Relevant bibliographies by topics / Genotype and Phenotype Relationship

Academic literature on the topic 'Genotype and Phenotype Relationship'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Genotype and Phenotype Relationship"

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Wilson, David Sloan, and Alexandra Wells. "Radical Epistasis and the Genotype-Phenotype Relationship." Artificial Life 2, no. 1 (October 1994): 117–28. http://dx.doi.org/10.1162/artl.1994.2.1.117.

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Models of evolution often assume that the offspring of two genotypes, which are genetically intermediate by definition, are also phenotypically intermediate. The continuity between genotype and phenotype interferes with the process of evolution on multipeaked adaptive landscapes because the progeny of genotypes that lie on separate adaptive peaks fall into valleys of low fitness. This problem can be solved by epistasis, which disrupts the continuity between genotype and phenotype. In a five-locus sexual haploid model with maximum epistasis, natural selection in multipeak landscapes evolves a set of genotypes that a) occupy the adaptive peaks and b) give rise to each other by recombination. The epistatic genetic system therefore “molds” the phenotypic distribution to the adaptive landscape, without assortative mating or linkage disequilibrium. If the adaptive landscape is changed, a new set of genotypes quickly evolves that satisfies conditions a and b, above, for the new peaks. Our model may be relevant to a number of recalcitrant problems in biology and also stands in contrast to Kauffman's [3] NK model of evolution on rugged fitness surfaces, in which epistasis and recombination tend to constrain the evolutionary process.
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Spiegel, Ronen, Hanna Mandel, Ann Saada, Issy Lerer, Ayala Burger, Avraham Shaag, Stavit A. Shalev, et al. "Delineation of C12orf65-related phenotypes: a genotype–phenotype relationship." European Journal of Human Genetics 22, no. 8 (January 15, 2014): 1019–25. http://dx.doi.org/10.1038/ejhg.2013.284.

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Guilfoile, Patrick, and Stephen Plum. "The Relationship Between Phenotype & Genotype." American Biology Teacher 62, no. 4 (April 2000): 288–91. http://dx.doi.org/10.1662/0002-7685(2000)062[0288:trbpg]2.0.co;2.

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Romano, V., G. Anello, and S. Kaufman. "Genotype-phenotype relationship in PAH deficiency." Journal of Inherited Metabolic Disease 21 (August 1998): 13–16. http://dx.doi.org/10.1023/a:1005428215950.

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Li, Ruowang, Rui Duan, Rachel L. Kember, Daniel J. Rader, Scott M. Damrauer, Jason H. Moore, and Yong Chen. "A regression framework to uncover pleiotropy in large-scale electronic health record data." Journal of the American Medical Informatics Association 26, no. 10 (July 27, 2019): 1083–90. http://dx.doi.org/10.1093/jamia/ocz084.

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Abstract Objective Pleiotropy, where 1 genetic locus affects multiple phenotypes, can offer significant insights in understanding the complex genotype–phenotype relationship. Although individual genotype–phenotype associations have been thoroughly explored, seemingly unrelated phenotypes can be connected genetically through common pleiotropic loci or genes. However, current analyses of pleiotropy have been challenged by both methodologic limitations and a lack of available suitable data sources. Materials and Methods In this study, we propose to utilize a new regression framework, reduced rank regression, to simultaneously analyze multiple phenotypes and genotypes to detect pleiotropic effects. We used a large-scale biobank linked electronic health record data from the Penn Medicine BioBank to select 5 cardiovascular diseases (hypertension, cardiac dysrhythmias, ischemic heart disease, congestive heart failure, and heart valve disorders) and 5 mental disorders (mood disorders; anxiety, phobic and dissociative disorders; alcohol-related disorders; neurological disorders; and delirium dementia) to validate our framework. Results Compared with existing methods, reduced rank regression showed a higher power to distinguish known associated single-nucleotide polymorphisms from random single-nucleotide polymorphisms. In addition, genome-wide gene-based investigation of pleiotropy showed that reduced rank regression was able to identify candidate genetic variants with novel pleiotropic effects compared to existing methods. Conclusion The proposed regression framework offers a new approach to account for the phenotype and genotype correlations when identifying pleiotropic effects. By jointly modeling multiple phenotypes and genotypes together, the method has the potential to distinguish confounding from causal genotype and phenotype associations.
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Letteboer, T. G. W. "Genotype-phenotype relationship in hereditary haemorrhagic telangiectasia." Journal of Medical Genetics 43, no. 4 (September 9, 2005): 371–77. http://dx.doi.org/10.1136/jmg.2005.035451.

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GALANELLO, RENZO, and ANTONIO CAO. "Relationship between Genotype and Phenotype: Thalassemia Intermediaa." Annals of the New York Academy of Sciences 850, no. 1 COOLEY'S ANEM (June 1998): 325–33. http://dx.doi.org/10.1111/j.1749-6632.1998.tb10489.x.

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Bronsveld, I., R. A. de Nooijer, H. G. M. Arets, F. Teding van Berkhout, C. K. van der Ent, Y. de Rijke, and H. R. de Jonge. "R117H homozygosity and the genotype–phenotype relationship." Journal of Cystic Fibrosis 9 (June 2010): S11. http://dx.doi.org/10.1016/s1569-1993(10)60042-2.

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Pera, Angelo, Raffaello Sostegni, Marco Daperno, Elena Ercole, Cristiana Laudi, Rodolfo Rocca, Caterina Rigazio, Marco Astegiano, and Giuseppe Rocca. "Genotype–phenotype relationship in inflammatory bowel disease." European Journal of Internal Medicine 11, no. 4 (August 2000): 204–9. http://dx.doi.org/10.1016/s0953-6205(00)00092-3.

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Sun, Yi-Min, Yan-Bin Zhang, and Zhi-Ying Wu. "Huntington’s Disease: Relationship Between Phenotype and Genotype." Molecular Neurobiology 54, no. 1 (January 7, 2016): 342–48. http://dx.doi.org/10.1007/s12035-015-9662-8.

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Dissertations / Theses on the topic "Genotype and Phenotype Relationship"

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Kemble, Henry. "The genotype-phenotype relationship across different scales." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC178/document.

