Relevant bibliographies by topics / Genomic Wide Association Study (GWAS)

Academic literature on the topic 'Genomic Wide Association Study (GWAS)'

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Published: 9 March 2023

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Journal articles on the topic "Genomic Wide Association Study (GWAS)"

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Shaffer, J. R., E. Feingold, and M. L. Marazita. "Genome-wide Association Studies." Journal of Dental Research 91, no. 7 (May 4, 2012): 637–41. http://dx.doi.org/10.1177/0022034512446968.

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The genomic era of biomedical research has given rise to the genome-wide association study (GWAS) approach, which attempts to discover novel genes affecting an outcome by testing a large number ( i.e., hundreds of thousands to millions) of genetic variants for association. This article discusses the issues surrounding the GWAS approach with emphasis on the prospects and challenges relevant to the oral health research community.
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Wolking, Stefan, Herbert Schulz, Anne T. Nies, Mark McCormack, Elke Schaeffeler, Pauls Auce, Andreja Avbersek, et al. "Pharmacoresponse in genetic generalized epilepsy: a genome-wide association study." Pharmacogenomics 21, no. 5 (April 2020): 325–35. http://dx.doi.org/10.2217/pgs-2019-0179.

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Aim: Pharmacoresistance is a major burden in epilepsy treatment. We aimed to identify genetic biomarkers in response to specific antiepileptic drugs (AEDs) in genetic generalized epilepsies (GGE). Materials & methods: We conducted a genome-wide association study (GWAS) of 3.3 million autosomal SNPs in 893 European subjects with GGE – responsive or nonresponsive to lamotrigine, levetiracetam and valproic acid. Results: Our GWAS of AED response revealed suggestive evidence for association at 29 genomic loci (p <10-5) but no significant association reflecting its limited power. The suggestive associations highlight candidate genes that are implicated in epileptogenesis and neurodevelopment. Conclusion: This first GWAS of AED response in GGE provides a comprehensive reference of SNP associations for hypothesis-driven candidate gene analyses in upcoming pharmacogenetic studies.
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Xiaopeng, Song, Feng Jie, Cui Zixia, Zhang Chuanliang, and Sun Daojie. "Genome-wide association study for anther length in some elite bread wheat germplasm." Czech Journal of Genetics and Plant Breeding 54, No. 3 (September 5, 2018): 109–14. http://dx.doi.org/10.17221/70/2017-cjgpb.

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The anther is a crucial organ for the development of the spike in bread wheat (Triticum aestivum L.). Long anthers contain large amounts of pollen grains; thus, they are favourable for cross-pollination and increase resilience against adverse environmental conditions. We conducted a genome-wide association study (GWAS) of anther length in 305 elite wheat lines evaluated during 2013–2015 in two locations and two growing seasons. The mapping panel was genotyped using a high-density Illumina iSelect 90K single nucleotide polymorphism (SNP) array. The GWAS used 18763 SNPs and identified 17 markers associated with anther length in wheat. The loci were mainly distributed across the chromosomes 3A, 3B and 7B. Further studies are required to determine if these are candidate genomic regions of anther length. In addition, anther length had high heritability, and positive correlations between anther length and grain weight per spike were observed.
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Mei, Hao, Lianna Li, Fan Jiang, Jeannette Simino, Michael Griswold, Thomas Mosley, and Shijian Liu. "snpGeneSets: An R Package for Genome-Wide Study Annotation." G3 Genes|Genomes|Genetics 6, no. 12 (December 1, 2016): 4087–95. http://dx.doi.org/10.1534/g3.116.034694.

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Abstract Genome-wide studies (GWS) of SNP associations and differential gene expressions have generated abundant results; next-generation sequencing technology has further boosted the number of variants and genes identified. Effective interpretation requires massive annotation and downstream analysis of these genome-wide results, a computationally challenging task. We developed the snpGeneSets package to simplify annotation and analysis of GWS results. Our package integrates local copies of knowledge bases for SNPs, genes, and gene sets, and implements wrapper functions in the R language to enable transparent access to low-level databases for efficient annotation of large genomic data. The package contains functions that execute three types of annotations: (1) genomic mapping annotation for SNPs and genes and functional annotation for gene sets; (2) bidirectional mapping between SNPs and genes, and genes and gene sets; and (3) calculation of gene effect measures from SNP associations and performance of gene set enrichment analyses to identify functional pathways. We applied snpGeneSets to type 2 diabetes (T2D) results from the NHGRI genome-wide association study (GWAS) catalog, a Finnish GWAS, and a genome-wide expression study (GWES). These studies demonstrate the usefulness of snpGeneSets for annotating and performing enrichment analysis of GWS results. The package is open-source, free, and can be downloaded at: https://www.umc.edu/biostats_software/.
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Krivoruchko, Alexander, Olesya Yatsyk, Anastasiya Kanibolockaya, and Valery Kulintsev. "Genome-wide association study (GWAS) of high productivity classes in the Karachaevsky sheep breed." Journal of Central European Agriculture 22, no. 4 (2021): 669–77. http://dx.doi.org/10.5513/jcea01/22.4.3238.

