Exploiting the diversity of tomato: the development of a phenotypically and genetically detailed germplasm collection
[EN] A collection of 163 accessions, including Solanum pimpinellifolium, Solanum lycopersicum var. cerasiforme and Solanum lycopersicum var. lycopersicum, was selected to represent the genetic and morphological variability of tomato at its centers of origin and domestication: Andean regions of Peru and Ecuador and Mesoamerica. The collection is enriched with S. lycopersicum var. cerasiforme from the Amazonian region that has not been analyzed previously nor used extensively. The collection has been morphologically characterized showing diversity for fruit, flower and vegetative traits. Their genomes were sequenced in the Varitome project and are publicly available (solgenomics.net/projects/…
Morphological Similarity and Ecological Overlap in Two Rotifer Species
Co-occurrence of cryptic species raises theoretically relevant questions regarding their coexistence and ecological similarity. Given their great morphological similitude and close phylogenetic relationship (i.e., niche retention), these species will have similar ecological requirements and are expected to have strong competitive interactions. This raises the problem of finding the mechanisms that may explain the coexistence of cryptic species and challenges the conventional view of coexistence based on niche differentiation. The cryptic species complex of the rotifer Brachionus plicatilis is an excellent model to study these questions and to test hypotheses regarding ecological differentia…
Discovery of a Major QTL Controlling Trichome IV Density in Tomato Using K-Seq Genotyping
[EN] Trichomes are a common morphological defense against pests, in particular, type IV glandular trichomes have been associated with resistance against different invertebrates. Cultivated tomatoes usually lack or have a very low density of type IV trichomes. Therefore, for sustainable management of this crop, breeding programs could incorporate some natural defense mechanisms, such as those afforded by trichomes, present in certain Solanum species. We have identified a S. pimpinellifolium accession with very high density of this type of trichomes. This accession was crossed with a S. lycopersicum var. cerasiforme and a S. lycopersicum var. lycopersicum accessions, and the two resulting F2 …
Haplotype analyses reveal novel insights into tomato history and domestication driven by long-distance migrations and latitudinal adaptations.
Abstract A novel haplotype-based approach that uses Procrustes analysis and automatic classification was used to provide further insights into tomato history and domestication. Agrarian societies domesticated species of interest by introducing complex genetic modifications. For tomatoes, two species, one of which had two botanical varieties, are thought to be involved in its domestication: the fully wild Solanum pimpinellifolium (SP), the wild and semi-domesticated Solanum lycopersicum var. cerasiforme (SLC) and the cultivated S. l. var. lycopersicum (SLL). The Procrustes approach showed that SP evolved into SLC during a gradual migration from the Peruvian deserts to the Mexican rainforests…
The effect of environmental uncertainty and diapause investment on the occurrence of specialist and generalist species
The evolution of specialist and generalist strategies is a central topic in ecology with strong implications for the biodiversity and structure of communities. Environmental unpredictability has been suggested as a key factor affecting the relative advantages of generalist species. However, life cycle features, like diapause, can also play a major role in the competitive dynamics between generalists and specialists. Zooplanktonic communities of continental waters are suitable models to study this; they inhabit water bodies that vary temporally with different degrees of uncertainty and rely on the production of diapause stages to survive across the year. We developed a simple theoretical mod…
Development of environmental health competencies through compulsory education. A polyhedral approach based on the SDGs
This paper focuses on the competencies in environmental health acquired by students during compulsory education. Questionnaires addressing environmental health problems were completed by 923 students of primary and secondary schools from five different Spanish regions. The results for five challenging situations related to hunger, consumerism, climate change, pollution in the cities and allergies are analysed according to the internal coherence of each sub-competency, i.e., addressing knowledge, skills and attitudes towards these topics. Our results show that problems related to air and water pollution were the most commonly described by the students. Focusing on competency achievement, the…
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 …
Inquiry-based science education in primary school in Spain : teachers’ practices
Teaching science by inquiry allows students to develop scientific skills, which is key during primary school, and enhances learning. In this study we present the results of a survey to 63 primary school teachers in Spain about their practices in science class and their knowledge about inquiry-based science education (IBSE). Our results show that concept-based paradigm of science is predominant. Scientific skills, besides observation, are not developed, and the concept of research is restricted to bibliographic search. Teachers believe that IBSE is feasible in the Spanish educative system, although they identify the length of the curriculum and the lack of time are the main obstacles.
