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Journal articles on the topic "SNPs genotyping"
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Xu, Han, Sihuan Zhang, Xiaoyan Zhang, Ruihua Dang, Chuzhao Lei, Hong Chen, and Xianyong Lan. "Evaluation of novel SNPs and haplotypes within the <i>ATBF1</i> gene and their effects on economically important production traits in cattle." Archives Animal Breeding 60, no. 3 (August 29, 2017): 285–96. http://dx.doi.org/10.5194/aab-60-285-2017.
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Abstract. AT motif binding factor 1 (ATBF1) gene can promote the expression level of the growth hormone 1 (GH1) gene by binding to the enhancers of the POU1F1 and PROP1 genes; thus, it affects the growth and development of livestock. Considering that the ATBF1 gene also has a close relationship with the Janus kinase–signal transductor and activator of transcription (JAK–STAT) pathway, the objective of this work was to identify novel single-nucleotide polymorphism (SNP) variations and their association with growth traits in native Chinese cattle breeds. Five novel SNPs within the ATBF1 gene were found in 644 Qinchuan and Jinnan cattle for first time using 25 pairs of screening and genotyping primers. The five novel SNPs were named as AC_000175:g.140344C>G (SNP1), g.146573T>C (SNP2), g.205468C>T (SNP3), g.205575A>G (SNP4) and g.297690C<T (SNP5). Among them, SNP1 and SNP2 were synonymous coding SNPs, while SNP5 was a missense coding SNP, and the other SNPs were intronic. Haplotype analysis found 18 haplotypes in the two breeds, and three and five closely linked loci were revealed in Qinchuan and Jinnan breeds, respectively. Association analysis revealed that SNP1 was significantly associated with the height across the hip in Qinchuan cattle. SNP2 was found to be significantly related to chest circumference and body side length traits in Jinnan cattle. SNP3 was found to have significant associations with four growth traits in Qinchuan cattle. Moreover, the different combined genotypes, SNP1–SNP3, SNP1–SNP4 and SNP2–SNP5 were significantly associated with the growth traits in cattle. These findings indicated that the bovine ATBF1 gene had marked effects on growth traits, and the growth-trait-related loci can be used as DNA markers for maker-assisted selection (MAS) breeding programs in cattle.
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Claassen, Daniel O., Jody Corey-Bloom, E. Ray Dorsey, Mary Edmondson, Sandra K. Kostyk, Mark S. LeDoux, Ralf Reilmann, et al. "Genotyping single nucleotide polymorphisms for allele-selective therapy in Huntington disease." Neurology Genetics 6, no. 3 (May 14, 2020): e430. http://dx.doi.org/10.1212/nxg.0000000000000430.
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BackgroundThe huntingtin gene (HTT) pathogenic cytosine-adenine-guanine (CAG) repeat expansion responsible for Huntington disease (HD) is phased with single nucleotide polymorphisms (SNPs), providing targets for allele-selective treatments.ObjectiveThis prospective observational study defined the frequency at which rs362307 (SNP1) or rs362331 (SNP2) was found on the same allele with pathogenic CAG expansions.MethodsAcross 7 US sites, 202 individuals with HD provided blood samples that were processed centrally to determine the number and size of CAG repeats, presence and heterozygosity of SNPs, and whether SNPs were present on the mutant HTT allele using long-read sequencing and phasing.ResultsHeterozygosity of SNP1 and/or SNP2 was identified in 146 (72%) individuals. The 2 polymorphisms were associated only with the mHTT allele in 61% (95% high density interval: 55%, 67%) of individuals.ConclusionsThese results are consistent with previous reports and demonstrate the feasibility of genotyping, phasing, and targeting of HTT SNPs for personalized treatment of HD.
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Min, Josine L., Nico Lakenberg, Margreet Bakker-Verweij, Eka Suchiman, Dorret I. Boomsma, P. Eline Slagboom, and Ingrid Meulenbelt. "High Microsatellite and SNP Genotyping Success Rates Established in a Large Number of Genomic DNA Samples Extracted From Mouth Swabs and Genotypes." Twin Research and Human Genetics 9, no. 4 (August 1, 2006): 501–6. http://dx.doi.org/10.1375/twin.9.4.501.
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AbstractIn this article, we present the genomic DNA yield and the microsatellite and single nucleotide polymorphism (SNP) genotyping success rates of genomic DNA extracted from a large number of mouth swab samples. In total, the median yield and quality was determined in 714 individuals and the success rates in 378,480 genotypings of 915 individuals. The median yield of genomic DNA per mouth swab was 4.1 μg (range 0.1–42.2 μg) and was not reduced when mouth swabs were stored for at least 21 months prior to extraction. A maximum of 20 mouth swabs is collected per participant. Mouth swab samples showed in, respectively, 89% for 390 microsatellites and 99% for 24 SNPs a genotyping success rate higher than 75%. A very low success rate of genotyping (0%–10%) was obtained for 3.2% of the 915 mouth swab samples using microsatellite markers. Only 0.005% of the mouth swab samples showed a geno-typing success rate lower than 75% (range 58%–71%) using SNPs. Our results show that mouth swabs can be easily collected, stored by our conditions for months prior to DNA extraction and result in high yield and high-quality DNA appropriate for genotyping with high success rate including whole genome searches using microsatellites or SNPs.
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Rustgi, S., R. Bandopadhyay, H. S. Balyan, and P. K. Gupta. "EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure." Czech Journal of Genetics and Plant Breeding 45, No. 3 (October 6, 2009): 106–16. http://dx.doi.org/10.17221/16/2009-cjgpb.
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The present study involves discovery, validation and use of single-nucleotide polymorphisms (SNPs) in bread wheat utilizing 48 EST-contigs (individual contigs having 20-89 ESTs, derived from 2 to 11 different genotypes). In order to avoid a problem due to homoeologous relationships, the ESTs in each contig were classified into 175 sub-contigs (3.7 sub-contigs/EST-contig) using characteristic homoeologue sequence variants (HSVs), which had a density of 1 HSV every 136.7 bp. In silico analysis of sub-contigs led to the discovery of 230 candidate EST-SNPs with a density of 1SNP/273.9 bp. Locus specific primers (each primer pair flanking 1–18 SNPs) were designed utilizing one sub-contig each from 42 EST-contigs that contained SNPs, the remaining 6 contigs having no SNPs. To provide locus specificity to the PCR products, each primer was tagged with an HSV at its 3' end. Only 10 primer pairs, which gave each a characteristic solitary band, were utilized to validate EST-SNPs over 30 diverse bread wheat genotypes; 7 SNPs were validated through resequencing the PCR products. Allele specific primers were designed and utilized for genotyping of 50 diverse bread wheat accessions (including 30 bread wheat genotypes previously used for validation of SNPs), with an aim to test their utility in genotyping and map construction. The allele specific primers allowed the classification of 50 genotypes in two alternative allele groups for each SNP as expected, thus suggesting their utility for genotyping. Of the above 7 validated SNPs, 4 belonged to a solitary locus (PKS37); 7 haplotypes were available at this locus. Altogether, the results suggested that EST-SNPs constitute an important source of molecular markers for studies on wheat genomics.
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Li, Peng-Le, Mo-Hua Yang, Xiao-Long Jiang, Huan Xiong, Hui-Liang Duan, Feng-Lan Zou, Qian-Yu Xu, Wei Wang, Yong-Hui Hong, and Neng-Qing Lin. "De Novo SNP Discovery and Genotyping of Masson Pine (Pinus massoniana Lamb.) via Genotyping-by-Sequencing." Forests 14, no. 2 (February 14, 2023): 387. http://dx.doi.org/10.3390/f14020387.