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Liu, Nana, Jiayuan Xu, Huaigui Liu, Shijie Zhang, Miaoxin Li, Yao Zhou, Wen Qin, Mulin Jun Li, and Chunshui Yu. "Hippocampal transcriptome-wide association study and neurobiological pathway analysis for Alzheimer’s disease." PLOS Genetics 17, no. 2 (February 25, 2021): e1009363. http://dx.doi.org/10.1371/journal.pgen.1009363.

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Genome-wide association studies (GWASs) have identified multiple susceptibility loci for Alzheimer’s disease (AD), which is characterized by early and progressive damage to the hippocampus. However, the association of hippocampal gene expression with AD and the underlying neurobiological pathways remain largely unknown. Based on the genomic and transcriptomic data of 111 hippocampal samples and the summary data of two large-scale meta-analyses of GWASs, a transcriptome-wide association study (TWAS) was performed to identify genes with significant associations between hippocampal expression and AD. We identified 54 significantly associated genes using an AD-GWAS meta-analysis of 455,258 individuals; 36 of the genes were confirmed in another AD-GWAS meta-analysis of 63,926 individuals. Fine-mapping models further prioritized 24 AD-related genes whose effects on AD were mediated by hippocampal expression, including APOE and two novel genes (PTPN9 and PCDHA4). These genes are functionally related to amyloid-beta formation, phosphorylation/dephosphorylation, neuronal apoptosis, neurogenesis and telomerase-related processes. By integrating the predicted hippocampal expression and neuroimaging data, we found that the hippocampal expression of QPCTL and ERCC2 showed significant difference between AD patients and cognitively normal elderly individuals as well as correlated with hippocampal volume. Mediation analysis further demonstrated that hippocampal volume mediated the effect of hippocampal gene expression (QPCTL and ERCC2) on AD. This study identifies two novel genes associated with AD by integrating hippocampal gene expression and genome-wide association data and reveals candidate hippocampus-mediated neurobiological pathways from gene expression to AD.
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Nakagawa, Hidewaki. "Prostate cancer genomics by high-throughput technologies: genome-wide association study and sequencing analysis." Endocrine-Related Cancer 20, no. 4 (April 26, 2013): R171—R181. http://dx.doi.org/10.1530/erc-13-0113.

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Prostate cancer (PC) is the most common malignancy in males. It is evident that genetic factors at both germline and somatic levels play critical roles in prostate carcinogenesis. Recently, genome-wide association studies (GWAS) by high-throughput genotyping technology have identified more than 70 germline variants of various genes or chromosome loci that are significantly associated with PC susceptibility. They include multiple 8q24 loci, prostate-specific genes, and metabolism-related genes. Somatic alterations in PC genomes have been explored by high-throughput sequencing technologies such as whole-genome sequencing and RNA sequencing, which have identified a variety of androgen-responsive events and fusion transcripts represented by E26 transformation-specific (ETS) gene fusions. Recent innovations in high-throughput genomic technologies have enabled us to analyze PC genomics more comprehensively, more precisely, and on a larger scale in multiple ethnic groups to increase our understanding of PC genomics and biology in germline and somatic studies, which can ultimately lead to personalized medicine for PC diagnosis, prevention, and therapy. However, these data indicate that the PC genome is more complex and heterogeneous than we expected from GWAS and sequencing analyses.
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Yin, Ruimin, Binbin Song, Jingjing Wang, Chaodan Shao, Yufen Xu, and HongGang Jiang. "Genome-Wide Association and Transcriptome-Wide Association Studies Identify Novel Susceptibility Genes Contributing to Colorectal Cancer." Journal of Immunology Research 2022 (July 1, 2022): 1–14. http://dx.doi.org/10.1155/2022/5794055.

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Background. Colorectal cancer (CRC) is among the most common cancers diagnosed worldwide. Although genome-wide association studies have effectively identified the genetic basis of CRC, there is still unexplained variability in genetic risk. Transcriptome-wide association studies (TWAS) integrate summary statistics from CRC genome-wide association studies (GWAS) with gene expression data to prioritize these GWAS findings and uncover additional gene-trait correlations. Methods. First, we carried out a post-GWAS analysis using summary statistics from a large-scale GWAS of CRC ( n = 4,562 cases, n = 382,756 controls). Second, combined with the expression weight sets from GTEx (v7), susceptibility genes were identified with the FUSION software. Colocalization, conditional and fine-mapping analyses, phenome-wide association study (pheWAS), and Mendelian randomization were employed to further characterize the observed correlations. Results. In the post-GWAS analyses, we first identified new genome-wide significant associations: three genomic risk loci were identified at 8q24.21 (rs6983267, P = 6.98 × 10 − 12 ), 15q13.3 (rs58658771, P = 1.40 × 10 − 10 ), and 18q21.1 (rs6507874, P = 1.91 × 10 − 14 ). In addition, the TWAS also identified four loci statistically significantly associated with CRC risk, largely explained by expression regulation, including six candidate genes (DUSP10, POU5F1B, C11orf53, COLCA1, COLCA2, and GREM1-AS1). We further discovered evidence that low expression of COLCA2 is correlated with CRC risk with Mendelian randomization. Conclusions. We discovered novel CRC risk loci and candidate functional genes by merging gene expression and GWAS summary data, offering new insight into the molecular processes underlying CRC development. This makes it easier to prioritize potential genes for follow-up functional research in CRC.
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Dwiningsih, S.Si., M.Si., Ph.D, Yheni. "Genome-Wide Association Study of Complex Traits in Maize Detects Genomic Regions and Genes for Increasing Grain Yield and Grain Quality." Advance Sustainable Science Engineering and Technology 4, no. 2 (November 6, 2022): 0220209. http://dx.doi.org/10.26877/asset.v4i2.12678.

