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[EN] The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a `SyntenyViewer¿ to view genome synteny between different cucurbit species and an `RNA-Seq¿ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system., USDA National Institute of Food and Agriculture Specialty Crop Research Initiative [2015-51181-24285]; US-Israel Binational Agricultural Research and Development Fund [IS-3333-02, IS-3877-06CR and IS-4223-09C]; USDA Agricultural Research Service, and by SNC Laboratoire ASL, de Ruiter Seeds B.V., Enza Zaden B.V., Gautier Semences S.A., Nunhems B.V., Rijk Zwaan B.V., Sakata Seed Inc, Semillas Fito S.A., Seminis Vegetable Seeds Inc, Syngenta Seeds B.V., Takii and Company Ltd, Vilmorin and Cie S.A. and Zeraim Gedera Ltd, all of them as part of the support to the International Cucurbit Genomics Initiative (ICuGI). Funding for open access charge: USDA National Institute of Food and Agriculture.

Melons (Cucumis melo L.) and peaches (Prunus persica (L.) Batsch) are two commercially important fruit species in the European Union. The quality improvement of melon and peach cultivars is determinant to maintain and increase their acceptance and consumption. In this context, the main objective of this thesis was to investigate key quality attributes of melon and peach fruit cultivars through the correlation of sensory and instrumental methodologies. The correlation of sensory and instrumental methods allowed to identify specific parameters with a positive or negative contribution to the sensory perception of melon and peach fruits, either directly or by their interaction with other quality traits. The combination of these methodologies provided important information for a comprehensive assessment of quality and their application can improve melon and peach fruit quality without compromising other valuable quality traits El meló (Cucumis melo L.) i el préssec (Prunus persica (L.) Batsch) són dues espècies fruiteres d'interès econòmic a la Unió Europea. La millora en la qualitat de varietats de meló i préssec és fonamental per a mantenir i incrementar la seva acceptació i consum. En aquest context, l'objectiu central d'aquesta tesi va ser investigar els principals paràmetres de qualitat de diferents cultivars de meló i préssec mitjançant la correlació d'anàlisis sensorials i instrumentals. La correlació de mètodes sensorials i instrumentals va permetre identificar aquells paràmetres amb impacte positiu o negatiu sobre la percepció sensorial de fruits de meló i préssec, bé directament o mitjançant interacció amb altres trets de qualitat. La combinació d'aquestes metodologies va proporcionar informació important per a una millor avaluació de la qualitat i la seva aplicació permetrà la millora en la qualitat de fruits de meló i préssec sense comprometre altres trets de qualitat d'interès The doctoral thesis presented herein was developed in the framework of the Strategic Plan of the National Institute for Agricultural and Food Research and Technology (INIA) and agrifood research in Spain of the State Secretariat of Research, Development, and Innovation of the Ministry of Economy and Competitiveness, through the subvention of the project RTA2011-00123-00-00 and an FPI-INIA grant

We study the effect of organic farming practices on several taxa in olive groves and vineyards. Sessile organisms show a stronger response to treatment, their diversity being higher in organic vineyards. Vagile organism show a less intense response, with the most mobile taxa (birds) showing no farming treatment related differences. Organic olive groves are preferred over conventional groves by some endangered bat species (Rhinolophus spp.), thus stressing their importance for bat conservation. We analize the regulatory ecosystems services bats exert in rice paddies. Bats predate on both agricultural pests (moths and midges) and disease-bearing pests (mosquitoes). The intensity with which they track pests is linked to the cost-benefit trade-off, more evidently shifting their hunting grounds when bigger pests are available. Their economic impact has been assessed in terms of the avoided pesticide cost per hectare of rice crop and year at around 50€ Evaluem l’efecte del maneig ecològic de vinyes i oliverars sobre diversos grups taxonòmics. Els organismes sèssils mostren diversitats majors en ecològic. Els organismes vàgils mostren una resposta més moderada, i els organismes més mòbils analitzats (aus) no mostren diferencies entre pràctiques agrícoles. Els oliverars ecològics són seleccionats positivament per part d’especies amenaçades de ratpenats (Rhinolophus spp.), posant-se de manifest la seva importància per a la conservació. Analitzem els serveis ecosistèmics de regulació que els ratpenats exerceixen en els arrossars. Els ratpenats depreden tant sobre plagues agrícoles (arnes i quironòmids) com sobre vectors de malalties humanes (mosquits). La intensitat amb la que segueixen els moviments de les plagues per alimentar-se’n depèn del compromís cost-benefici, canviant les seves zones d’alimentació de forma evident quan hi ha plagues de major mida. L’impacte econòmic en quant als costos evitats de pesticida per hectàrea y any s’ha estimat en uns 50€ Programa de Doctorat en Medi Ambient

