381 results on '"Carputo, Domenico"'
Search Results
352. Glycoalkaloid content and chemical composition of potatoes improved with nonconventional breeding approaches
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Vincenzo Fogliano, Teodoro Cardi, Edgardo Filippone, Domenico Carputo, Fabrizio Esposito, Esposito, F., Fogliano, V., Cardi, T., Carputo, D., Filippone, Edgardo, and Carputo, Domenico
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Chipping quality ,Genotype ,Genetically modified crops ,Biology ,Transfection ,Glycoalkaloid ,Antioxidant activity ,Botany ,Cultivar ,Hybrid ,Plant Proteins ,Solanum tuberosum ,Transgenic potatoes ,Substantial equivalence ,Chitinases ,Interspecific hybrids ,food and beverages ,Chlorogenic acid ,General Chemistry ,biology.organism_classification ,Plants, Genetically Modified ,Solanine ,Somatic fusion ,Food Technology ,General Agricultural and Biological Sciences ,Genetic Engineering ,Solanaceae - Abstract
This paper reports the results of chemical analyses performed on two distinct groups of new potato genotypes. The first group contained five clones transformed with the gene ech42 encoding for an endochitinase. The second included 21 interspecific hybrids between the cultivated potato Solanum tuberosum and the wild species S. commersonii, obtained either by somatic fusion or by sexual hybridization. Tubers from transgenic plants were analyzed for several morphological and biochemical parameters to ascertain the substantial equivalence between the transgenic genotypes and the original cultivar Desiree. The interspecific hybrids were analyzed for the same parameters in order to identify genotypes with novel improved chemical characteristics and with low levels of glycoalkaloids deriving from the wild species and potentially hazardous to human health. For transgenic tubers, the results provided evidence that indicates the substantial equivalence between the transgenic genotypes and the cultivated control for the considered traits. The results suggest that chitinase gene insertion did not alter other metabolic pathways of potato tubers and did not cause unintentional pleiotropic effects. As far as interspecific hybrids are concerned, wide variability for all of the parameters analyzed was found. For some useful traits (e.g., soluble solids and proteins, dry matter content) the interspecific hybrids performed better than both the cultivated control and the wild species. In a number of genotypes, glycoalkaloid levels were close to or lower than those of the control varieties, suggesting that selection for low glycoalkaloid content is possible. The results also indicated that glycoalkaloids from S. commersonii may be lost rapidly. Indeed, some hybrids were found to have the same glycoalkaloid profile as S. tuberosum. Finally, the results showed that among the parameters considered, glycoalkaloid content is the most sensitive to variation. Therefore, glycoalkaloid determination should be used for routine control of genotypes produced by interspecific hybridization.
- Published
- 2002
353. Tuber quality and soft rot resistance of hybrids between Solanum tuberosum and the incongruent wild relative S. commersonii
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Carputo, D., Frusciante, L., Monti, L., Parisi, M., amalia barone, Carputo, Domenico, Frusciante, Luigi, Monti, L., Parisi, M., Barone, Amalia, and Carputo, D.
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food and beverages - Abstract
Tetraploid BC3 hybrids between sexually incompatible species Solanum commersonii and S. tuberosum were characterized for tuber quality (stolon length, tuber eye depth, chipping color from 3-month storage at 5 C, and specific gravity) and soft rot resistance traits. For all analysed morphological traits, except stolon length, genotypes resembled the S. tuberosum phenotype. On average, the specific gravity of selected genotypes was quite high (1.087), and 12 of them had a value >1.090. As for chip-processing ability, 4.8% of genotypes chipped well directly from cold storage, and 14.3% after reconditioning. All but one of these genotypes also possessed a high specific gravity of tubers. Variability was found for resistance to Erwinia carotovora subsp. carotovora. In particular, 24% of hybrids had a rotted area diameter < 4 mm and were classified as resistant. The average percentage of commersonii-specific markers still present in the BC3 hybrids was 22%, ranging from 9% to 37%. Genotypes combining good qualitative tuber traits with a wild genome content lower than the average value of the population were selected for further breeding efforts. The importance of molecular-assisted selection is discussed.
- Published
- 2002
354. Metodologie innovative per il miglioramento genetico della patata precoce
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CARPUTO D., BARONE, AMALIA, CARBONE S., FRUSCIANTE, LUIGI, Carputo, Domenico, Barone, Amalia, Carbone, S., Frusciante, Luigi, and Carputo, D.