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Masson pine (Pinus massoniana Lamb.) is an important tree species in China, but its genomic research has been hindered due to a large genome size. Genotyping-by-sequencing (GBS) has been a powerful approach to revolutionize the field of genomic research by facilitating the discovery of thousands of single nucleotide polymorphisms (SNPs) and genotyping in non-model organisms, at relatively low cost. Here, we performed de novo SNP discovery and genotyping in 299 trees via the genotyping-by-sequencing (GBS) approach. The effort produced 9.33 × 109 sequence reads, 265,525 SNP-associated contigs, and 6,739,240 raw SNPs. Further filtering and validation of the SNP-associated contigs for reliable SNPs were performed using blasting against the Pinus tabuliformis reference genome, functional annotation, technical replicates, and custom parameter settings for the optimization. The 159,372 SNP-associated contigs were aligned and validated for SNP prediction, in which 60,038 contigs were searched with hits in the NCBI nr database. We further improved the SNP discovery and genotyping with multiple technical replicates and custom parameter settings filtering. It was found that the use of blasting, annotation, technical replicates, and specific parameter settings removed many unreliable SNPs and identified 20,055 more precise and reliable SNPs from the 10,712 filtered contigs. We further demonstrated the informativeness of the identified SNPs in the inference of some genetic diversity and structure. These findings should be useful to stimulate genomic research and genomics-assisted breeding of Masson pine.
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Calvo, Jorge H., Magdalena Serrano, Flavie Tortereau, Pilar Sarto, Laura P. Iguacel, María A. Jiménez, José Folch, José L. Alabart, Stéphane Fabre, and Belén Lahoz. "Development of a SNP parentage assignment panel in some North-Eastern Spanish meat sheep breeds." Spanish Journal of Agricultural Research 18, no. 4 (October 27, 2020): e0406. http://dx.doi.org/10.5424/sjar/2020184-16805.
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Aim of study: To validate two existing single nucleotide polymorphism (SNP) panels for parentage assignment in sheep, and develop a cost effective genotyping system to use in some North-Eastern Spanish meat sheep populations for accurate pedigree assignment.Area of study: SpainMaterial and methods: Nine sheep breeds were sampled: Rasa Aragonesa (n=38), Navarra (n=39), Ansotana (n=41), Xisqueta (n=41), Churra Tensina (n=38), Maellana (39), Roya Bilbilitana (n=24), Ojinegra (n=36) and Cartera (n=39), and these animals were genotyped with the Illumina OvineSNP50 BeadChip array. Genotypes were extracted from the sets of 249 SNPs and 163 SNPs for parentage assignment designed in France and North America, respectively. Validation of a selected cost-effective genotyping panel of 158 SNPs from the French panel were performed by Kompetitive allele specific PCR (KASP). Additionally, some functional SNPs (n=15) were also genotyped.Main results: The set of 249 SNPs for parentage assignment showed better diversity, probability of identity, and exclusion probabilities than the set of 163 SNPs. The average minor allele frequency for the set of 249, 163 and 158 SNPs were 0.41 + 0.01, 0.39 + 0.01 and 0.42 + 0.01, respectively. The parentage assignment rate was highly dependent to the percentage of putative sires genotyped.Research highlights: The described method is a cost-effective genotyping system combining the genotyping of SNPs for the parentage assignment with some functional SNPs, which was successfully used in some Spanish meat sheep breeds.
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Graham, Natalie, Emily Telfer, Tancred Frickey, Gancho Slavov, Ahmed Ismael, Jaroslav Klápště, and Heidi Dungey. "Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don)." Forests 13, no. 2 (January 24, 2022): 176. http://dx.doi.org/10.3390/f13020176.
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Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial breeding. Leveraging off a previously developed exome capture panel, we tested the performance of 438,744 single nucleotide polymorphisms (SNPs) on a screening array (NZPRAD01) and then selected 36,285 SNPs for a final genotyping array (NZPRAD02). These SNPs aligned to 15,372 scaffolds from the Pinus taeda L. v. 1.01e assembly, and 20,039 contigs from the radiata pine transcriptome assembly. The genotyping array was tested on more than 8000 samples, including material from archival progenitors, current breeding trials, nursery material, clonal lines, and material from Australia. Our analyses indicate that the array is performing well, with sample call rates greater than 98% and a sample reproducibility of 99.9%. Genotyping in two linkage mapping families indicated that the SNPs are well distributed across the 12 linkage groups. Using genotypic data from this array, we were also able to differentiate representatives of the five recognized provenances of radiata pine, Año Nuevo, Monterey, Cambria, Cedros and Guadalupe. Furthermore, principal component analysis of genotyped trees revealed clear patterns of population structure, with the primary axis of variation driven by provenance ancestry and the secondary axis reflecting breeding activities. This represents the first commercial use of genomics in a radiata pine breeding program.
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Chiapparino, E., D. Lee, and P. Donini. "Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS–PCR." Genome 47, no. 2 (April 1, 2004): 414–20. http://dx.doi.org/10.1139/g03-130.
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Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism. These polymorphisms can be used in plants as simple genetic markers for many breeding applications, for population studies, and for germplasm fingerprinting. The great increase in the available DNA sequences in the databases has made it possible to identify SNPs by "database mining", and the single most important factor preventing their widespread use appears to be the genotyping cost. Many genotyping platforms rely on the use of sophisticated, automated equipment coupled to costly chemistry and detection systems. A simple and economical method involving a single PCR is reported here for barley SNP genotyping. Using the tetra-primer ARMS–PCR procedure, we have been able to assay unambiguously five SNPs in a set of 132 varieties of cultivated barley. The results show the reliability of this technique and its potential for use in low- to moderate-throughput situations; the association of agronomically important traits is discussed.Key words: single nucleotide polymorphisms (SNPs), genotyping, barley, tetra-primers ARMS–PCR.
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Germer, Søren, and Russell Higuchi. "Single-Tube Genotyping without Oligonucleotide Probes." Genome Research 9, no. 1 (January 1, 1999): 72–78. http://dx.doi.org/10.1101/gr.9.1.72.
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We report the development of a self-contained (homogeneous), single-tube assay for the genotyping of single-nucleotide polymorphisms (SNPs), which does not rely on fluorescent oligonucleotide probes. The method, which we call Tm-shift genotyping, combines allele-specific PCR with the discrimination between amplification products by their melting temperatures (Tm). Two distinct forward primers, each of which contains a 3′-terminal base that corresponds to one of the two SNP allelic variants, are combined with a common reverse primer in a single-tube reaction. A GC-tail is attached to one of the forward allele-specific primers to increase theTm of the amplification product from the corresponding allele. PCR amplification, Tmanalysis, and allele determination of genomic template DNA are carried out on a fluorescence-detecting thermocycler with a dye that fluoresces when bound to dsDNA. We demonstrate the accuracy and reliability ofTm-shift genotyping on 100 samples typed for two SNPs, and recommend it both as a simple and inexpensive diagnostic tool for genotyping medically relevant SNPs and as a high-throughput SNP genotyping method for gene mapping.
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Ahmed, Mahbubl, Chee Goh, Edward Saunders, Clara Cieza-Borrella, Zsofia Kote-Jarai, Fredrick R. Schumacher, and Ros Eeles. "Germline genetic variation in prostate susceptibility does not predict outcomes in the chemoprevention trials PCPT and SELECT." Prostate Cancer and Prostatic Diseases 23, no. 2 (November 27, 2019): 333–42. http://dx.doi.org/10.1038/s41391-019-0181-y.
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Abstract Background The development of prostate cancer can be influenced by genetic and environmental factors. Numerous germline SNPs influence prostate cancer susceptibility. The functional pathways in which these SNPs increase prostate cancer susceptibility are unknown. Finasteride is currently not being used routinely as a chemoprevention agent but the long term outcomes of the PCPT trial are awaited. The outcomes of the SELECT trial have not recommended the use of chemoprevention in preventing prostate cancer. This study investigated whether germline risk SNPs could be used to predict outcomes in the PCPT and SELECT trial. Methods Genotyping was performed in European men entered into the PCPT trial (n = 2434) and SELECT (n = 4885). Next generation genotyping was performed using Affymetrix® Eureka™ Genotyping protocols. Logistic regression models were used to test the association of risk scores and the outcomes in the PCPT and SELECT trials. Results Of the 100 SNPs, 98 designed successfully and genotyping was validated for samples genotyped on other platforms. A number of SNPs predicted for aggressive disease in both trials. Men with a higher polygenic score are more likely to develop prostate cancer in both trials, but the score did not predict for other outcomes in the trial. Conclusion Men with a higher polygenic risk score are more likely to develop prostate cancer. There were no interactions of these germline risk SNPs and the chemoprevention agents in the SELECT and PCPT trials.