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Avec la révolution moléculaire en biologie, une compréhension des mécanismes de la relation génotype-phénotype est devenue possible. Récemment, les progrès réalisés dans la synthèse et le séquençage de l’ADN ont permis le développement d’expériences de deep-mutational scanning capable de quantifier divers phénotypes pour un ensemble de génotypes sur toute la longueur d’un gène. Ces ensembles de données sont non seulement intéressants en eux-mêmes, mais permettent également de tester de manière rigoureuse des modèles phénotypiques quantitatifs. Nous avons utilisé cette technologie pour caractériser les cartes séquence-fitness de 3 systèmes bactériens modèles: un régulateur global, la CRP, une enzyme de résistance aux antibiotiques, la β-lactamase, et une petite voie métabolique constituée des enzymes AraA et AraB. Ces systèmes ont été choisis pour éclairer les rôles de différentes caractéristiques dans la formation de la relation génotype-fitness (réseaux de régulations, stabilité des protéines et flux métabolique). Nous constatons que la tendance globale des effets sur le fitness semble prévaloir sur les tendances spécifiques. Ceci nous conduit à penser qu’une grande partie de la relation entre le génotype et le fitness pourrait être expliquée à partir de la forme des fonctions de phénotype-fitness. Par ailleurs, nous voyons que la caractérisation de la relation génotype-fitness dans différents systèmes peut être un moyen puissant d’obtenir des informations sur les phénotypes pertinents
With the molecular revolution in Biology, a mechanistic understanding of the genotype-phenotype relationship became possible. Recently, advances in DNA synthesis and sequencing have enabled the development of deep-mutational scanning experiments, capable of scoring comprehensive libraries of genotypes for a variety of phenotypes over the length of entire genes. Such datasets are not only interesting in themselves, but also allow rigorous testing of quantitative phenotypic models. We used this technology to characterise sequence-fitness maps for 3 model bacterial systems: a global regulator, CRP, an antibiotic-resistance enzyme, β-lactamase, and a small metabolic pathway, consisting of the enzymes AraA and AraB. These different systems were chosen to illuminate the roles of different mechanistic features in shaping the genotype-fitness relationship (regulatory wiring, protein stability and metabolic flux). We find that smooth patterns of fitness effects tend to prevail over idiosyncrasy, indicating that much of the genotype-fitness relationship could be understood from the global shape of smooth underlying phenotype-fitness functions. On the flip side, we see that characterising the genotype-fitness relationship in different systems can be a powerful way to glean phenotypic insights
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Jacques, Adam Matthew. "Hypertrophic and dilated cardiomyopathies, the relationship of genotype to phenotype." Thesis, Imperial College London, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.550457.

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Most familial dilated and hypertrophic cardiomyopathies are caused by mutations in sarcomeric proteins. What remains to be answered is how mutations cause the cardiac phenotype and why mutations in the same protein can cause cardiomyopathies at different ends of the phenotypic spectrum. We collected human myocardium from HCM patients undergoing surgical myectomy, and familial and acquired DCM patients, undergoing cardiac transplantation. Patients were phenotyped before operation and blood taken for genotyping. We used the ProQ Diamond, Western Blot and in vitro motility assays to assess levels of phosphorylation, expression and function respectively of sarcomeric proteins. In HCM patients with myosin binding protein C mutations expression of MyBPC was reduced by 24% in myofilaments arguing strongly for happloinsufficiency as the disease causing mechanism. HCM myosin and MyBPC mutations, also affect cardiac contractility by dominant negative effects. Myosin mutation, Va1606Met, has direct and indirect effects on cardiac contraction. Filament sliding speed was greater and relaxation at pCa9 less complete than with other HCM myosins tested without mutations. The DCM troponin C mutation, Gly159Asp, acts as a poison polypeptide, changing thin filament regulation. Ca2+ -sensitivity of G159D troponin C was independent of the level of troponin phosphorylation. The uncoupling of the relationship between troponin phosphorylation and Ca2+-sensitivity, provides a novel mechanism for initiation of familial DCM. Post-translational modifications in sarcomeric proteins occur independently of genotype. Troponin I is dephosphorylated in DCM and HCM, leading to changes in Ca2+-sensitivity and cross-bridge turnover rate. Also both troponin and myosin from HCM tissue is functionally abnormal and MyBPC phosphorylation is reduced. In acquired heart failure dephosphorylation of Serines 23/24 on troponin I could account for the contractile defect in seen and MyBPC phosphorylation is also decreased. In summary we observed a hypocontractile molecular phenotype in HCM human heart tissue, similar to that seen in heart failure. These findings conflict with the observed clinical phenotype seen in HCM, which is often regarded as a hyperdynamic or hypercontractile state.
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O'Brien, Kirtsy K. "Genotype - phenotype relationships in late onset dementia." Thesis, University of Newcastle Upon Tyne, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.402161.

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Vrcelj, Katarina. "Genotype and phenotype relationships in neurodevelopmental disorders." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:a7a9d22c-c92d-4078-9065-b9a9275c49a9.

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NeuroDevelopmental Disorders (NDDs) are a group of heterogeneous neuropsychiatric conditions, encompassing Developmental Delay (DD), Intellectual Disability (ID), Autism Spectrum Disorder (ASD) and Gilles de la Tourette Syndrome (GTS). NDDs often involve a life-long need of supportive services and represent a major economic and societal burden in Europe and the United States. Hitherto, no safe and effective treatment strategies are available, underpinning the urgency of deciphering their elusive aetiology. NDDs have a strong genetic component. Accordingly, the mechanistic understanding of disease involves (1) the description of mutational landscapes, (2) the molecular and cellular of characterisation of genetic variants and (3) their integration at circuit and system levels. In this thesis, we tackled these theoretical underpinnings to provide insights into the genetics of NDDs and the onset of associated clinical abnormalities. Firstly, aiming to shape the genetic architecture of GTS, a condition characterised by the presence of motor and vocal tics, we undertook a whole-genome CNV study of a cohort of Danish GTS cases and healthy controls. Using statistical and functional genomics approaches, we proposed novel potential candidate genes and implicated the disruption of early neurodevelopmental and late synaptic processes in the aetiology of GTS. Secondly, to elucidate the vast phenotypic heterogeneity of NDDs, we conducted a systematic investigation of genotype and phenotype relationships in DD, ID and ASD. Taking advantage of extensive phenotypic and genetic data available for DD/ID and ASD patients, we grouped individuals based on their functional rare CNV and gene disruptions but did not to identify distinguishing clinical archetypes. Instead, we showed converging molecular perturbations underlie the onset of globally more similar clinical presentations and investigated the role of common variants in modulating their expressivity. Lastly, we established the relevance of mouse models in the study of human disease. By applying comprehensive genomics approaches to over 1,000 mouse neuroanatomical knockouts, we implicated early neurodevelopmental and adult synaptic processes in the aetiology of ID and brain malformations. Furthermore, we showed that functionally converging genetic disturbances translate at the phenotypic level and proposed novel candidate ID genes.
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Squance, Michael Graham. "Computational modelling of the relationship between Miscanthus genotype, phenotype and environment." Thesis, Aberystwyth University, 2014. http://hdl.handle.net/2160/ca10d87a-2e3e-4e35-b156-7bdb80c3efb1.