- Published
- 2001
355. Use and usefulness of Endosperm Balance Number
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CARPUTO D., MONTI L., WERNER J., FRUSCIANTE, LUIGI, Carputo, Domenico, Monti, L., Werner, J., Frusciante, Luigi, and Carputo, D.
- Published
- 1999
356. The role of the cytoskeleton in potato meiosis
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Flora Alfano, Cammareri, M., Carputo, D., Errico, A., Conicella, C., Alfano, F., Cammareri, M., Carputo, Domenico, Errico, Angela, and Conicella, C.
- Published
- 1998
357. Discrepancy between spindle anomalies and 2n pollen production in Solanum interspecific hybrids
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amalia barone, Carputo, D., La Rotonda, G., Frusciante, L., Barone, Amalia, Carputo, Domenico, LA ROTONDA, G., Frusciante, Luigi, Carputo, D, and LA ROTONDA, G
- Published
- 1997
358. RESISTANCE TO BLACKLEG AND TUBER SOFT ROT IN SEXUAL AND SOMATIC INTERSPECIFIC HYBRIDS WITH DIFFERENT GENETIC BACKGROUND
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Astolfo Zoina, Luigi Frusciante, Domenico Carputo, Teodoro Cardi, Mario Speggiorin, Carputo, D, Cardi, T, Speggiorin, M, Zoina, A, Frusciante, Luigi, Carputo, Domenico, Cardi, T., Speggiorin, M., and Zoina, A.
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biology ,Tubercle ,fungi ,Blackleg ,food and beverages ,Plant Science ,Plant disease resistance ,biology.organism_classification ,Somatic fusion ,Botany ,Genotype ,Ploidy ,Agronomy and Crop Science ,Solanaceae ,Hybrid - Abstract
Diploid interspecific hybrids from crosses betweenSolanum tuberosum haploids andS. canasense, S. multidissectum, andS. tarijense, along with tetraploid and hexaploid somatic hybrids S.tuberosum (+)S. commersonii, were screened for resistance to blackleg and tuber soft rot byErwinia carotovora subsp.atroseptica andE. carotovora subsp.carotovora. Among the diploid hybrids, those involving clone mlt la of S.multidissectum and tar 2b ofS. tarijense yielded the highest number of genotypes resistant to both blackleg and tuber soft rot. By contrast, all the hybrids involving clone tar 1lb ofS. tarijense were susceptible to both bacterial diseases. As far as resistance of somatic hybrids is concerned, the most interesting genotype was the tetraploid one which showed resistance to both blackleg and tuber soft rot Significant correlations were found betweenE. carotovora subsp.atroseptica andE. carotovora subsp.carotovora both in resistance to blackleg and in resistance to tuber soft rot, suggesting that resistance to the two subspecies is controlled by the same gene/s or that the relevant genes are linked. On the other hand, correlations between blackleg and tuber soft rot were never significant, indicating that different mechanisms may control resistance in tuber and stems. Alternatively, the resistance could be controlled by the same gene/s under a different spatial/temporal expression pattern. Twelve diploid sexual hybrids and one tetraploid somatic hybrid were selected for resistance to blackleg and/or tuber soft rot and for tuber characteristics.
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- 1997
359. Production and use of seedling tubers from True Potato Seed (TPS) for potato cultivation in Italy
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M. Pentimalli, Domenico Carputo, Luigi Frusciante, Carputo, Domenico, Pentimalli, M., and Frusciante, Luigi
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biology ,Tubercle ,Field experiment ,Significant difference ,biology.organism_classification ,Solanum tuberosum ,Population density ,Plant population ,Horticulture ,Agronomy ,Seedling ,Agronomy and Crop Science ,Solanaceae ,Food Science - Abstract
The effect of varying plant population on the production of tubers from potato seedlings was investigated during 1992 and 1993 using three different plant densities: 35, 70, 100 plants/m2. Increasing the plant population significantly increased the number of tubers produced, but no significant difference was found between the plant densities of 70 and 100 plants/m2. The seedling tubers produced in nursery beds were tested in the field for ware potato production using different sized tubers. The best performances were obtained using tubers 30–40 mm. Significant differences were evident among the 7 true potato seed (TPS) families used, but data grouped by type of cross did not indicate any significant difference between 4X×4X and 4X×2X crossing groups.
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- 1996
360. 2n pollen production in Solanum phureja-S. tuberosum hybrids
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FILOTICO F., CARPUTO D., BARONE, AMALIA, Filotico, F., Carputo, Domenico, Barone, Amalia, and Carputo, D.