[Objective]: Peach brachytic dwarfism determined by Dwarf gene (Dw) is an undesired trait segregating in some peach breeding programs. Recently, a single nucleotide polymorphism (SNP) mutation in the gibberellin insensitive dwarf 1 (GID1) peach gene causing brachytic dwarfism was described. In this research we wanted to validate this marker in an F2 population of the ‘Nectavantop’ peach cultivar (Nv) to include it as a marker assisted selection tool for peach breeding programs., [Results]: The observed segregation of the trait was in agreement with that of a recessive gene, the individuals homozygous for the recessive allele (dwdw) presenting the dwarf genotype. Dw was mapped to the distal part of linkage group 6 as previously described. The SNP marker based on the causal mutation previously described did not segregate in Nv F2 population. The sequence of the GID1c gene in Nv revealed a second SNP in its coding sequence which cosegregated with the dwarf phenotype. This SNP was predicted by the SNAP2 software to cause a major functional change and was validated in the dwarf peach cultivar ‘Small sunning’. These results suggest the existence of at least two independent mutations of the Dw gene causing the peach brachytic dwarf phenotype., We acknowledge fnancial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016–2019 (SEV‐2015‐0533)” and project AGL2012-40228, and from the CERCA Programme from the Generalitat de Catalunya.

The application of microorganisms to control the growth of foodborne pathogens is an alternative to the use of chemical additives. In this work, Pseudomonas graminis CPA-7 was tested as a biocontrol agent against Salmonella enterica and Listeria monocytogenes on fresh-cut pear under conditions that simulate its commercial application at 5 ± 1 °C (under a modified atmosphere and antioxidant solution). The quality of the fresh-cut fruit, including the ethanol and acetaldehyde contents and the volatile profile, was determined. After the storage period, the L. monocytogenes population was reduced by 1-log unit by the presence of CPA-7; however, CPA-7 was not found to have antagonistic activity against S. enterica. The fruit quality (total soluble solids content and titratable acidity) was not negatively affected by CPA-7. The ethanol and acetaldehyde contents increased during the shelf-life of the fruit regardless of the presence of CPA-7. Some volatile compounds were key factors for discriminating samples from the two groups (the control group and the group that was inoculated with CPA-7). Some components are common in the volatile profile of pear (methyl acetate, 3-methylbutyl acetate, 1-butanol, 1-hexanol, and hexanal), and thus increases in their contents could enhance consumers flavour perception. Authors are grateful to the Spanish Ministry of Science and Innovation (AGL-2012-38671 research project), Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (AGAUR fellowship 2015-FI-B100156 (M. Belén Iglesias) and 2017-FI-B200164 (Lorena Zudaire)), European Regional Development Fund (FEDER), and CERCA Programme (Generalitat de Catalunya) for their financial support. We also thank Marina Anguera, Patricia Gálvez and Mariona Guardiola for their technical support.

Fleshy fruits using ethylene to regulate ripening have developed multiple times in the history of angiosperms, presenting a clear case of convergent evolution whose molecular basis remains largely unknown. Analysis of the fruitENCODE data consisting of 361 transcriptome, 71 accessible chromatin, 147 histone and 45 DNA methylation profiles reveals three types of transcriptional feedback circuits controlling ethylene-dependent fruit ripening. These circuits are evolved from senescence or floral organ identity pathways in the ancestral angiosperms either by neofunctionalisation or repurposing pre-existing genes. The epigenome, H3K27me3 in particular, has played a conserved role in restricting ripening genes and their orthologues in dry and ethylene-independent fleshy fruits. Our findings suggest that evolution of ripening is constrained by limited hormone molecules and genetic and epigenetic materials, and whole-genome duplications have provided opportunities for plants to successfully circumvent these limitations., This work is supported by Hong Kong UGC GRF-14119814/14104515 and Area of Excellence Scheme AoE/M-403/16 to S.Z., Shenzhen Peacock-KQTD201101 to J.Z., Spanish Ministry of Economy and Competitively grant AGL2015-64625-C2-1-R, Centro de Excelencia Severo Ochoa 2016-2020 and the CERCA Programme/Generalitat de Catalunya to J.G.-M., and National Science Foundation IOS-1339287 to Z.F. and J.G.