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This review describes the current status of genome-wide association study (GWAS) of the major crops in maize (Zea mays L.) concentrate on performing association mapping as a novel method in associating genetic and complex traits, current strategy in analyzing of phenotype and genotype data to identify population structure and linkage disequilibrium. GWAS has an important role in food security because this method identified many crucial genomic regions of important traits in the most commercialize crops of the world, such as maize. These complex traits including yield, grain quality, biofortification, biotic and abiotic resistance. GWAS has many advantages correlated with reducing genotyping cost and research time, increasing mapping resolution and larger allele number. Meanwhile, GWAS has two main limitations related to population size and the number of markers. There are many software packages for data analysis in GWAS. The most commonly software that was used in GWAS especially in this crop is TASSEL because frequently updated. Recently, many research papers concentrated on GWAS in maize. GWAS analysis accelerated identification of genetic regions, candidate genes within these genomic regions and their metabolomic analysis correlated to the complex traits in maize for increasing grain yield and grain quality to fulfill the market demands.
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Kirichenko, A. V., A. S. Zlobin, T. I. Shashkova, N. A. Volkova, B. S. Iolchiev, V. A. Bagirov, P. M. Borodin, L. С. Karssen, Y. A. Tsepilov, and Y. S. Aulchenko. "The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep." Vavilov Journal of Genetics and Breeding 26, no. 4 (July 7, 2022): 378–84. http://dx.doi.org/10.18699/vjgb-22-46.

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In recent years, the number of genome-wide association studies (GWAS) carried out for various economically important animal traits has been increasing. GWAS discoveries provide summary statistics that can be used both for targeted marker-oriented selection and for studying the genetic control of economically important traits of farm animals. In contrast to research in human genetics, GWAS on farm animals often does not meet generally accepted standards (availability of information about effect and reference alleles, the size and direction of the effect, etc.). This greatly complicates the use of GWAS results for breeding needs. Within the framework of human genetics, there are several technological solutions for researching the harmonized results of GWAS, including one of the largest, the GWAS-MAP platform. For other types of living organisms, including economically important agricultural animals, there are no similar solutions. To our knowledge, no similar solution has been proposed to date for any of the species of economically important animals. As part of this work, we focused on creating a platform similar to GWAS-MAP for working with the results of GWAS of sheep, since sheep breeding is one of the most important branches of agriculture. By analogy with the GWAS-MAP platform for storing, unifying and analyzing human GWAS, we have created the GWAS-MAP|ovis platform. The platform currently contains information on more than 34 million associations between genomic sequence variants and traits of meat production in sheep. The platform can also be used to conduct colocalization analysis, a method that allows one to determine whether the association of a particular locus with two different traits is the result of pleiotropy or whether these traits are associated with different variants that are in linkage disequilibrium. This platform will be useful for breeders to select promising markers for breeding, as well as to obtain information for the introduction of genomic breeding and for scientists to replicate the results obtained.
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Dissertations / Theses on the topic "Genomic Wide Association Study (GWAS)"

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Kaplan, Abdullah. "Genomic Selection and Genome-Wide Association Study in Populus trichocarpa and Pinus taeda." Thesis, Virginia Tech, 2016. http://hdl.handle.net/10919/82501.