Dissertations / Theses on the topic "SNPs genotyping"
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Simmons, Stacy. "Genotyping for Response to Physical Training." Wright State University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=wright1565880927061102.
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Hammond, Naomi Rachel. "Improved approaches to multiplexed PCR and to the genotyping of SNPs by mass spectrometry." Thesis, University of Southampton, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.438509.
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Chacon, Cortes Diego Fernando. "Study of miRNA polymorphisms and their potential association with breast cancer risk in Australian Caucasian populations." Thesis, Queensland University of Technology, 2015. https://eprints.qut.edu.au/89768/15/89768%28thesis%29.pdf.
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This project established a large and well characterised prospective breast cancer DNA biobank and used this biobank to conduct genetic studies in breast cancer. The thesis presented the results of these high-throughput genotyping studies in two separate Australian Caucasian case-control populations and identified association between three novel genetic variants in microRNA genes and breast cancer risk.
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Merchant-Patel, Shreema. "Development of rapid and highly resolving combinatorial genotyping schemes for Campylobacter jejuni and Campylobacter coli." Thesis, Queensland University of Technology, 2009. https://eprints.qut.edu.au/33194/1/Shreema_Merchant-Patel_Thesis.pdf.
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Campylobacter jejuni followed by Campylobacter coli contribute substantially to the economic and public health burden attributed to food-borne infections in Australia. Genotypic characterisation of isolates has provided new insights into the epidemiology and pathogenesis of C. jejuni and C. coli. However, currently available methods are not conducive to large scale epidemiological investigations that are necessary to elucidate the global epidemiology of these common food-borne pathogens. This research aims to develop high resolution C. jejuni and C. coli genotyping schemes that are convenient for high throughput applications.
Real-time PCR and High Resolution Melt (HRM) analysis are fundamental to the genotyping schemes developed in this study and enable rapid, cost effective, interrogation of a range of different polymorphic sites within the Campylobacter genome. While the sources and routes of transmission of campylobacters are unclear, handling and consumption of poultry meat is frequently associated with human campylobacteriosis in Australia. Therefore, chicken derived C. jejuni and C. coli isolates were used to develop and verify the methods described in this study.
The first aim of this study describes the application of MLST-SNP (Multi Locus Sequence Typing Single Nucleotide Polymorphisms) + binary typing to 87 chicken C. jejuni isolates using real-time PCR analysis. These typing schemes were developed previously by our research group using isolates from campylobacteriosis patients. This present study showed that SNP + binary typing alone or in combination are effective at detecting epidemiological linkage between chicken derived Campylobacter isolates and enable data comparisons with other MLST based investigations. SNP + binary types obtained from chicken isolates in this study were compared with a previously SNP + binary and MLST typed set of human isolates. Common genotypes between the two collections of isolates were identified and ST-524 represented a clone that could be worth monitoring in the chicken meat industry. In contrast, ST-48, mainly associated with bovine hosts, was abundant in the human isolates. This genotype was, however, absent in the chicken isolates, indicating the role of non-poultry sources in causing human Campylobacter infections. This demonstrates the potential application of SNP + binary typing for epidemiological investigations and source tracing.
While MLST SNPs and binary genes comprise the more stable backbone of the Campylobacter genome and are indicative of long term epidemiological linkage of the isolates, the development of a High Resolution Melt (HRM) based curve analysis method to interrogate the hypervariable Campylobacter flagellin encoding gene (flaA) is described in Aim 2 of this study. The flaA gene product appears to be an important pathogenicity determinant of campylobacters and is therefore a popular target for genotyping, especially for short term epidemiological studies such as outbreak investigations. HRM curve analysis based flaA interrogation is a single-step closed-tube method that provides portable data that can be easily shared and accessed. Critical to the development of flaA HRM was the use of flaA specific primers that did not amplify the flaB gene. HRM curve analysis flaA interrogation was successful at discriminating the 47 sequence variants identified within the 87 C. jejuni and 15 C. coli isolates and correlated to the epidemiological background of the isolates. In the combinatorial format, the resolving power of flaA was additive to that of SNP + binary typing and CRISPR (Clustered regularly spaced short Palindromic repeats) HRM and fits the PHRANA (Progressive hierarchical resolving assays using nucleic acids) approach for genotyping. The use of statistical methods to analyse the HRM data enhanced sophistication of the method. Therefore, flaA HRM is a rapid and cost effective alternative to gel- or sequence-based flaA typing schemes.
Aim 3 of this study describes the development of a novel bioinformatics driven method to interrogate Campylobacter MLST gene fragments using HRM, and is called ‘SNP Nucleated Minim MLST’ or ‘Minim typing’. The method involves HRM interrogation of MLST fragments that encompass highly informative “Nucleating SNPS” to ensure high resolution. Selection of fragments potentially suited to HRM analysis was conducted in silico using i) “Minimum SNPs” and ii) the new ’HRMtype’ software packages. Species specific sets of six “Nucleating SNPs” and six HRM fragments were identified for both C. jejuni and C. coli to ensure high typeability and resolution relevant to the MLST database. ‘Minim typing’ was tested empirically by typing 15 C. jejuni and five C. coli isolates. The association of clonal complexes (CC) to each isolate by ‘Minim typing’ and SNP + binary typing were used to compare the two MLST interrogation schemes. The CCs linked with each C. jejuni isolate were consistent for both methods. Thus, ‘Minim typing’ is an efficient and cost effective method to interrogate MLST genes. However, it is not expected to be independent, or meet the resolution of, sequence based MLST gene interrogation. ‘Minim typing’ in combination with flaA HRM is envisaged to comprise a highly resolving combinatorial typing scheme developed around the HRM platform and is amenable to automation and multiplexing.
The genotyping techniques described in this thesis involve the combinatorial interrogation of differentially evolving genetic markers on the unified real-time PCR and HRM platform. They provide high resolution and are simple, cost effective and ideally suited to rapid and high throughput genotyping for these common food-borne pathogens.
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Söderholm, Simon. "The Complex Genetics of Multiple Sclerosis : A preliminary study of MS-associated SNPs prior to a larger genotyping project." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-129423.
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Biomedical research have been revolutionized by recent technological advances, both in the fields of molecular biology and computer science, turning the biomolecular and genetic research into “big data science”. One of the main objectives have been to improve our understanding of complex human diseases. Among those diseases, multiple sclerosis (MS) is considered as one of the most common. MS is a chronic autoimmune disease that cause inflammation and damage to the central nervous system. In this study, a set of bioinformatics analyses have been conducted on SNP data, as an initial step to gain more information prior to an upcoming genotyping project. The results showed extensive regulatory properties for the 761 selected SNPs, which is consistent with current scientific knowledge, and also identified another 332 SNPs in linkage to these. However, during the study some issues have also been identified, which need to be addressed going forward.
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Carvalho, Thaysa Buss. "Avaliação de SNPs (Single Nucleotide Polymorphisms) nas diferentes formas clínicas da doença de Chagas." Universidade Estadual Paulista (UNESP), 2018. http://hdl.handle.net/11449/152931.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
A doença de Chagas (DC), causada pelo protozoário Trypanosoma cruzi (T. cruzi), ainda é considerada como um problema de saúde pública em muitos países da América Latina. De acordo com a Organização Mundial da Saúde, estima-se que entre seis a sete milhões de pessoas no mundo estejam infectadas. Indivíduos na fase crônica da doença podem ser classificados como assintomáticos ou sintomáticos (estes, desenvolvendo as formas clínicas cardíaca, digestiva ou mista). Os assintomáticos correspondem a 70% dos indivíduos nessa fase e, embora apresentem sorologia positiva para anticorpos anti T-cruzi, não desenvolvem manifestações clínicas da doença. O motivo pelo qual alguns pacientes permanecem assintomáticos, e outros desenvolvem sintomas severos, ainda é desconhecido. Fatores genéticos do hospedeiro são bastante relevantes e podem explicar a heterogeneidade encontrada em pacientes que vivem com a doença em áreas endêmicas. Diante disso, o presente trabalho teve como objetivo avaliar SNPs (Single Nucleotide Polymorphisms) no gene TNF-α (rs1800629) e ACAT-1 (rs1044925) em indivíduos com DC crônica e verificar se os mesmos estão relacionados com a susceptibilidade para manifestação de formas clínicas sintomáticas com uso da técnica PCR-RFLP. Foram genotipadas 124 amostras para o gene TNF-α e 135 para o gene ACAT-1. Foi observada associação significativa da presença do alelo A do gene TNF- α em indivíduos sintomáticos em relação aos assintomáticos (p = 0,045). Também houve associação significativa entre o alelo G (p = 0,008) e o genótipo GG (p = 0,001) do gene TNF-α e os genótipos AA (p = 0,047) e AC (p = 0,016) do gene ACAT-1 nos indivíduos assintomáticos em relação aos sintomáticos. Nossos resultados sugerem que a presença do alelo A do gene TNF-α possa estar relacionada com a presença de manifestações clínicas sintomáticas na fase crônica da doença e o alelo G, bem como, genótipo GG possam estar associados com ausência de sintomas clínicos em indivíduos nessa fase. A respeito do SNP do gene ACAT-1, nossos dados sugerem efeito protetor dos genótipos AA e AC segundo apresentação de sintomas da doença na fase crônica, o que representa dado inédito em chagásicos.