- Published
- 1995
361. Effect of mulching and plant density on out-of-season organic potato growth, yield and quality
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Caruso, G., Carputo, D., Stefano Conti, Borrelli, C., Maddaluno, P., Frusciante, L., Caruso, Gianluca, Carputo, Domenico, Conti, Stefano, Borrelli, C., Maddaluno, P., and Frusciante, Luigi
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Biodegradable mulch, plant leaf area and dry matter, production, Solanum tuberosum L., tuber vitamin C - Abstract
Research was carried out on potato (Solanum tuberosum L., cv. Spunta) growing in the fi eld in the Campania region (southern Italy) in 2007 and 2008, adopting organic farming practices, in order to evaluate the effects of two mulching treatments (black biodegradable fi lm and bare soil) and six plant densities (12.5, 10.0, 8.3, 7.1, 6.2 and, as a control, 5.3 plants per m2) on growth, yield and quality of “new potato” winter-spring and summer-autumn crops. Only in the case of the summer-autumn crop cycle, mulching resulted in a higher yield, plant dry matter and leaf area compared with the bare soil control, while in both crop cycles this latter treatment induced a delay in harvest. The winter-spring cycle gave a higher production of 40-70 mm tubers, while the summer-autumn cycle resulted in a higher vitamin C content. For the winter-spring crop cycle, the plant density of 8.3 plants·m-2 resulted in the highest yield for food-use tubers, whereas the highest production of seed tubers was obtained with a density of 12.5 plants·m-2. The plant density of 8.3 plants·m-2 also resulted in the highest plant dry matter and leaf area. For the summer-autumn crop cycle, the 10 plants·m-2 density gave the highest production of 40-70 mm calibre tubers, as well as the highest plant dry matter and leaf area. In this cycle, the 6.3 plants·m-2 density resulted in the highest production of 70-80 mm calibre tubers. In terms of cost effectiveness, the choice of biodegradable mulching could save the expense of manual weed control and, in the case of the summer-autumn crop cycle, it is also associated with a higher yield. Overall, tuber yield increased with plant density but the fi nal production was also affected by the crop cycle. This may depend on the different environmental conditions and duration which characterized each cultural cycle and, therefore, affected the vegetative development of organic new potatoes.
362. Shoot regeneration and chromosome doubling in accessions of 2x(1EBN) and 4x(2EBN) wild Solanum species
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Marina Iovene, Frusciante, L., Carputo, D., Iovene, . M., Frusiante, L., Carputo, Domenico, Iovene, Marina, and Frusciante, Luigi
363. Chromosome pairing in Solanum commersonii-S. tuberosum sexual hybrids detected by commersonii-specific RAPDs and cytological analysis
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amalia barone, Sebastiano, A., Carputo, D., Barone, Amalia, Sebastiano, A., and Carputo, Domenico
364. Cytological and genetic studies on 2n pollen formation mechanisms in diploid Phureja-Tuberosum hybrids
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amalia barone, Carputo, D., La Rotonda, G., Sebastiano, A., Frusciante, L., Barone, Amalia, Carputo, D., LA ROTONDA, G., Sebastiano, A., Frusciante, Luigi, and Carputo, Domenico
365. Field performance and resistance to tuber soft rot of potato clones derived from sexual polyploidization
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Antonio Di Matteo, Caruso, G., Barone, A., Aversano, R., Frusciante, L., Carputo, D., DI MATTEO, Antonio, Caruso, Gianluca, Barone, Amalia, Aversano, Riccardo, Frusciante, Luigi, and Carputo, Domenico
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sexual polyploidization, resistance, potato, tuber soft rot - Abstract
Unilateral sexual polyploidization through 4x x 2x crosses is widely used to introgress genes from the diploid gene pool to the tetraploid cultivated potato Solanum tuberosum. Clones of eight 4x x 2x families, from crosses between four tetraploid cultivated potatoes and two diploid S. phureja – S. tuberosum hybrids, producing 2n pollen, were evaluated for yield performances and resistance to tuber soft rot. Significant differences in terms of tuber yield and number were found between families and clones, with several clones outyielding their tetraploid parents. The source of variation due to females (4x females GCA) was significant for both tuber yield and number. A number of clones displayed inheritance of resistance to tuber soft rot. No relationship was found between agronomic traits and resistance to soft rot. Results suggest that the genotypes produced represent genetic material with good potentiality in the constitution of new genotypes with interesting trait combinations.