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…
Founder effects drive the genetic structure of passively dispersed aquatic invertebrates
Populations of passively dispersed organisms in continental aquatic habitats typically show high levels of neutral genetic differentiation, despite their high dispersal capabilities. Several evolutionary factors, including founder events and local adaptation, and life cycle features such as high population growth rates and the presence of propagule banks, have been proposed to be responsible for this paradox. Here, we have modeled the colonization process in these organisms to assess the impact of migration rate, growth rate, population size, local adaptation and life-cycle features on their population genetic structure. Our simulation results show that the strongest effect on population st…
Genomic variation in tomato, from wild ancestors to contemporary breeding accessions
[EN] Background: Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection. Results: Our results revealed a pat…
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)
European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci
A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent seco…
Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild
The vast variation in floral traits across angiosperms is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection or by low trait ability to respond even if selection is present. We studied a plant predominantly pollinated by one bee species across its range. We measured heritability …
AtPGAP1 functions as a GPI inositol-deacylase required for efficient transport of GPI-anchored proteins
Abstract Glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) play an important role in a variety of plant biological processes including growth, stress response, morphogenesis, signaling, and cell wall biosynthesis. The GPI anchor contains a lipid-linked glycan backbone that is synthesized in the endoplasmic reticulum (ER) where it is subsequently transferred to the C-terminus of proteins containing a GPI signal peptide by a GPI transamidase. Once the GPI anchor is attached to the protein, the glycan and lipid moieties are remodeled. In mammals and yeast, this remodeling is required for GPI-APs to be included in Coat Protein II-coated vesicles for their ER export and subsequent t…
Life-history variation, environmental fluctuations and competition in ecologically similar species: modeling the case of rotifers
Competition for resources can lead to species exclusion. However, this exclusion may be avoided if species show differential adaptation to physical environment. Empirical studies on competition are difficult when species are phylogenetically close and have complex life cycles. This is the case of B. plicatilis and B. manjavacas, two cryptic rotifer species differing in their salinity niches and in life-history traits related to sex and diapause. These differences have been suggested to promote the stable co-occurrence observed in natural populations of these species. However, in a previous empirical study, the outcome of competition between both species was always exclusion. Here, we theore…
Persistent genetic signatures of colonization inBrachionus manjavacasrotifers in the Iberian Peninsula
Recent phylogeographical assessments have consistently shown that continental zooplankton display high levels of population subdivision, despite the high dispersal capacity of their diapausing propagules. As such, there is an apparent paradox between observed cosmopolitanism in the zooplankton that is associated with long-distance dispersal, and strong phylogeographical structures at a regional scale. Such population dynamics, far from migration-drift equilibrium, have been shown in the rotifer species complex Brachionus plicatilis, a group of over a dozen species inhabiting salt lakes and coastal lagoons worldwide. Here we present the mitochondrial DNA phylogeography of one of these specie…
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…
Life-cycle switching and coexistence of species with no niche differentiation.