Chagas disease (CD), caused by the protozoan Trypanosoma cruzi (T. cruzi), is still considered a public health problem in many Latin America countries. According to the World Health Organization, it is estimated that between six and seven million people worldwide are infected. Disease’s chronic phase individuals may be classified as asymptomatic or symptomatic (these, developing as clinical cardiac, digestive or mixed forms). Asymptomatic individuals account for 70% of the patients at this stage and, although they have positive serology for anti-T-cruzi antibodies, they do not develop it’s clinical manifestations. The reason why some patients remain asymptomatic, and others develop severe symptoms, is still unknown. Host’s genetic factors are quite relevant and may explain the heterogeneity found in patients living with the disease in endemic areas. The objective of this study was to evaluate SNPs in the TNF-α (rs1800629) and ACAT-1 (rs1044925) genes in individuals with chronic CD and to verify if the polymorphisms are related to the susceptibility to manifestation of symptomatic clinical forms using the PCR-RFLP technique. Were genotyped 124 samples for the TNF-α gene and 135 for the ACAT-1 gene. Significant association for the presence of the A allele of the TNF-α gene was observed for symptomatic individuals in relation to the asymptomatic ones (p = 0.045). There was also a significant association between the G allele (p = 0.008) and the GG genotype (p = 0.001) of the TNF-α gene and the AA (p = 0.047) and AC (p = 0.016) genotypes of the ACAT-1 gene for asymptomatic patients. Our results suggests that the presence of the TNF-α gene A allele may be related to the presence of symptomatic clinical manifestations in the chronic phase of the disease and the G allele as well as the GG genotype may be associated with absence of clinical symptoms in individuals at this stage. Regarding the ACAT-1 gene SNP, our data suggests a protective effect of AA and AC genotypes according to the to the presentation of chronic disease symptoms, which is an unprecedented finding in chagasic patients.
CAPES: 1578310
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Stephens, Alex J. "The development of rapid genotyping methods for methicillin-resistant Staphylococcus aureus." Thesis, Queensland University of Technology, 2008. https://eprints.qut.edu.au/20172/1/Alexander_Stephens_Thesis.pdf.
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Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen that is endemic in hospitals all over the world. It has more recently emerged as a serious threat to the general public in the form of community-acquired MRSA. MRSA has been implicated in a wide variety of diseases, ranging from skin infections and food poisoning to more severe and potentially fatal conditions, including; endocarditis, septicaemia and necrotising pneumonia. Treatment of MRSA disease is complicated and can be unsuccessful due to the bacterium's remarkable ability to develop antibiotic resistance.
The considerable economic and public health burden imposed by MRSA has fuelled attempts by researchers to understand the evolution of virulent and antibiotic resistant strains and thereby improve epidemiological management strategies. Central to MRSA transmission management strategies is the implementation of active surveillance programs, via which unique genetic fingerprints, or genotypes, of each strain can be identified. Despite numerous advances in MRSA genotyping methodology, there remains a need for a rapid, reproducible, cost-effective method that is capable of producing a high level of genotype discrimination, whilst being suitable for high throughput use. Consequently, the fundamental aim of this thesis was to develop a novel MRSA genotyping strategy incorporating these benefits.
This thesis explored the possibility that the development of more efficient genotyping strategies could be achieved through careful identification, and then simple interrogation, of multiple, unlinked DNA loci that exhibit progressively increasing mutation rates. The baseline component of the MRSA genotyping strategy described in this thesis is the allele-specific real-time PCR interrogation of slowly evolving core single nucleotide polymorphisms (SNPs). The genotyping SNP set was identified previously from the Multi-locus sequence typing (MLST) sequence database using an in-house software package named Minimum SNPs. As discussed in Chapter Three, the genotyping utility of the SNP set was validated on 107 diverse Australian MRSA isolates, which were largely clustered into groups of related strains as defined by MLST. To increase the resolution of the SNP genotyping method, a selection of binary virulence genes and antimicrobial resistance plasmids were tested that were successful at sub typing the SNP groups.
A comprehensive MRSA genotyping strategy requires characterisation of the clonal background as well as interrogation of the hypervariable Staphylococcal Cassette Chromosome mec (SCCmec) that carries the β-lactam resistance gene, mecA. SCCmec genotyping defines the MRSA lineages; however, current SCCmec genotyping methods have struggled to handle the increasing number of SCCmec elements resulting from a recent explosion of comparative genomic analyses. Chapter Four of this thesis collates the known SCCmec binary marker diversity and demonstrates the ability of Minimum SNPs to identify systematically a minimal set of binary markers capable of generating maximum genotyping resolution. A number of binary targets were identified that indeed permit high resolution genotyping of the SCCmec element. Furthermore, the SCCmec genotyping targets are amenable for combinatorial use with the MLST genotyping SNPs and therefore are suitable as the second component of the MRSA genotyping strategy.
To increase genotyping resolution of the slowly evolving MLST SNPs and the SCCmec binary markers, the analysis of a hypervariable repeat region was required. Sequence analysis of the Staphylococcal protein A (spa) repeat region has been conducted frequently with great success. Chapter Five describes the characterisation of the tandem repeats in the spa gene using real-time PCR and high resolution melting (HRM) analysis. Since the melting rate and precise point of dissociation of double stranded DNA is dependent on the size and sequence of the PCR amplicon, the HRM method was used successfully to identify 20 of 22 spa sequence types, without the need for DNA sequencing.
The accumulation of comparative genomic information has allowed the systematic identification of key MRSA genomic polymorphisms to genotype MRSA efficiently. If implemented in its entirety, the strategy described in this thesis would produce efficient and deep-rooted genotypes. For example, an unknown MRSA isolate would be positioned within the MLST defined population structure, categorised based on its SCCmec lineage, then subtyped based on the polymorphic spa repeat region. Overall, by combining the genotyping methods described here, an integrated and novel MRSA genotyping strategy results that is efficacious for both long and short term investigations. Furthermore, an additional benefit is that each component can be performed easily and cost-effectively on a standard real-time PCR platform.
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Stephens, Alex J. "The development of rapid genotyping methods for methicillin-resistant Staphylococcus aureus." Queensland University of Technology, 2008. http://eprints.qut.edu.au/20172/.
Full textAbstract:
Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen that is endemic in hospitals all over the world. It has more recently emerged as a serious threat to the general public in the form of community-acquired MRSA. MRSA has been implicated in a wide variety of diseases, ranging from skin infections and food poisoning to more severe and potentially fatal conditions, including; endocarditis, septicaemia and necrotising pneumonia. Treatment of MRSA disease is complicated and can be unsuccessful due to the bacterium's remarkable ability to develop antibiotic resistance.
The considerable economic and public health burden imposed by MRSA has fuelled attempts by researchers to understand the evolution of virulent and antibiotic resistant strains and thereby improve epidemiological management strategies. Central to MRSA transmission management strategies is the implementation of active surveillance programs, via which unique genetic fingerprints, or genotypes, of each strain can be identified. Despite numerous advances in MRSA genotyping methodology, there remains a need for a rapid, reproducible, cost-effective method that is capable of producing a high level of genotype discrimination, whilst being suitable for high throughput use. Consequently, the fundamental aim of this thesis was to develop a novel MRSA genotyping strategy incorporating these benefits.
