Relevant bibliographies by topics / Genomic resources

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Genomic resources'

Author: Grafiati
Published: 7 September 2022
Last updated: 1 February 2023

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Journal articles on the topic "Genomic resources"

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Gustafson, J. Perry, Patrick E. McGuire, and Calvin O. Qualset. "Genomic Resources." Genetics 168, no. 2 (October 2004): 583–84. http://dx.doi.org/10.1534/genetics.104.036731.

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Rusk, Nicole. "Functional genomic resources." Nature Methods 9, no. 1 (December 28, 2011): 35. http://dx.doi.org/10.1038/nmeth.1820.

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Li, Xiu-Qing, Rebecca Griffiths, David De Koeyer, Charlotte Rothwell, Vicki Gustafson, Sharon Regan, and Barry Flinn. "Functional genomic resources for potato." Canadian Journal of Plant Science 88, no. 4 (July 1, 2008): 573–81. http://dx.doi.org/10.4141/cjps07048.

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Considerable functional genomic resources have been developed by the potato research community in the past decade, including expressed sequence tag (EST) libraries, SAGE libraries, microarrays, molecular-function maps, and mutant populations. This article reviews the types, characteristics, strengths, limitations, and appropriate applications of these resources for genomic research and discusses perspectives on future directions. This wide selection of resources available to potato researchers complements efforts to sequence the entire genome and advances made in the development of saturated genetic maps. Key words: Solanum, potato, genomics, expressed sequence tag, microarray, longSAGE, data mining
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Fairley, Susan, Ernesto Lowy-Gallego, Emily Perry, and Paul Flicek. "The International Genome Sample Resource (IGSR) collection of open human genomic variation resources." Nucleic Acids Research 48, no. D1 (October 4, 2019): D941—D947. http://dx.doi.org/10.1093/nar/gkz836.

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Abstract To sustain and develop the largest fully open human genomic resources the International Genome Sample Resource (IGSR) (https://www.internationalgenome.org) was established. It is built on the foundation of the 1000 Genomes Project, which created the largest openly accessible catalogue of human genomic variation developed from samples spanning five continents. IGSR (i) maintains access to 1000 Genomes Project resources, (ii) updates 1000 Genomes Project resources to the GRCh38 human reference assembly, (iii) adds new data generated on 1000 Genomes Project cell lines, (iv) shares data from samples with a similarly open consent to increase the number of samples and populations represented in the resources and (v) provides support to users of these resources. Among recent updates are the release of variation calls from 1000 Genomes Project data calculated directly on GRCh38 and the addition of high coverage sequence data for the 2504 samples in the 1000 Genomes Project phase three panel. The data portal, which facilitates web-based exploration of the IGSR resources, has been updated to include samples which were not part of the 1000 Genomes Project and now presents a unified view of data and samples across almost 5000 samples from multiple studies. All data is fully open and publicly accessible.
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Šafář, J., J. Janda, J. Bartoš, M. Kubaláková, P. Kovářová, J. Číhalíková, H. Šimková, et al. "Development of BAC resources for genomic research on wheat." Czech Journal of Genetics and Plant Breeding 41, Special Issue (July 31, 2012): 202. http://dx.doi.org/10.17221/6173-cjgpb.

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Havey, Michael, Kenneth Sink, Maria Jenderek, and Christopher Town. "Genomic Resources for Asparagales." Aliso 22, no. 1 (2006): 305–10. http://dx.doi.org/10.5642/aliso.20062201.25.

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Antin, Parker B., and Jay H. Konieczka. "Genomic resources for chicken." Developmental Dynamics 232, no. 4 (2005): 877–82. http://dx.doi.org/10.1002/dvdy.20339.

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Overby, Casey, John Connolly, Christopher Chute, Joshua Denny, Robert Freimuth, Andrea Hartzler, Ingrid Holm, et al. "Practical considerations for implementing genomic information resources." Applied Clinical Informatics 07, no. 03 (July 2016): 870–82. http://dx.doi.org/10.4338/aci-2016-04-ra-0060.

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SummaryTo understand opinions and perceptions on the state of information resources specifically targeted to genomics, and approaches to delivery in clinical practice.We conducted a survey of genomic content use and its clinical delivery from representatives across eight institutions in the electronic Medical Records and Genomics (eMERGE) network and two institutions in the Clinical Sequencing Exploratory Research (CSER) consortium in 2014.Eleven responses representing distinct projects across ten sites showed heterogeneity in how content is being delivered, with provider-facing content primarily delivered via the electronic health record (EHR) (n=10), and paper/pamphlets as the leading mode for patient-facing content (n=9). There was general agreement (91%) that new content is needed for patients and providers specific to genomics, and that while aspects of this content could be shared across institutions there remain site-specific needs (73% in agreement).This work identifies a need for the improved access to and expansion of information resources to support genomic medicine, and opportunities for content developers and EHR vendors to partner with institutions to develop needed resources, and streamline their use – such as a central content site in multiple modalities while implementing approaches to allow for site-specific customization. Citation: Rasmussen LV, Overby CL, Connolly J, Chute CG, Denny JC, Freimuth RR, Hartzler AL, Holm IA, Manzi S, Pathak J, Peissig PL, Smith M, Williams MS, Shirts BH, Stoffel EM, Tarczy-Hornoch P, Rohrer Vitek CR, Wolf WA, Starren J. Practical considerations for implementing genomic information resources – experiences from eMERGE and CSER.
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Bryan, Glenn J., and Ingo Hein. "Genomic Resources and Tools for Gene Function Analysis in Potato." International Journal of Plant Genomics 2008 (December 18, 2008): 1–9. http://dx.doi.org/10.1155/2008/216513.

