our results suggest that LtxA induces lysosomal damage, cytosol acidification, which is followed by cell death in K562-puro/LFA-1 cells.
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Affiliation(s)
- N Balashova
- Department of Pathology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - A Dhingra
- Department of Biochemistry, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - K Boesze-Battaglia
- Department of Biochemistry, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - E T Lally
- Department of Pathology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
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Mandadi N, Hendrickson C, Handanahal S, Rajappa T, Pai N, Javeed S, Verghese A, Rai A, Pappu A, Nagaraj G, Dhingra A. Genome sequences of Photorhabdus luminescens strains isolated from entomopathogenic nematodes from southern India. Genom Data 2015; 6:46-7. [PMID: 26697329 PMCID: PMC4664677 DOI: 10.1016/j.gdata.2015.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 07/17/2015] [Accepted: 07/26/2015] [Indexed: 12/02/2022]
Abstract
We report here draft whole genome sequences of three novel strains of Photorhabdus luminescens of 5.2–5.3 Mbps in size, and with a G + C content of 42.5% (each). Symbiotic γ-proteobacteria belonging to the genera, Photorhabdus (Family: Enterobacteriaceae) with their natural vectors, the entomopathogenic nematodes (EPN) (Phylum: Nematoda; Order: Rhabditida; Family: Heterorhabditidae), have emerged as important biological control agents of insect pests, and are capable of production and delivery of diverse compounds to influence host biology [1], [2], [3]. Analysis of these genomes is expected to provide enhanced insight into mechanisms of virulence, insecticidal toxin genetic diversity, antibiotic resistance and monoxenicity. The nucleotide sequence information for the three strains NBAII PLHb105, NBAII HiPL101 and NBAII H75HRPL105 has been deposited in NCBI Nucleotide database and is accessible via AZAB00000000, JTHJ00000000 and JXUR00000000 accession numbers respectively.
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Affiliation(s)
- Nagesh Mandadi
- ICAR-National Bureau of Agricultural Insect Resources (ICAR), P. B. No. 2491, H.A. Farm Post, Bengaluru, 560024, Karnataka, India
| | - Christopher Hendrickson
- Department of Horticulture, PO Box 646414, Washington State University, Pullman, WA 99164, USA
| | - Savithri Handanahal
- Department of Biochemistry, Indian Institute of Science, Malleshwaram Post, Bengaluru, 560012, Karnataka, India
| | - Thippeswamy Rajappa
- ICAR-National Bureau of Agricultural Insect Resources (ICAR), P. B. No. 2491, H.A. Farm Post, Bengaluru, 560024, Karnataka, India
| | - Nikhita Pai
- ICAR-National Bureau of Agricultural Insect Resources (ICAR), P. B. No. 2491, H.A. Farm Post, Bengaluru, 560024, Karnataka, India
| | - Saleem Javeed
- ICAR-National Bureau of Agricultural Insect Resources (ICAR), P. B. No. 2491, H.A. Farm Post, Bengaluru, 560024, Karnataka, India
| | - Abraham Verghese
- ICAR-National Bureau of Agricultural Insect Resources (ICAR), P. B. No. 2491, H.A. Farm Post, Bengaluru, 560024, Karnataka, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistical Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Aneesh Pappu
- Department of Horticulture, PO Box 646414, Washington State University, Pullman, WA 99164, USA
| | - Geetha Nagaraj
- Chromous Biotech Ltd., Sahakar Bhavan, Sahakara Nagar, Bengaluru, 560 0692, Karnataka, India
| | - Amit Dhingra
- Department of Horticulture, PO Box 646414, Washington State University, Pullman, WA 99164, USA
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Naveed K, Mitter N, Harper A, Dhingra A, Pappu HR. Comparative analysis of virus-specific small RNA profiles of three biologically distinct strains of Potato virus Y in infected potato (Solanum tuberosum) cv. Russet Burbank. Virus Res 2014; 191:153-60. [PMID: 25036885 DOI: 10.1016/j.virusres.2014.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/02/2014] [Accepted: 07/07/2014] [Indexed: 11/17/2022]
Abstract