This thesis explored the possibility that the development of more efficient genotyping strategies could be achieved through careful identification, and then simple interrogation, of multiple, unlinked DNA loci that exhibit progressively increasing mutation rates. The baseline component of the MRSA genotyping strategy described in this thesis is the allele-specific real-time PCR interrogation of slowly evolving core single nucleotide polymorphisms (SNPs). The genotyping SNP set was identified previously from the Multi-locus sequence typing (MLST) sequence database using an in-house software package named Minimum SNPs. As discussed in Chapter Three, the genotyping utility of the SNP set was validated on 107 diverse Australian MRSA isolates, which were largely clustered into groups of related strains as defined by MLST. To increase the resolution of the SNP genotyping method, a selection of binary virulence genes and antimicrobial resistance plasmids were tested that were successful at sub typing the SNP groups.
A comprehensive MRSA genotyping strategy requires characterisation of the clonal background as well as interrogation of the hypervariable Staphylococcal Cassette Chromosome mec (SCCmec) that carries the β-lactam resistance gene, mecA. SCCmec genotyping defines the MRSA lineages; however, current SCCmec genotyping methods have struggled to handle the increasing number of SCCmec elements resulting from a recent explosion of comparative genomic analyses. Chapter Four of this thesis collates the known SCCmec binary marker diversity and demonstrates the ability of Minimum SNPs to identify systematically a minimal set of binary markers capable of generating maximum genotyping resolution. A number of binary targets were identified that indeed permit high resolution genotyping of the SCCmec element. Furthermore, the SCCmec genotyping targets are amenable for combinatorial use with the MLST genotyping SNPs and therefore are suitable as the second component of the MRSA genotyping strategy.
To increase genotyping resolution of the slowly evolving MLST SNPs and the SCCmec binary markers, the analysis of a hypervariable repeat region was required. Sequence analysis of the Staphylococcal protein A (spa) repeat region has been conducted frequently with great success. Chapter Five describes the characterisation of the tandem repeats in the spa gene using real-time PCR and high resolution melting (HRM) analysis. Since the melting rate and precise point of dissociation of double stranded DNA is dependent on the size and sequence of the PCR amplicon, the HRM method was used successfully to identify 20 of 22 spa sequence types, without the need for DNA sequencing.
The accumulation of comparative genomic information has allowed the systematic identification of key MRSA genomic polymorphisms to genotype MRSA efficiently. If implemented in its entirety, the strategy described in this thesis would produce efficient and deep-rooted genotypes. For example, an unknown MRSA isolate would be positioned within the MLST defined population structure, categorised based on its SCCmec lineage, then subtyped based on the polymorphic spa repeat region. Overall, by combining the genotyping methods described here, an integrated and novel MRSA genotyping strategy results that is efficacious for both long and short term investigations. Furthermore, an additional benefit is that each component can be performed easily and cost-effectively on a standard real-time PCR platform.
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Montes, Vergara Donicer Eduardo [UNESP]. "Prospecção de assinaturas de seleção em regiões de QTL associadas com características reprodutivas em novilhas Nelore." Universidade Estadual Paulista (UNESP), 2016. http://hdl.handle.net/11449/137897.
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Características reprodutivas, como a ocorrência de prenhez precoce, são mais importantes economicamente ao comparar-se com as características de crescimento. Desta forma, o aumento da taxa de fertilidade e emprego de animais geneticamente superiores é determinante no progresso da produtividade nas fazendas comerciais de produção de carne bovina. A seleção modifica as frequências alélicas de uma população ao transmitir as variantes gênicas mais interessantes. Considerando o desequilíbrio de ligação, alguns locos adjacentes às mutações favoráveis são transmitidos ao longo das gerações. Estes são conhecidos como assinaturas de seleção e podem ser identificados com o uso de “chips” de SNP e metodologias estatísticas adequadas. Com o objetivo de identificar assinaturas de seleção recentes em QTL previamente mapeados para características reprodutivas de fêmeas bovinas ligadas à precocidade sexual, foram genotipadas 2.035 fêmeas da raça Nelore (Bos taurus indicus) com o chip “Illumina BovineHD BeadChip”. Posteriormente foi inferida a fase de ligação dos SNPs e a reconstrução dos haplótipos. A detecção de assinaturas de seleção foi realizada por meio da aplicação da metodologia “Relative Extended Haplotype Homozygosity” (REHH). A identificação de genes que contribuem para a importância da característica nestas regiões foi feita com a ferramenta Map Viewer do “National Center for Biotechnology Information”- NCBI e GBrowse carregada com o genoma bovino versão UMD 3.1. Foram detectadas 2.756 regiões núcleo, com tamanho médio 27,6 ± 29,1 Kb, abrangendo 70,1 Mb dos 25 cromossomos estudados. Dos SNPs utilizados, 17.312 participaram da formação das regiões núcleo, com o mínimo de 10 no BTA27 e o máximo de 20 SNPs nos cromossomos 1, 3-7, 9-15,18-21, e 23-24. Foram identificadas 40 assinaturas de seleção recentes com diferentes níveis de significância e 56 genes A maioria dos genes localizados nas regiões de assinaturas de seleção tem relação com os processos biológicos de metabolismo mitocondrial, desenvolvimento pós-embrionário, regulação da taxa de ovulação e fertilidade, resposta imune, metabolismo de triglicerídeo, proliferação celular e neurônios receptores olfativos. A investigação de mecanismos regulatórios da expressão dos genes associados aos processos biológicos descritos pode oferecer conhecimentos sobre os mecanismos moleculares que afetam a característica ocorrências de prenhez precoce, na raça Nelore.
Some reproductive traits such as early pregnancy are more profitable than those related to growth. Increasing fertility rate and using genetically superior animals are crucial in productivity of meat commercial farms. Artificial selection modifies allele frequencies of a cattle population by transmitting the most significant gene variants. Considering linkage disequilibrium, some loci adjacent to favorable mutations are transmitted across generations. Known as signatures of selection, such locations can be identified by the SNP chips, and appropriate statistical methods. To determine recent selection signature in quantitative trait loci (QTL) previously mapped for reproductive cow features linked to sexual precocity, 2,035 Nelore (Bos taurus indicus) females were genotyped by Illumina Bovine chip. After, inferring the connection phase of SNPs allowed haplotype reconstruction. Selection signatures were detected by Relative Extended Haplotype Homozygosity (REHH) method. Genes supposedly important were recognized by Map Viewer from the National Center for Biotechnology Information (NCBI), and also through a loaded GBrowse with bovine genome UMD, version 3.1. A total of 2,756 core regions were detected, with an average size of 27.6 ± 29.1 Kb, covering 70.1 Mb of 25 chromosomes. 17,312 SNPs are involved in the formation of core regions with at least 10 on BTA27, and a maximum of 20 SNPs on 1, 3-7, 9-15, 18-21, and 23-24 chromosomes. We identify 40 possible recent selection signatures, with different levels of significance, and 56 positional candidate genes. Most of genes located in selection signature regions are related to biological processes of mitochondrial metabolism, post-embryonic development, ovulation rate regulation and fertility, immune response, triglyceride metabolism, cell proliferation, and olfactory receptor neurons. The investigation of regulatory mechanisms of gene expression associated with biological processes described can provide knowledge on the molecular mechanisms affecting characteristic of early pregnancy occurrences in Nellore.
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Price, Erin Peta. "Development of novel combinatorial methods for genotyping the common foodborne pathogen Campylobacter jejuni." Thesis, Queensland University of Technology, 2007. https://eprints.qut.edu.au/16601/1/Erin_Peta_Price_Thesis.pdf.
Full textAbstract:
Campylobacter jejuni is the commonest cause of bacterial foodborne gastroenteritis in industrialised countries. Despite its significance, it remains unclear how C. jejuni is disseminated in the environment, whether particular strains are more pathogenic than others, and by what routes this bacterium is transmitted to humans. One major factor hampering this knowledge is the lack of a standardised method for fingerprinting C. jejuni. Therefore, the overall aim of this project was to develop systematic and novel genotyping methods for C. jejuni.