366. Highlights of meiotic genes in Arabidopsis thaliana
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L. Monti, Domenico Carputo, C. Conicella, F. Consiglio, C., Conicella, F. Consiglio, ., Carputo, Domenico, and Monti, Luigi
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Genetics ,biology ,Arabidopsis ,Fertility ,Meiosis ,Mutants ,fungi ,Synapsis ,food and beverages ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Plant reproduction ,Apomixis ,Arabidopsis thaliana ,Agronomy and Crop Science ,Molecular Biology ,Gene ,Cytokinesis ,Biotechnology - Abstract
Meiosis is a fascinating and complex phenomenon and, despite its central role in sexual plant reproduction, little is known on the molecular mechanisms involved in this process. We review the progress made in recent years using Arabidopsis thaliana mutants for isolating meiotic genes. In particular, emphasis is given on the description of mutants affecting either the regular commitment to meiosis, or the mechanisms of synapsis, recombination, and cytokinesis. We believe that the isolation of genes affecting some crucial meiotic events may represent the first step towards the practical use of meiotic genes in plant breeding. The introduction of deviations in the meiotic pathway into sexual crops will have important implications for the exploitation of apomixis and sexual polyploidization. Key words : Arabidopsis, meiosis, mutants, fertility. African Journal of Biotechnology Vol. 2 (12), pp.516-520, December 2003
367. FDR and FDR+SDR 2n pollen for true potato seed production
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Sebastiano, A., Carputo, D., Maria Federica Consiglio, Filotico, F., Frusciante, L., Barone, A., Sebastiano, A., Carputo, Domenico, Consiglio, F., Filotico, F., Frusciante, Luigi, and Barone, Amalia
368. Exploring CDF gene family in wild potato under salinity stress unveils promising candidates for developing climate-resilient crops.
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Docimo T, Paesano A, D'Agostino N, D'Amelia V, Garramone R, Carputo D, and Aversano R
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- Multigene Family, Transcription Factors genetics, Transcription Factors metabolism, Stress, Physiological genetics, Phylogeny, Solanum tuberosum genetics, Solanum tuberosum metabolism, Solanum tuberosum growth & development, Gene Expression Regulation, Plant, Plant Proteins genetics, Plant Proteins metabolism, Crops, Agricultural genetics, Crops, Agricultural growth & development, Salt Stress genetics
- Abstract
The DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors involved in diverse biological processes, including response to biotic and abiotic stresses. Members of this family have been reported in the cultivated potato Solanum tuberosum, but clues to the roles of several Dof genes are still lacking. Potato wild relatives represent a genetic reservoir for breeding as they could provide useful alleles for adaptation to the environment and tolerance to biotic and abiotic stresses. We performed an in silico analysis to identify genes belonging to the Dof family in the wild potato S. commersonii, confirming that the identified Dof genes can be grouped in four classes (A, B, C, D), as reported for cultivated potato. A special focus was dedicated to Cycling Dof Factors (CDFs), which play a crucial role in plant responses to abiotic stresses. Analysis of available RNA-seq data confirmed CDF genes as regulated by stresses and often in a tissue specific manner. To ascertain their involvement in the stress response, S. tuberosum and S. commersonii plantlets growing in vitro were subjected to salt stress (80mM NaCl) for short (2 days) and prolonged (7 days) times. Analysis of phenotypic traits and qRT-PCR expression profiles of target CDF genes in aerial and root tissues showed differences between the two species. In addition, after saline treatment, changes in total phenols, proline, and malondialdehyde suggested a diverse perception of saline stress in S. commersonii vs. S. tuberosum. Overall, this study provided useful clues to the involvement of CDF genes in salt response and promoted the identification of potential candidate genes for further functional studies., (© 2024. The Author(s).)
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- 2024
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369. Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties.