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Several major global challenges being faced in the 21st century, ranging from climate change, energy security and food security to the sustainable living. Innovative solutions are needed to address those challenges. Miscanthus is a highly productive C4 grass which naturally occurs in Asia with the potential use for as a bioenergy crop. Recent advances in technologies such as genomics, phenomics, bioinformatics and modelling, provide a unique opportunity to accelerate the domestication process of Miscanthus. Modern breeding programmes aim to utilise genetic information to assist in breeding decisions. High-throughput technologies such as genotyping-by-sequencing (GBS) generate massive datasets. Conventional analysis methods cannot handle large multi-dimensional datasets, therefore new methodologies are needed. This research aims to use machine learning to model marker trait association and genotype by environmental interaction on Miscanthus. Three studies were performed in this research: 1) Develop a machine learning based QTL analysis tool to detect QTL on a Miscanthus flowering time mapping population. 2) Conduct marker-trait associations in a GBS analysis. 3) Establish a predictive model to understand drought and thermal effects on flowering time in Miscanthus. The machine learning algorithm, random forest, was used to develop a QTL analysis tool, referred to as RFQTL. RFQTL identified several flowering QTL, with reduced computation time, consistent with conventional QTL analysis. Within the GBS study machine learning detected markers which when aligned with the Sorghum genome several homolog QTLs were found for the traits investigated. Using the prediction model of flowering time we were able to show that drought delays flowering whereas increased temperature led to earlier flowering. This research has demonstrated the power of machine learning as an effective method for marker trait association and genotype by environment modelling. It has great potential to play a crucial role in crop improvement and provide further scientific insights for genetic research.
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Brunklaus, Andreas. "Genotype phenotype relationships in SCN1A related childhood epilepsies." Thesis, University of Glasgow, 2013. http://theses.gla.ac.uk/4518/.

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Most mutations in SCN1A-related epilepsies are novel and when an infant presents with febrile seizures (FS) it is uncertain if they will have simple FS, FS+ or develop a severe epilepsy such as Dravet Syndrome. The main aim of this work has been to translate specific genetic findings in SCN1A related epilepsies not only to the phenotype, but to examine the implications this has on treatment and quality of life in children and their families. Clinical and genetic data were collected from 273 individuals with SCN1A mutations identified in our laboratory between November 2005 and February 2010. I examined whether the mutation class, distribution or nature of amino acid substitution correlated with the epilepsy phenotype, using the Grantham Score (GS) as a measure of physicochemical difference between amino acids. From structured referral data I analysed a range of clinical characteristics including epilepsy phenotype, seizure precipitants, EEG data, imaging studies, mutation class and response to medication and determined predictors of developmental outcome. I developed novel ideas on how to characterise mutations in SCN1A related epilepsies, showing that phenotypes are not determined by chance, but are in part determined by defined physico-chemical changes affecting a specific location in the protein structure. I was able to demonstrate that these principles not only apply to the SCN1A gene but also to the wider voltage gated sodium channel family and related diseases. This study has been the largest to date to systematically examine the prognostic, clinical and demographic features of Dravet syndrome. The overall incidence of Dravet syndrome was found to be at least one in every 28,600 UK births. Clinical features predicting a worse developmental outcome included status epilepticus, interictal EEG abnormalities in the first year of life and a motor disorder. No significant effect was seen for seizure precipitants, MRI abnormalities or mutation class (truncating vs. missense). Sodium valproate, benzodiazepines and topiramate were reported the most helpful medications and aggravation of seizures was reported for carbamazepine and lamotrigine. Health related quality of life (HRQOL) has emerged as a widely accepted measure to evaluate how chronic disease impacts on an individual’s well-being and I examined in detail the comorbidities and predictors of health related quality of life in Dravet syndrome. HRQOL was evaluated with two epilepsy-specific instruments, the Impact of Pediatric Epilepsy Scale (IPES) and the Epilepsy & Learning Disabilities Quality of Life Questionnaire (ELDQOL), a generic HRQOL instrument the Pediatric Quality of Life Inventory (PedsQL) and a behavioural screening tool, the Strength and Difficulties Questionnaire (SDQ). 163 individuals with Dravet syndrome and their families participated in the questionnaire study. HRQOL was significantly lower for children with Dravet syndrome compared to normative data. One third of children had conduct problems and two thirds had hyperactive or inattentive behaviour. Regression analysis revealed that behavioural problems were the strongest predictors of poorer HRQOL. Identification of specific comorbidities will help us to better recognise and understand the needs of children and families with Dravet syndrome and facilitate a distinct multi-disciplinary approach to management. Genetic testing in the epilepsies has become an increasingly accessible clinical tool and this is the first study to assess the impact of SCN1A testing on patient management from both carer and physician perspectives. The vast majority of parents whose children tested positive for a mutation reported genetic testing helpful, leading to treatment changes resulting in fewer seizures, and improved access to therapies and respite care. Nearly half of the physicians reported that a positive test facilitated diagnosis earlier than with clinical and EEG data alone. In two thirds it prevented additional investigations and altered the treatment approach; it influenced medication choice in three quarters of cases and through medication change improved seizure control in forty percent. In addition to confirming a clinical diagnosis, a positive SCN1A test enabled early diagnosis, influenced treatment choice and facilitated improvements in clinical management, especially in the very young. Finally I hope that this work will contribute to a better understanding of the causes of SCN1A related epilepsies. Furthermore I hope that it will provide evidence to aid earlier diagnosis and treatment of children with severe infantile epilepsies and that it will offer more information for genetic counselling. These improvements in epilepsy care and seizure control could help prevent or reduce the disability associated with SCN1A related epilepsies such as learning and behaviour problems and would improve the quality of life for children and families.
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Jeerooburkhan, Noorjahan Bibi. "Phenotype and genotype relationship in nitric oxide and pterin pathways in man." Thesis, University College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269759.