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Forest tree breeding methods rank among the most efficient ways to increase productivity and quality of forests. With the advent of high-throughput genotyping technology, genome-enabled breeding has started to gain importance and may overcome some weaknesses of traditional tree breeding. Genomic Selection (GS), which involves using genome-wide markers to predict breeding values of individuals in a population, has been proposed for animal and plant breeding programs. GS enables very accurate selection decisions through estimation of genomic estimated breeding values (GEBVs). While the goal of GS is to predict phenotype from genotype, it does not identify the underlying genes that have important roles in a trait. Genome-Wide Association Studies (GWAS) approaches are therefore complementary to GS, enabling identification of these genes, which may be useful for marker-assisted selection in some traits. In this study, we first estimated heritability for several adaptive traits (cold hardiness, dbh, bud flush, height, and bud set) in a population of Populus trichocarpa and for height, diameter, and stem straightness in Pinus taeda. GEBVs accuracies were estimated using a ridge regression–best linear unbiased prediction (rrBLUP) model, and these accuracies were compared with estimated heritabilities. GWAS was also performed for the both imputed and non–imputed data of P. taeda population using TASSEL (Trait Analysis by aSSociation Evolution and Linkage) software, as well as rrBLUP and FFBSKAT (Fast Family-Based Sequence Kernel Association Test) packages in R. Heritabilities ranged from 0.34 to 0.56 for P. trichocarpa and 0.14 to 0.37 for P.taeda. GWAS identified 3244 associations for dbh, 4077 associations for stem straightness, and 5280 SNPs for height (p≤0.05) in TASSEL using the reduced model (marker data only), whereas 2729, 3272 and 3531 associations were found with the full model where we also included population structure as a covariate. FFBSKAT showed a similar number of SNP associations (2989, 3046 and 3058). There was an inflation of SNP associations (~20k) found in rrBLUP, which suggests population structure was not effectively controlled. The GEBVs accuracies ranged from 0.09 and 0.22 for P.trichocarpa and 0.09 to 0.23 for P.taeda using rrBLUP method. Testing the effect of repetation on the accuracy of GEBV for poplar showed that there was no significant difference between the number of cycles. Also, there was no significant difference the accuracy of GEBVs in pine between two different imputation methods, the marker mean value and Beagle software.
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Ghaffar, Ammarah. "Identifying and understanding the molecular mechanisms of migraine via functional interpretation of genome-wide association study (GWAS) data." Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/236251/7/Ammarah_Ghaffar_Thesis_2_.pdf.

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Migraine is the most common brain disorder, affecting almost 14% of the adult population, yet its molecular mechanisms and pathogenic tissue(s) remain unclear. In this thesis, I have developed a novel approach that uses genome-wide association study (GWAS) summary statistics and expression quantitative trait loci (eQTL) data to impute genetically regulated tissue-specific gene expression and prioritise disease-relevant pathogenic tissues. In subsequent studies, I compared three transcriptome imputation models to characterise genome-wide significant migraine GWAS risk loci and identified 14 novel migraine risk loci that were confirmed to be true risk loci in a recent larger migraine GWAS.
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Trivedi, Sapna. "A genetic association study in ANCA associated vasculitis." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.607655.

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Risslén, Rebecca. "Genome-wide association study to find SNPs associated with circulating levels of the protein FGF-21." Thesis, Umeå universitet, Institutionen för fysik, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-173011.

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Colorectal cancer (CRC) is one of the most common types of cancer globally. In Sweden, every year over 6000 individuals are diagnosed with CRC making it the fourth most common form of cancer in the country. The symptoms of the disease occur late in its development, therefore diagnosis is often delayed, which has a negative effect on mortality. Once an individual starts to experience symptoms, a colonoscopy is performed to examine the colon and set a diagnosis. However, colonoscopy is straining for the individual and costly for the health care system. Therefore, a complementary risk screening method is needed to help identify high-risk individuals. Two separate studies have shown that individuals who develop CRC also have increased levels of the fibroblast protein (FGF-21). Thus, there is an interest in potentially using FGF-21 as a risk screening marker in a blood test for filtering out the high-risk individuals of colorectal cancer. However, it is not known whether FGF-21 is part of the causal pathway leading to CRC development or only a marker of increased risk. Therefore, more work is needed to better understand the role of FGF-21 in CRC disease. This study represents the first step in identifying if FGF-21 has any causal role in CRC. To do this I have tried to identify single genetic variants (so-called SNPs) in the human DNA that are associated with circulating levels of FGF-21 by conducting a genome-wide association study (GWAS). The genome and protein data used in the GWAS originated from 131 individuals participating in the Västerbotten Intervention Programme. Preliminary results showed no significant SNPs among the study subjects when correcting for multiple tests at a significance level of 5%. Although there were no significant findings I did find several indications of potential associations and the small size of the dataset might explain why they did not reach significance. The analytical pipeline I have created as part of this project will be used in a larger dataset where it will be possible to both verify potential associations from this study and hopefully identify other interesting SNPs. Any confirmed findings will in the future be used in a Mendelian Randomization study where the association between having SNPs that increase your levels of FGF-21 and the risk of CRC will be assessed. If such an association could be confirmed it would indicate that FGF-21 plays a causal role in CRC development.
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Floyd, James A. B. "Analysis of high-density SNP data from complex populations." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/4926.

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Data from a Croatian isolate population are analysed in a genome-wide association study (GWAS) for a variety of disease-related quantitative traits. A novel genomewide approach to analysing pedigree-based association data called GRAMMAR is utilised. One of the significant findings, for uric acid, is followed up in greater detail, and is replicated in another isolate population, from Orkney. The associated SNPs are located in the SLC2A9 gene, coding for a known glucose transporter, which leads to identification of SLC2A9 as a urate transporter too (Vitart et al., 2008). These SNPs are later implicated in affecting gout, a disease known to be linked with high serum uric acid levels, in an independent study (Dehghan et al., 2008). Subsequently, investigation into different ways in which to use SNP data to identify quantitative trait loci (QTL) for genome-wide association (GWA) studies is performed. Several multi-marker approaches are compared to single SNP analysis using simulated phenotypes and real genotype data, and results show that for rare variants haplotype analysis is the most effective method of detection. Finally, the multi-marker methods are compared with single SNP analysis on the real uric acid data. Interpretation of real data results was complicated due to low sample size, since only founder and unrelated individuals may be used for population-based haplotype analysis, nonetheless, results of the prior analyses of simulated data indicate that multi-marker methods, in particular haplotypes, may greatly facilitate detection of QTL with low minor allele frequency in GWA studies.
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Fatima, Fizza. "Genome-Wide Association Study for Disease Traits In Wheat and Its Wild Relatives." Thesis, Université d'Ottawa / University of Ottawa, 2020. http://hdl.handle.net/10393/40900.