Chapter Three describes the use of single nucleotide polymorphisms (SNPs) derived from the multilocus sequence typing (MLST) database of C. jejuni and the closely related Campylobacter coli for genotyping these pathogens. The MLST database contains DNA sequence data for over 4000 strains, making it the largest comparative database available for these organisms. Using the in-house software package "Minimum SNPs", seven SNPs were identified from the C. jejuni/C. coli MLST database that gave a Simpson's Index of Diversity (D), or resolving power, of 0.98. An allele-specific real-time PCR method was developed and tested on 154 Australian C. jejuni and C. coli isolates. The major advantage of the seven SNPs over MLST is that they are cheaper, faster and simpler to interrogate than the sequence-based MLST method. When the SNP profiles were combined with sequencing of the rapidly evolving flaA short variable region (flaA SVR) locus, the genotype distributions were comparable to those obtained by MLST-flaA SVR.
Recent technological advances have facilitated the characterisation of entire bacterial genomes using comparative genome hybridisation (CGH) microarrays. Chapter Four of this thesis explores the large volume of CGH data generated for C. jejuni and eight binary genes (genes present in some strains but absent in others) were identified that provided complete discrimination of 20 epidemiologically unrelated strains of C. jejuni. Real-time PCR assays were developed for the eight binary genes and tested on the Australian isolates. The results from this study showed that the SNP-binary assay provided a sufficient replacement for the more laborious MLST-flaA SVR sequencing method.
The clustered regularly interspaced short palindromic repeat (CRISPR) region is comprised of tandem repeats, with one half of the repeat region highly conserved and the other half highly diverse in sequence. Recent advances in real-time PCR enabled the interrogation of these repeat regions in C. jejuni using high-resolution melt differentiation of PCR products. It was found that the CRISPR loci discriminated epidemiologically distinct isolates that were indistinguishable by the other typing methods (Chapter Five). Importantly, the combinatorial SNP-binary-CRISPR assay provided resolution comparable to the current 'gold standard' genotyping methodology, pulsed-field gel electrophoresis.
Chapter Six describes a novel third module of "Minimum SNPs", 'Not-N', to identify genetic targets diagnostic for strain populations of interest from the remaining population. The applicability of Not-N was tested using bacterial and viral sequence databases. Due to the weakly clonal population structure of C. jejuni and C. coli, Not-N was inefficient at identifying small numbers of SNPs for the major MLST clonal complexes. In contrast, Not-N completely discriminated the 13 major subtypes of hepatitis C virus using 15 SNPs, and identified binary gene targets superior to those previously found for phylogenetic clades of C. jejuni, Yersinia enterocolitica and Clostridium difficile, demonstrating the utility of this additional module of "Minimum SNPs".
Taken together, the presented work demonstrates the potentially far-reaching applications of novel and systematic genotyping assays to characterise bacterial pathogens with high accuracy and discriminatory power. This project has exploited known genetic diversity of C. jejuni to develop highly targeted assays that are akin to the resolution of the current 'gold standard' typing methods. By targeting differentially evolving genetic markers, an epidemiologically relevant, high-resolution fingerprint of the isolate in question can be determined at a fraction of the time, effort and cost of current genotyping procedures. The outcomes from this study will pave the way for improved diagnostics for many clinically significant pathogens as the concept of hierarchal combinatorial genotyping gains momentum amongst infectious disease specialists and public health-related agencies.
Books on the topic "SNPs genotyping"
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Henry, R. J., ed. Plant genotyping II: SNP technology. Wallingford: CABI, 2008. http://dx.doi.org/10.1079/9781845933821.0000.
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J, Henry Robert, ed. Plant genotyping II: SNP technology. Wallingford, UK: CABI, 2008.
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1962-, Hajeer Ali, Worthington Jane 1961-, and John Sally 1964-, eds. SNP and microsatellite genotyping: Markers for genetic analysis. Natick, MA: Eaton Pub., 2000.
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Lewis, Myles, and Tim Vyse. Genetics of connective tissue diseases. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0042.
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The advent of genome-wide association studies (GWAS) has been an exciting breakthrough in our understanding of the genetic aetiology of autoimmune diseases. Substantial overlap has been found in susceptibility genes across multiple diseases, from connective tissue diseases and rheumatoid arthritis (RA) to inflammatory bowel disease, coeliac disease, and psoriasis. Major technological advances now permit genotyping of millions of single nucleotide polymorphisms (SNPs). Group analysis of SNPs by haplotypes, aided by completion of the Hapmap project, has improved our ability to pinpoint causal genetic variants. International collaboration to pool large-scale cohorts of patients has enabled GWAS in systemic lupus erythematosus (SLE), systemic sclerosis and Behçet's disease, with studies in progress for ANCA-associated vasculitis. These 'hypothesis-free' studies have revealed many novel disease-associated genes. In both SLE and systemic sclerosis, identified genes map to known pathways including antigen presentation (MHC, TNFSF4), autoreactivity of B and T lymphocytes (BLK, BANK1), type I interferon production (STAT4, IRF5) and the NFκB pathway (TNIP1). In SLE alone, additional genes appear to be involved in dysregulated apoptotic cell clearance (ITGAM, TREX1, C1q, C4) and recognition of immune complexes (FCGR2A, FCGR3B). Future developments include whole-genome sequencing to identify rare variants, and efforts to understand functional consequences of susceptibility genes. Putative environmental triggers for connective tissue diseases include infectious agents, especially Epstein-Barr virus; cigarette smoking; occupational exposure to toxins including silica; and low vitamin D, due to its immunomodulatory effects. Despite numerous studies looking at toxin exposure and connective tissue diseases, conclusive evidence is lacking, due to either rarity of exposure or rarity of disease.
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Eyre, Steve, and Jane Worthington. Genetics of rheumatoid arthritis. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0040.
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A range of epidemiological studies have clearly established that susceptibility to rheumatoid arthritis (RA) is determined by both genetic and environmental factors. Studies over the last five decades have used a variety of approaches to identify the genetic variants associated with disease. HLA DRB1 was the first RA susceptibility locus to be discovered and has the largest effect size. We describe current understanding of the complexities of HLA association for RA. Linkage and small-scale association studies prior to 2007 provided convincing evidence for only one more RA susceptibility locus, PTPN22. Major breakthroughs in high-throughput genotyping and systematic discovery and mapping of hundreds of thousands of single nucleotide polymorphisms (SNPs) led to large-scale genome-wide association studies used for the first time for RA in 2007. This approach has had a dramatic impact on our knowledge of the susceptibility loci for RA, such that over 60 risk variants have now been robustly identified. We present an overview of these studies and the loci that have been identified. We consider how this knowledge is contributing to a greater understanding of the aetiology and pathology of the disease and in turn how this can influence management of patients presenting with an inflammatory arthritis. We consider some of the unanswered questions and the approaches that will need to be taken to address them.
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Eyre, Steve, Jane Worthington, and Sebastien Viatte. Genetics of rheumatoid arthritis. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199642489.003.0040_update_003.
Full textAbstract:
A range of epidemiological studies have clearly established that susceptibility to rheumatoid arthritis (RA) is determined by both genetic and environmental factors. Studies over the last five decades have used a variety of approaches to identify the genetic variants associated with disease. HLA DRB1 was the first RA susceptibility locus to be discovered and has the largest effect size. We describe current understanding of the complexities of HLA association for RA. Linkage and small-scale association studies prior to 2007 provided convincing evidence for only one more RA susceptibility locus, PTPN22. Major breakthroughs in high-throughput genotyping, and systematic discovery and mapping of hundreds of thousands of single nucleotide polymorphisms (SNPs) led to large-scale genome-wide association studies used for the first time for RA in 2007. Widespread utilization of this approach has had a dramatic impact on our knowledge of the susceptibility loci for RA, such that over 100 risk variants have now been robustly identified. We present an overview of these studies and the loci that have been identified. We consider how this knowledge is contributing to a greater understanding of the aetiology and pathology of the disease, and in turn how this can influence management of patients presenting with an inflammatory arthritis. We consider some of the unanswered questions and the approaches that will need to be taken to address them.