We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net. The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species., This work was supported by the Spanish Ministry of Economy and Competitiveness grant AGL2015–64625-C2-1-R, Severo Ochoa Programme for Centres of Excellence in R&D 2016–2010 (SEV-2015–0533) and the CERCA Programme/Generalitat de Catalunya to JGM. VR was supported by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement No 665919.

Transposable elements (TEs) are a major driver of plant genome evolution. A part from being a rich source of new genes and regulatory sequences, TEs can also affect plant genome evolution by modifying genome size and shaping chromosome structure. TEs tend to concentrate in heterochromatic pericentromeric regions and their proliferation may expand these regions. Here, we show that after the split of melon and cucumber, TEs have expanded the pericentromeric regions of melon chromosomes that, probably as a consequence, show a very low recombination frequency. In contrast, TEs have not proliferated to a high extent in cucumber, which has small TE-dense pericentromeric regions and shows a relatively constant recombination rate along chromosomes. These differences in chromosome structure also translate in differences in gene nucleotide diversity. Although gene nucleotide diversity is essentially constant along cucumber chromosomes, melon chromosomes show a bimodal pattern of genetic variability, with a gene-poor region where variability is negatively correlated with gene density. Interestingly, genes are not homogeneously distributed in melon, and the high variable low-recombining pericentromeric regions show a higher concentration of melon-specific genes whereas genes shared with cucumber and other plants are essentially found in gene-rich chromosomal arms. The results presented here suggest that melon pericentromeric regions may allow gene sequences to evolve more freely than in other chromosomal compartments which may allow new ORFs to arise and eventually be selected. These results show that TEs can drastically change the structure of chromosomes creating different chromosomal compartments imposing different constraints for gene evolution., This work was supported by Ministerio de Economia y Competitividad grants AGL2013-43244-R and AGL2016-78992-R to J.C., Ministerio de Economia y Competitividad grant AGL2015-64625-C2-1-R to J.G.-M. and Centro de Excelencia Severo Ochoa 2016–2020, and the CERCA Programme/Generalitat de Catalunya to J.C., J.G.-M. and S.R.-O.

Most almond cultivars are self-incompatible, and so to obtain a yield they need to be pollinated with cross-compatible cultivars. For an efficient use of these cultivars in growing and breeding, over the years many have been S-genotyped. This information has been included in consecutive tables of cross-incompatibility groups, which are essentially an update of the previously proposed. However, the information of these tables has not always been reconciled and their inconsistencies have not been corrected. In this work the S-genotypes of 15 Spanish almond local cultivars, included in a research program for the preservation of almond biodiversity, were determined for the first time. For this, PCR with consensus primers for the Prunus S-RNases, PCR using S-RNase allele specific primers designed herein, and also cloning and sequencing were performed. As a result, a new S-RNase allele numbered as S53 could be identified, and a compilation table of almond cross-incompatibility groups is provided including the information from this and previous studies. In this novel Table, twelve new cross-incompatibility groups have been established, two former groups were omitted, and those cultivars with inconsistent genotypes have been removed. The information of this table will facilitate the use of a very high number of almond cultivars in research and breeding. Determination of the S-genotype might be considered as an important addition to a set of identity markers of almond genetic resources, what is of particular interest in the characterization of the agricultural biodiversity. info:eu-repo/semantics/acceptedVersion