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Harris, Tegan Maree. "B-lactamase-mediated resistance to antimicrobials : the relationship between genotype and phenotype." Thesis, Queensland University of Technology, 2014. https://eprints.qut.edu.au/77835/1/Tegan_Harris_Thesis.pdf.

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This thesis examined the ability to predict the emergence of bacteria resistant to antibiotics using genetic markers in the bacteria. Bacteria containing the genetic markers were able to become resistant to antibiotics, whereas bacteria that did not have the genetic markers remained susceptible. Existing techniques can identify the presence of resistance by looking at the characteristics of the bacteria during growth. However, having the ability to predict antibiotic resistance before it emerges could improve the preservation of currently available antibiotics and minimise treatment failure.
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Hart, Lesley Ruth. "Dissecting the genotype to phenotype relationships of genomic disorders." Thesis, University of Sussex, 2013. http://sro.sussex.ac.uk/id/eprint/47112/.

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Over the last decade, major advances in the development and application of microarray-based comparative genomic hybridisation (aCGH) technology have significantly contributed to our understanding of Genomic Disorders. My aims here were to provide insight into the genotype to phenotype relationships of three Genomic Disorders; CUL4B-deleted X-Linked Mental Retardation (XLMR), Wolf-Hirschhorn Syndrome (WHS) and 16p11.2 Copy Number Variant Disorder. CUL4B encodes a structural component of the Cullin-RING-ligase 4-containing class of E3 ubiquitin ligases. CUL4B-deleted XLMR represents a syndromal form of mental retardation whereby patients exhibit other clinical features aside from the MR, such as seizures, growth retardation and disrupted sexual development. I used CUL4B-deleted patient-derived cell lines to investigate the impacts of CUL4B loss on mitochondrial function. I have shown that loss of CUL4B is associated with a distinct set of mitochondrial phenotypes, identifying CUL4B-deleted XLMR as a disorder associated with mitochondrial dysfunction. Furthermore, I have uncovered a reciprocal relationship between CUL4B and Cereblon, providing evidence of a potential role for the CUL4-CRBN E3 ligase complex in maintaining mitochondrial function. Deletion or duplication of the 16p11.2 region is associated with macro-/microcephaly respectively. Here, I have evaluated the cellular consequences of 16p11.2 CNV, specifically with regards KCTD13 expression, DNA replication and checkpoint activation. WHS is typically caused by a small hemizygous telomeric deletion of the 4p16.1 region. Haploinsufficiency of 4p16.1 is associated with microcephaly, growth retardation and complex developmental abnormalities. I investigated the impacts of LETM1 copy number change in WHS patient-derived cells. Here, I have shown that copy number change of LETM1 specifically segregates with mitochondrial dysfunction, likely underlying the seizure phenotype exhibited by the large subgroup of WHS patients whose deletions incorporate LETM1 as well as the rarer instances of the reciprocal duplication. In this thesis I use patient-derived cell lines from three Genomic Disorders as a fundamental tool providing new pathomechanistic insight into the clinical presentation of these conditions.
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Hartman, Deirdre. "Investigation of Genotype-Phenotype relationships of sodium control mechanisms in hypertension." Thesis, St George's, University of London, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.498075.

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Books on the topic "Genotype and Phenotype Relationship"

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Cummings, Jeffrey L., Michel Poncet, John Hardy, and Yves Christen, eds. Genotype — Proteotype — Phenotype Relationships in Neurodegenerative Diseases. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/b137738.

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Zielonka, Stefan, and Simon Krah, eds. Genotype Phenotype Coupling. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-4939-9853-1.

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Sue, Malcolm, and Goodship Timothy H. J, eds. Genotype to phenotype. 2nd ed. Oxford: BIOS Scientific, 2001.

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Pontarotti, Pierre, ed. Evolutionary Biology: Biodiversification from Genotype to Phenotype. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-19932-0.

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Dr, Cooper David N., and Upadhyaya M, eds. Neurofibromatosis type 1: From genotype to phenotype. Oxford: Bios Scientific, 1998.

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Hallgrímsson, Benedikt. Epigenetics: Linking genotype and phenotype in development and evolution. Berkeley: University of California Press, 2011.

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1941-, Hall Brian Keith, ed. Epigenetics: Linking genotype and phenotype in development and evolution. Berkeley: University of California Press, 2010.

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Soravia, Claudio. Genotype-phenotype correlative studies in familial colorectal cancer predisposition syndromes. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1999.

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Phillips, Lesley. The distribution of phenotypic and genotypic characters within streptomycetes and their relationship to antibioticproduction. [s.l.]: typescript, 1992.

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The Dependent Gene: The Fallacy of "Nature vs. Nurture". New York: A W. H. Freeman book, Times Books, Henry Holt and Co., 2002.

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Book chapters on the topic "Genotype and Phenotype Relationship"

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Allen, Emily G., Maureen A. Leehey, Flora Tassone, and Stephanie Sherman. "Genotype/Phenotype Relationships in FXTAS." In FXTAS, FXPOI, and Other Premutation Disorders, 129–60. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-33898-9_7.

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Allen, Emily, Maureen A. Leehey, Flora Tassone, and Stephanie Sherman. "Genotype/Phenotype Relationships in FXTAS." In The Fragile X-Associated Tremor Ataxia Syndrome (FXTAS), 95–122. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-5805-1_7.

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Graff-Radford, Neill R. "Presenilin Mutations: Variations in the Behavioral Phenotype with an Emphasis on the Frontotemporal Dementia Phenotype." In Genotype — Proteotype — Phenotype Relationships in Neurodegenerative Diseases, 93–101. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/3-540-26522-8_8.

