1
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Patella A, Palumbo F, Galla G, Barcaccia G. The Molecular Determination of Hybridity and Homozygosity Estimates in Breeding Populations of Lettuce ( Lactuca sativa L.). Genes (Basel) 2019; 10:E916. [PMID: 31717592 PMCID: PMC6895879 DOI: 10.3390/genes10110916] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/26/2022] Open
Abstract
The development of new varieties of horticultural crops benefits from the integration of conventional and molecular marker-assisted breeding schemes in order to combine phenotyping and genotyping information. In this study, a selected panel of 16 microsatellite markers were used in different steps of a breeding programme of lettuce (Lactuca sativa L., 2 n = 18). Molecular markers were first used to genotype 71 putative parental lines and to plan 89 controlled crosses designed to maximise recombination potentials. The resulting 871 progeny plants were then molecularly screened, and their marker allele profiles were compared with the profiles expected based on the parental lines. The average cross-pollination success rate was 68 ± 33%, so 602 F1 hybrids were completely identified. Unexpected genotypes were detected in 5% of cases, consistent with this species' spontaneous out-pollination rate. Finally, in a later step of the breeding programme, 47 different F3 progenies, selected by phenotyping for a number of morphological descriptors, were characterised in terms of their observed homozygosity and within-population genetic uniformity and stability. Ten of these populations had a median homozygosity above 90% and a median genetic similarity above 95% and are, therefore, particularly suitable for pre-commercial trials. In conclusion, this study shows the synergistic effects and advantages of conventional and molecular methods of selection applied in different steps of a breeding programme aimed at developing new varieties of lettuce.
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Affiliation(s)
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro PD, Italy; (A.P.); (G.G.); (G.B.)
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2
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Ravazzolo L, Trevisan S, Manoli A, Boutet-Mercey SP, Perreau FO, Quaggiotti S. The Control of Zealactone Biosynthesis and Exudation is Involved in the Response to Nitrogen in Maize Root. PLANT & CELL PHYSIOLOGY 2019; 60:2100-2112. [PMID: 31147714 DOI: 10.1093/pcp/pcz108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
Nitrate acts as a signal in regulating plant development in response to environment. In particular nitric oxide, auxin and strigolactones (SLs) were supposed to cooperate to regulate the maize root response to this anion. In this study, a combined approach based on liquid chromatography-quadrupole/time-of-flight tandem mass spectrometry and on physiological and molecular analyses was adopted to specify the involvement of SLs in the maize response to N. Our results showed that N deficiency strongly induces SL exudation, likely through stimulating their biosynthesis. Nitrate provision early counteracts and also ammonium lowers SL exudation, but less markedly. Exudates obtained from N-starved and ammonium-provided seedlings stimulated Phelipanche germination, whereas when seeds were treated with exudates harvested from nitrate-provided plants no germination was observed. Furthermore, our findings support the idea that the inhibition of SL production observed in response to nitrate and ammonium would contribute to the regulation of lateral root development. Moreover, the transcriptional regulation of a gene encoding a putative maize WBC transporter, in response to various nitrogen supplies, together with its mRNA tissue localization, supported its role in SL allocation. Our results highlight the dual role of SLs as molecules able to signal outwards a nutritional need and as endogenous regulators of root architecture adjustments to N, thus synchronizing plant growth with nitrogen acquisition.