The fruit production is threatened by several bacterial diseases, such as fire blight of apple and pear, bacterial canker of kiwifruit, bacterial spot of stone fruits, and angular leaf spot of strawberry. The conventional pesticides that are available for the control of these diseases are mainly copper compounds and they have a limited efficacy and negative impact on environment. Therefore, there is a need to develop alternative and sustainable management tools. This Ph.D. Thesis contributes to the development of a novel microbial biopesticide based on lactic acid bacteria. Two Lactobacillus plantarum strains were selected due to their broad-spectrum activity. In order to improve the epiphytic survival of both strains in plants and to get more consistency in their biocontrol efficacy, a physiological adaptive strategy was defined to increase the water-stress tolerance. Also, a monitoring method was developed to evaluate the population dynamics of a L. plantarum strain. La producció de fruita està afectada per diferents malalties bacterianes de quarantena com el foc bacterià de les pomeres i pereres, el xancre bacterià del kiwi, la taca bacteriana dels fruiters de pinyol i la taca angular de les fulles de maduixera. Els plaguicides disponibles pel seu control són principalment compostos cúprics els quals tenen una eficàcia limitada i un impacte negatiu en el medi ambient. Existeix la necessitat de desenvolupar eines de control alternatives i més sostenibles. Aquesta tesi contribueix en el desenvolupament d’un bioplaguicida microbià basat en bacteris de l’àcid làctic. Es van seleccionar dues soques de Lactobacillus plantarum amb activitat d’ampli espectre i es va definir una estratègia fisiològica d’adaptació per incrementar la tolerància a l’estrès per manca d’aigua i així millorar la supervivència epifítica a la planta. També es va desenvolupar un mètode de monitoratge per avaluar les dinàmiques poblacionals d’una soca de L. plantarum.

Codling moth, Cydia pomonella (L.) is a key pest of global importance that affects apple fruit production and whose populations have developed resistance to insecticides in many apple production areas. In Spain, enhanced cytochrome P450 polysubstrate monooxygenase (PSMO) activity is the main mechanism involved in insecticide detoxification by codling moth, although acetylcholinesterase (AChE) target site mutations have been described in two populations. However, the extent of AChE and knockdown resistance (kdr) mutations in Spain is unknown. To assess the actual occurrence of AChE and kdr mutations concurrently with the frequency of moths with PSMO enhanced activity (R-PSMO), 32 Spanish field populations from four apple-growing areas of Spain and two susceptible laboratory strains were evaluated. R-PSMO was significantly higher in 23 chemically treated field populations from Extremadura, Catalonia and Aragon, with proportions that varied between 25% and 90%, but no significant differences among strains and the non-chemically treated orchards (organic or abandoned) were observed. The AChE mutation (F290V) was detected in all field populations from Catalonia (n=21) and in three field populations from Aragon (n=5), with resistant phenotype proportions varying from 34.2% to 97.5% and from 7.2% to 65% in Catalonia and Aragon, respectively. In addition, the kdr mutation (L1014F) was detected in twelve Catalonian field populations, at rates of incidence ranging between 2.6% and 56.8%. A positive correlation between R-PSMO and AChE mutation was found. The origin of the mutations and their ability to persist and spread in field populations with different management systems is discussed. The authors thank the fruit growers and pest control advisors of the different Spanish apple-growing areas for their help in accessing and identifying apple orchards and Mónica Pérez for her technical help. This work was funded by grant Fondo de Desarrollo Científico y Tecnológico, FONDECYT 11130599 (CONICYT), Chile, to M.A. Rodríguez, by grant AGL2013-49164 of the Spanish Ministry for Science and Innovation, to J. Avilla and D. Bosch, and by the CERCA Programme/Generalitat de Catalunya.

[Background]: Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools., [Results]: In order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: “Védrantais”, from the cantalupensis group, and “Piel de Sapo”, from the inodorus group. Both have desirable quality traits for the market, but their fruits differ in traits such as rind and flesh color, sugar content, ripening behavior, size and shape. We used a genotyping-by-sequencing strategy to construct a dense genetic map, which included around five thousand variants distributed in 824 bins. The RIL population was phenotyped for quality and morphology traits, and we mapped 33 stable QTLs involved in sugar and carotenoid content, fruit and seed morphology and major loci controlling external color of immature fruit and mottled rind. The median confidence interval of the QTLs was 942 kb, suggesting that the high density of the genetic map helped in increasing the mapping resolution. Some of these intervals contained less than a hundred annotated genes, and an integrative strategy combining gene expression and resequencing data enabled identification of candidate genes for some of these traits., [Conclusion]: Several QTLs controlling fruit quality traits in melon were identified and delimited to narrow genomic intervals, using a RIL population and a GBS-based genetic map., This work was supported by the Spanish Ministry of Economy and Competitiveness grant AGL2015–64625-C2–1-R, Severo Ochoa Programme for Centres of Excellence in R&D 2016–2010 (SEV-2015-0533) and the CERCA Programme/Generalitat de Catalunya to JGM. LP was supported by a FPI grant from the Spanish Ministry of Economy and Competitiveness. VR was supported by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement No 6655919.

Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars ‘Zin Dai’ and ‘Crimson Lady’ (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae., This project was supported in part by the USDA-NIFA-Specialty Crop Research Initiative project, RosBREED: Enabling marker-assisted breeding in Rosaceae (2009-51181-05808) to KG, and RosBREED 2: Combining disease resistance with horticultural quality in new rosaceous cultivars (2014-51181-22378) to KG. The Spanish Ministry of Economy and Competitiveness (project RTA2015-00050-00-00, Severo Ochoa Program for Centres of Excellence in R&D 201-2019 (SEV-2015-0533) and CERCA Programme-Generalitat de Catalunya). This work was in part supported by the Ministero delle Politiche Agricole Alimentari e Forestali (MiPAAF, Italy) through the projects DRUPOMICS (grant DM14999/7303/08), and 'MAS.PES: apricot and peach breeding by molecular-assisted selection' a project funded by private and public agencies.

Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond., This work has been funded under the EU seventh Framework Programme by the FruitBreedomics project No. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops (http://www.fruitbreedomics.com/).

In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond., The authors gratefully acknowledge financial support from the following: Hort Innovation (the grower-owned, not-for-profit research and development corporation for Australian horticulture), which supported this research using the almond industry and development levy and contributions from the Australian Government; the Commonwealth Scientific and Industrial Research Organization; the South Australian River Murray Sustainability Program (IRSPR2-004) administered by Primary Industries and Regions South Australia; and the Spanish Ministry of Economy and Competitiveness [project AGL2015-68329-R, Severo Ochoa Program for Centres of Excellence in R&D 201-2019 (SEV-2015-0533), CERCA Program of the Generalitat de Catalunya]. S.N.G. was the recipient of an Australian Postgraduate Award administered by the University of Adelaide.

L’èxit de les jornades tècniques de l’arròs ens posiciona com una plataforma de transferència referent en el sector arrosser, amb l’objectiu d’exposar i debatre les darreres innovacions tecnològiques. Benvinguts a aquesta trobada d’experts i professionals del sector arrosser. El éxito de las jornadas técnicas del arroz nos posiciona como una plataforma de transferencia referente en el sector arrocero, con el objetivo de exponer y debatir las últimas innovaciones tecnológicas. Les damos la bienvenida a este encuentro de expertos y profesionales del sector arrocero.

Microalgae oil has been identified as a reliable resource for biodiesel production due to its high lipid productivity and potential cultivation in non-fertile locations. However, high scale production of microalgae based biodiesel depends on the optimization of the entire process to be economically feasible. The present work combine the optimization of microalgae downstream processes with computational tools for the modeling of different scenarios of the harvesting, oil extraction and transesterification with data obtained at pilot scale. This approach detects process bottlenecks that could have led to an overestimation of the potentiality of the microalgae lipids as a resource for the biodiesel production. Reduction of the cultivation step is mandatory to consider the microalgae-based biodiesel competitive with respect to the fossil diesels. The required biodiesel market price for the best alternative assessed is $5700 per MT where only the biomass production (cultivation/harvesting) is responsible of the 65% of the cost., Durante las últimas décadas, se ha prestado mucha atención a la producción de biodiesel a partir de microalgas (alta productividad y contenido lipídico). Sin embargo la viabilidad de su producción depende del proceso global y la optimización de cada una de las etapas del proceso. El presente trabajo combina una serie de propuestas de optimización de los procesos post-cultivos demostrados a escala piloto (concentración mediante filtración-dinámica y extracción/transesterificación directa de lípidos) y herramientas computacionales para detectar posibles sobre-estimaciones en la capacidad de las microalgas como fuente de producción de biodiesel. Según caso-base es necesaria la reducción de inversión inicial del proceso de producción de biomasa, (cultivo y concentrado) responsables del 65% del costo (5700$/MT) de producción de biodiesel a partir de microalgas para que el proceso sea económicamente viable.