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Karlstrom, Helena, William S. Brooks, John B. J. Kwok, Jillian J. Kril, Glenda M. Halliday, and Peter R. Schofield. "Variable Phenotype of Alzheimer's Disease with Spastic Paraparesis." In Genotype — Proteotype — Phenotype Relationships in Neurodegenerative Diseases, 73–92. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/3-540-26522-8_7.

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Cummings, Jeffrey L. "Neurodegenerative Disorders as Proteinopathies: Phenotypic Relationships." In Genotype — Proteotype — Phenotype Relationships in Neurodegenerative Diseases, 1–10. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/3-540-26522-8_1.

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Rademakers, Rosa, Julie van der Zee, Samir Kumar-Singh, Bart Dermaut, Marc Cruts, and Christine Van Broeckhoven. "Chromosome 17-linked Frontotemporal dementia with Ubiquitin-Positive, Tau-Negative Inclusions." In Genotype — Proteotype — Phenotype Relationships in Neurodegenerative Diseases, 117–37. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/3-540-26522-8_10.

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Hardy, John. "Towards a Molecular Classification of Neurodegenerative Disease." In Genotype — Proteotype — Phenotype Relationships in Neurodegenerative Diseases, 11–23. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/3-540-26522-8_2.

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Gwinn-Hardy, Katrina. "Racial and Ethnic Influences on the Expression of the Genotype in Neurodegenerative Diseases." In Genotype — Proteotype — Phenotype Relationships in Neurodegenerative Diseases, 25–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/3-540-26522-8_3.

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Praticò, Domenico. "Causes and Consequences of Oxidative Stress in Neurodegenerative Diseases." In Genotype — Proteotype — Phenotype Relationships in Neurodegenerative Diseases, 37–44. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/3-540-26522-8_4.

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Galasko, Douglas. "Early Onset Familial Alzheimer's Disease: Is a Mutation Predictive of Pathology?" In Genotype — Proteotype — Phenotype Relationships in Neurodegenerative Diseases, 45–59. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/3-540-26522-8_5.

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Conference papers on the topic "Genotype and Phenotype Relationship"

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Muller-Quernheim, J., J. C. Schupp, S. Freitag-Wolf, B. Frye, G. Zissel, C. Grohé, V. Mihailovic-Vucinic, et al. "Genotype-Phenotype-Relationships in Sarcoidosis." In American Thoracic Society 2022 International Conference, May 13-18, 2022 - San Francisco, CA. American Thoracic Society, 2022. http://dx.doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4880.

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Darabos, Christian, Britney E. Graham, Ting Hu, and Jason H. Moore. "Bipartite networks to study the genotype-to-phenotype relationship in cellular automata models." In Proceeding of the fifteenth annual conference companion. New York, New York, USA: ACM Press, 2013. http://dx.doi.org/10.1145/2464576.2480789.

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Loubani, M., M. Müller, D. J. Backhoff, T. Paul, and U. Krause. "Clinical Course of Patients with Long-QT Syndrome: Is There a Genotype–Phenotype Relationship?" In 52nd Annual Meeting of the German Society for Pediatric Cardiology. Georg Thieme Verlag KG, 2020. http://dx.doi.org/10.1055/s-0040-1705546.

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COHEN, K. BRETONNEL, YAEL GARTEN, NIGAM SHAH, and UDO HAHN. "TEXT AND KNOWLEDGE MINING FOR PHARMACOGENOMICS: GENOTYPE-PHENOTYPE-DRUG RELATIONSHIPS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2011. http://dx.doi.org/10.1142/9789814366496_0036.

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Sahni, Nidhi, and Song Yi. "Abstract 5555: Integrative network variomics reveals complex genotype to phenotype relationships in cancer." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-5555.

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Horani, A., J. PAN, J. Xu, and S. L. Brody. "Modeling Genotype-Phenotype Relationships in Primary Ciliary Dyskinesia Using CRISPR Gene Editing in Mice." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a7663.

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Rubbo, B., A. Shoemark, M. Legendre, M. Fassad, E. Haarman, S. Best, I. C. M. Bon, et al. "Topological Data Analysis Coupled with Machine Learning Reveals New Genotype-Phenotype Relationships in Primary Ciliary Dyskinesia." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a5691.

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Darabos, Christian, Britney Graham, Ting Hu, and Jason Moore. "Bipartite Networks Show the Genotype-to-Phenotype Relationship in Biological Systems Models: A Study of the Robustness, Evolvability, and Accessibility in Linear Cellular Automata." In European Conference on Artificial Life 2013. MIT Press, 2013. http://dx.doi.org/10.7551/978-0-262-31709-2-ch051.

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Otter, Tim. "Genotype, phenotype and ontogeny." In the 2005 workshops. New York, New York, USA: ACM Press, 2005. http://dx.doi.org/10.1145/1102256.1102323.

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Moreno, Matthew Andres, Wolfgang Banzhaf, and Charles Ofria. "Learning an evolvable genotype-phenotype mapping." In GECCO '18: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2018. http://dx.doi.org/10.1145/3205455.3205597.

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Reports on the topic "Genotype and Phenotype Relationship"

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Nowell, Susan A. Sulfotransferase 1A1 (SULT1A1) Genotype and Phenotype in Relation to Efficacy of Tamoxifen Treatment. Fort Belvoir, VA: Defense Technical Information Center, November 2003. http://dx.doi.org/10.21236/ada421960.

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Paterson, Andrew H., Yehoshua Saranga, and Dan Yakir. Improving Productivity of Cotton (Gossypsum spp.) in Arid Region Agriculture: An Integrated Physiological/Genetic Approach. United States Department of Agriculture, December 1999. http://dx.doi.org/10.32747/1999.7573066.bard.