Deep sequencing technology has enabled the analysis of small RNA profiles of virus-infected plants and could provide insights into virus-host interactions. Potato virus Y is an economically important viral pathogen of potato worldwide. In this study, we investigated the nature and relative levels of virus-derived small interfering RNAs (vsiRNAs) in potato cv. Russet Burbank infected with three biologically distinct and economically important strains of PVY, the ordinary strain (PVY-O), tobacco veinal-necrotic strain (PVY-N) and tuber necrotic strain (PVY-NTN). The analysis showed an overall abundance of vsiRNAs of 20-24nt in PVY-infected plants. Considerable differences were present in the distribution of vsiRNAs as well as total small RNAs. The 21nt class was the most prevalent in PVY-infected plants irrespective of the virus strain, whereas in healthy potato plants, the 24nt class was the most dominant. vsiRNAs were derived from every position in the PVY genome, though certain hotspots were identified for each of the PVY strains. Among the three strains used, the population of vsiRNAs of different size classes was relatively different with PVY-NTN accumulating the highest level of vsiRNAs, while PVY-N infected plants had the least population of vsiRNAs. Unique vsiRNAs mapping to PVY genome in PVY-infected plants amounted to 3.13, 1.93 and 1.70% for NTN, N and O, respectively. There was a bias in the generation of vsiRNAs from the plus strand of the genome in comparison to the negative strand. The highest number of total vsiRNAs was from the cytoplasmic inclusion protein gene (CI) in PVY-O and PVY-NTN strains, whereas from PVY-N, the NIb gene produced maximum total vsiRNAs. These findings indicate that the three PVY strains interact differently in the same host genetic background and provided insights into virus-host interactions in an important food crop.
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Affiliation(s)
- Khalid Naveed
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Artemus Harper
- Department of Horticulture, Washington State University, Pullman, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, USA.
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46
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Yin C, Hulbert SH, Schroeder KL, Mavrodi O, Mavrodi D, Dhingra A, Schillinger WF, Paulitz TC. Role of bacterial communities in the natural suppression of Rhizoctonia solani bare patch disease of wheat (Triticum aestivum L.). Appl Environ Microbiol 2013; 79:7428-38. [PMID: 24056471 PMCID: PMC3837727 DOI: 10.1128/aem.01610-13] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/17/2013] [Indexed: 11/20/2022] Open
Abstract
Rhizoctonia bare patch and root rot disease of wheat, caused by Rhizoctonia solani AG-8, develops as distinct patches of stunted plants and limits the yield of direct-seeded (no-till) wheat in the Pacific Northwest of the United States. At the site of a long-term cropping systems study near Ritzville, WA, a decline in Rhizoctonia patch disease was observed over an 11-year period. Bacterial communities from bulk and rhizosphere soil of plants from inside the patches, outside the patches, and recovered patches were analyzed by using pyrosequencing with primers designed for 16S rRNA. Taxa in the class Acidobacteria and the genus Gemmatimonas were found at higher frequencies in the rhizosphere of healthy plants outside the patches than in that of diseased plants from inside the patches. Dyella and Acidobacteria subgroup Gp7 were found at higher frequencies in recovered patches. Chitinophaga, Pedobacter, Oxalobacteriaceae (Duganella and Massilia), and Chyseobacterium were found at higher frequencies in the rhizosphere of diseased plants from inside the patches. For selected taxa, trends were validated by quantitative PCR (qPCR), and observed shifts of frequencies in the rhizosphere over time were duplicated in cycling experiments in the greenhouse that involved successive plantings of wheat in Rhizoctonia-inoculated soil. Chryseobacterium soldanellicola was isolated from the rhizosphere inside the patches and exhibited significant antagonism against R. solani AG-8 in vitro and in greenhouse tests. In conclusion, we identified novel bacterial taxa that respond to conditions affecting bare patch disease symptoms and that may be involved in suppression of Rhizoctonia root rot and bare batch disease.