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Potato, a highly heterozygous tetraploid, is undergoing an exciting phase of genomics resource development. The potato research community has established extensive genomic resources, such as large expressed sequence tag (EST) data collections, microarrays and other expression profiling platforms, and large-insert genomic libraries. Moreover, potato will now benefit from a global potato physical mapping effort, which is serving as the underlying resource for a full potato genome sequencing project, now well underway. These tools and resources are having a major impact on potato breeding and genetics. The genome sequence will provide an invaluable comparative genomics resource for cross-referencing to the other Solanaceae, notably tomato, whose sequence is also being determined. Most importantly perhaps, a potato genome sequence will pave the way for the functional analysis of the large numbers of potato genes that await discovery. Potato, being easily transformable, is highly amenable to the investigation of gene function by biotechnological approaches. Recent advances in the development of Virus Induced Gene Silencing (VIGS) and related methods will facilitate rapid progress in the analysis of gene function in this important crop.
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Howe, Kevin L., Bruno Contreras-Moreira, Nishadi De Silva, Gareth Maslen, Wasiu Akanni, James Allen, Jorge Alvarez-Jarreta, et al. "Ensembl Genomes 2020—enabling non-vertebrate genomic research." Nucleic Acids Research 48, no. D1 (October 10, 2019): D689—D695. http://dx.doi.org/10.1093/nar/gkz890.

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Abstract Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.
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Dissertations / Theses on the topic "Genomic resources"

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Voutsina, Nikol. "Elucidating the genomics of nutritional and morphological traits in watercress (Nasturtium officinale R. Br.) : the first genomic resources." Thesis, University of Southampton, 2017. https://eprints.soton.ac.uk/425884/.

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Watercress (Nasturtium officinale R. Br.; Brassicaceae) has a long history of human use for medicine and consumption. In recent years, it has received a large deal of attention as one of the most nutrient-dense foods. Despite this, watercress remains largely underdeveloped with limited breeding resources through which to meet current and future intensifying market demands, such as for a more compact morphology, enhanced nutritional benefits and resource-use efficiency. The aim of this PhD has been to characterize the genetic structure of nutritional and morphological traits in watercress and develop molecular breeding tools that will inform and facilitate future work on this crop. To this end, Chapter 1 provides an overview of pre-existing knowledge on watercress and reviews the opportunities offered by Next Generation Sequencing tools for undeveloped crops. Chapter 2 describes the application of RNASeq towards de novo assembly and functional annotation the watercress transcriptome for the first time. Differential expression analysis resulted in a catalogue of significant genes for antioxidant capacity and glucosinolate content in watercress and identified orthologs to known phenylpropanoid and glucosinolate biosynthetic pathway genes. In Chapter 3, the first genetic linkage map and QTL analysis were completed for this crop, utilizing Genotyping-By-Sequencing for marker discovery. In a novel undertaking to identify QTL for chemopreventive qualities in a plant genome, the toxicity of watercress to human cancer cells was mapped successfully explaining 20 % of variation in this trait. As the development of new cultivars remains central to this work, Chapter 4 reports on the first commercial trials of the new ‘Boldrewood’ accession, aimed at informing its commercialization process. Excitingly, this study also highlighted previously unknown trends in phytonutrient character of the crops across a temporal gradient, which suggests the potential for increasing consumer health benefit by alternations to crop management practices. The sum of this work has resulted in significant advances in the understanding of watercress genetics and genomics and the production of valuable resources for its future preservation and advancement.
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Wang, Biao. "Development and Application of Genomic Resources in Non-model Bird Species." Doctoral thesis, Uppsala, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-183645.

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Understanding the genetic basis of biological processes is a fundamental component of modern ecology and evolutionary biology studies. With the recent advent of next generation sequencing (NGS) technologies, it is now possible to perform large genome and transcriptome projects for ecologically important non-model species. In this thesis, I focused on the development and application of genomic resources of two non-model bird species, the black grouse (Tetrao tetrix) and the great snipe (Gallinago media). Using the chicken genome as a reference, I developed a reference guided NGS pipeline to assemble the complete draft genome of black grouse. The draft genome has a good coverage of the main 29 chromosomes of the chicken genome. The genome was used to develop a vast number of genetic markers. Comparing this genome with that of other species, I identified the genomic regions which were important for the lineage specific evolution of black grouse. I also sequenced and characterised the spleen transcriptome of the black grouse. I identified and validated a large number of gene-based microsatellite markers from the transcriptome and identified and confirmed the expression of immune related genes. Using a similar RNA-Seq approach, I also sequenced the blood transcriptomes of 14 great snipe males with different mating success. I identified genes and single nucleotide polymorphisms (SNPs) which might be related to male mating success in this species, both in terms of gene expression levels and genetic variation structure. For the immunologically important major histocompatibility complex (MHC) gene region of black grouse, I constructed a fosmid library and used it to sequence the complete core MHC region of this species. This resource allowed me to perform a comprehensive comparative genomics analysis of the galliform MHC, by which I found that some genes in this region were affected by selective forces. I was also able to develop a single locus genotyping protocol for the duplicated MHC BLB (class IIB) genes and found that the two black grouse BLB loci followed different evolutionary trajectories. This thesis set an example of developing genomic resources in non-model species and applying them in addressing questions relevant to ecology and evolutionary biology.
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Ramsey, John, Alex Wilson, Vos Martin de, Qi Sun, Cecilia Tamborindeguy, Agnese Winfield, Gaynor Malloch, et al. "Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design." BioMed Central, 2007. http://hdl.handle.net/10150/610401.

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BACKGROUND:The green peach aphid, Myzus persicae (Sulzer), is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species.RESULTS:Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). Aphids for library construction were raised on Arabidopsis thaliana, Nicotiana benthamiana, Brassica oleracea, B. napus, and Physalis floridana (with and without Potato leafroll virus infection). The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. Furthermore, 2423 genes that are novel to science and potentially aphid-specific were identified. Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes.CONCLUSION:New genomic resources have been developed for M. persicae, an agriculturally important insect pest. These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. These resources will help elucidate the adaptations that allow M. persicae to develop compatible interactions with its host plants, complementing ongoing work illuminating plant molecular responses to phloem-feeding insects.
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章明明 and Ming-ming Cheung. "An examination of the regulation of gene expression using microarray and genomic resources." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2002. http://hub.hku.hk/bib/B31225809.