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Objectives: We seek to establish the basis for improving cotton productivity under arid conditions, by studying the water use efficiency - evaporative cooling interrelationship. Specifically, we will test the hypothesis that cotton productivity under arid conditions can be improved by combining high seasonal WUE with efficient evaporative cooling, evaluate whether high WUE and/or evaporative cooling are based on specific physiological factors such as diurnal flexibility in stomatal conductance, stomatal density, photosynthetic capacity, chlorophyll fluorescence, and plant water status. Genes influencing both WUE and evaporative cooling, as well as other parameters such as economic products (lint yield, quality, harvest index) of cotton will also be mapped, in order to evaluate influences of water relations on these parameters. Approach: Carbon isotope ratio will be used to evaluate WUE, accompanied by additional parameters to elucidate the relationship between WUE, evaporative cooling, and cotton productivity. A detailed RFLP map will be used to determine the number, location, and phenotypic effects of genes underlying genetic variation in WUE between cultivated cottons, as well as test associations of these genes with traits of economic importance such as harvest index, lint yield, and lint quality. Major Conclusions: Productivity and quality of cotton grown under well-watered versus water-limited conditions was shown to be partly accounted for by different quantitative trait loci (QTLs). Among a suite of physiological traits often found to differ between genotypes adapted to arid versus well-watered conditions, genetic mapping implicated only reduced plant osmotic potential in improved cotton productivity under arid conditions. Our findings clearly implicate OP as a major component of cotton adaptation to arid conditions. However, testing of further physiological hypotheses is clearly needed to account for additional QTL alleles conferring higher seed-cotton yield under arid conditions, such as three of the five we found. Near-isogenic lines being made for QTLs discovered herein will offer a powerful new tool useful toward identification of the underlying gene(s) by using fine-scale mapping approaches (Paterson et al 1990). Implications: Adaptation to both arid and favorable conditions can be combined into the same genotype. We have identified diagnostic DNA markers that are being applied to creation of such desirable genotypes. Simultaneous improvement of productivity (and/or quality) for both arid and irrigated conditions will require more extensive field testing and the manipulation of larger numbers of genes, reducing the expected rate of genetic gain These difficulties may be at least partly ameliorated by efficiencies gained through identification and use of diagnostic DNA markers. Genomic tools and approaches may expedite adaptation of crops to arid cultivation, help to test roles of additional physiological factors, and guide the isolation of the underlying genes that protect crop performance under arid conditions.
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D'haeseleer, P. FY07 LDRD Final Report Comparative Analysis of Genome Composition with Respect to Genotype-to-Phenotype Mapping and Metabolic Capability. Office of Scientific and Technical Information (OSTI), February 2008. http://dx.doi.org/10.2172/926416.

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Hovav, Ran, Peggy Ozias-Akins, and Scott A. Jackson. The genetics of pod-filling in peanut under water-limiting conditions. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597923.bard.

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Pod-filling, an important yield-determining stage is strongly influenced by water stress. This is particularly true for peanut (Arachishypogaea), wherein pods are developed underground and are directly affected by the water condition. Pod-filling in peanut has a significant genetic component as well, since genotypes are considerably varied in their pod-fill (PF) and seed-fill (SF) potential. The goals of this research were to: Examine the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Detect global changes in mRNA and metabolites levels that accompany PF and SF. Explore the response of the duplicate peanut pod transcriptome to drought stress. Study how entire duplicated PF regulatory processes are networked within a polyploid organism. Discover locus-specific SNP markers and map pod quality traits under different environments. The research included genotypes and segregating populations from Israel and US that are varied in PF, SF and their tolerance to water deficit. Initially, an extensive field trial was conducted to investigate the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Significant irrigation and genotypic effect was observed for the two main PF related traits, "seed ratio" and "dead-end ratio", demonstrating that reduction in irrigation directly influences the developing pods as a result of low water potential. Although the Irrigation × Genotype interaction was not statistically significant, one genotype (line 53) was found to be more sensitive to low irrigation treatments. Two RNAseq studies were simultaneously conducted in IL and the USA to characterize expression changes that accompany shell ("source") and seed ("sink") biogenesis in peanut. Both studies showed that SF and PF processes are very dynamic and undergo very rapid change in the accumulation of RNA, nutrients, and oil. Some genotypes differ in transcript accumulation rates, which can explain their difference in SF and PF potential; like cvHanoch that was found to be more enriched than line 53 in processes involving the generation of metabolites and energy at the beginning of seed development. Interestingly, an opposite situation was found in pericarp development, wherein rapid cell wall maturation processes were up-regulated in line 53. Although no significant effect was found for the irrigation level on seed transcriptome in general, and particularly on subgenomic assignment (that was found almost comparable to a 1:1 for A- and B- subgenomes), more specific homoeologous expression changes associated with particular biosynthesis pathways were found. For example, some significant A- and B- biases were observed in particular parts of the oil related gene expression network and several candidate genes with potential influence on oil content and SF were further examined. Substation achievement of the current program was the development and application of new SNP detection and mapping methods for peanut. Two major efforts on this direction were performed. In IL, a GBS approach was developed to map pod quality traits on Hanoch X 53 F2/F3 generations. Although the GBS approach was found to be less effective for our genetic system, it still succeeded to find significant mapping locations for several traits like testa color (linkage A10), number of seeds/pods (A5) and pod wart resistance (B7). In the USA, a SNP array was developed and applied for peanut, which is based on whole genome re-sequencing of 20 genotypes. This chip was used to map pod quality related traits in a Tifrunner x NC3033 RIL population. It was phenotyped for three years, including a new x-ray method to phenotype seed-fill and seed density. The total map size was 1229.7 cM with 1320 markers assigned. Based on this linkage map, 21 QTLs were identified for the traits 16/64 weight, kernel percentage, seed and pod weight, double pod and pod area. Collectively, this research serves as the first fundamental effort in peanut for understanding the PF and SF components, as a whole, and as influenced by the irrigation level. Results of the proposed study will also generate information and materials that will benefit peanut breeding by facilitating selection for reduced linkage drag during introgression of disease resistance traits into elite cultivars. BARD Report - Project4540 Page 2 of 10
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Valverde, Rodrigo A., Aviv Dombrovsky, and Noa Sela. Interactions between Bell pepper endornavirus and acute viruses in bell pepper and effect to the host. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598166.bard.