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Wheat is the most widely grown crop in the world and as such, is an essential source of energy and nutrition. The challenges that breeders presently face is to increase production to feed the rising population of the world, while also accounting for climate change, pollution, water and environmental stresses. As genetic uniformity of modern cultivars has increased vulnerability to pests and diseases, the wild relatives of wheat offer a rich source of genetic diversity and stress tolerance traits, that can be harnessed and transferred in to modern wheat. In this study, we used array-based genotyping to explore genetic diversity in 385 domesticated and non-domesticated lines of wheat and their wild relatives. Genetic characterization using the wheat 90K array, and subsequent filtering and validation mapped 9,570 single nucleotide polymorphic markers onto the wheat reference genome. Phylogenetic analyses illustrated four major clades, clearly separating the wild species from the domesticated, and the ancient Triticum turgidum species from modern T. turgidum cultivars. Using this diverse germplasm, a genome-wide association study (GWAS) was performed for leaf rust, the most widespread rust disease of wheat. Identification of novel sources of resistance is necessary to maintain disease resistance and stay ahead in the plant-pathogen evolutionary arms race. GWAS was conducted using eight statistical models for infection types against six leaf rust isolates and leaf rust severity rated in field trials for 3-4 years at 2-3 locations in Canada. Functional annotation of genes containing significant quantitative trait nucleotides (QTNs) identified 96 disease-related nucleotide associated with leaf rust resistance. A total of 21 QTNs were in haplotype blocks or within flanking markers of at least 16 known leaf rust (Lr) resistance genes. The remaining significant QTNs were considered loci that putatively harbor new Lr resistance genes. Future efforts to validate these loci will help understand their role in disease resistance and promote their utility for marker-assisted selection in pre-breeding.
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Pooler, Tammy. "Genome-Wide Association Study on the Sleep Symptom of Post Traumatic Stress Disorder." ScholarWorks, 2015. https://scholarworks.waldenu.edu/dissertations/1273.

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Posttraumatic stress disorder (PTSD) is a psychiatric condition that presents with 3 main symptoms're-experiencing, avoidance/numbing, and hyper arousal'after an individual experiences a traumatic event. Recent evidence suggests a potential genetic basis for PTSD and a sub symptom of hyper arousal, sleep, as a potential pathway for PTSD development, but no study has identified candidate genes associated with specific symptoms such as sleep difficulty. Based on a conceptual framework in which specific genes are associated with the onset of PTSD, this study used a genome-wide association study (GWAS) method with a case control study design to compare the genomes of individuals with and without PTSD. A secondary GWAS dataset from a study on alcohol dependence in European and African Americans was obtained from the National Center for Biotechnology Information. PTSD cases and controls were analyzed using PLINK software. Signals from 2 single nucleotide polymorphisms (SNPs), which have not been previously associated with PTSD, exceeded the established genome-wide threshold: SNP rs13160949 on chromosome 5 (p = 7.33x10-9, OR: 1.565) and SNP rs2283877 on chromosome 22 (p = 2.55x10-8, OR: 1.748). Neither SNP, though, maintained genomewide significance following corrected tests for multiple testing, population stratification, and false discovery, so the planned analysis for possible associations with PTSD by symptom category then by the sub symptom of sleep could not be completed. The results of this study suggest that PTSD may be the result of polygenic SNPs with weak effects, which supports a recent study indicating the disease may be highly polygenic. Positive social change implications include bringing attention to the clinical and research community that PTSD may involve complex polygenic factors in need of further study.
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Aterido, Ballonga Adrià 1990. "Identification of clinically relevant genetic variation in immune-mediated inflammatory diseases using genome-wide approaches." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/666363.