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Affiliation(s)
- Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Kurtis L. Schroeder
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Olga Mavrodi
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Dmitri Mavrodi
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Amit Dhingra
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, USA
| | - William F. Schillinger
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Timothy C. Paulitz
- USDA Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, Washington, USA
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Garczynski SF, Coates BS, Unruh TR, Schaeffer S, Jiwan D, Koepke T, Dhingra A. Application of Cydia pomonella expressed sequence tags: Identification and expression of three general odorant binding proteins in codling moth. Insect Sci 2013; 20:559-574. [PMID: 23956229 PMCID: PMC4255946 DOI: 10.1111/j.1744-7917.2012.01560.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/05/2012] [Indexed: 06/02/2023]
Abstract
The codling moth, Cydia pomonella, is one of the most important pests of pome fruits in the world, yet the molecular genetics and the physiology of this insect remain poorly understood. A combined assembly of 8 341 expressed sequence tags was generated from Roche 454 GS-FLX sequencing of eight tissue-specific cDNA libraries. Putative chemosensory proteins (12) and odorant binding proteins (OBPs) (18) were annotated, which included three putative general OBP (GOBP), one more than typically reported for other Lepidoptera. To further characterize CpomGOBPs, we cloned cDNA copies of their transcripts and determined their expression patterns in various tissues. Cloning and sequencing of the 698 nt transcript for CpomGOBP1 resulted in the prediction of a 163 amino acid coding region, and subsequent RT-PCR indicated that the transcripts were mainly expressed in antennae and mouthparts. The 1 289 nt (160 amino acid) CpomGOBP2 and the novel 702 nt (169 amino acid) CpomGOBP3 transcripts are mainly expressed in antennae, mouthparts, and female abdomen tips. These results indicate that next generation sequencing is useful for the identification of novel transcripts of interest, and that codling moth expresses a transcript encoding for a new member of the GOBP subfamily.
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Affiliation(s)
| | - Brad S. Coates
- USDA-ARS, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011
| | - Thomas R. Unruh
- USDA-ARS, Yakima Agricultural Research Laboratory, Wapato, WA 98951
| | - Scott Schaeffer
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
| | - Derick Jiwan
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
| | - Tyson Koepke
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
| | - Amit Dhingra
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
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Koepke T, Schaeffer S, Harper A, Dicenta F, Edwards M, Henry RJ, Møller BL, Meisel L, Oraguzie N, Silva H, Sánchez-Pérez R, Dhingra A. Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms. Plant Biotechnol J 2013; 11:883-93. [PMID: 23763653 PMCID: PMC3775899 DOI: 10.1111/pbi.12081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/27/2013] [Accepted: 04/08/2013] [Indexed: 05/08/2023]
Abstract
Prunus is an economically important genus with a wide range of physiological and biological variability. Using the peach genome as a reference, sequencing reads from four almond accessions and one sweet cherry cultivar were used for comparative analysis of these three Prunus species. Reference mapping enabled the identification of many biological relevant polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall scaffold coverage, we identified many potentially interesting regions including hundreds of small scaffolds with no coverage from any individual. Non-sense mutations account for about 70 000 of the 13 million identified single nucleotide polymorphisms (SNPs). Blast2GO analyses on these non-sense SNPs revealed several interesting results. First, non-sense SNPs were not evenly distributed across all gene ontology terms. Specifically, in comparison with peach, sweet cherry is found to have non-sense SNPs in two 1-aminocyclopropane-1-carboxylate synthase (ACS) genes and two 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the nonclimacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were identified by comparing sweet and bitter almond sequences. To the best of our knowledge, this is the first report in plants of non-sense SNP abundance in a genus being linked to specific GO terms.