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Hajeer, Ali. Snp And Microsatellite Genotyping: Markers For Genetic Analysis (MOLECULAR LABORATORY METHODS (BIOTECHNIQUES BOOKS)). EATON PUBLISHING, 2000.
Find full textBook chapters on the topic "SNPs genotyping"
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Barreiro, Luis B., Ricardo Henriques, and Musa M. Mhlanga. "High-Throughput SNP Genotyping: Combining Tag SNPs and Molecular Beacons." In Methods in Molecular Biology, 255–76. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-411-1_17.
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Bortolin, Susan. "Multiplex Genotyping for Thrombophilia-Associated SNPs by Universal Bead Arrays." In DNA and RNA Profiling in Human Blood, 59–72. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-553-4_6.
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Dabrowski, Piotr Wojciech, Kati Bourquain, and Andreas Nitsche. "Multiplex Pyrosequencing®: Simultaneous Genotyping Based on SNPs from Distant Genomic Regions." In Methods in Molecular Biology, 337–47. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2715-9_23.
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Bayer, Philipp Emanuel. "Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies." In Plant Bioinformatics, 285–92. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3167-5_16.
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Bayer, Philipp Emanuel. "Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies." In Plant Bioinformatics, 405–13. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2067-0_20.
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Peatman, Eric. "SNP Genotyping Platforms." In Next Generation Sequencing and Whole Genome Selection in Aquaculture, 123–32. Oxford, UK: Wiley-Blackwell, 2010. http://dx.doi.org/10.1002/9780470958964.ch8.
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Studer, Bruno, and Roland Kölliker. "SNP Genotyping Technologies." In Diagnostics in Plant Breeding, 187–210. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-5687-8_9.
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Royo, Jose Luis, and Jose Jorge Galán. "Pyrosequencing for SNP Genotyping." In Methods in Molecular Biology, 123–33. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-411-1_7.
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Singh, B. D., and A. K. Singh. "High-Throughput SNP Genotyping." In Marker-Assisted Plant Breeding: Principles and Practices, 367–400. New Delhi: Springer India, 2015. http://dx.doi.org/10.1007/978-81-322-2316-0_13.
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Mohanrao, Manmode Darpan, Senapathy Senthilvel, Yarabapani Rushwanth Reddy, Chippa Anil Kumar, and Palchamy Kadirvel. "Amplifluor-Based SNP Genotyping." In Methods in Molecular Biology, 191–200. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3024-2_13.
Full textConference papers on the topic "SNPs genotyping"
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Ma, Jie, Sheng Ning, and Pengfeng Xiao. "Multiple SNPs genotyping by ligation of universal probes on 3D DNA microarray." In 2010 3rd International Conference on Biomedical Engineering and Informatics (BMEI). IEEE, 2010. http://dx.doi.org/10.1109/bmei.2010.5639397.
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Lee, Y. L., M. Bosse, W. Coppieters, R. F. Veerkamp, L. Karim, C. Oget-Ebrad, T. Druet, et al. "542. Rare CNVs in the bovine genome are not captured well by 50K density genotyping array SNPs." In World Congress on Genetics Applied to Livestock Production. The Netherlands: Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_542.
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Sharma, Vineeta, Pallavi Singhal, Anoop Kumar, V. G. Ramachandran, Shukla Das, and Mausumi Bharadwaj. "Association of TNF-α–rs 281865419 polymorphism with reproductive tract infections in Indian population." In 16th Annual International Conference RGCON. Thieme Medical and Scientific Publishers Private Ltd., 2016. http://dx.doi.org/10.1055/s-0039-1685357.
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Aim: To investigate the presence of reproductive tract infections (RTIs) in symptomatic and asymptomatic women in North India and association of SNPs in TNF? gene (rs-281865419 C/T) with susceptibility to these RTIs. Methods: We collected 100 symptomatic (cases) and 100 asymptomatic women (controls) samples and screened them for RTIs. Then genotyping of TNF-? gene was performed by PCR-RFLP. Results: Among cases the frequencies of RTIs infection is higher than control. The prevalence of HPV, C. trachomatis, T. vaginalis, Bacterial vaginosis and N. gonorrhoeae are 28% and 6%; 11%, 32% respectively while in controls it was 5%, 2%, 1% and 8% and 1%. In the present study we found that the frequency of wild homozygous genotype (TT) was lower in cases 30% (6/20) as compared to controls 60% (12/20). The frequency of the heterozygous polymorphic genotype (CT) was higher in cases 65% (65/100) as compared to controls 32% (32/100). It was interesting to note that the frequency of the polymorphic homozygous genotype (CC) was higher in cases 15% (15/100) than controls 2% (2/100). While the frequency of the carrier genotype (CT + TT) was found to be more in cases 70% (70/100) than in controls 40/100 (40%). This study shows that T allele may be risk factor for reproductive tract infections as its percentage is higher in cases as compare to normal controls. Conclusion: TNF-? rs-281865419 locus may serve as an important biomarker for RTIs predisposition in Indian population though larger sample size is needed to validate the findings.
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Sharma, Vineeta, Pallavi Singhal, Anoop Kumar, V. G. Ramachandran, Shukla Das, and Mausumi Bharadwaj. "Association of TNF-α rs-281865419 polymorphism with reproductive tract infections in Indian population." In 16th Annual International Conference RGCON. Thieme Medical and Scientific Publishers Private Ltd., 2016. http://dx.doi.org/10.1055/s-0039-1685270.
Full textAbstract:
Aim: To investigate the presence of reproductive tract infections (RTIs) in symptomatic and asymptomatic women in North India and association of SNPs in TNFα gene (rs-281865419 C/T) with susceptibility to these RTIs. Methods: We collected 100 symptomatic (cases) and 100 asymptomatic women (controls) samples and screened them for RTIs. Then genotyping of TNF-α gene was performed by PCR-RFLP. Results: Among cases the frequencies of RTIs infection is higher than control. The prevalence of HPV, C. trachomatis, T. vaginalis, Bacterial vaginosis and N. gonorrhoeae are 28% & 6%; 11%, 32% respectively while in controls it was 5%, 2%, 1% and 8% & 1%. In the present study we found that the frequency of wild homozygous genotype (TT) was lower in cases 30% (6/20) as compared to controls 60% (12/20). The frequency of the heterozygous polymorphic genotype (CT) was higher in cases 65% (65/100) as compared to controls 32% (32/100). It was interesting to note that the frequency of the polymorphic homozygous genotype (CC) was higher in cases 15% (15/100) than controls 2% (2/100). While the frequency of the carrier genotype (CT + TT) was found to be more in cases 70% (70/100) than in controls 40/100 (40%). This study shows that T allele may be risk factor for Reproductive tract infections as its percentage is higher in cases as compare to normal controls. Conclusion: TNF-? rs-281865419 locus may serve as an important biomarker for RTIs predisposition in Indian population though larger sample size is needed to validate the findings.
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SHARAN, R., A. BEN-DOR, and Z. YAKHINI. "MULTIPLEXING SCHEMES FOR GENERIC SNP GENOTYPING ASSAYS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812704856_0014.
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Machado, Vitor Pereira, Edis Bellini Júnior, Lucas Gazarini, Clarisse Lobo, and Claudia Bonini-Domingos. "Association of genetic markers with ischemic stroke in pediatric patients with sickle cell anemia." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.293.
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Introduction: Sickle cell anemia (SCA) is characterized by complex clinical heterogeneity. Amongst them, ischemic stroke (IS) stands out because it affects 8% to 12% of patients up to the age of 20, with a mortality rate of 20% in untreated cases. Objectives: To evaluate the association of SNPs -786T/C NOS3 and C667T MTHFR in the occurrence of IS in SCA pediatric patients undergoing regular blood transfusion. Methods: Ninety SCA pediatric patients 12.1±3.3 years old being followed-up at HEMORIO/RJ, divided into Patients with IS in hypertransfusion (n=20) and Patients without IS not transfused (n=70). Results: IS Group: genotypic frequencies: -786T/C NOS3, 4 (20%) CC, 4 (20%) CT and 22 (60%) TT; C667T MTHFR, 3 (15%) TT, 2 (10%) CT and 15 (75%) CC. Group without IS: genotypic frequencies: -786T/C NOS3, 1 (1.4%) CC, 25 (35.7%) CT and 44 (62.8%) TT; C667T MTHFR, 1 (1.4%) TT, 18 (25.7%) CT and 51 (72.8%) CC. Chisquare test revealed association of SNPs -786T/C NOS3 (p = 0,017) and C667T MTHFR (p = 0,004) with the occurrence of stroke in SCA patients, in which the frequency of homozygous mutants is higher in the IS group than in the control group (-786T/C NOS3 20% vs. 1.4% and C667T MTHFR 15% vs. 1.4%). Conclusions: The polymorphisms evaluated influenced the occurrence of IS in SCA pediatric patients especially when carrying recessive alleles. Studies with larger sample sizes and similar inclusion/exclusion criteria is needed.