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Affiliation(s)
- Laura Ravazzolo
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Universit� 16, Legnaro, Padova, Italy
| | - Sara Trevisan
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Universit� 16, Legnaro, Padova, Italy
| | - Alessandro Manoli
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Universit� 16, Legnaro, Padova, Italy
| | - Stï Phanie Boutet-Mercey
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Franï Ois Perreau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Viale dell'Universit� 16, Legnaro, Padova, Italy
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3
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de Lima PHC, Barcelos RM, Klein RC, Vidigal PMP, Montandon CE, Fabres-Klein MH, Dergam JA, Mafra C. Sequencing and comparative analysis of the Amblyomma sculptum mitogenome. Vet Parasitol 2017; 247:121-128. [DOI: 10.1016/j.vetpar.2017.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 10/08/2017] [Accepted: 10/14/2017] [Indexed: 11/25/2022]
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4
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Di Lorenzo T, Melita M, Cifoni M, Galassi DMP, Iannucci A, Biricolti S, Gori M, Baratti M. Effect of ammonia on the gene expression levels of the freshwater cyclopoid Eucyclops serrulatus. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2017; 51:138-141. [PMID: 28238699 DOI: 10.1016/j.etap.2017.02.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/16/2017] [Accepted: 02/18/2017] [Indexed: 06/06/2023]
Abstract
Ammonia pollution is a critical issue in Europe, since more than half of the European freshwater bodies actually fail to meet EU quality standards for this chemical. In this study, the response of stress-related genes to a sublethal ammonia concentration has been investigated in the adults of the freshwater cyclopoid Eucyclops serrulatus. Two short-term exposures (12h and 24h) at 12mg/L NH4+ have been tested. Results indicate that 12mg/L NH4+ causes a significant increase in the expression of some proteins, namely CAT, HSP90 and HSP40, suggesting an activation of the protecting antioxidant system after both 12h and 24h.
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Affiliation(s)
- Tiziana Di Lorenzo
- Institute of Ecosystem Study (ISE), CNR, Sesto Fiorentino, Firenze, Italy
| | - Marco Melita
- Institute of Ecosystem Study (ISE), CNR, Sesto Fiorentino, Firenze, Italy
| | - Marco Cifoni
- Institute of Ecosystem Study (ISE), CNR, Sesto Fiorentino, Firenze, Italy; Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Diana M P Galassi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Alessio Iannucci
- Institute of Ecosystem Study (ISE), CNR, Sesto Fiorentino, Firenze, Italy
| | - Stefano Biricolti
- Department Agrifood Production and Environmental Sciences (DISPAA), Sesto Fiorentino, Firenze, Italy
| | - Massimo Gori
- Department Agrifood Production and Environmental Sciences (DISPAA), Sesto Fiorentino, Firenze, Italy
| | - Mariella Baratti
- Institute of Ecosystem Study (ISE), CNR, Sesto Fiorentino, Firenze, Italy.
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5
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Jaramillo ML, Ammar D, Quispe RL, Guzman F, Margis R, Nazari EM, Müller YMR. Identification and evaluation of reference genes for expression studies by RT-qPCR during embryonic development of the emerging model organism, Macrobrachium olfersii. Gene 2016; 598:97-106. [PMID: 27825774 DOI: 10.1016/j.gene.2016.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/25/2016] [Accepted: 11/02/2016] [Indexed: 11/28/2022]
Abstract
RT-qPCR is a sensitive and highly efficient technique that is widely used in gene expression analysis and to provide insight into the molecular mechanisms underlying embryonic development. The freshwater prawn, Macrobrachium olfersii is an emerging model organism, but, the stable reference genes of this species need to be identified and validated for RT-qPCR analysis. Thus, the aim of this study was to evaluate the expression stability of six genes (β-act, GAPDH, EF-1α, RpL8, RpS6, AK) in embryos and in adult tissues (cerebral ganglia, muscle and hepatopancreas) of M. olfersii. The expression stabilities of these genes were evaluated using geNorm, NormFinder, BestKeeper, ΔCt method and integrated tool RefFinder. In the general ranking, RpL8 and RpS6 were the most stable genes in embryos, while RpS6 and RpL8 were the most stable in a combined adult tissue analysis. Analysis of the adult tissues revealed that β-act and AK were the most stable genes in cerebral ganglia, RpL8 and AK in muscle, and RpS6 and β-act in hepatopancreas. EF-1α and GAPDH were the least stable genes and as normalizer genes in RT-qPCR affected expression of the Distal-less gene during M. olfersii development. This study provides suitable reference genes for RT-qPCR analysis and allows future studies of the gene expression in M. olfersii for understanding the molecular mechanisms of their development. To our knowledge, this is the first published study that identifies and evaluates reference genes for RT-qPCR analysis in M. olfersii and could be useful as basis for evaluations of reference genes in other prawns.