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Cheung, Ming-ming. "An examination of the regulation of gene expression using microarray and genomic resources /." Hong Kong : University of Hong Kong, 2002. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25205717.

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Jeffries, Daniel Lee. "Genetic and genomic approaches to the conservation of the threatened crucian carp Carassius carassius (L.) : phylogeography, hybridisation and introgression." Thesis, University of Hull, 2015. http://hydra.hull.ac.uk/resources/hull:13225.

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Biological invasions can have dramatic detrimental impacts on ecosystems, however they also represent rich opportunities to study the evolutionary processes associated with them. Hybridisation and subsequent introgression are two such processes and are common among native and non-native species. The crucian carp, Carassius carassius (L.), is a European freshwater fish that is threatened throughout much of its native range by several factors including hybridisation and introgression with three non-native species, the goldfish, Carassius auratus (L.), the gibel carp, Carassius gibelio (Bloch), and the common carp, Cyprinus carpio (L.). The conservation of C. carassius is hampered by a lack of phylogeographic knowledge for the species and no knowledge of the extent or impact of hybridisation and introgression. Contemporary genomic approaches such as Restriction Site Associated DNA sequencing (RADseq) can offer unprecedented insights into such research areas, however RADseq comes with several sources of potential bias. Exploratory analyses in Chapter 2 show that two sources of bias in particular, null alleles and over merged ohnolog loci, are highly important in this dataset, but can be filtered using population genetics statistics. The filtered dataset is used in phylogeographic analyses in Chapter 3, along with microsatellite and mitochondrial DNA and show that C. carassius exists as two major lineages in Europe, which diverged approximately 2.26 million years ago, and should be treated as separate units for conservation. These lineages result from the C. carassius postglacial recolonisation routes thtough Europe, which are highly distinct from the general patterns seen in other freshwater fish species. These phylogeographic results showed high similarity between C. carassius in England and those in continental Europe, calling into question the presently assumed native status of C. carassius in England, which has been contentious in the past. Empirical tests of this status using microsatellites showed that, in fact, C. carassius is most likely introduced in England around the 15th century, raising interesting discussions pertaining to their conservation in the England. Lastly, in Chapter 5, microsatellite and RADseq approaches show that hybridisation between C. carassius and non-native species is prevalent where they are sympatric, however backcrosses are rare, and there is no evidence of further introgression between the species studied. Taken together, these results suggest that postzygotic mechanisms of isolation limit interspecific gene flow, and conservationists should focus further research on the direct impacts of non-native species and F1 hybrids.
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Munoz-Torres, Monica Cecilia. "Comparative genomics and molecular evolution new genomic resources for the Hymenoptera and evolutionary studies on the genes of the Nasonia vitripennis Hox complex /." Connect to this title online, 2009. http://etd.lib.clemson.edu/documents/1246558786/.

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Nogueira, Marques João Pedro. "Using genomic tools to understand species differentiation and admixture in hares and mice." Thesis, Université de Montpellier (2022-….), 2022. http://www.theses.fr/2022UMONG010.