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Villano C, Procino S, Blaiotta G, Carputo D, D'Agostino N, Di Serio E, Fanelli V, La Notte P, Miazzi MM, Montemurro C, Taranto F, and Aversano R
- Abstract
Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence of spontaneous somatic mutations has played a pivotal role in shaping the diverse landscape of grapevine agrobiodiversity. These naturally occurring selections, termed 'clones,' represent a vast reservoir of potentially valuable traits and alleles that hold promise for enhancing grape quality and bolstering plant resilience against environmental and biotic challenges. Despite their potential, many of these clones remain largely untapped.In light of this context, this study aims to delve into the population structure, genetic diversity, and distinctive genetic loci within a collection of 138 clones derived from six Campanian and Apulian grapevine varieties, known for their desirable attributes in viticulture and winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis and fixation index (FST) calculations were conducted both between populations and at individual loci. Notably, varieties originating from the same geographical region exhibited pronounced genetic similarity.The resulting SNP dataset facilitated the identification of approximately two hundred loci featuring divergent markers (FST ≥ 0.80) within annotated exons. Several of these loci exhibited associations with essential traits like phenotypic adaptability and environmental responsiveness, offering compelling opportunities for grapevine breeding initiatives. By shedding light on the genetic variability inherent in these treasured traditional grapevines, our study contributes to the broader understanding of their potential. Importantly, it underscores the urgency of preserving and characterizing these valuable genetic resources to safeguard their intra-varietal diversity and foster future advancements in grapevine cultivation., Competing Interests: Author CM was employed by the company SINAGRI S.r.l. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Villano, Procino, Blaiotta, Carputo, D’Agostino, Di Serio, Fanelli, La Notte, Miazzi, Montemurro, Taranto and Aversano.)
- Published
- 2023
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370. Functional characterization of DcMYB11, an R2R3 MYB associated with the purple pigmentation of carrot petiole.
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D'Amelia V, Curaba J, Abid MA, Esposito S, Cavagnaro P, Carputo D, and Iorizzo M
- Subjects
- Anthocyanins, Pigmentation, Alleles, Crops, Agricultural, Daucus carota
- Abstract
Main Conclusion: DcMYB11, an R2R3 MYB gene associated with petiole anthocyanin pigmentation in carrot, was functionally characterized. A putative enhancer sequence is able to increase DcMYB11 activity. The accumulation of anthocyanin pigments can exhibit different patterns across plant tissues and crop varieties. This variability allowed the investigation of the molecular mechanisms behind the biosynthesis of these pigments in several plant species. Among crops, carrots have a well-defined anthocyanin pigmentation pattern depending on the genic background. In this work, we report on the discovery of DNA structural differences affecting the activity of an R2R3 MYB (encoded by DcMYB11) involved in anthocyanin regulation in carrot petiole. To this end, we first verified the function of DcMYB11 using heterologous systems and identified three different alleles which may explain differences in petiole pigmentation. Characterization of the DcMYB11 alleles at the 5' upstream sequence unveiled a sequence that functions as a putative enhancer. In conclusion, this study provides novel insight into the molecular mechanisms controlling anthocyanin accumulation in carrot. By these outcomes, we expanded our knowledge on the cis-regulatory sequences in plants., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
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- 2023
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371. Targeted mutagenesis of StISAC stabilizes the production of anthocyanins in potato cell culture.
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D'Amelia V, Staiti A, D'Orso F, Maisto M, Piccolo V, Aversano R, and Carputo D
- Abstract
To increase the production of decorated anthocyanins in potato cell cultures, we knocked out a novel potato gene, named Inducer Silencing of Anthocyanins in Cell culture ( StISAC ), using CRISPR-Cas9 editing. Our results provided evidence that mutant cell lines doubled the accumulation level of anthocyanins biosynthesized. Moreover, the production of these important pigments was stabilized over time. Our study overcame important challenges in the efficient biotechnological production of these valuable pigments and reported the function of a novel anthocyanin biosynthesis repressor gene., Competing Interests: VDA, AS, RA, and DC declare to be co‐authors of a patent governing the information disclosed here (Italian patent application n. 102021000000785, filled on 18 Jan 2021). The other authors have no competing interests to declare., (© 2022 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd.)
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- 2022
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372. Multi-omics data integration provides insights into the post-harvest biology of a long shelf-life tomato landrace.
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Cigliano RA, Aversano R, Di Matteo A, Palombieri S, Termolino P, Angelini C, Bostan H, Cammareri M, Consiglio FM, Della Ragione F, Paparo R, Valkov VT, Vitiello A, Carputo D, Chiusano ML, D'Esposito M, Grandillo S, Matarazzo MR, Frusciante L, D'Agostino N, and Conicella C
- Abstract
In this study we investigated the transcriptome and epigenome dynamics of the tomato fruit during post-harvest in a landrace belonging to a group of tomatoes (Solanum lycopersicum L.) collectively known as "Piennolo del Vesuvio", all characterized by a long shelf-life. Expression of protein-coding genes and microRNAs as well as DNA methylation patterns and histone modifications were analysed in distinct post-harvest phases. Multi-omics data integration contributed to the elucidation of the molecular mechanisms underlying processes leading to long shelf-life. We unveiled global changes in transcriptome and epigenome. DNA methylation increased and the repressive histone mark H3K27me3 was lost as the fruit progressed from red ripe to 150 days post-harvest. Thousands of genes were differentially expressed, about half of which were potentially epi-regulated as they were engaged in at least one epi-mark change in addition to being microRNA targets in ~5% of cases. Down-regulation of the ripening regulator MADS-RIN and of genes involved in ethylene response and cell wall degradation was consistent with the delayed fruit softening. Large-scale epigenome reprogramming that occurred in the fruit during post-harvest likely contributed to delayed fruit senescence., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved.)