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Rheumatoid arthritis, psoriasis, psoriatic arthritis, systemic lupus erythematosus, Crohn’s disease and ulcerative colitis are six of the most prevalent immune-mediated inflammatory diseases (IMIDs) and are associated with a high socio-economic impact. There is compelling evidence that IMIDs are genetically complex diseases. To date, however, the genetic component of IMIDs has been only partially explained. Identifying new clinically relevant variation is therefore of major clinical interest. The objective of the present thesis was to identify new genetic variation underlying IMIDs. The research activity here presented is the result of analyzing high-throughput genomic data from a large cohort of IMID patients collected by the IMID Consortium. Using genome-wide approaches and functional analyses, we have identified new genetic variants associated to IMID susceptibility, IMID clinical phenotypes and specific treatment outcomes. Taken together, these findings contribute to better understanding the genetic basis of IMIDs and suggest more specific and preventive therapeutic strategies.
L’artritis reumatoide, la psoriasis, l’artritis psoriàsica, el lupus eritematós sistèmic, la malaltia de Crohn i la colitis ulcerosa són sis malalties inflamatòries mediades per immunitat (IMIDs) d’elevada prevalença i amb un fort impacte socioeconòmic. Totes elles comparteixen un component genètic important. No obstant, a dia d’avui, només s’ha caracteritzat una part dels factors genètics de les IMIDs. La identificació de factors genètics clínicament rellevants presenta doncs un gran interès clínic per tal d’incorporar la informació genètica a la pràctica mèdica. L’objectiu d’aquesta tesi és identificar noves variants genètiques associades a les IMIDs. La recerca que es presenta és el resultat d’analitzar dades genòmiques d’una gran cohort de pacients amb IMIDs, els quals es van obtenir a través del consorci IMID Consortium. Mitjançant estratègies d’anàlisi de genoma complet i estudis funcionals, en aquesta tesi s’han identificat noves variants genètiques associades al risc de desenvolupar IMIDs així com als seus fenotips clínics i tractament. Aquesta tesi contribueix significativament a la caracterització del component genètic de les IMIDs i, des d’un punt de vista clínic, suggereix noves estratègies terapèutiques.
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Thompson, Katherine L. "Using ancestral information to search for quantitative trait loci in genome-wide association studies." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1372410951.

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Shen, Hanyang, Bizu Gelaye, Hailiang Huang, Marta B. Rondon, Sixto Sanchez, and Laramie E. Duncan. "Polygenic prediction and GWAS of depression, PTSD, and suicidal ideation/self-harm in a Peruvian cohort." Springer Nature, 2020. http://hdl.handle.net/10757/652459.

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Genome-wide approaches including polygenic risk scores (PRSs) are now widely used in medical research; however, few studies have been conducted in low- and middle-income countries (LMICs), especially in South America. This study was designed to test the transferability of psychiatric PRSs to individuals with different ancestral and cultural backgrounds and to provide genome-wide association study (GWAS) results for psychiatric outcomes in this sample. The PrOMIS cohort (N = 3308) was recruited from prenatal care clinics at the Instituto Nacional Materno Perinatal (INMP) in Lima, Peru. Three major psychiatric outcomes (depression, PTSD, and suicidal ideation and/or self-harm) were scored by interviewers using valid Spanish questionnaires. Illumina Multi-Ethnic Global chip was used for genotyping. Standard procedures for PRSs and GWAS were used along with extra steps to rule out confounding due to ancestry. Depression PRSs significantly predicted depression, PTSD, and suicidal ideation/self-harm and explained up to 0.6% of phenotypic variation (minimum p = 3.9 × 10−6). The associations were robust to sensitivity analyses using more homogeneous subgroups of participants and alternative choices of principal components. Successful polygenic prediction of three psychiatric phenotypes in this Peruvian cohort suggests that genetic influences on depression, PTSD, and suicidal ideation/self-harm are at least partially shared across global populations. These PRS and GWAS results from this large Peruvian cohort advance genetic research (and the potential for improved treatments) for diverse global populations.
National Institutes of Health
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Books on the topic "Genomic Wide Association Study (GWAS)"

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Gondro, Cedric, Julius van der Werf, and Ben Hayes. Genome-Wide Association Studies and Genomic Prediction. Humana Press, 2017.

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Media, Springer Science+Business, ed. Genome-wide association studies and genomic prediction. Humana Press, 2013.

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Thun, Michael J., Martha S. Linet, James R. Cerhan, Christopher A. Haiman, and David Schottenfeld. Introduction. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0001.

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This Introduction provides a broad overview of the scientific advances and crosscutting developments that increasingly influence epidemiologic research on the causes and prevention of cancer. High-throughput technologies have identified the molecular “driver” events in tumor tissue that underlie the multistage development of many types of cancer. These somatic (largely acquired) alterations disrupt normal genetic and epigenetic control over cell maintenance, division and survival. Tumor classification is also changing to reflect the genetic and molecular alterations in tumor tissue, as well as the anatomic, morphologic, and histologic phenotype of the cancer. Genome-wide association studies (GWAS) have identified more than 700 germline (inherited) genetic loci associated with susceptibility to various forms of cancer, although the risk estimates for almost all of these are small to modest and their exact location and function remain to identified. Advances in genomic and other “OMIC” technologies are identifying biomarkers that reflect internal exposures, biological processes and intermediate outcomes in large population studies. While research in many of these areas is still in its infancy, mechanistic and molecular assays are increasingly incorporated into etiologic studies and inferences about causation. Other sections of the book discuss the global public health impact of cancer, the growing list of exposures known to affect cancer risk, the epidemiology of over 30 types of cancer by tissue of origin, and preventive interventions that have dramatically reduced the incidence rates of several major cancers.
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Cutter, Asher D. A Primer of Molecular Population Genetics. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198838944.001.0001.