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Oscoz Irurozqui, Maitane, Maria Guardiola-Ripoll, Carmen Almodóvar-Payà, Salavador Sarró, Amalia Guerrero-Pedraza, Edith Pomarol-Clotet, and Mar Fatjó-Vilas. "Cannabis use and genes of endocannabinoid system: their role in psychotic symptoms and cognition in first-episode psychosis." In 22° Congreso de la Sociedad Española de Patología Dual (SEPD) 2020. SEPD, 2020. http://dx.doi.org/10.17579/sepd2020o031.
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Objectives. To evaluate the association of cannabis use, genes of the endocannabinoid system and their interaction on clinical symptoms and cognitive performance in patients with a first-episode of pyschosis. Background. The role of both cannabis use and individual genetic background has been shown in the risk for psychosis. However, the influence of cannabis and variability at endocannabinoid genes on the psychosis outcome still remains inconclusive. Materials and Methods. The sample comprised 43 Caucasian individuals with a first-episode of psychosis (mean age(sd)=25.80(6.39) years, 76.7% males, 51.2% cannabis users).There were no differences in age and sex between cannabis users and non-users. Genetic variability was assessed by genotyping one Single Nucleotide Polymorphism (SNP) in each gene (CNR1-rs1049353 and CNR2-rs2501431). Clinical (PANSS, GAF) and neuropsychological (WAIS, WMS, BADS) scales were administered. Results and conclusions. Genotypic frequencies did not differ between cannabis users and non-users. Cannabis use was associated with better manipulative abilities (IQ-M-WAIS, p=0.029) and better executive function (BADS, p=0.036). CNR1-T allele carriers presented higher disorganized and negative syndrome scores (p=0.001 and p=0.044, respectively). The interaction models evidenced a combined effect of CNR1 and cannabis use on the negative syndrome-PANSS (p=0.037). These results suggest the role of cannabis use and genetic background on cognitive and psychopathological outcomes in first-episode psychosis. However, evidence is still scant, and further investigation in larger samples is needed.
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"PROPOSAL FOR A FILTERLESS FLUORESCENCE SENSOR FOR SNP GENOTYPING." In International Conference on Biomedical Electronics and Devices. SciTePress - Science and and Technology Publications, 2012. http://dx.doi.org/10.5220/0003774201850189.
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"Application of Amplifluor-like SNP markers in plant genotyping." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-162.
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Liu, Zheng, Bin Liu, Yan Deng, and Nongyue He. "The state of field of high-throughput SNP genotyping system." In 2011 International Symposium on Bioelectronics and Bioinformatics (ISBB). IEEE, 2011. http://dx.doi.org/10.1109/isbb.2011.6107674.
Full textReports on the topic "SNPs genotyping"
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Hultman, Keith, and Eve Mellgren. Fetching SNPs: A Dog Genotyping Laboratory for Undergraduate Biology. Genetics Society of America Peer-Reviewed Education Portal, September 2014. http://dx.doi.org/10.1534/gsaprep.2014.001.
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Medrano, Juan, Adam Friedmann, Moshe (Morris) Soller, Ehud Lipkin, and Abraham Korol. High resolution linkage disequilibrium mapping of QTL affecting milk production traits in Israel Holstein dairy cattle. United States Department of Agriculture, March 2008. http://dx.doi.org/10.32747/2008.7696509.bard.
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Original objectives: To create BAC contigs covering two QTL containing chromosomal regions (QTLR) and obtain BAC end sequence information as a platform for SNP identification. Use the SNPs to search for marker-QTL linkage disequilibrium (LD) in the test populations (US and Israel Holstein cattle). Identify candidate genes, test for association with dairy cattle production and functional traits, and confirm any associations in a secondary test population. Revisions in the course of the project: The selective recombinant genotyping (SRG) methodology which we implemented to provide moderate resolution QTL mapping turned out to be less effective than expected, due to problems introduced by incomplete marker informativity. This required a no-cost one-year extension of the project. Aside from this, the project was implemented essentially as envisaged, but only with respect to a single QTLR and single population association-test. Background to the topic. Dairy cattle breeders are looking to marker-assisted selection (MAS) as a means of identifying genetically superior sires and dams. MAS based on population-wide LD can be many times more effective than MAS based on within-family linkage mapping. In this proposal we developed a protocol leading from family based QTL mapping to population-wide LD between markers and the QTL Major conclusions, solutions, achievements. The critical importance of marker informativity for application of the SRG design in outcrossing random mating populations was identified, and an alternative Fractioned Pool Design (FPD) based on selective DNA pooling was developed. We demonstrated the feasibility of constructing a BAC contig across a targeted chromosomal region flanking the marker RM188 on bovine chromosome BTA4, which was shown in previous work to contain a QTL affecting milk production traits. BAC end sequences were obtained and successfully screened for SNPs. LD studies of these SNPs in the Israel population, and of an independent set of SNPs taken across the entire proximal region of BTA4 in the USA population, showed a much lower degree of LD than previously reported in the literature. Only at distances in the sub-cM level did an appreciable fraction of SNP marker-pairs show levels of LD useful for MAS. In contrast, studies in the Israel population using microsatellite markers, presented an equivalent degree of LD at a 1-5 separation distance. SNP LD appeared to reflect historical population size of Bostaurus (Ne=5000- 10,000), while microsatellite LD appeared to be in proportion to more recent effective population size of the Holstein breed (Ne=50-100). An appreciable fraction of the observed LD was due to Family admixture structure of the Holstein population. The SNPs MEOX2/IF2G (found within the gene SETMAR at 23,000 bp from RM188) and SNP23 were significantly associated with PTA protein, Cheese dollars and Net Merit Protein in the Davis bull resource population, and were also associated with protein and casein percentages in the Davis cow resource population. Implications. These studies document a major difference in degree of LD presented by SNPs as compared to microsatellites, and raise questions as to the source of this difference and its implications for QTL mapping and MAS. The study lends significant support to the targeted approach to fine map a previously identified QTL. Using high density genotyping with SNP discovered in flanking genes to the QTL, we have identified important markers associated with milk protein percentage that can be tested in markers assisted selection programs.
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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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Hassen, Abebe T., Jack C. M. Dekkers, Susan J. Lamont, Rohan L. Fernando, Santiago Avendano, John Ralph, Jim McKay, and William G. Hill. High-density SNP Genotyping Analysis of Broiler Breeding Lines. Ames (Iowa): Iowa State University, January 2007. http://dx.doi.org/10.31274/ans_air-180814-1049.
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Breiman, Adina, Jan Dvorak, Abraham Korol, and Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7697121.bard.
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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.
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Saatchi, Mahdi, and Dorian J. Garrick. Developing a Reduced SNP Panel for Low-cost Genotyping in Beef Cattle. Ames (Iowa): Iowa State University, January 2014. http://dx.doi.org/10.31274/ans_air-180814-1140.
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Gorbach, Danielle M., Bin Fan, Suneel K. Onteru, Xia Zhao, Zhi-Qiang Du, Dorian J. Garrick, Jack C. M. Dekkers, and Max F. Rothschild. Genome-Wide Association Studies for Important Economic Traits in Domestic Animals Using High Density SNP Genotyping. Ames (Iowa): Iowa State University, January 2010. http://dx.doi.org/10.31274/ans_air-180814-980.
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Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, August 2011. http://dx.doi.org/10.32747/2011.7592655.bard.
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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.
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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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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.
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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.