- Published
- 2022
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373. Whole-Genome Doubling Affects Pre-miRNA Expression in Plants.
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Esposito S, Aversano R, Tripodi P, and Carputo D
- Abstract
Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs' precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species ( Arabidopsis thaliana L., Morus alba L., Brassica rapa L. , Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.
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- 2021
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374. Applications and Trends of Machine Learning in Genomics and Phenomics for Next-Generation Breeding.
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Esposito S, Carputo D, Cardi T, and Tripodi P
- Abstract
Crops are the major source of food supply and raw materials for the processing industry. A balance between crop production and food consumption is continually threatened by plant diseases and adverse environmental conditions. This leads to serious losses every year and results in food shortages, particularly in developing countries. Presently, cutting-edge technologies for genome sequencing and phenotyping of crops combined with progress in computational sciences are leading a revolution in plant breeding, boosting the identification of the genetic basis of traits at a precision never reached before. In this frame, machine learning (ML) plays a pivotal role in data-mining and analysis, providing relevant information for decision-making towards achieving breeding targets. To this end, we summarize the recent progress in next-generation sequencing and the role of phenotyping technologies in genomics-assisted breeding toward the exploitation of the natural variation and the identification of target genes. We also explore the application of ML in managing big data and predictive models, reporting a case study using microRNAs (miRNAs) to identify genes related to stress conditions.
- Published
- 2019
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375. Inferring RPW8-NLRs's evolution patterns in seed plants: case study in Vitis vinifera.
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Andolfo G, Villano C, Errico A, Frusciante L, Carputo D, Aversano R, and Ercolano MR
- Subjects
- Ascomycota, Evolution, Molecular, Gene Expression Profiling, Genome, Plant, Neuregulin-1, Phylogeny, Plant Diseases genetics, Plant Diseases microbiology, Transcriptome, Disease Resistance genetics, Genes, Plant genetics, Seeds genetics, Seeds metabolism, Vitis genetics, Vitis metabolism
- Abstract
Main Conclusion: Genomic and transcriptomic studies in plants and, more in deep, in grapevine reveal that the disease-resistance RNL gene family is highly variable. RNLs (RPW8-NLRs) are a phylogenetically distinct class of nucleotide oligomerization domain (NOD)-like receptors (NLRs) identified in plants. Two RNLs, namely, the NRG1 (N Requirement Gene 1) and the ADR1 (Activated Disease Resistance 1), have been characterized; however, little is known about the RNL evolutionary history in higher plants. To trace the diversification of RNL gene subfamily, we scanned the NLR proteins of 73 plant genomes belonging to 29 taxa, revealing a noticeable diversification across species and within the same genus or botanic family together with a conspicuous expansion in important crop species. To explore the RNL variability in Vitis vinifera and gain information with respect to their structure, evolutionary diversification of five grape genomes ('Aglianico', 'Falanghina', 'Sultanina', 'Tannat', and 'Nebbiolo') has been compared to the reference genome ('Pinot Noir'). The number of RNLs ranged from 6 ('Sultanina') to 14 ('Nebbiolo'), in contrast to the 10 'Pinot Noir' RNLs. The phylogenetic study on grapevine RNLs revealed that all collapsed into NRG1-clade, rather than four. To investigate more in depth the means of intraspecific variability of grape RNL copies, a transcriptomic profiling in response to powdery mildew (PM) infection was carried out through qRT-PCRs and public databases interrogation. The RNL expression variability identified in transcriptome data sets supports the hypothesis of a functional expansion/contraction in grapevine varieties. Although no direct correlations between grapevine PM-resistance and RNL expression was identified, our work can provide good candidates for functional studies able to elucidate the putative "helper" role of RNLs in grape immune signalling.
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- 2019
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376. LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions.