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The study of molecular population genetics seeks to understand the micro-evolutionary principles underlying DNA sequence variation and change. It addresses such questions as: Why do individuals differ as much as they do in their DNA sequences? What are the genomic signatures of adaptations? How often does natural selection dictate changes to DNA and accumulate as differences between species? How does the ebb and flow in the abundance of individuals over time get marked onto chromosomes to record genetic history? The concepts used to answer such questions also apply to analysis of personal genomics, genome-wide association studies, phylogenetics, landscape and conservation genetics, forensics, molecular anthropology, and selection scans. This Primer of Molecular Population Genetics introduces the bare essentials of the theory and practice of evolutionary analysis through the lens of DNA sequence change in populations. Intended as an introductory text for upper-level undergraduates and junior graduate students, this Primer also provides an accessible entryway for scientists from other areas of biology to appreciate the ideas and practice of molecular population genetics. With the revolutionary advances in genomic data acquisition, understanding molecular population genetics is now a fundamental requirement for today’s life scientists.
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Book chapters on the topic "Genomic Wide Association Study (GWAS)"

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Galik, Elizabeth, Shin Fukudo, Yukari Tanaka, Yori Gidron, Tavis S. Campbell, Jillian A. Johnson, Kristin A. Zernicke, et al. "Genome-Wide Association Study (GWAS)." In Encyclopedia of Behavioral Medicine, 852–54. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-1005-9_697.

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Wagner, Peter, Frank C. Mooren, Hidde J. Haisma, Stephen H. Day, Alun G. Williams, Julius Bogomolovas, Henk Granzier, et al. "Genome-Wide Association Study (GWAS)." In Encyclopedia of Exercise Medicine in Health and Disease, 363. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-540-29807-6_2436.

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Simonson, Matthew A. "Genome-Wide Association Study (GWAS)." In Encyclopedia of Behavioral Medicine, 936–39. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-39903-0_697.

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Sale, Michèle M., Josyf C. Mychaleckyj, and Wei-Min Chen. "Planning and Executing a Genome Wide Association Study (GWAS)." In Methods in Molecular Biology, 403–18. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-378-7_25.

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Shrestha, Vivek, Mani Awale, and Avinash Karn. "Genome Wide Association Study (GWAS) on Disease Resistance in Maize." In Disease Resistance in Crop Plants, 113–30. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-20728-1_6.

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Kumari, Meenu, Lakesh Muduli, Prabina Kumar Meher, and Sukanta Kumar Pradhan. "Genome-Wide Association Study (GWAS) for Trait Analysis in Crops." In Springer Protocols Handbooks, 295–307. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2533-0_15.

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Liu, Xiaojing, and Yi Jia. "Genome Wide Association Studies (GWAS) and Their Clinical Applications in Asthma." In Genomic Approach to Asthma, 31–44. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-8764-6_3.

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Mühleisen, Thomas W., and Sven Cichon. "Genome-wide association studies." In Genes, brain, and emotions, 51–62. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198793014.003.0005.

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Genome-wide association studies (GWAS) have evolved over the past ten years into a very successful tool for investigating the genetic architecture of multifactorial human traits and disorders. One major advantage of GWAS is that they do not require any a priori knowledge about the biological mechanisms underlying the traits and disorders under study. This chapter describes the scientific and technological developments that made GWAS possible and the underlying basic concept of these studies. The chapter considers what has been learned from GWAS in psychiatric research so far, what are the limitations, and looks forward to the future of GWAS.
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Kheirallah, A. K., S. Miller, I. P. Hall, and I. Sayers. "Translating Lung Function Genome-Wide Association Study (GWAS) Findings." In Advances in Genetics, 57–145. Elsevier, 2016. http://dx.doi.org/10.1016/bs.adgen.2015.12.002.

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"Reviewing a Genome-Wide Association Study (GWAS) Journal Article." In Active Learning Exercises. 2215 Constitution Avenue, N.W. Washington, DC 20037-2985: The American Pharmacists Association, 2013. http://dx.doi.org/10.21019/ale.2000.114.

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Conference papers on the topic "Genomic Wide Association Study (GWAS)"

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Wang, Liya, Doreen Ware, Nirav Merchant, and Carol Lushbough. "Building an open Genome Wide Association Study (GWAS) platform." In 2013 IEEE International Conference on Cluster Computing (CLUSTER). IEEE, 2013. http://dx.doi.org/10.1109/cluster.2013.6702696.

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Singer, William, Bo Zhang, Dajun Yu, David Holshouser, Haibo Huang, Keren Brooks, Maria Rosso, and Mark Reiter. "Evaluating Breeding and Management Solutions for Methionine Content in Soybean." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/qvdx5082.

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Soybean is widely recognized as a valuable crop and plant protein source due to its ideal amino acid profile. However, deficient methionine content in soybean seeds limits the nutritional utility. Therefore, a genome-wide association study (GWAS) utilizing 311 soybean accessions from maturity groups IV and V was performed alongside genomic prediction models to determine genetic underpinnings and breeding potential. Additionally, sulfur fertilization source and rate were evaluated for their impact on methionine content in soybean seeds. Across four environments, 23 novel single nucleotide polymorphisms (SNPs) were identified as being associated with methionine content, and average prediction accuracy (r2) ranged from 0.03 to 0.62 for genomic prediction models. Across six locations, soybean plots treated with ammonium sulfate (AMS) exhibited statistically increased methionine content when compared to other sulfur fertilizers. When combined, these results highlight the complex genetic and environmental controls for methionine content in soybean seeds and will positively contribute to protein quality improvement in soybean.
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Yan, Yan, Connor Burbridge, Jinhong Shi, Juxin Liu, and Anthony Kusalik. "Comparing Four Genome-Wide Association Study (GWAS) Programs with Varied Input Data Quantity." In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2018. http://dx.doi.org/10.1109/bibm.2018.8621425.