The increasing evidence of coexistence of cryptic species with no recognized niche differentiation has called attention to mechanisms reducing competition that are not based on niche-differentiation. Only sex-based mechanisms have been shown to create the negative feedback needed for stable coexistence of competitors with completely overlapping niches. Here we show that density-dependent sexual and diapause investment can mediate coexistence of facultative sexual species having identical niches. We modelled the dynamics of two competing cyclical parthenogens with species-specific density-dependent sexual and diapause investment and either equal or different competitive abilities. We show th…
Electronic supplementary materials for “A stable pollination environment limits current but not potential evolution of floral traits” by Castellanos et al. from Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild
A single document containing Supplementary methods, Tables and Figures)
Loss of
The early secretory pathway involves bidirectional transport between the endoplasmic reticulum (ER) and the Golgi apparatus and is mediated by coat protein complex I (COPI)-coated and coat protein complex II (COPII)-coated vesicles. COPII vesicles are involved in ER to Golgi transport meanwhile COPI vesicles mediate intra-Golgi transport and retrograde transport from the Golgi apparatus to the ER. The key component of COPI vesicles is the coatomer complex, that is composed of seven subunits (α/β/β'/γ/δ/ε/ζ). In Arabidopsis two genes coding for the β-COP subunit have been identified, which are the result of recent tandem duplication. Here we have used a loss-of-function approach to study the…
Long-Term Coexistence of Rotifer Cryptic Species
Despite their high morphological similarity, cryptic species often coexist in aquatic habitats presenting a challenge in the framework of niche differentiation theory and coexistence mechanisms. Here we use a rotifer species complex inhabiting highly unpredictable and fluctuating salt lakes to gain insights into the mechanisms involved in stable coexistence in cryptic species. We combined molecular barcoding surveys of planktonic populations and paleogenetic analysis of diapausing eggs to reconstruct the current and historical coexistence dynamics of two highly morphologically similar rotifer species, B. plicatilis and B. manjavacas. In addition, we carried out laboratory experiments using …
Measuring the potential for growth in populations investing in diapause
AbstractThe intrinsic rate of population increase (r) is a common performance measure in many ecological and evolutionary studies. However, in life cycles with diapause investment resources are split into a short-term (current population growth) and a long-term (population survival through periods of unsuitable habitat conditions) component, which complicates the use of r as a single performance measure. Here we propose a new measure that integrates both performance components into a single parameter, the potential intrinsic growth rate, rpot. This is the rate of increase that a population/genotype would have if no investment in diapausing stages would occur. We show that rpot can be comput…
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…
Life-history traits, abiotic environment and coexistence: The case of two cryptic rotifer species
Abstract Trade-offs are important in life-history evolution and coexistence of competitors. However, how alternative life-history optima might promote competitor coexistence has received little attention. The rotifers Brachionus plicatilis and Brachionus manjavacas are two cryptic species with a considerable ecological overlap in relation to biotic factors. These species often co-occur in temporal brackish ponds characterised by environmental fluctuations. In these rotifers, sexual reproduction results in diapausing stages, which are able to survive through adverse conditions but constrain current population growth. In the present work, the differential responses of both cryptic rotifer spe…
Sex ratio, reproductive mode and genetic diversity inTriops cancriformis
SUMMARY 1. Aquatic invertebrates display a wide array of alternative reproductive modes from apomixis to hermaphroditism and cyclical parthenogenesis. These have important effects on genetic diversity and population structure. Populations of the ‘living fossil’ Triops cancriformis display a range of sex ratios, and various reproductive modes are thought to underlie this variation. Using sex ratio information and histological analyses European populations have been inferred to be gonochoric (with separate males and females), selfing hermaphroditic and androdioecious, a rare reproductive mode in which selfing hermaphrodites coexist with variable proportions of males. In addition, some populat…
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. …
Long-term competitive dynamics of two cryptic rotifer species: diapause and fluctuating conditions.
Life-history traits may have an important role in promoting species coexistence. However, the complexity of certain life cycles makes it difficult to draw conclusions about the conditions for coexistence or exclusion based on the study of short-term competitive dynamics. Brachionus plicatilis and B. manjavacasare two cryptic rotifer species co-occurring in many lakes on the Iberian Peninsula. They have a complex life cycle in which cyclical parthenogenesis occurs with diapausing stages being the result of sexual reproduction. B. plicatilis and B. manjavacasare identical in morphology and size, their biotic niches are broadly overlapping, and they have similar competitive abilities. However,…
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
Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs
We describe the application of a simple, low-cost, and effective method of DNA extraction (hot sodium hydroxide and Tris, HotSHOT) to the diapausing propagules of continental aquatic invertebrates for its use in PCR amplification. We illustrate the use of the technique in cladocerans, rotifers, anostracans, notostracans, and copepod diapausing eggs. We compare the performance of the HotSHOT technique to the currently most widely used method for DNA extraction of zooplankton eggs and individuals, the chelating resin (or Chelex) technique. The HotSHOT technique overcomes several of the problems posed by Chelex and permits easy optimization for its use with 96-well plates for high-throughput D…
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 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 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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