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Esposito S, Barteri F, Casacuberta J, Mirouze M, Carputo D, and Aversano R
- Subjects
- Cold Temperature, Evolution, Molecular, Genetic Markers genetics, Solanum physiology, Solanum tuberosum genetics, Solanum tuberosum physiology, Stress, Physiological, Genome, Plant genetics, Genomics, Retroelements ethics, Solanum genetics, Terminal Repeat Sequences genetics
- Abstract
Main Conclusion: Copia/Ale is the youngest lineage in both Solanum tuberosum and S. commersonii. Within it, we identified nightshade, a new LTR element active in the cultivated potato. From an evolutionary perspective, long-terminal repeat retrotransposons (LTR-RT) activity during stress may be viewed as a mean by which organisms can keep up rates of genetic adaptation to changing conditions. Potato is one of the most important crop consumed worldwide, but studies on LTR-RT characterization are still lacking. Here, we assessed the abundance, insertion time and activity of LTR-RTs in both cultivated Solanum tuberosum and its cold-tolerant wild relative S. commersonii genomes. Gypsy elements were more abundant than Copia ones, suggesting that the former was somehow more successful in colonizing potato genomes. However, Copia elements, and in particular, the Ale lineage, are younger than Gypsy ones, since their insertion time was in average ~ 2 Mya. Due to the ability of LTR-RTs to be circularized by the host DNA repair mechanisms, we identified via mobilome-seq a Copia/Ale element (called nightshade, informal name used for potato family) active in S. tuberosum genome. Our analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in potato.
- Published
- 2019
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377. Dicer-like and RNA-dependent RNA polymerase gene family identification and annotation in the cultivated Solanum tuberosum and its wild relative S. commersonii.
- Author
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Esposito S, Aversano R, D'Amelia V, Villano C, Alioto D, Mirouze M, and Carputo D
- Subjects
- Gene Duplication genetics, Gene Expression Regulation, Plant genetics, Phylogeny, Real-Time Polymerase Chain Reaction, Sequence Alignment, Solanum enzymology, Solanum tuberosum enzymology, Stress, Physiological genetics, DNA-Directed RNA Polymerases genetics, Genes, Plant genetics, RNA-Dependent RNA Polymerase genetics, Ribonuclease III genetics, Solanum genetics, Solanum tuberosum genetics
- Abstract
Main Conclusion: We provide advances in DCL and RDR gene diversity in Solanaceae. We also shed light on DCL and RDR gene expression in response to cold stress. DICER-like (DCL) and RNA-dependent RNA polymerase (RDR) genes form the core components to trigger small non-coding RNA (ncRNA) production. In spite of this, little is known about the two gene families in non-model plant species. As their genome sequences are now available, the cultivated potato (Solanum tuberosum) and its cold-tolerant wild relative Solanum commersonii offer a valuable opportunity to advance our understanding of the above genes. To determine the extent of diversification and evolution of DCLs and RDRs in these species, we performed a comparative analysis. Seven DCLs were identified in the two species, whereas seven and six RDR genes were found in S. tuberosum and S. commersonii, respectively. Based on phylogenetic analysis with DCLs and RDRs from several species, we provide evidence for an increase in their number in both potato species. We also disclosed that tandem duplications played a major role in the evolution of these gene families in Solanaceae. DCL and RDR expression was investigated in different tissues and under cold and virus stresses, with divergent profiles of the tandem duplicated genes being found in different tissues. DCL paralogs showed a contrasting expression in S. tuberosum and S. commersonii following cold stress and virus infection. By contrast, no change in RDR transcript activity was detected following both stresses. Overall, this study provides the first comparative genomic analysis of the core components of the RNAi machinery in Solanaceae and offers a scaffold for future functional analysis of these gene families.
- Published
- 2018
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378. Repeated Stand-Replacing Crown Fires Affect Seed Morphology and Germination in Aleppo pine.