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Park, Zewon, Ko-Woon Choi, Doo Won Seo, Sunae Ryu, Jong Gu Lee, and Woo Yong Oh. "Genome-Wide Association Study (GWAS) for the Infliximab Responsiveness in Korean Inflammatory Bowel Disease Patients." In BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3107411.3108218.

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Wang, Qiang, Xiaoming Lu, Matthew T. Weirauch, and Peter Nigrovic. "903 Decoding genome-wide association study (GWAS) hits for lupus using massively parallel reporter assays." In LUPUS 21ST CENTURY 2022 CONFERENCE, Abstracts of Sixth Scientific Meeting of North American and European Lupus Community, Tucson, AZ, USA – September 20–23, 2022. Lupus Foundation of America, 2022. http://dx.doi.org/10.1136/lupus-2022-lupus21century.54.

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Elrayess, Mohamed, Fatima Al-Khelaifi, Noha Yousri, and Omar Al-Bagha. "Genome-Wide Association study Identifies a Novel Association Between a Cardiovascular Gene Polymorphism and Superior Athletic Performance." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0111.

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Research into the genetic predisposition to superior athletic performance has been a hindered by the underpowered studies and the small effect size of identified genetic variants. The aims of this study were to investigate the association of common single-nucleotide polymorphisms (SNPs) with endurance athlete status in a large cohort of elite European athletes using GWAS approach, followed by replication studies in Russian and Japanese elite athletes and functional validation using metabolomics analysis. Results: The association of 476,728 SNPs of Illumina DrugCore Gene chip and endurance athlete status was investigated in 796 European international-level athletes (645 males, 151 females) by comparing allelic frequencies between athletes specialized in sports with high (n=662) and low/moderate (n=134) aerobic component. Validation of results was performed by comparing the frequencies of the most significant SNPs between 242 and 168 elite Russian high and low/moderate aerobic athletes, respectively, and between 60 elite Japanese endurance athletes and 406 controls. A meta-analysis has identified rs1052373 (GG homozygotes) in Myosin Binding Protein (MYBPC3; implicated in cardiac hypertrophic myopathy) gene to be associated with endurance athlete status (P=1.43E-08, odd ratio 2.2). Homozygotes carriers of rs1052373 G allele in Russian athletes had significantly greater VO2max than carriers of the AA+AG (P = 0.005). Subsequent metabolomics analysis revealed several amino acids and lipids associated with rs1052373 G allele (1.82x10-05) including the testosterone precursor androstenediol (3beta, 17beta) disulfate. Conclusion: This is the first report of genome-wide significant SNP and related metabolites associated with elite athlete status. Further investigations of the functional relevance of the identified SNPs and metabolites in relation to enhanced athletic performance are warranted.
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Polfus, Linda M., S. Lani Park, Yesha M. Patel, Sharon E. Murphy, David Conti, Christopher Haiman, Daniel O. Stram, and Loïc Le Marchand. "Abstract 232: Genome-wide association study (GWAS) of total nicotine equivalents: A composite biomarker of nicotine uptake." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-232.

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Yeh, Kuan-Hung, Ching-Heng Lin, Tzu-Hung Hsiao, and Tzu-Pin Lu. "Genome-Wide Association Study (GWAS) on Metabolic Syndrome in Subjects with Abdominal Obesity in a Taiwanese Population." In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2020. http://dx.doi.org/10.1109/bibm49941.2020.9313373.

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Chen, Yian A., Zhihua Chen, Ya-Yu Tsai, Xiaotao Qu, Edwin Iversen, Jill Barnholtz-Sloan, Brooke L. Fridley, et al. "Abstract 4729: Pathway and gene set analyses for epithelial ovarian cancer (EOC) genome-wide association study (GWAS)." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-4729.

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Bowden, S., I. Kalliala, M. Wielscher, B. Bodinier, J. Flanagan, M. Chadeau-Hyam, M.-R. Jarvelin, and M. Kyrgiou. "P15 Cervical intraepithelial neoplasia and cervical cancer: a genome wide association study (GWAS) of the UK biobank cohort." In ESGO Annual Meeting Abstracts. BMJ Publishing Group Ltd, 2019. http://dx.doi.org/10.1136/ijgc-2019-esgo.78.

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Reports on the topic "Genomic Wide Association Study (GWAS)"

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Seroussi, Eyal, and George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, September 2010. http://dx.doi.org/10.32747/2010.7593397.bard.

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Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.
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Sela, Hanan, Eduard Akhunov, and Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598170.bard.

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The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.
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