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Affiliation(s)
- Michael L Jaramillo
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Dib Ammar
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil; Centro Universitário - Católica de Santa Catarina, 89203-005 Joinville, SC, Brazil
| | - Ruth L Quispe
- Universidade Federal de Santa Catarina, Programa de Pós-Graduação em Neurociências, Campus Universitário, 88040-900 Florianópolis, SC, Brazil
| | - Frank Guzman
- Universidade Federal do Rio Grande do Sul, PPGBCM, Centro de Biotecnologia, 91501-970 Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Departamento de Biofisica, 91501-970 Porto Alegre, RS, Brazil
| | - Evelise M Nazari
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil.
| | - Yara M R Müller
- Universidade Federal de Santa Catarina, Departamento de Biologia Celular, Embriologia e Genética, 88040-900 Florianópolis, Santa Catarina, Brazil
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Anindyajati, Artarini AA, Riani C, Retnoningrum DS. Plasmid Copy Number Determination by Quantitative Polymerase Chain Reaction. Sci Pharm 2016; 84:89-101. [PMID: 27110501 PMCID: PMC4839616 DOI: 10.3797/scipharm.isp.2015.02] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/15/2015] [Indexed: 01/24/2023] Open
Abstract
Recombinant therapeutic proteins are biopharmaceutical products that develop rapidly for years. Recombinant protein production in certain hosts requires vector expression harboring the gene encoding the corresponding protein. Escherichia coli is the prokaryote organism mostly used in recombinant protein production, commonly using a plasmid as the expression vector. Recombinant protein production is affected by plasmid copy number harboring the encoded gene, hence the determination of plasmid copy number also plays an important role in establishing a recombinant protein production system. On the industrial scale, a low copy number of plasmids are more suitable due to their better stability. In the previous study we constructed pCAD, a plasmid derived from the low copy number pBR322 plasmid. This study was aimed to confirm pCAD’s copy number by quantitative polymerase chain reaction (qPCR). Plasmid copy number was determined by comparing the quantification signal from the plasmid to those from the chromosome. Copy number was then calculated by using a known copy number plasmid as a standard. Two pairs of primers, called tdk and ori, were designed for targeting a single gene tdk in the chromosome and a conserved domain in the plasmid’s ori, respectively. Primer quality was analyzed in silico using PrimerSelect DNASTAR and PraTo software prior to in vitro evaluation on primer specificity and efficiency as well as optimization of qPCR conditions. Plasmid copy number determination was conducted on E. coli lysates harboring each plasmid, with the number of cells ranging from 102–105 cells/μL. Cells were lysed by incubation at 95ºC for 10 minutes, followed by immediate freezing at −4°C. pBR322 plasmid with the copy number of ~19 copies/cell was used as the standard, while pJExpress414-sod plasmid possessing the high copy number pUC ori was also determined to test the method being used. In silico analysis based on primer-primer and primer-template interactions showed that both primer pairs were acceptable and were predicted to have good performance. Those predictions were in agreement with the in vitro test that gave a single band in the PCR product’s electropherogram and a single peak in DNA amplicon’s melting curve with a Tm value of 79.01 ± 0.11°C for the tdk primer and 81.53 ± 0.29°C for the ori primer. The efficiency of each primer was 1.95 and 1.97, respectively. The calculation result of pCAD’s copy number was 13.1 ± 0.3 copies/cell, showing that pCAD’s low copy number has been determined and confirmed. Meanwhile, it was 576.3 ± 91.9 copies/cell for pJExpress414-sod, in accordance with the hypothesis that pUC ori regulates the high copy number plasmid. In conclusion, the designed primers and qPCR conditions used in this study can be used to determine plasmid copy number for plasmids with pBR322 and pUC ori. The method should be tested further on plasmids harboring other type of ori.