- Author
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Saracino A, Bellino A, Allevato E, Mingo A, Conti S, Rossi S, Bonanomi G, Carputo D, and Mazzoleni S
- Abstract
Post-fire reproductive niche of Aleppo pine ( Pinus halepensis ) is deeply interlaced with fire products. Indeed, the high pH and low osmotic potentials of ash beds under burnt crowns constitute the main constraints to seed germination. In this study, we aim to investigate whether fire recurrence, through the physico-chemical constraints imposed by the ash beds, affects the reproduction ability of P. halepensis at the germination stage. To this aim, Aleppo pine seeds were collected in neighboring even-aged stands subjected to 0, 1, or 2 fires (namely fire cohorts), and seed morphology and germination performance, in terms of cumulative germination and germination kinetics, were studied under increasing osmotic potentials (from 0.0 to -1.2 MPa) and pH (from 6 to 11). Besides fire history, the role of ontogenetic age of mother plants on seed morphology and germination was also investigated. Differences in seed morphology among the three cohorts have been highlighted in a multivariate context, with anisotropic enlargement of the seeds produced by pine stands experiencing repeated fires. The patterns of seed germination varied primarily in relation to the fire cohort, with seeds from the pine stand experiencing repeated fires exhibiting enhanced tolerance to pH stress. Conversely, germination performances under osmotic constraints mainly depends on tree ontogenetic stage, with an involvement of fire history especially in the timing of seed germination. Our results suggest that, at least in the short term, fire recurrence does not constrain the reproduction ability of Aleppo pine. These results highlight the need for further research to elucidate the mechanisms behind these responses to recurrent fires.
- Published
- 2017
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379. The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives.
- Author
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Aversano R, Contaldi F, Ercolano MR, Grosso V, Iorizzo M, Tatino F, Xumerle L, Dal Molin A, Avanzato C, Ferrarini A, Delledonne M, Sanseverino W, Cigliano RA, Capella-Gutierrez S, Gabaldón T, Frusciante L, Bradeen JM, and Carputo D
- Subjects
- Acclimatization, Biological Evolution, Phylogeny, Solanum classification, Solanum tuberosum classification, Genome, Plant genetics, Solanum genetics, Solanum tuberosum genetics
- Abstract
Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes., (© 2015 American Society of Plant Biologists. All rights reserved.)
- Published
- 2015
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380. Use of SSR and retrotransposon-based markers to interpret the population structure of native grapevines from southern Italy.
- Author
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Villano C, Carputo D, Frusciante L, Santoro X, and Aversano R
- Subjects
- DNA, Plant, Genetic Variation, Genotype, Italy, Phylogeny, Vitis classification, DNA Fingerprinting methods, Microsatellite Repeats, Retroelements, Vitis genetics
- Abstract
Native grapevines are the quintessential elements of Southern Italy winemaking, and genomic characterization plays a role of primary importance for preservation and sustainable use of these unexploited genetic resources. Among the various molecular techniques available, SSR and retrotransposons-based markers result to be the most valuable for cultivars and biotypes distinctiveness. A total of 62 accessions including 38 local grape cultivars were analyzed with 30 SSR, four REMAP and one IRAP markers to assess their genetic diversity and obtain a complete genomic profiling. The use of VrZAG79, VrZAG112, VVS2, VVMD25 and VVMD5 combined with retrotransposon-based markers proved to be the most discriminating and polymorphic markers for the rapid and unambiguous identification of minority grapevines from Campania region, which is considered one of the most appreciated Italian districts for wine production. Results revealed 58 SSR marker-specific alleles, 22 genotype-specific SSR alleles, and four REMAP and IRAP private bands. Cases of synonymy and homonymy were discovered. In conclusion, we provided evidences that the integrating SSR and retrotransposon-based markers is an effective strategy to assess the genetic diversity of autochthonous grapes, allowing their easy identification.
- Published
- 2014
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381. The role of 2n gametes and endosperm balance number in the origin and evolution of polyploids in the tuber-bearing Solanums.
- Author
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Carputo D, Frusciante L, and Peloquin SJ
- Subjects
- Solanum metabolism, Biological Evolution, Germ Cells metabolism, Polyploidy, Solanum genetics
- Abstract
Polyploidization has played a major role in the origin and evolution of polyploid species. In this article we outline the unique characteristics of 2n gametes and implications of their participation in the evolution of polyploid Solanum species. The genetic consequences of 2n gametes indicate that sexual polyploidization results in greater variability, fitness, and heterozygosity than does somatic doubling. Further, the mechanisms of 2n gamete formation and the frequency of 2n gamete-forming genes in present polyploids and their ancestral species provide additional evidence of their involvement. Equally important is the endosperm, via the endosperm balance number (EBN) incompatibility system, in complementing the role of 2n gametes. In fact, the EBN system acts as a screen for either 1n or 2n gametes, depending on the EBN and chromosome numbers of parental species. EBN in combination with 2n gametes maintains the ploidy integrity of diploid ancestral species, while providing the flexibility for either unilateral or bilateral sexual polyploidization.
- Published
- 2003
- Full Text
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