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Cette thèse a contribué, en utilisant le séquençage haut débit de génomes, à la compréhension de l’histoire de la divergence conduisant à la spéciation, et des causes et conséquences des échanges génétiques entre espèces.Ce travail a contribué au développement des ressources génomiques pour étudier la génomique des populations de lièvres, en produisant le premier assemblage de novo d’un génome de lièvre (Lepus timidus), et en évaluant son utilité en comparaison au génome de référence du lapin, préalablement disponible. Nous avons aussi produit le premier transcriptome de L. timidus, le plus complet de ceux disponibles pour les lièvres. En combinaison avec des données publiées sur L. europaeus, nous avons trouvé les différences fixées entre les deux espèces, qui peuvent être utilisées pour construire des outils pour étudier les échanges interspécifiques dans les zones d’hybridation.Nous avons contribué à la compréhension de l’introgression massive documentée du génome mitochondrial de L. timidus vers L. granatensis dans la péninsule ibérique, en reconstituant l’évolution démographique post-glaciaire de cette dernière à partir de la variation génétique actuelle. Nous avons démontré que cette introgression s’est faite à la faveur de l’envahissement du territoire de l’espèce donneuse par la receveuse, soulignant l’importance de la démographie et de la biogéographie pour favoriser l’introgression.A partir de séquences de génomes complets, nous avons étudié la différenciation et le re-mélange en Iran, la région d’origine des trois sous-espèces connues de souris domestique (Mus musculus domesticus, musculus et castaneus), source de leur expansion au reste de l’Eurasie, conduisant à leurs distributions parapatriques actuelles. Nous avons découvert au centre de l’Iran une population différenciée de ces trois sous-espèces, et inféré qu’elle résulte d’un mélange passé entre M. m. domesticus (environ 40%) et une population apparentée à M. m. musculus. Les lignées domesticus et musculus se sont donc largement mélangées à proximité de leur région d’origine, mais apparaissent isolées suite à leurs expansions géographiques indépendantes vers l’Europe, où elles forment une zone de tension étroite, un patron évocateur d’une espèce en anneau. Ceci offre un modèle exceptionnel pour étudier l’évolution et les déterminants de l’isolement reproductif entre ces sous-espèces. Nos analyses suggèrent un avantage sélectif du chromosome Y de la lignée musculus dans ce contexte de mélange en Iran central.Nous avons aussi découvert au NW de l’Iran une population d’origine majoritairement domesticus, avec des contributions de ses deux voisins (musculus et Iran central), mais qui a fixé une lignée de chromosome Y de la branche musculus. Nous trouvons que cette introgression massive de Y est accompagnée par la co-introgression de gènes impliqués dans la fertilité mâle, particulièrement sur le chromosome X. Nous avons testé le lien potentiel de cette invasion de Y avec une course aux armements entre le X et le Y qui pourrait biaiser les sex-ratios, et ainsi pu aborder la question du rôle des conflits génétiques comme promoteurs de l’introgression. Entre sous-espèces, nous avons trouvé une corrélation entre les nombres de copies Y et X de familles ampliconiques (gènes Sly/Slx) dont l’interaction est connue pour contrôler le sex-ratio de manière antagoniste en fonction de la dose. Plus de copies dans la lignée musculus suggère des propriétés distortrices plus fortes. Toutefois nous argumentons que ce conflit X-Y n’est pas le moteur de l’invasion du Y, qui résulterait plutôt d’un avantage intrinsèque du Y musculus en situation de mélange entre sous-espèces. La propension du Y musculus à envahir les régions où musculus se mélange avec d’autres sous-espèces semble générale et observée dans d’autres régions géographiques. Le conflit entraînerait la co-introgression ou la coévolution des régions ampliconiques du X dans les zones de mélange
The present thesis has contributed, using high throughput genome sequencing, to understanding the history of divergence leading to speciation, and the causes and consequences of genetic exchanges between species, in hares and mice.First, this work has contributed to the development of the genomic resources available to study hare population genomics, by providing the first de novo assembly of a hare genome (for the mountain hare, Lepus timidus), and assessing its utility as compared to the rabbit assembly, previously available. We have also generated the first mountain hare transcriptome, and the most complete among the currently available Lepus transcriptomes. In combination with published data on the European brown hare (L. europaeus), we pinpointed candidate fixed differences between the two species that can be used to build genotyping tools to monitor gene exchange in contact zones.Second, we have contributed to the understanding of the documented massive introgression of the mitochondrial genome from the mountain hare to the Iberian hare (L. granatensis) in Iberia, by reconstructing the post-glacial demographic dynamics of the latter species using Single Nucleotide Polymorphism data. We demonstrated that this introgression occurred at the favor of the invasive replacement of the donor species by the recipient one during the last deglaciation, thus showing the importance of demographic and biogeographic history in driving introgression.Third, using whole genome sequencing, we studied genetic differentiation and admixture in Iran, the region of origin of the three described house mouse subspecies (M. m. domesticus, musculus and castaneus), source of their expansion to the rest of Eurasia, leading to their present parapatric distributions. We discovered in Central Iran a population that is differentiated from these three subspecies, and inferred that it results from an ancient admixture between M. m. domesticus (about 40%) and a population related to M. m. musculus. The domesticus and musculus lineages thus admixed extensively close to their region of origin, but appear genetically isolated after their independent geographical expansions to Europe, where they form a narrow tension zone, a pattern evocative of a ring species. This offers an exceptional model to further study the evolution and determinants of reproductive isolation between these subspecies. Our analyses also suggest a selective advantage of non-domesticus Y chromosome in this context of admixture in Central Iran.We also discovered in North Western Iran a population that is mostly of domesticus origin, with inferred admixture from its geographical neighbours (musculus and central Iran), but which has fixed a Y chromosome lineage related to that of musculus. We show that this massive Y introgression is accompanied by co-introgression of genes with functions related to male fertility, especially on the X chromosome. We tested the potential link of this Y invasion with an arms-race between the X and Y chromosomes that could bias sex-ratio, and therefore address the question of the potential role of genetic conflicts in promoting introgression. Among subspecies we found a correlation between copy numbers of Y and X ampliconic families (Sly/Slx genes) whose interaction is known to control sex chromosome transmission in a dosage dependent manner. Higher copy numbers in the musculus lineage suggest stronger distortion properties. We however argue that this X-Y conflict is not the cause of massive Y introgression, which would rather reflect an intrinsic advantage of the musculus Y lineage in zones of admixture between the subspecies. The ability of the musculus Y chromosome to invade zones where musculus admixes with other subspecies seems to be a ubiquitous pattern, observed in other geographic regions. The conflict would rather cause co-introgression or co-evolution of the X ampliconic region in admixed populations
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Verbruggen, Bas. "Generating genomic resources for two crustacean species and their application to the study of White Spot Disease." Thesis, University of Exeter, 2016. http://hdl.handle.net/10871/25535.