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Based on the type of relationship with the host, plant viruses can be grouped as acute or persistent. Acute viruses are well studied and cause disease. In contrast, persistent viruses do not appear to affect the phenotype of the host. The genus Endornavirus contains persistent viruses that infect plants without causing visible symptoms. Infections by endornaviruses have been reported in many economically important crops, such as avocado, barley, common bean, melon, pepper, and rice. However, little is known about the effect they have on their plant hosts. The long term objective of the proposed project is to elucidate the nature of the symbiotic interaction between Bell pepper endornavirus (BPEV) and its host. The specific objectives include: a) to evaluate the phenotype and fruit yield of endornavirus-free and endornavirus-infected bell pepper near-isogenic lines under greenhouse conditions; b) to conduct gene expression studies using endornavirus-free and endornavirus-infected bell pepper near-isogenic lines; and c) to study the interactions between acute viruses, Cucumber mosaic virus Potato virus Y, Pepper yellow leaf curl virus, and Tobacco etch virus and Bell pepper endornavirus. It is likely that BPEV in bell pepper is in a mutualistic relationship with the plant and provide protection to unknown biotic or abiotic agents. Nevertheless, it is also possible that the endornavirus could interact synergistically with acute viruses and indirectly or directly cause harmful effects. In any case, the information that will be obtained with this investigation is relevant to BARD’s mission since it is related to the protection of plants against biotic stresses.
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Hunter, Martha S., and Einat Zchori-Fein. Rickettsia in the whitefly Bemisia tabaci: Phenotypic variants and fitness effects. United States Department of Agriculture, September 2014. http://dx.doi.org/10.32747/2014.7594394.bard.

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The sweet potato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae) is a major pest of vegetables, field crops, and ornamentals worldwide. This species harbors a diverse assembly of facultative, “secondary” bacterial symbionts, the roles of which are largely unknown. We documented a spectacular sweep of one of these, Rickettsia, in the Southwestern United States in the B biotype (=MEAM1) of B. tabaci, from 1% to 97% over 6 years, as well as a dramatic fitness benefit associated with it in Arizona but not in Israel. Because it is critical to understand the circumstances in which a symbiont invasion can cause such a large change in pest life history, the following objectives were set: 1) Determine the frequency of Rickettsia in B. tabaci in cotton across the United States and Israel. 2) Characterize Rickettsia and B. tabaci genotypes in order to test the hypothesis that genetic variation in either partner is responsible for differences in phenotypes seen in the two countries. 3) Determine the comparative fitness effects of Rickettsia phenotypes in B. tabaci in Israel and the United States. For Obj. 1, a survey of B. tabaci B samples revealed the distribution of Rickettsia across the cotton-growing regions of 13 sites from Israel and 22 sites from the USA. Across the USA, Rickettsia frequencies were heterogeneous among regions, but were generally at frequencies higher than 75% and close to fixation in some areas, whereas in Israel the infection rates were lower and declining. The distinct outcomes of Rickettsia infection in these two countries conform to previouslyreported phenotypic differences. Intermediate frequencies in some areas in both countries may indicate a cost to infection in certain environments or that the frequencies are in flux. This suggests underlying geographic differences in the interactions between bacterial symbionts and the pest. Obj. 2, Sequences of several Rickettsia genes in both locations, including a hypervariableintergenic spacer gene, suggested that the Rickettsia genotype is identical in both countries. Experiments in the US showed that differences in whitefly nuclear genotype had a strong influence on Rickettsia phenotype. Obj. 3. Experiments designed to test for possible horizontal transmission of Rickettsia, showed that these bacteria are transferred from B. tabaci to a plant, moved inside the phloem, and could be acquired by other whiteflies. Plants can serve as a reservoir for horizontal transmission of Rickettsia, a mechanism that may explain the occurrence of phylogenetically-similarsymbionts among unrelated phytophagous insect species. This plant-mediated transmission route may also exist in other insect-symbiont systems, and since symbionts may play a critical role in the ecology and evolution of their hosts, serve as an immediate and powerful tool for accelerated evolution. However, no such horizontal transmission of Rickettsia could be detected in the USA, underlining the difference between the interaction in both countries, or between B. tabaci and the banded wing whitefly on cotton in the USA (Trialeurodes sp. nr. abutiloneus) and the omnivorous bug Nesidiocoristenuis. Additionally, a series of experiments excluded the possibility that Rickettsia is frequently transmitted between B. tabaci and its parasitoid wasps Eretmocerusmundus and Encarsiapergandiella. Lastly, ecological studies on Rickettsia effects on free flight of whiteflies showed no significant influence of symbiont infection on flight. In contrast, a field study of the effects of Rickettsia on whitefly performance on caged cotton in the USA showed strong fitness benefits of infection, and rapid increases in Rickettsia frequency in competition population cages. This result confirmed the benefits to whiteflies of Rickettsia infection in a field setting.
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Blum, Abraham, and Henry T. Nguyen. Molecular Tagging of Drought Resistance in Wheat: Osmotic Adjustment and Plant Productivity. United States Department of Agriculture, November 2002. http://dx.doi.org/10.32747/2002.7580672.bard.

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Drought stress is a major limitation to bread wheat (Triticumaestivum L.) productivity and its yield stability in arid and semi-arid regions of world including parts of Israel and the U.S. Currently, breeding for sustained yields under drought stress is totally dependent on the use of yield and several key physiological attributes as selection indices. The attempt to identify the optimal genotype by evaluating the phenotype is undermining progress in such breeding programs. Osmotic adjustment (OA) is an effective drought resistance mechanism in many crop plants. Evidence exists that there is a genetic variation for OA in wheat and that high OA capacity supports wheat yields under drought stress. The major objective of this research was to identify molecular markers (RFLPs, restriction fragment length polymorphisms; and AFLPs, amplified fragment length polymorph isms) linked to OA as a major attribute of drought resistance in wheat and thus to facilitate marker-assisted selection for drought resistance. We identified high and low OA lines of wheat and from their cross developed recombinant inbred lines (RILs) used in the molecular tagging of OA in relation to drought resistance in terms of plant production under stress. The significant positive co-segregation of OA, plant water status and yield under stress in this RIL population provided strong support for the important role of OA as a drought resistance mechanism sustaining wheat production under drought stress. This evidence was obtained in addition to the initial study of parental materials for constructing this RIL population, which also gave evidence for a strong correlation between OA and grain yield under stress. This research therefore provides conclusive evidence on the important role of OA in sustaining wheat yield under drought stress. The measurement of OA is difficult and the selection for drought resistance by the phenotypic expression of OA is practically impossible. This research provided information on the genetic basis of OA in wheat in relations to yield under stress. It provided the basic information to indicate that molecular marker assisted selection for OA in wheat is possible. The RIL population has been created by a cross between two agronomic spring wheat lines and the high OA recombinants in this population presented very high OA values, not commonly observed in wheat. These recombinants are therefore an immediate valuable genetic recourse for breeding well-adapted drought resistant wheat in Texas and Israel. We feel that this work taken as a whole eliminate the few previous speculated . doubts about the practical role of OA as an important mechanism of drought resistance in economic crop plants. As such it should open the way, in terms of both concept and the use of marker assisted selection, for improving drought resistance in wheat by deploying high osmotic adjustment.
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Mizrahi, Itzhak, and Bryan A. White. Uncovering rumen microbiome components shaping feed efficiency in dairy cows. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600020.bard.