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Affiliation(s)
- Anindyajati
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | - A Anita Artarini
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | - Catur Riani
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | - Debbie S Retnoningrum
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, 40132, Bandung, Indonesia
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7
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Manoli A, Trevisan S, Voigt B, Yokawa K, Baluška F, Quaggiotti S. Nitric Oxide-Mediated Maize Root Apex Responses to Nitrate are Regulated by Auxin and Strigolactones. FRONTIERS IN PLANT SCIENCE 2016; 6:1269. [PMID: 26834770 PMCID: PMC4722128 DOI: 10.3389/fpls.2015.01269] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/28/2015] [Indexed: 05/20/2023]
Abstract
Nitrate (NO3 (-)) is a key element for crop production but its levels in agricultural soils are limited. Plants have developed mechanisms to cope with these NO3 (-) fluctuations based on sensing nitrate at the root apex. Particularly, the transition zone (TZ) of root apex has been suggested as a signaling-response zone. This study dissects cellular and molecular mechanisms underlying NO3 (-) resupply effects on primary root (PR) growth in maize, confirming nitric oxide (NO) as a putative modulator. Nitrate restoration induced PR elongation within the first 2 h, corresponding to a stimulation of cell elongation at the basal border of the TZ. Xyloglucans (XGs) immunolocalization together with Brefeldin A applications demonstrated that nitrate resupply induces XG accumulation. This effect was blocked by cPTIO (NO scavenger). Transcriptional analysis of ZmXET1 confirmed the stimulatory effect of nitrate on XGs accumulation in cells of the TZ. Immunolocalization analyses revealed a positive effect of nitrate resupply on auxin and PIN1 accumulation, but a transcriptional regulation of auxin biosynthesis/transport/signaling genes was excluded. Short-term nitrate treatment repressed the transcription of genes involved in strigolactones (SLs) biosynthesis and transport, mainly in the TZ. Enhancement of carotenoid cleavage dioxygenases (CCDs) transcription in presence of cPTIO indicated endogenous NO as a negative modulator of CCDs activity. Finally, treatment with the SLs-biosynthesis inhibitor (TIS108) restored the root growth in the nitrate-starved seedlings. Present report suggests that the NO-mediated root apex responses to nitrate are accomplished in cells of the TZ via integrative actions of auxin, NO and SLs.
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Affiliation(s)
- Alessandro Manoli
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PaduaPadua, Italy
| | - Sara Trevisan
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PaduaPadua, Italy
| | - Boris Voigt
- Department of Plant Cell Biology, Institute of Cellular and Molecular Botany, University of BonnBonn, Germany
| | - Ken Yokawa
- Department of Plant Cell Biology, Institute of Cellular and Molecular Botany, University of BonnBonn, Germany
- Department of Biological Sciences, Tokyo Metropolitan UniversityTokyo, Japan
| | - František Baluška
- Department of Plant Cell Biology, Institute of Cellular and Molecular Botany, University of BonnBonn, Germany
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PaduaPadua, Italy
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8
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Cukrov D, Zermiani M, Brizzolara S, Cestaro A, Licausi F, Luchinat C, Santucci C, Tenori L, Van Veen H, Zuccolo A, Ruperti B, Tonutti P. Extreme Hypoxic Conditions Induce Selective Molecular Responses and Metabolic Reset in Detached Apple Fruit. FRONTIERS IN PLANT SCIENCE 2016; 7:146. [PMID: 26909091 PMCID: PMC4754620 DOI: 10.3389/fpls.2016.00146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/28/2016] [Indexed: 05/05/2023]
Abstract
The ripening physiology of detached fruit is altered by low oxygen conditions with profound effects on quality parameters. To study hypoxia-related processes and regulatory mechanisms, apple (Malus domestica, cv Granny Smith) fruit, harvested at commercial ripening, were kept at 1°C under normoxic (control) and hypoxic (0.4 and 0.8 kPa oxygen) conditions for up to 60 days. NMR analyses of cortex tissue identified eight metabolites showing significantly different accumulations between samples, with ethanol and alanine displaying the most pronounced difference between hypoxic and normoxic treatments. A rapid up-regulation of alcohol dehydrogenase and pyruvate-related metabolism (lactate dehydrogenase, pyruvate decarboxylase, alanine aminotransferase) gene expression was detected under both hypoxic conditions with a more pronounced effect induced by the lowest (0.4 kPa) oxygen concentration. Both hypoxic conditions negatively affected ACC synthase and ACC oxidase transcript accumulation. Analysis of RNA-seq data of samples collected after 24 days of hypoxic treatment identified more than 1000 genes differentially expressed when comparing 0.4 vs. 0.8 kPa oxygen concentration samples. Genes involved in cell-wall, minor and major CHO, amino acid and secondary metabolisms, fermentation and glycolysis as well as genes involved in transport, defense responses, and oxidation-reduction appeared to be selectively affected by treatments. The lowest oxygen concentration induced a higher expression of transcription factors belonging to AUX/IAA, WRKY, HB, Zinc-finger families, while MADS box family genes were more expressed when apples were kept under 0.8 kPa oxygen. Out of the eight group VII ERF members present in apple genome, two genes showed a rapid up-regulation under hypoxia, and western blot analysis showed that apple MdRAP2.12 proteins were differentially accumulated in normoxic and hypoxic samples, with the highest level reached under 0.4 kPa oxygen. These data suggest that ripe apple tissues finely and specifically modulate sensing and regulatory mechanisms in response to different hypoxic stress conditions.