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Affiliation(s)
- Tyson Koepke
- Department of Horticulture, Washington State University, Pullman WA, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, USA
| | - Scott Schaeffer
- Department of Horticulture, Washington State University, Pullman WA, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, USA
| | - Artemus Harper
- Department of Horticulture, Washington State University, Pullman WA, USA
| | - Federico Dicenta
- Department of Plant Breeding, CEBAS-CSIC, PO BOX 164, 30100 Espinardo, Murcia, Spain
| | - Mark Edwards
- Southern Cross University, Lismore NSW 2480, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia QLD 4072
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Lee Meisel
- INTA-Universidad de Chile, Santiago, Chile
| | - Nnadozie Oraguzie
- IAREC, Department of Horticulture, Washington State University, Prosser, WA, USA
| | - Herman Silva
- Laboratorio de Genómica Funcional & Bioinformática, Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile, 8820808, La Pintana Santiago, Chile
| | - Raquel Sánchez-Pérez
- Department of Plant Breeding, CEBAS-CSIC, PO BOX 164, 30100 Espinardo, Murcia, Spain
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
- Corresponding authors:
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman WA, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, USA
- Corresponding authors:
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Koepke T, Dhingra A. Rootstock scion somatogenetic interactions in perennial composite plants. Plant Cell Rep 2013; 32:1321-37. [PMID: 23793453 PMCID: PMC4244527 DOI: 10.1007/s00299-013-1471-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 06/06/2013] [Accepted: 06/06/2013] [Indexed: 05/19/2023]
Abstract
The ancient plant production practice of grafting which instantly imparts new physiological properties to the desirable scion still remains shrouded in mystery. Yet, grafting remains a widely used technique in the production of several horticultural species. In a composite grafted plant, rootstocks control many aspects of scion growth and physiology including yield and quality attributes as well as biotic and abiotic stress tolerance. Broadly, physical, physiological, biochemical and molecular mechanisms have been reviewed to develop an integrated understanding of this enigmatic process that challenges existing genetic paradigms. This review summarizes the reported mechanisms underlying some of the economically important traits and identifies several key points to consider when conducting rootstock scion interaction experiments. Study of the somatogenetic interactions between rootstock and scion is a field that is ripe for discovery and vast improvements in the coming decade. Further, utilization of rootstocks based on a better understanding of the somatogenetic interactions is highly relevant in the current agricultural environment where there is a need for sustainable production practices. Rootstocks may offer a non-transgenic approach to rapidly respond to the changing environment and expand agricultural production of annual and perennial crops where grafting is feasible in order to meet the global food, fiber and fuel demands of the future.
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Affiliation(s)
- Tyson Koepke
- Department of Horticulture, Washington State University, 149 Johnson Hall, Pullman, WA 99164, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, 149 Johnson Hall, Pullman, WA 99164, USA
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50
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Jiwan D, Roalson EH, Main D, Dhingra A. Antisense expression of peach mildew resistance locus O (PpMlo1) gene confers cross-species resistance to powdery mildew in Fragaria x ananassa. Transgenic Res 2013; 22:1119-31. [PMID: 23728780 DOI: 10.1007/s11248-013-9715-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 05/24/2013] [Indexed: 01/13/2023]
Abstract
Powdery mildew (PM) is one of the major plant pathogens. The conventional method of PM control includes frequent use of sulfur-based fungicides adding to production costs and potential harm to the environment. PM remains a major scourge for Rosaceae crops where breeding approaches mainly resort to gene-for-gene resistance. We have tested an alternate source of PM resistance in Rosaceae. Mildew resistance locus O (MLO) has been well studied in barley due to its role in imparting broad spectrum resistance to PM. We identified PpMlo1 (Prunus persica Mlo) in peach and characterized it further to test if a similar mechanism of resistance is conserved in Rosaceae. Due to its recalcitrance in tissue culture, reverse genetic studies involving PpMloI were not feasible in peach. Therefore, Fragaria x ananassa LF9 line, a taxonomic surrogate, was used for functional analysis of PpMlo1. Agrobacterium-mediated transformation yielded transgenic strawberry plants expressing PpMlo1 in sense and antisense orientation. Antisense expression of PpMlo1 in transgenic strawberry plants conferred resistance to Fragaria-specific powdery mildew, Podosphaera macularis. Phylogenetic analysis of 208 putative Mlo gene copies from 35 plant species suggests a large number of duplications of this gene family prior to the divergence of monocots and eudicots, early in eudicot diversification. Our results indicate that the Mlo-based resistance mechanism is functional in Rosaceae, and that Fragaria can be used as a host to test mechanistic function of genes derived from related tree species. To the best of our knowledge, this work is one of the first attempts at testing the potential of using a Mlo-based resistance strategy to combat powdery mildew in Rosaceae.
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Affiliation(s)
- Derick Jiwan
- Department of Horticulture, Washington State University, PO Box 646414, Pullman, WA, 99164, USA
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