Genetically modified crops are submitted to strict regulation to ensure the safety of consumers and the environment. To complement the comparison between GM plants and their counterparts, in the present Thesis, we evaluated the possible unexpected effects of the transgene on the host plant, by means of transcriptomic technologies. More exactly, we studied three pathogen-resistant GM rice lines: S-afp, expressing constitutively the antifungal protein AFP; and S-bp217 and S-bp213, expressing undecapeptide BP100 derivatives, which were developed in the UdG in the context of this Thesis. Although the high phytotoxicity of the BP100 derivatives on the host plant the transcriptional changes observed in S-afp, S-bp217 and S-bp213 compared to the conventional line Senia were similar that those observed in other GM crops, of other species and with different transgenes, and only the half of them was attributed to the insertion and/or expression of the transgene., Les plantes modificades genèticament (MG) destinades a comercialització estan sotmeses a estricta legislació per garantir la seguretat del consumidor i del medi ambient. Per complementar la comparativa entre plantes MG i convencionals, en aquesta tesi s’ha abordat l’avaluació dels possibles efectes no esperats del transgèn sobre la planta hoste, mitjançant tècniques de transcriptòmica. Concretament s’han estudiat línies d'arròs MG que presenten fenotips de resistència a patògens: S-afp, que expressa constitutivament la proteïna antifúngica AFP, i S-bp213 i S-bp217, que expressen derivats de l’undecapèptid BP100, desenvolupat a la UdG, que s’han obtingut també en el marc d’aquesta tesi. Malgrat l’elevada fitotoxicitat dels derivats de BP100 enfront la planta hoste, els canvis transcripcionals de S-afp, S-bp213 i S-bp217 respecte la línia convencional Senia són similars als observats en altres events MG, de diferents espècies i amb diferents transgens; i només la meitat d’ells s’ha atribuit a la presència o expressió del transgèn.

Els anys 2008 i 2009 es va dur a terme un assaig en una plantació de pomera cv. Golden Smoothee® per a avaluar l’efecte de la poda mecànica del dosser foliar i la poda mecànica d’arrels sobre el rendiment de l’arbre, el pes promig del fruit i la qualitat del fruit. Els resultats confirmen que la poda mecànica del dosser foliar no redueix el rendiment de fruits de qualitat comercial i tampoc afecta la qualitat dels fruits; la poda d’arrels quan es duu a terme durant l’hivern tampoc suposa cap reducció de rendiment ni de qualitat dels fruits de pomera.

Amb la finalitat de garantir la seguretat dels consumidors i del medi ambient, a la UE els aliments modificats genèticament (MG) estan sotmesos a un rigorós procés d'autorització que inclou: caracterització molecular del transgèn i anàlisis comparatives a nivell nutricional i agronòmic. L'ús de tècniques de profiling per avaluar la possible existència d'efectes no esperats derivats de la inserció i/o expressió del transgèn s'ha proposat com a una eina complementària per l'avaluació de la seguretat alimentària. L'objectiu de la present tesis és avaluar la variabilitat associada a la inserció i expressió de transgens en plantes, utilitzant com a exemple el blat de moro MON810. Es pretén complementar les aproximacions ja existents basades en l'estudi de paràmetres concrets mitjançant les tècniques de profiling. Des del punt de vista transcriptòmic i proteòmic, les varietats de blat de moro MON810 semblen ser substancialment equivalents a les seves varietats comparables no-MG. En conseqüència, és possible la producció de plantes MG amb el mínim d'efectes no esperats., To ensure the safety of consumers and the environment, genetically modified (GM) food and feed are submitted to strict legislation. The EU establishes an authorisation procedure requiring: molecular characterisation of the transgene and compositional and agronomic comparative analysis. The use of profiling approaches to evaluate the possible occurrence of unintended effects derived from the insertion and/or expression of the transgene has been proposed as complementary tool for safety assessment. The objective of this thesis was to evaluate the variability associated to the insertion and expression of transgenes in plants, using as example MON810 maize. We aim to complement the existing targeted approaches by providing more unbiased information on the basis of profiling techniques. From the transcriptomics and proteomics perspectives, MON810 maize varieties seem to be substantially equivalent to their non-GM comparators. Thus, the production of GM plants with minimal unexpected effects is possible.