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Affiliation(s)
- Dubravka Cukrov
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
| | - Monica Zermiani
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, University of PadovaPadova, Italy
| | | | - Alessandro Cestaro
- Centro Ricerca e Innovazione, Fondazione Edmund Mach di San Michele all'AdigeTrento, Italy
| | - Francesco Licausi
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
| | | | | | | | - Hans Van Veen
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
| | - Andrea Zuccolo
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
| | - Benedetto Ruperti
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, University of PadovaPadova, Italy
| | - Pietro Tonutti
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
- *Correspondence: Pietro Tonutti
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9
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Abstract
Design of primers and probes is one of the most crucial factors affecting the success and quality of quantitative real-time PCR (qPCR) analyses, since an accurate and reliable quantification depends on using efficient primers and probes. Design of primers and probes should meet several criteria to find potential primers and probes for specific qPCR assays. The formation of primer-dimers and other non-specific products should be avoided or reduced. This factor is especially important when designing primers for SYBR(®) Green protocols but also in designing probes to ensure specificity of the developed qPCR protocol. To design primers and probes for qPCR, multiple software programs and websites are available being numerous of them free. These tools often consider the default requirements for primers and probes, although new research advances in primer and probe design should be progressively added to different algorithm programs. After a proper design, a precise validation of the primers and probes is necessary. Specific consideration should be taken into account when designing primers and probes for multiplex qPCR and reverse transcription qPCR (RT-qPCR). This chapter provides guidelines for the design of suitable primers and probes and their subsequent validation through the development of singlex qPCR, multiplex qPCR, and RT-qPCR protocols.
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Zermiani M, Zonin E, Nonis A, Begheldo M, Ceccato L, Vezzaro A, Baldan B, Trentin A, Masi A, Pegoraro M, Fadanelli L, Teale W, Palme K, Quintieri L, Ruperti B. Ethylene negatively regulates transcript abundance of ROP-GAP rheostat-encoding genes and affects apoplastic reactive oxygen species homeostasis in epicarps of cold stored apple fruits. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:7255-70. [PMID: 26428066 PMCID: PMC4765793 DOI: 10.1093/jxb/erv422] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Apple (Malus×domestica Borkh) fruits are stored for long periods of time at low temperatures (1 °C) leading to the occurrence of physiological disorders. 'Superficial scald' of Granny Smith apples, an economically important ethylene-dependent disorder, was used as a model to study relationships among ethylene action, the regulation of the ROP-GAP rheostat, and maintenance of H2O2 homeostasis in fruits during prolonged cold exposure. The ROP-GAP rheostat is a key module for adaptation to low oxygen in Arabidopsis through Respiratory Burst NADPH Oxidase Homologs (RBOH)-mediated and ROP GTPase-dependent regulation of reactive oxygen species (ROS) homeostasis. Here, it was shown that the transcriptional expression of several components of the apple ROP-GAP machinery, including genes encoding RBOHs, ROPs, and their ancillary proteins ROP-GEFs and ROP-GAPs, is coordinately and negatively regulated by ethylene in conjunction with the progressive impairment of apoplastic H2O2 homeostatic levels. RNA sequencing analyses showed that several components of the known ROP- and ROS-associated transcriptional networks are regulated along with the ROP-GAP rheostat in response to ethylene perception. These findings may extend the role of the ROP-GAP rheostat beyond hypoxic responses and suggest that it may be a functional regulatory node involved in the integration of ethylene and ROS signalling pathways in abiotic stress.
