0000000001299136
AUTHOR
Belén Picó
Viral diseases causing the greatest economic losses to the tomato crop. II. The Tomato yellow leaf curl virus — a review
Abstract Tomato yellow leaf curl geminivirus (TYLCV), transmitted by the whitefly Bemisia tabaci (Gennadius) is one of the most devastating diseases of cultivated tomato (Lycopersicon esculentum Mill.). TYLCV causes economic losses up to 100% in tomato crop in many tropical and subtropical regions, and is spreading towards new areas. The increasing economic importance of TYLCV has resulted in the need for accurate detection and identification procedures, stimulating intensive research efforts focused on virus biology, diversity, and epidemiology to develop successful control strategies. Breeding for resistance appears to be the best approach to control this disease, but to date only partial…
Exploring the miRNA-mediated response to combined stresses in melon plants
AbstractClimate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop-productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of melon’s response to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or …
De novoassembly of the zucchini genome reveals a whole-genome duplication associated with the origin of theCucurbitagenus
Summary The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the …
Additional file 5: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
Phenotypic values of RILs carrying Zucchini and Scallop alleles in the detected QTL regions. Means and standard errors of the phenotypic value of RILs belonging to the alternative allelic classes (Zuchini versus Scallop) for the markers in the LOD peak regions of each significant QTL are shown. Data of the three environments, combined and separate, are shown to validate the effects of the different QTLs (Paip2014, Paip2015, and UPV2015). (DOCX 39 kb)
Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits
[EN] Cucurbita pepo contains two cultivated subspecies, each of which encompasses four fruit-shape morphotypes (cultivar groups). The Pumpkin, Vegetable Marrow, Cocozelle, and Zucchini Groups are of subsp. pepo and the Acorn, Crookneck, Scallop, and Straightneck Groups are of subsp. ovifera. Recently, a de novo assembly of the C. pepo subsp. pepo Zucchini genome was published, providing insights into its evolution. To expand our knowledge of evolutionary processes within C. pepo and to identify variants associated with particular morphotypes, we performed whole-genome resequencing of seven of these eight C. pepo morphotypes. We report for the first time whole-genome resequencing of the four…
Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network
Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple …
Additional file 2: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
Average percentage of genome covered with the GBS reads with a read depth from > 1 to > 20. (PPTX 713 kb)
Synthetic conversion of leaf chloroplasts into carotenoid-rich plastids reveals mechanistic basis of natural chromoplast development
Plastids, the defining organelles of plant cells, undergo physiological and morphological changes to fulfill distinct biological functions. In particular, the differentiation of chloroplasts into chromoplasts results in an enhanced storage capacity for carotenoids with industrial and nutritional value such as beta-carotene (provitamin A). Here, we show that synthetically inducing a burst in the production of phytoene, the first committed intermediate of the carotenoid pathway, elicits an artificial chloroplast-to-chromoplast differentiation in leaves. Phytoene overproduction initially interferes with photosynthesis, acting as a metabolic threshold switch mechanism that weakens chloroplast i…
An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
[EN] Background: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species. Results: We report the Genoty…
A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
[EN] Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,0…
Additional file 1: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
Phenotyped traits in the RIL population. (DOCX 13 kb)
A Major QTL Located in Chromosome 8 of Cucurbita moschata Is Responsible for Resistance to Tomato Leaf Curl New Delhi Virus
[EN] Tomato leaf curl New Delhi virus (ToLCNDV) is a bipartite whitefly transmitted begomovirus, responsible since 2013 of severe damages in cucurbit crops in Southeastern Spain. Zucchini (Cucurbita pepo) is the most affected species, but melon (Cucumis melo) and cucumber (Cucumis sativus) are also highly damaged by the infection. The virus has spread across Mediterranean basin and European countries, and integrated control measures are not being enough to reduce economic losses. The identification of resistance genes is required to develop resistant cultivars. In this assay, we studied the inheritance of the resistance to ToLCNDV previously identified in two Cucurbita moschata accessions. …
Additional file 4: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
a) LOD peaks of the QTLs identified in the RIL population for vine, flowering and fruit traits. Lines represent the thresholds p 0.01 and 0.05. Results of CIM analysis with a 20 cM windows are shown for each trait. First box show QTL results with data from all the environments and the other three boxes show the QTL results for single environments Paip2014, Paip2015 and UPV2015. b) Means and errors of the phenotype of alternative allelic classes, homozygous Zucchini (AA) and homozygous Scallop (BB), are shown for each QTL, calculated with the full set of data and with the data form each environment separately. c) Genetic correlations (r x,y) between locations for each trait (*p
Additional file 7 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 6: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
List of genes underlying the significant QTLs involved in vine, flowering and fruit traits variation annotated in the last version of the C. pepo genome (v 3.2) available [13]. (XLSX 146 kb)
Additional file 11 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 8 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 3: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
a) Genetic map developed using the GBS approach with the RIL population derived from the cross Zucchini x Scallop. The genetic and physical position of each of the the 7,718 SNP markers (in the C. pepo genome version 3.2) is indicated and the flanking sequenced of each SNPs is also included. b) Physical position and annotation (in the C. pepo genome version 3.2) of the SNPs that showed statistically significant distorted segregation. Chi-square p-values were corrected for multiple testing using Benjamini and Yekutieli correction [36]. Distorted SNPs are integrated with the 7,718 non-distorted SNPs used for the map construction for which the genetic position is also indicated. c) Main region…
Additional file 4 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 3 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 10 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 4 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 13 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 6 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 5 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 9 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 9 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 7 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 6 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 2 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 1 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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Additional file 5 of A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms
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