Amb l'objectiu de contribuir al coneixement de la diversitat existent en el germoplasma tradicional espanyol de blat fariner per a característiques relacionades amb la adaptació a l'ambient mediterrani i determinar el seu valor com a font de gens d'interès per a la millora d'aquest cereal, es va caracteritzar una col·lecció de 120 varietats tradicionals espanyoles en un assaig de camp en condicions de secà. Es va determinar la duració de les fases de desenvolupament, es va estudiar el creixement mitjançant fotografia digital i es determinà el contingut en clorofil·la, la depressió de la temperatura de la coberta vegetal i la reflectància espectral en diferents estadis. Els resultats van permetre quantificar la variabilitat disponible en aquest germoplasma e identificar dos grups de varietats.

La jornada és una presentació de plantacions d’espècies per a producció de fusta de qualitat com una possibilitat productiva per a algunes finques. Es farà un recorregut dels aspectes a considerar a l’hora de realitzar aquest tipus de plantacions; des de com fomenta l’administració la implantació d’aquestes produccions, quins models de gestió es poden aplicar, quines espècies i materials vegetals podem trobar al mercat i què és fusta de qualitat i com assolir l’objectiu de produir-la. La visita a una plantació de nogueres sotmesa a un maneig adequat per a aquest tipus d’explotacions serà la visió pràctica de la jornada.

La present tesi doctoral es centra en l'aplicació dels bacteris de l'àcid lactic (BAL) com a agents bioprotectors davant microorganismes patògens i deteriorants.Es van aïllar i seleccionar BAL de fruites i hortalisses fresques i es van assajar in vitro davant 5 microorganismes fitopatògens i 5 patògens humans.Es van realitzar assajos d'eficàcia en pomes Golden Delicious amb tots els aïllats enfront les infeccions causades pel fong Penicillium expansum. La soca més eficaç era Weissella cibaria TM128, que reduïa el diàmetre de les infeccions en un 50%.Les soques seleccionades es van assajar enfront els patògens Salmonella typhimurium, Escherichia coli i Listeria monocytogenes en enciams Iceberg i pomes Golden Delicious.Els BAL interferien eficientment amb el creixemet de S. typhimurium, and L. monocytogenes, però van mostrar poc efecte enfront E. coli.Finalment, es van realitzar assajos dosi-resposta amb les soques Leuconostoc mesenteroides CM135, CM160 and PM249 enfront L. monocytogenes. De totes les soques assajades, la soca CM160 va ser la més efectiva., The present thesis focuses on the use of lactic acid bacteria as bioprotective cultures to inhibit pathogenic and spoilage microorganisms.Lactic acid bacteria were isolated and selected from fresh fruit and vegetables and tested in vitro against five plant pathogens and five human pathogen test bacteria.Efficacy trials with all the isolates were performed in Golden Delicious apples against the blue mould rot infections, caused by Penicillium expansum. The highest effectivity found in this assay was of about 50%, with strain Weissella cibaria TM128.Selected lactic acid bacteria were tested against Salmonella typhimurium, Escherichia coli and Listeria monocytogenes in Iceberg lettuce and Golden Delicious apples. Lactic acid bacteria interfered efficiently with the growth of S. typhimurium, and L. monocytogenes, but showed little effectivity over E. coli.Finally, dose-response assays were done with Leuconostoc mesenteroides strains CM135, CM160 and PM249 against L. monocytogenes.Among the three strains tested, strain CM160 showed the highest effectivity.