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Affiliation(s)
- Monica Zermiani
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Elisabetta Zonin
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Alberto Nonis
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Maura Begheldo
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Luca Ceccato
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Alice Vezzaro
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Barbara Baldan
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Annarita Trentin
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Marco Pegoraro
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
| | - Livio Fadanelli
- Edmund Mach Foundation, San Michele all'Adige, 38123 Trento, Italy
| | - William Teale
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany
| | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany Centre for Biological Systems Analysis, Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany Freiburg Institute for Advanced Sciences (FRIAS), Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany Freiburg Initiative for Systems Biology (FRISYS), Albert-Ludwigs-University of Freiburg, D-79104 Freiburg, Germany
| | - Luigi Quintieri
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, 35131 Padova, Italy
| | - Benedetto Ruperti
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, 35020 Legnaro, Italy
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11
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Trevisan S, Manoli A, Ravazzolo L, Botton A, Pivato M, Masi A, Quaggiotti S. Nitrate sensing by the maize root apex transition zone: a merged transcriptomic and proteomic survey. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3699-715. [PMID: 25911739 PMCID: PMC4473975 DOI: 10.1093/jxb/erv165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nitrate is an essential nutrient for plants, and crops depend on its availability for growth and development, but its presence in agricultural soils is far from stable. In order to overcome nitrate fluctuations in soil, plants have developed adaptive mechanisms allowing them to grow despite changes in external nitrate availability. Nitrate can act as both nutrient and signal, regulating global gene expression in plants, and the root tip has been proposed as the sensory organ. A set of genome-wide studies has demonstrated several nitrate-regulated genes in the roots of many plants, although only a few studies have been carried out on distinct root zones. To unravel new details of the transcriptomic and proteomic responses to nitrate availability in a major food crop, a double untargeted approach was conducted on a transition zone-enriched root portion of maize seedlings subjected to differing nitrate supplies. The results highlighted a complex transcriptomic and proteomic reprogramming that occurs in response to nitrate, emphasizing the role of this root zone in sensing and transducing nitrate signal. Our findings indicated a relationship of nitrate with biosynthesis and signalling of several phytohormones, such as auxin, strigolactones, and brassinosteroids. Moreover, the already hypothesized involvement of nitric oxide in the early response to nitrate was confirmed with the use of nitric oxide inhibitors. Our results also suggested that cytoskeleton activation and cell wall modification occurred in response to nitrate provision in the transition zone.
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Affiliation(s)
- Sara Trevisan
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Alessandro Manoli
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Laura Ravazzolo
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Alessandro Botton
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Micaela Pivato
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy Proteomics Centre of Padova University, VIMM and Padova University Hospital, Via Giuseppe Orus, 2, 35129 Padova, Italy
| | - Antonio Masi
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Silvia Quaggiotti
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro (PD), Italy
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Choosing between RT-qPCR and RNA-seq: a back-of-the-envelope estimate towards the definition of the break-even-point. Anal Bioanal Chem 2015; 406:3533-6. [PMID: 24687434 DOI: 10.1007/s00216-014-7687-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Manoli A, Begheldo M, Genre A, Lanfranco L, Trevisan S, Quaggiotti S. NO homeostasis is a key regulator of early nitrate perception and root elongation in maize. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:185-200. [PMID: 24220653 PMCID: PMC3883287 DOI: 10.1093/jxb/ert358] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Crop plant development is strongly dependent on nitrogen availability in the soil and on the efficiency of its recruitment by roots. For this reason, the understanding of the molecular events underlying root adaptation to nitrogen fluctuations is a primary goal to develop biotechnological tools for sustainable agriculture. However, knowledge about molecular responses to nitrogen availability is derived mainly from the study of model species. Nitric oxide (NO) has been recently proposed to be implicated in plant responses to environmental stresses, but its exact role in the response of plants to nutritional stress is still under evaluation. In this work, the role of NO production by maize roots after nitrate perception was investigated by focusing on the regulation of transcription of genes involved in NO homeostasis and by measuring NO production in roots. Moreover, its involvement in the root growth response to nitrate was also investigated. The results provide evidence that NO is produced by nitrate reductase as an early response to nitrate supply and that the coordinated induction of non-symbiotic haemoglobins (nsHbs) could finely regulate the NO steady state. This mechanism seems to be implicated on the modulation of the root elongation in response to nitrate perception. Moreover, an improved agar-plate system for growing maize seedlings was developed. This system, which allows localized treatments to be performed on specific root portions, gave the opportunity to discern between localized and systemic effects of nitrate supply to roots.