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Over the last decades the crustacean aquaculture sector has been steadily growing, in order to meet global demands for its products. A major hurdle for further growth of the industry is the prevalence of viral disease epidemics that are facilitated by the intense culture conditions. A devastating virus impacting on the sector is the White Spot Syndrome Virus (WSSV), responsible for over US $10 billion in losses in shrimp production and trade. The Pathogenicity of WSSV is high, reaching 100 % mortality within 3-10 days in penaeid shrimps. In contrast, the European shore crab Carcinus maenas has been shown to be relatively resistant to WSSV. Uncovering the basis of this resistance could help inform on the development of strategies to mitigate the WSSV threat. C. maenas has been used widely in studies on ecotoxicology and host-pathogen interactions. However, like most aquatic crustaceans, the genomic resources available for this species are limited, impairing experimentation. Therefore, to facilitate interpretations of the exposure studies, we first produced a C. maenas transcriptome and genome scaffold assembly. We also produced a transcriptome for the European lobster (Homarus gammarus), an ecologically and commercially important crustacean species in United Kingdom waters, for use in comparing WSSV responses in this, a susceptible species, and C. maenas. For the C. maenas transcriptome assembly we isolated and pooled RNA from twelve different tissues and sequenced RNA on an Illumina HiSeq 2500 platform. After de novo assembly a transcriptome encompassing 212,427 transcripts was produced. Similar, the H. gammarus transcriptome was based on RNA from nine tissues and contained 106,498 transcripts. The transcripts were filtered and annotated using a variety of tools (including BLAST, MEGAN and RSEM) and databases (including GenBank, Gene Ontology and KEGG). The annotation rate for transcripts in both transcriptomes was around 20-25 % which appears to be common for aquatic crustacean species, as a result of the lack of well annotated gene sequences for this clade. Since it is likely that the host immune system would play an important role in WSSV infection we characterized the IMD, JAK/STAT, Toll-like receptor and other innate immune system pathways. We found a strong overlap between the immune system pathways in C. maenas and H. gammarus. In addition we investigated the sequence diversity of known WSSV interacting proteins amongst susceptible penaeid shrimp/lobster and the more resistant C. maenas. There were differences in viral receptor sequences, like Rab7, that correlate with a less efficient infection by WSSV. To produce the genome scaffold assembly for C. maenas we isolated DNA from muscle tissue and produced both paired-end and mate pair libraries for processing on the Illumina HiSeq 2500 platform. A de novo draft genome assembly consisting of 338,980 scaffolds and covering 362 Mb (36 % of estimated genome size) was produced, using SOAP-denovo2 coupled with the BESST scaffolding system. The generated assembly was highly fragmented due to the presence of repetitive areas in the C. maenas genome. Using a combination of ab initio predictors, RNA-sequencing data from the transcriptome datasets and curated C. maenas sequences we produced a model encompassing 10,355 genes. The gene model for C. maenas Dscam, a gene potentially involved in (pan)crustacean immune memory, was investigated in greater detail as manual curation can improve on the results of ab initio predictors. The scaffold containing C. maenas Dscam was fragmented, thus only contained the latter exons of the gene. The assembled draft genome and transcriptomes for C. maenas and H. gammarus are valuable molecular resources for studies involving these and other aquatic crustacean species. To uncover the basis of their resistance to WSSV, we infected C. maenas with WSSV and measured mRNA and miRNA expression for 7 time points spread over a period of 28 days, using RNA-Seq and miRNA-Seq. The resistance of C. maenas to WSSV infection was confirmed by the fact that no mortalities occurred. In these animals replicating WSSV was latent and detected only after 7 days, and this occurred in five of out 28 infected crabs only. Differential expression of transcripts and miRNAs were identified for each time point. In the first 12 hours post exposure we observed decreased expression of important regulators in endocytosis. Since it is established that WSSV enters the host cells through endocytosis and that interactions between the viral protein VP28 and Rab7 are important in successful infection, it is likely that changes in this process could impact WSSV infection success. Additionally we observed an increased expression of transcripts involved in RNA interference pathways across many time points, indicating a longer term response to initial viral exposure. miRNA sequencing showed several miRNAs that were differentially expressed. The most striking finding was a novel C. maenas miRNA that we found to be significantly downregulated in every WSSV infected individual, suggesting that it may play an important role in mediating the response of the host to the virus. In silico target prediction pointed to the involvement of this miRNA in endocytosis regulation. Taken together we hypothesize that C. maenas resistance to WSSV involves obstruction of viral entry by endocytosis, a process probably regulated through miRNAs, resulting in inefficient uptake of virions.
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Galata, Valentina [Verfasser]. "Resources for the analysis of bacterial and microbial genomic data with a focus on antibiotic resistance / Valentina Galata." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2020. http://d-nb.info/1214240755/34.

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Books on the topic "Genomic resources"

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-14871-2.

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-14255-0.

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-14387-8.

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-16057-8.

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-20447-0.

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-20450-0.

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-14228-4.

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21102-7.

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21201-7.

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Kole, Chittaranjan, ed. Wild Crop Relatives: Genomic and Breeding Resources. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21250-5.

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Book chapters on the topic "Genomic resources"

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del Rosario, Ricardo Cruz-Herrera. "Genomic Resources." In Encyclopedia of Systems Biology, 838–39. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_1041.

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Jayakodi, Murukarthick, and Tae-Jin Yang. "Genomic Resources for Ginseng Genome Studies." In The Ginseng Genome, 143–48. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-30347-1_11.

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Shah, Saumya, Shubhra Rastogi, and Ajit Kumar Shasany. "Genomic Resources of Ocimum." In The Ocimum Genome, 99–110. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-97430-9_8.

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King, Graham J., and Abdul Baten. "Brassica napus Genomic Resources." In Compendium of Plant Genomes, 233–44. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-43694-4_14.

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Sareen, Sindhu, Pawan Saini, Charan Singh, Pradeep Kumar, and Sonia Sheoran. "Genomics and molecular physiology for improvement of drought tolerance in wheat." In Molecular breeding in wheat, maize and sorghum: strategies for improving abiotic stress tolerance and yield, 51–81. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789245431.0004.

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Abstract This chapter discusses the complexity of drought tolerance in wheat focusing the morphological, biochemical, physiological and molecular responses. The breeding approaches, such as traditional and genomics-assisted strategies, for drought tolerance in wheat are described. Future perspectives are also mentioned. Before wheat genome sequencing, it was very difficult to dissect drought tolerance genomic regions because of large genome size and repetitive sequences. But with the availability of sequencing approaches, a large number of genomic resources has become available which extend the scope of utilization of advanced genomics approaches such as GWAM and GS, MutMap+, etc. A new genome editing approach, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPRassociated protein 9 (Cas9) system, can also be utilized for enhancement of drought tolerance in wheat. Therefore, integration of genomic approaches with precise phenotyping is the need of the hour for improving drought tolerance in wheat.
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Zhang, Jiaren, Yanliang Jiang, Fanyue Sun, Yu Zhang, Ruijia Wang, Chao Li, Shikai Liu, and Zhanjiang john Liu. "Genomic Resources for Functional Genomics in Aquaculture Species." In Functional Genomics in Aquaculture, 41–77. Oxford, UK: Wiley-Blackwell, 2012. http://dx.doi.org/10.1002/9781118350041.ch2.

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Cianzio, Silvia R., Randy C. Shoemaker, and Dirk V. Charlson. "Genomic Resources of Agronomic Crops." In Iron Nutrition in Plants and Rhizospheric Microorganisms, 449–66. Dordrecht: Springer Netherlands, 2006. http://dx.doi.org/10.1007/1-4020-4743-6_22.

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Dwivedi, Sangam, Hari Upadhyaya, Senapathy Senthilvel, Charles Hash, Kenji Fukunaga, Xiamin Diao, Dipak Santra, David Baltensperger, and Manoj Prasad. "Millets: Genetic and Genomic Resources." In Plant Breeding Reviews, 247–375. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118100509.ch5.