La soca EPS125 ha mostrat ser un efectiu agent de control biològic de diferents patògens fúngics de postcollita en diferents fruits. Degut a la seva elevada eficàcia, es va plantejar desenvolupar aquesta soca comercialment i per aquest motiu en el present treball es plantejà complementar la informació necessària pel seu registre. D'acord amb els resultats obtinguts mitjançant proves fenotípiques i genotípiques, la soca EPS125 queda inclosa dins l'espècie Pantoea agglomerans (Enterobacter agglomerans-Erwinia herbicola). En relació a la utilització de fonts de carboni, en el perfil i contingut d'àcids grassos cel·lulars i en el polimorfisme en la longitud dels fragments de macrorestricció genòmica (MRFLP), la soca EPS125 mostrà trets característics que la diferencien d'altres soques. Els dos marcadors moleculars (125.2 i 125.3) específics per la soca EPS125 dissenyats en el present treball mostraren ser semiespecífics per la seva detecció mitjançant la tècnica PCR i Real Time PCR. Quedant pendent l'anàlisi d'especificitat de l'ús combinat dels dos marcadors moleculars en una reacció PCR multiplex. P. agglomerans EPS125 ha mostrat ser molt efectiva en el control de Penicillium expansum en poma amb una dosi efectiva mitjana de 2.7x105 a 7x105 ufc/ml, i una ratio de 25-101 cèl·lules de la soca EPS125 per inactivar una espora del patogen segons el model de saturació hiperbòlica. Segons les aproximacions fenotípiques i estudis genotípics realitzats, sembla que els mecanismes de biocontrol utilitzats per la soca EPS125 contra P. expansum en poma estan directament relacionats amb la capacitat de formació de biofilm per aquesta soca., Strain EPS125 has shown effectiveness against a wide range of fungal pathogens in a large variety of fruit. However, to develop this strain as commercial biopesticide an extensive characterization is essential. For this reason, the objective of this PhD thesis was to complete the necessary information for its future registration.According to morphological and biochemical tests, strain EPS125 pertain to Pantoea agglomerans (Enterobacter agglomerans-Erwinia herbicola) species. This strain showed typical traits different from other bacteria in relation to the ability to use several carbon sources, the fatty acid profiles and the macrorestriction fragment length polymorphism (MRFLP) pattern. The two DNA molecular markers of P. agglomerans EPS125 (125.2 and 125.3) obtained in the present work were semispecific in the detection of strain EPS125 by means of PCR and Real Time PCR. However, the combined use of the two primer sets in a multiplex PCR reaction would be specific. P. agglomerans EPS125 was highly effective against P. expansum in apple fruit having a median effective dose from 2.7x105 to 7x105 cfu/ml and a ratio of 101 and 25 EPS125 cells to inactivate one pathogen spore according to the hyperbolic saturation model. Biocontrol mechanisms used by P. agglomerans EPS125 against P. expansum in apple fruit may be related with the ability of biofilm formation by this strain as show phenotypic approaches and genotypic studies.

Una sitja és una cavitat subterrània destinada a emmagatzemar la collita, especialment de cereals. Amb el manteniment d'unes condicions ideal de temperatura i humitat els cereals s'hi poden conservar durant un llarg període de temps, que segons Varró podria arribar als 50 anys. Aquestes excepcionals possibilitats han possibilitat que l'emmagatzematge en sitges fos un dels mètodes de conservació de cereals a llarg termini més utilitzat en les societats pre-industrials de tot el món.La sitja estàndard del nord-est de Catalunya és aquella que era excavada a l'argila, no portava revestiment i tenia la boca en forma de tub, de 0,77 m de diàmetre màxim per 0,42 de profunditat. El perfil era de tipus còncau, amb el diàmetre màxim situat en el terç central de la sitja, i un fons indistintament còncau o pla. La profunditat i el diàmetre màxim es situarien entre 1,75 i 2 m., amb un marge de diferència reduïdíssim entre ambdues mesures. La capacitat resultant d'aquestes dimensions se situaria entre 1 i 3 tones de cereals, que en termes estàndards de producció seria el resultat de la collita d'una extensió d'entre 1,5 i 4 hectàrees de terreny.ASBTRACT:A silo is an underground cavity designed to store the harvest, especially grain. With the maintenance of ideal conditions of temperature and moisture grains can be preserved for a long period of time, according to Varró it could reach 50 years. These exceptional opportunities have enabled the storage silos to be one of the methods of long-term conservation of grain used in most pre-industrial societies around the world.The standard silo from the North-East of Catalonia was excavated in clay,it had no siding and its mouth was tube-shaped, up to 0.77 m of maximum diameter to 0.42 deep. The profile was concave, with maximum diameter located in the central third of the silo, and a background either concave or flat. The depth and maximum diameter are located between 1.75 and 2 m, with a very little margin of difference between the two measures. The capacity resulting from these dimensions would be located between 1 and 3 tons of cereals, which in terms of production standards it would mean a harvest of between 1.5 and 4 hectares of ground.