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Affiliation(s)
- Alessandro Manoli
- Department of Agriculture, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Agripolis, Viale dell’Università, 16, 35020 Legnaro (PD), Italy
| | - Maura Begheldo
- Department of Agriculture, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Agripolis, Viale dell’Università, 16, 35020 Legnaro (PD), Italy
| | - Andrea Genre
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Sara Trevisan
- Department of Agriculture, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Agripolis, Viale dell’Università, 16, 35020 Legnaro (PD), Italy
| | - Silvia Quaggiotti
- Department of Agriculture, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Agripolis, Viale dell’Università, 16, 35020 Legnaro (PD), Italy
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14
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Pinosa F, Begheldo M, Pasternak T, Zermiani M, Paponov IA, Dovzhenko A, Barcaccia G, Ruperti B, Palme K. The Arabidopsis thaliana Mob1A gene is required for organ growth and correct tissue patterning of the root tip. ANNALS OF BOTANY 2013; 112:1803-14. [PMID: 24201137 PMCID: PMC3838559 DOI: 10.1093/aob/mct235] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/22/2013] [Accepted: 08/20/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS The Mob1 family includes a group of kinase regulators conserved throughout eukaryotes. In multicellular organisms, Mob1 is involved in cell proliferation and apoptosis, thus controlling appropriate cell number and organ size. These functions are also of great importance for plants, which employ co-ordinated growth processes to explore the surrounding environment and respond to changing external conditions. Therefore, this study set out to investigate the role of two Arabidopsis thaliana Mob1-like genes, namely Mob1A and Mob1B, in plant development. METHODS A detailed spatio-temporal analysis of Mob1A and Mob1B gene expression was performed by means of bioinformatic tools, the generation of expression reporter lines and in situ hybridization of gene-specific probes. To explore the function of the two genes in plant development, knock-out and knock-down mutants were isolated and their phenotype quantitatively characterized. KEY RESULTS Transcripts of the two genes were detected in specific sets of cells in all plant organs. Mob1A was upregulated by several stress conditions as well as by abscisic acid and salicylic acid. A knock-out mutation in Mob1B did not cause any visible defect in plant development, whereas suppression of Mob1A expression affected organ growth and reproduction. In the primary root, reduced levels of Mob1A expression brought about severe defects in tissue patterning of the stem cell niche and columella and led to a decrease in meristem size. Moreover, loss of Mob1A function resulted in a higher sensitivity of root growth to abscisic acid. CONCLUSIONS Taken together, the results indicate that arabidopsis Mob1A is involved in the co-ordination of tissue patterning and organ growth, similarly to its orthologues in other multicellular eukaryotes. In addition, Mob1A serves a plant-specific function by contributing to growth adjustments in response to stress conditions.