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Khan, Haseena, Liwu Zhang, Dipnarayan Saha, Huawei Wei, Subhojit Datta, Pratik Satya, Jiban Mitra, and Gouranga Kar. "Jute Genomic Resources and Database." In Compendium of Plant Genomes, 247–58. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-91163-8_16.

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Jaiswal, Sarika, Mir Asif Iquebal, UB Angadi, Sunil Kumar, Anil Rai, Nagendra K. Singh, and Dinesh Kumar. "Mango Genomic Resources and Databases." In Compendium of Plant Genomes, 219–28. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-47829-2_13.

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Conference papers on the topic "Genomic resources"

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MacDonald, Anna, Margaret Byrne, JanineJanine Deakin, Mark Eldridge, Anna Fitzgerald, Rebecca Johnson, Stephanie Palmer, Andrew Young, Craig Moritz, and The Oz Mammals Genomics Consortium. "The Oz Mammals Genomics initiative: developing genomic resources for mammal conservation at a continental scale." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/108107.

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Oliver, Javier, Sandra Perdomo, and Felipe Vaca. "Abstract 1831: Cancer genomic resources and needs in the Latin American region." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-1831.

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Tasma, I. Made, Habib Rijzaani, Dani Satyawan, Ida Rosdianti, Edy Supriyanto, and Razak Purba. "Characterization of genomic variation on three Indonesian oil palm genotypes analyzed using next-generation sequencing HiSeq." In THE SECOND INTERNATIONAL CONFERENCE ON GENETIC RESOURCES AND BIOTECHNOLOGY: Harnessing Technology for Conservation and Sustainable Use of Genetic Resources for Food and Agriculture. AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0075392.

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"Understanding genomic resources of indigenous chickens for the rapid improvement of their production efficiency." In Technology Innovations and Collaborations in Livestock Production for Sustainable Food Systems. IAARD Press, 2021. http://dx.doi.org/10.14334/proc.intsem.lpvt-2021-p.7.

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Gardner, Brittany D., Janeth Sanchez, Michelle Doose, Sallie J. Weaver, Shobha Srinivasan, Andrew Freedman, and Janet S. de Moor. "Abstract PO-210: Distribution of genomic testing resources by oncology practice setting and rurality: A nationally representative analysis." In Abstracts: AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; October 2-4, 2020. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7755.disp20-po-210.

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Lakhan, Shaheen. "The Emergence of Modern Biotechnology in China." In InSITE 2006: Informing Science + IT Education Conference. Informing Science Institute, 2006. http://dx.doi.org/10.28945/3038.

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Science and technology of Republican China (1912-1949) often replicated the West in all hierarchies. However, in 1949 when the Chinese Communist Party (CCP) declared the nation the People's Republic of China, it had assumed Soviet pseudo-science, namely neo-Lamarckian and anti-Mendelian Lysenkoism, which led to intense propaganda campaigns that victimized intellectuals and natural scientists. Not until the 1956 Double Hundred Campaign had China engaging in meaningful exploration into modern genetics with advancements of Morgan. The CCP encouraged discussions on the impact of Lysenkoism which cultivated guidelines to move science forward. However, Mao ended the campaign by asserting the Anti-Rightist Movement (1957) that reinstated the persecution of intellectuals, for he believed they did not contribute to his socialist ethos of the working people. The Great Leap Forward (1958-1959), an idealist and unrealistic attempt to rapidly industrialize the nation, and the Cultural Revolution (1966-1976), a grand attempt to rid China of the "technological elite," extended China's lost years to a staggering two decades. Post-Mao China rapidly revived its science and technology frontier with specialized sciences: agricultural biotechnology, major genomic ventures, modernizing Traditional Chinese Medicine, and stem-cell research. Major revisions to the country’s patent laws increased international interest in China’s resources. However, bioethical and technical standards still need to be implemented and locally and nationally monitored if China’s scientific advances are to be globally accepted and commercialized.
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"Genetic resources of water caltrop Trapa L." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-013.

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"Plant genetic resources in India: management and utilization." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-174.

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Wang, Ting, and Thomas Ferrin. "Challenge session speakers: Engaging today's genomics resources." In 2013 IEEE Symposium on Biological Data Visualization (BioVis). IEEE, 2013. http://dx.doi.org/10.1109/biovis.2013.6664339.

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"Plant genetic resources for improving stress tolerance – examples for cereals." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-031.

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Reports on the topic "Genomic resources"

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Jean-Baptiste Ledoux, Jean-Baptiste Ledoux. Do Mediterranean corals have the genomic resources to face Marine Heat Waves? Experiment, June 2022. http://dx.doi.org/10.18258/27586.

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Rajarajan, Kunasekaran, Alka Bharati, Hirdayesh Anuragi, Arun Kumar Handa, Kishor Gaikwad, Nagendra Kumar Singh, Kamal Prasad Mohapatra, et al. Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts. World Agroforestry, 2020. http://dx.doi.org/10.5716/wp20050.pdf.

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Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.
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Abbott, Albert G., Doron Holland, Douglas Bielenberg, and Gregory Reighard. Structural and Functional Genomic Approaches for Marking and Identifying Genes that Control Chilling Requirement in Apricot and Peach Trees. United States Department of Agriculture, September 2009. http://dx.doi.org/10.32747/2009.7591742.bard.