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Ruminants provide human society with high quality food from non-human-edible resources, but their emissions negatively impact the environment via greenhouse gas production. The rumen and its resident microorganisms dictate both processes. The overall goal of this project was to determine whether a causal relationship exists between the rumen microbiome and the host animal's physiology, and if so, to isolate and examine the specific determinants that enable this causality. To this end, we divided the project into three specific parts: (1) determining the feed efficiency of 200 milking cows, (2) determining whether the feed- efficiency phenotype can be transferred by transplantation and (3) isolating and examining microbial consortia that can affect the feed-efficiency phenotype by their transplantation into germ-free ruminants. We finally included 1000 dairy cow metadata in our study that revealed a global core microbiome present in the rumen whose composition and abundance predicted many of the cows’ production phenotypes, including methane emission. Certain members of the core microbiome are heritable and have strong associations to cardinal rumen metabolites and fermentation products that govern the efficiency of milk production. These heritable core microbes therefore present primary targets for rumen manipulation towards sustainable and environmentally friendly agriculture. We then went beyond examining the metagenomic content, and asked whether microbes behave differently with relation to the host efficiency state. We sampled twelve animals with two extreme efficiency phenotypes, high efficiency and low efficiency where the first represents animals that maximize energy utilization from their feed whilst the later represents animals with very low utilization of the energy from their feed. Our analysis revealed differences in two host efficiency states in terms of the microbial expression profiles both with regards to protein identities and quantities. Another aim of the proposal was the cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of the cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort. In the context of the grant, the establishment of ruminant germ-free facility was possible and preliminary experiments were successful, which open up the way for direct applications of the new concepts discovered here, prior to the larger scale implementation at the agricultural level.
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Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597925.bard.

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Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.
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Sionov, Edward, Nancy Keller, and Shiri Barad-Kotler. Mechanisms governing the global regulation of mycotoxin production and pathogenicity by Penicillium expansum in postharvest fruits. United States Department of Agriculture, January 2017. http://dx.doi.org/10.32747/2017.7604292.bard.

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The original objectives of the study, as defined in the approved proposal, are: To characterize the relationship of CreA and LaeA in regulation of P T production To understand how PacC modulates P. expansumpathogenicity on apples To examine if other secondary metabolites are involved in virulence or P. expansumfitness To identify the signaling pathways leading to PAT synthesis Penicilliumexpansum, the causal agent of blue mould rot, is a critical health concern because of the production of the mycotoxinpatulin (PAT) in colonized apple fruit tissue. Although PAT is produced by many Penicilliumspecies, the factors activating its biosynthesis were not clear. This research focused on host and fungal mechanisms of activation of LaeA (the global regulator of secondary metabolism), PacC (the global pH modulator) and CreA (the global carbon catabolite regulator) on PAT synthesis with intention to establish P. expansumas the model system for understanding mycotoxin synthesis in fruits. The overall goal of this proposal is to identify critical host and pathogen factors that mechanistically modulate P. expansumgenes and pathways to control activation of PAT production and virulence in host. Several fungal factors have been correlated with disease development in apples, including the production of PAT, acidification of apple tissue by the fungus, sugar content and the global regulator of secondary metabolism and development, LaeA. An increase in sucrose molarity in the culture medium from 15 to 175 mM negatively regulated laeAexpression and PAT accumulation, but, conversely, increased creAexpression, leading to the hypothesis that CreA could be involved in P. expansumPAT biosynthesis and virulence, possibly through the negative regulation of LaeA. We found evidence for CreAtranscriptional regulation of laeA, but this was not correlated with PAT production either in vitro or in vivo, thus suggesting that CreA regulation of PAT is independent of LaeA. Our finding that sucrose, a key ingredient of apple fruit, regulates PAT synthesis, probably through suppression of laeAexpression, suggests a potential interaction between CreA and LaeA, which may offer control therapies for future study. We have also identified that in addition to PAT gene cluster, CreA regulates other secondary metabolite clusters, including citrinin, andrastin, roquefortine and communesins, during pathogenesis or during normal fungal growth. Following creation of P. expansumpacCknockout strain, we investigated the involvement of the global pH regulator PacC in fungal pathogenicity. We demonstrated that disruption of the pH signaling transcription factor PacC significantly decreased the virulence of P. expansumon deciduous fruits. This phenotype is associated with an impairment in fungal growth, decreased accumulation of gluconic acid and reduced synthesis of pectolytic enzymes. We showed that glucose oxidase- encoding gene, which is essential for gluconic acid production and acidification during fruit colonization, was significantly down regulated in the ΔPepacCmutant, suggesting that gox is PacC- responsive gene. We have provided evidence that deletion of goxgene in P. expansumled to a reduction in virulence toward apple fruits, further indicating that GOX is a virulence factor of P. expansum, and its expression is regulated by PacC. It is also clear from the present data that PacC in P. expansumis a key factor for the biosynthesis of secondary metabolites, such as PAT. On the basis of RNA-sequencing (RNA-seq) analysis and physiological experimentation, the P. expansumΔlaeA, ΔcreAand ΔpacCmutants were unable to successfully colonize apples for a multitude of potential mechanisms including, on the pathogen side, a decreased ability to produce proteolytic enzymes and to acidify the environment and impaired carbon/nitrogen metabolism and, on the host side, an increase in the oxidative defence pathways. Our study defines these global regulatory factors and their downstream signalling pathways as promising targets for the development of strategies to fight against this post-harvest pathogen.
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