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Affiliation(s)
- Francesco Pinosa
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Maura Begheldo
- Department of Agriculture, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Taras Pasternak
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Monica Zermiani
- Department of Agriculture, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Ivan A. Paponov
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Alexander Dovzhenko
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Gianni Barcaccia
- Department of Agriculture, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Benedetto Ruperti
- Department of Agriculture, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, viale dell'Università, 16, 35020 Legnaro (PD), Italy
| | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
- Centre for Biological Systems Analysis, Albert-Ludwigs-University of Freiburg, Habsburgerstrasse 49, D-79104 Freiburg, Germany
- Freiburg Institute for Advanced Sciences (FRIAS), Albert-Ludwigs-University of Freiburg, Albertstrasse 19, D-79104 Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), Albert-Ludwigs-University of Freiburg, Albertstrasse 19, D-79104 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
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15
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Nonis A, Vezzaro A, Ruperti B. Evaluation of RNA extraction methods and identification of putative reference genes for real-time quantitative polymerase chain reaction expression studies on olive (Olea europaea L.) fruits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:6855-6865. [PMID: 22703380 DOI: 10.1021/jf300419w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genome wide transcriptomic surveys together with targeted molecular studies are uncovering an ever increasing number of differentially expressed genes in relation to agriculturally relevant processes in olive (Olea europaea L). These data need to be supported by quantitative approaches enabling the precise estimation of transcript abundance. qPCR being the most widely adopted technique for mRNA quantification, preliminary work needs to be done to set up robust methods for extraction of fully functional RNA and for the identification of the best reference genes to obtain reliable quantification of transcripts. In this work, we have assessed different methods for their suitability for RNA extraction from olive fruits and leaves and we have evaluated thirteen potential candidate reference genes on 21 RNA samples belonging to fruit developmental/ripening series and to leaves subjected to wounding. By using two different algorithms, GAPDH2 and PP2A1 were identified as the best reference genes for olive fruit development and ripening, and their effectiveness for normalization of expression of two ripening marker genes was demonstrated.
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Affiliation(s)
- Alberto Nonis
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy
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16
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Vezzaro A, Krause ST, Nonis A, Ramina A, Degenhardt J, Ruperti B. Isolation and characterization of terpene synthases potentially involved in flavor development of ripening olive (Olea europaea) fruits. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:908-14. [PMID: 22475500 DOI: 10.1016/j.jplph.2012.01.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 01/24/2012] [Accepted: 01/25/2012] [Indexed: 05/08/2023]
Abstract
The flavor and taste of fruits are often determined by terpenes. We identified three cDNAs encoding putative terpene synthases from olive fruits of cv. Frantoio and Grignano. Heterologous expression in a bacterial system demonstrated that one of the terpene synthases, OeGES1, was an active monoterpene synthase that converted geranyl diphosphate to the monoterpene alcohol geraniol. The transcript accumulation pattern of this gene showed a peak during fruit ripening in both genotypes, indicating that the enzyme may be involved in the production of monoterpene flavor compounds in olive fruit. Although the putative terpene synthases OeTPS2 and OeTPS3 clustered with α-farnesene synthases and angiosperm monoterpene synthases, no detectable in vitro activity was found after expression in a bacterial system. Nevertheless, their transcripts sharply accumulated during fruit ripening starting from véraison.
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Affiliation(s)
- Alice Vezzaro
- Department of Environmental Agronomy and Crop Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy.
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Manoli A, Sturaro A, Trevisan S, Quaggiotti S, Nonis A. Evaluation of candidate reference genes for qPCR in maize. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:807-15. [PMID: 22459324 DOI: 10.1016/j.jplph.2012.01.019] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/26/2012] [Accepted: 01/30/2012] [Indexed: 05/18/2023]
Abstract
Quantitative real-time PCR (qPCR) is a powerful tool to measure gene expression levels. Accurate and reproducible results are dependent on the correct choice of the reference genes for data normalization. To date, screenings evaluating candidate reference gene stability for expression studies in maize have not been reported. In the present work, we analyzed the expression patterns of 12 genes in a set of 20 maize samples, obtained from different tissues of plants grown at various experimental conditions. Using genorm(PLUS), NormFinder and BestKeeper algorithms, the expression stability of three "classical" reference genes, such as ACT, TUB and 18S rRNA, and the newly identified candidates, was assessed. With respect to the algorithms, our results showed similar performance among genorm(PLUS), NormFinder and BestKeeper in evaluating the suitability of reference genes. Our data therefore showed that the currently and widely used reference genes for data normalization in maize were not the most stable expressed transcripts. Five of the new putative reference genes (CUL, FPGS, LUG, MEP and UBCP) exhibited the highest expression stability according to all algorithms. In conclusion, with this study, we provide a list of validated reference genes and their relative primer sequences to conduct reliable qPCR experiments in maize.
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Affiliation(s)
- Alessandro Manoli
- Department of Agricultural Biotechnologies, University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy
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