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Structural and functional genomic approaches for marking and identifying genes that control chilling requirement in apricot and peach trees. Specific aims: 1) Identify and characterize the genetic nature of chilling requirement for flowering and dormancy break of vegetative shoots in Prunusgermplasm through the utilization of existing apricot (NeweYa'ar Research Center, ARO) and peach (Clemson University) genetic mapping populations; 2) Use molecular genetic mapping techniques to identify markers flanking genomic regions controlling chilling; 3) Comparatively map the regions controlling chilling requirement in apricot and peach and locate important genomic regions influencing chilling requirement on the Prunus functional genomic database as an initial step for identification of candidate genes; 4) Develop from the functional genomics database a set of markers facilitating the development of cultivars with optimized chilling requirements for improved and sustained fruit production in warm-winter environments. Dormant apricot (prunus armeniaca L.) and peach [Prunus persica (L.) Batsch] trees require sustained exposure to low, near freezing, temperatures before vigorous floral and vegetative bud break is possible after the resumption of warm temperatures in the spring. The duration of chilling required (the chilling requirement, CR) is determined by the climatic adaptation of the particular cultivar, thus limiting its geographic distribution. This limitation is particularly evident when attempting to introduce superior cultivars to regions with very warm winter temperatures, such as Israel and the coastal southern United States. The physiological mechanism of CR is not understood and although breeding programs deliberately manipulate CR in apricot and peach crosses, robust closely associated markers to the trait are currently not available. We used segregating populations of apricot (100 Fl individuals, NeweYa'ar Research Center, ARO) and peach (378 F2 individuals, Clemson University) to discover several discreet genomic loci that regulate CR and blooming date. We used the extensive genomic/genetic resources available for Prunus to successfully combine our apricot and peach genetic data and identify five QTL with strong effects that are conserved between species as well as several QTL that are unique to each species. We have identified markers in the key major QTL regions for testing in breeding programs which we are carrying out currently; we have identified an initial set of candidate genes using the peach physical/transcriptome map and whole peach genome sequences and we are testing these currently to identify key target genes for manipulation in breeding programs. Our collaborative work to date has demonstrated the following: 1) CR in peach and apricot is predominantly controlled by a limited number ofQTL loci, seven detected in a peach F2 derived map comprising 65% of the character and 12 in an apricot Fl map comprising 71.6% and 55.6% of the trait in the Perfection and A. 1740 parental maps, respectively and that peach and apricot appear in our initial maps to share five genomic intervals containing potentially common QTL. 2) Application of common anchor markers of the Prunus/peach, physical/genetic map resources has allowed us not only to identify the shared intervals but also to have immediately available some putative candidate gene information from these intervals, the EVG region on LG1 in peach the TALY 1 region in apricot on LG2 in peach; and several others involved in vernalization pathways (LGI and LG7). 3) Mapped BACcontigs are easily defined from the complete physical map resources in peach through the common SSR markers that anchor our CR maps in the two species, 4) Sequences of BACs in these regions can be easily mined for additional polymorphic markers to use in MAS applications.
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Zhang, Hongbin B., David J. Bonfil, and Shahal Abbo. Genomics Tools for Legume Agronomic Gene Mapping and Cloning, and Genome Analysis: Chickpea as a Model. United States Department of Agriculture, March 2003. http://dx.doi.org/10.32747/2003.7586464.bard.

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The goals of this project were to develop essential genomic tools for modern chickpea genetics and genomics research, map the genes and quantitative traits of importance to chickpea production and generate DNA markers that are well-suited for enhanced chickpea germplasm analysis and breeding. To achieve these research goals, we proposed the following research objectives in this period of the project: 1) Develop an ordered BAC library with an average insert size of 150 - 200 kb (USA); 2) Develop 300 simple sequence repeat (SSR) markers with an aid of the BAC library (USA); 3) Develop SSR marker tags for Ascochyta response, flowering date and grain weight (USA); 4) Develop a molecular genetic map consisting of at least 200 SSR markers (Israel and USA); 5) Map genes and QTLs most important to chickpea production in the U.S. and Israel: Ascochyta response, flowering and seed set date, grain weight, and grain yield under extreme dryland conditions (Israel); and 6) Determine the genetic correlation between the above four traits (Israel). Chickpea is the third most important pulse crop in the world and ranks the first in the Middle East. Chickpea seeds are a good source of plant protein (12.4-31.5%) and carbohydrates (52.4-70.9%). Although it has been demonstrated in other major crops that the modern genetics and genomics research is essential to enhance our capacity for crop genetic improvement and breeding, little work was pursued in these research areas for chickpea. It was absent in resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. For instance, there were no large-insert BAC and BIBAC libraries, no sufficient and user- friendly DNA markers, and no intraspecific genetic map. Grain sizes, flowering time and Ascochyta response are three main constraints to chickpea production in drylands. Combination of large seeds, early flowering time and Ascochyta blight resistance is desirable and of significance for further genetic improvement of chickpea. However, it was unknown how many genes and/or loci contribute to each of the traits and what correlations occur among them, making breeders difficult to combine these desirable traits. In this period of the project, we developed the resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. In particular, we constructed the proposed large-insert BAC library and an additional plant-transformation-competent BIBAC library from an Israeli advanced chickpea cultivar, Hadas. The BAC library contains 30,720 clones and has an average insert size of 151 kb, equivalent to 6.3 x chickpea haploid genomes. The BIBAC library contains 18,432 clones and has an average insert size of 135 kb, equivalent to 3.4 x chickpea haploid genomes. The combined libraries contain 49,152 clones, equivalent to 10.7 x chickpea haploid genomes. We identified all SSR loci-containing clones from the chickpea BAC library, generated sequences for 536 SSR loci from a part of the SSR-containing BACs and developed 310 new SSR markers. From the new SSR markers and selected existing SSR markers, we developed a SSR marker-based molecular genetic map of the chickpea genome. The BAC and BIBAC libraries, SSR markers and the molecular genetic map have provided essential resources and tools for modern genetic and genomic analyses of the chickpea genome. Using the SSR markers and genetic map, we mapped the genes and loci for flowering time and Ascochyta responses; one major QTL and a few minor QTLs have been identified for Ascochyta response and one major QTL has been identified for flowering time. The genetic correlations between flowering time, grain weight and Ascochyta response have been established. These results have provided essential tools and knowledge for effective manipulation and enhanced breeding of the traits in chickpea.
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Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, August 2011. http://dx.doi.org/10.32747/2011.7592655.bard.

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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.
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Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.

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Tilapias are among the most important aquaculture commodities worldwide. Commercial production of tilapia is based on monosex culture of males. Current methods for producing all-male fingerlings, including hormone treatments and genetic manipulations, are not entirely reliable, in part because of the genetic complexity of sex determination and sexual differentiation in tilapias. The goals of this project are to map QTL and identify genes regulating sex determination in commonly cultured tilapia species, in order to provide a rational basis for designing reliable genetic approaches for producing all-male fingerlings. The original objectives for this research were: 1) to identify the gene underlying the QTL on LG1 through positional cloning and gene expression analysis; 2) to fine map the QTL on LG 3 and 23; and 3) to characterize the patterns of dominance and epistasis among QTL alleles influencing sex determination. The brain aromatase gene Cyp19b, a possible candidate for the genetic or environmental SD, was mapped to LG7 using our F2 mapping population. This region has not been identified before as affecting SD in tilapias. The QTL affecting SD on LG 1 and 23 have been fine-mapped down to 1 and 4 cM, respectively, but the key regulators for SD have not been found yet. Nevertheless, a very strong association with gender was found on LG23 for marker UNH898. Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Mating of males homozygous for MAA with normal females is underway for production of all-male populations. The first progeny reaching size allowing accurate sexing had 43 males and no females. During the course of the project it became apparent that in order to achieve those objectives there is a need to develop genomic infrastructures that were lacking. Efforts have been devoted to the development of genomic resources: a database consisting of nearly 117k ESTs representing 16 tissues from tilapia were obtained; a web tool based on the RepeatMasker software was designed to assist tilapia genomics; collaboration has been established with a sequencing company to sequence the tilapia genome; steps have been taken toward constructing a microarray to enable comparative analysis of the entire transcriptome that is required in order to detect genes that are differentially expressed between genders in early developmental stages. Genomic resources developed will be invaluable for studies of cichlid physiology, evolution and development, and will hopefully lead to identification of the key regulators of SD. Thus, they will have both scientific and agricultural implications in the coming years.
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Katzir, Nurit, James Giovannoni, and Joseph Burger. Genomic approach to the improvement of fruit quality in melon (Cucumis melo) and related cucurbit crops. United States Department of Agriculture, June 2006. http://dx.doi.org/10.32747/2006.7587224.bard.

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Fruit quality is determined by numerous genetic traits that affect taste, aroma, texture, pigmentation, nutritional value and duration of shelf-life. The molecular basis of many of these important traits is poorly understood and it’s understanding offers an excellent opportunity for adding value to agricultural products. Improvement of melon fruit quality was the primary goal of the project. The original objectives of the project were: The isolation of a minimum of 1000 fruit specific ESTs. The development of a microarray of melon fruit ESTs. The analysis of gene expression in melon using melon and tomato fruit enriched microarrays. A comprehensive study of fruit gene expression of the major cucurbit crops. In our current project we have focused on the development of genomics tools for the enhancement of melon research with an emphasis on fruit, specifically the first public melon EST collection. We have also developed a database to relay this information to the research community and developed a publicly available microarray. The release of this information was one of the catalysts for the establishment of the International Cucurbit Genomic Initiative (ICuGI, Barcelona, Spain, July 2005) aimed at collecting and generating up to 100,000 melon EST sequences in 2006, leveraging a significant expansion of melon genomic resources. A total of 1000 ESTs were promised under the original proposal (Objective 1). Non-subtracted mature fruit and young fruit flesh of a climacteric variety in addition to a non-climacteric variety resulted in the majority of additional EST sequences for a total of 4800 attempted reads. 3731 high quality sequences from independent ESTs were assembled, representing 2,467 melon unigenes (1,873 singletons, 594 contigs). In comparison, as of June 2004, a total of 170 melon mRNA sequences had been deposited in GENBANK. The current project has thus resulted in nearly five- fold the number of ESTs promised and ca. 15-fold increase in the depth of publicly available melon gene sequences. All of these sequences have been deposited in GENBANK and are also available and searchable via multiple approaches in the public database (http://melon.bti.cornell.edu). Our database was selected as the central location for presentation of public melon EST data of the International Cucurbit Genomic Initiative. With the available unigenes we recently constructed a microarray, which was successfully applied in hybridizations (planned public release by August 2006). Current gene expression analyses focus on fruit development and on comparative studies between climacteric and non-climacteric melons. Earlier, expression profiling was conducted using macroarrays developed at the preliminary stage of the project. This analysis replaced the study of tomato microarray following the recommendations of the reviewers and the panel of the original project. Comparative study between melon and other cucurbit crops have begun, mainly with watermelon, in collaboration with Dr. Amnon Levi (USDA-ARS). In conclusion, all four objectives have been addressed and achieved. In the continuation project that have been approved we plan to apply the genomic tools developed here to achieve detailed functional analyses of genes associated with major metabolic pathway.
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8

Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.
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Zamir, Dani, and Steven Tanksley. Fine Mapping and Genetic Interactions of Nearly-Isogenic Allelic Series Representing Yield and Quality QTLs Derived from Wild Tomato Species. United States Department of Agriculture, July 2002. http://dx.doi.org/10.32747/2002.7586460.bard.

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Wild germplasm represents a rich source of QTLs capable of enhancing productivity of crop plants. Using the molecular linkage map of tomato in conjunction with novel population structures, we have identified QTLs from five Lycopersicon species that improve key yield and quality associated traits of processing tomatoes. In this research we employed multi-testing sites for fine mapping analysis of the different components of the affected traits combined with genetic interaction studies. Our results demonstrate that 'exotic libraries', which comprise of marker-defined genomic regions taken from wild species and introgressed onto the background of elite crop lines, provide an important opportunity for improving of the agricultural performance of modem crop varieties. Furthermore, we showed that these genetic resources can also serve as reagents for the discovery and characterization of genes that underlie traits of agricultural value. The results set the stage for using the QTLs in marker assisted programs and for applying map-based cloning of the targeted QTL/genes. The cloning of QTLs revealed genes that control pathways for agricultural yield in tomato that may be common for other crop species.
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10

Gerald M. Rubin. Resources for Biological Annotation of the Drosophila Genome. Office of Scientific and Technical Information (OSTI), August 2005. http://dx.doi.org/10.2172/842216.

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