Tassel gwas study

Association mapping using TASSEL - YouTube

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9/14/2013 · This chanel develops and host various educational videos in the field of agriculture and applied genomics which will help for the students, teachers, scientists and seed industry personals for ...

Association mapping using TASSEL - YouTube

TASSEL - omicX

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Implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating ...

TASSEL - omicX

tasseladmin / Tassel 5 Source / wiki / UserManual ...

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Genome-wide Association Studies in Maize: Praise and Stargaze Yingjie Xiao 1 ,4, Haijun Liu , Liuji Wu2, Marilyn Warburton3 and Jianbing Yan1,* 1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China 2Synergetic Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China

tasseladmin / Tassel 5 Source / wiki / UserManual ...

Genome-wide Association Studies in Maize: Praise and Stargaze

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Few GWAS studies were conducted for mapping leaf rust resistance loci in both seedling and adult plant stages, and in elite bread wheat cultivars or breeding lines. Furthermore, to our knowledge, no study has utilized the recently developed high density iSelect 90K SNP array for GWAS analysis of leaf rust resistance in bread wheat.

Genome-wide Association Studies in Maize: Praise and Stargaze

Genome Wide Association Study of Seedling and Adult Plant ...

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Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers.

Genome Wide Association Study of Seedling and Adult Plant ...

TASSEL-GBS: A High Capacity Genotyping by Sequencing ...

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4/8/2015 · TASSEL genotype and phenotype formats. How to tabulate, analyze, and prepare graph from Likert Scale questionnaire data using Ms Excel.

TASSEL-GBS: A High Capacity Genotyping by Sequencing ...

TASSEL Data formats - YouTube

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Genome-Wide Association Study (GWAS) has become the leading method to identify genes underlying human diseases and agriculturally important traits. However, the genetic variants identified so far only explain a small portion of phenotypic variation .

TASSEL Data formats - YouTube

A SUPER Powerful Method for Genome Wide Association Study

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2/28/2014 · Herein, we describe the tassel-gbs pipeline in detail, as implemented in tassel 4, and we benchmark the pipeline based upon a large-scale, species-wide analysis of maize (Zea mays).There were three primary motivations behind the development of this software: (1) Support the use of GBS in high-throughput, accelerated plant breeding, (2) Accommodate the high genomic diversity that is …

A SUPER Powerful Method for Genome Wide Association Study

TASSEL-GBS: A High Capacity Genotyping by Sequencing ...

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performing GWAS. The command-line version of TASSEL, called the Pipeline, provides users the ability to program tasks using a script instead of the graphic user interface (GUI). This feature allows researchers to define tasks using a few lines of code and provides the ability to use TASSEL as part of an analysis pipeline or to

TASSEL-GBS: A High Capacity Genotyping by Sequencing ...

User Manual for TASSEL - West Virginia University

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I have conducted GWAS analysis through TASSEL software using SNPs generated from genotyping by sequencing data(GBS). ... How do I adjust the 'p' value of SNPs-phenotype association study for ...

User Manual for TASSEL - West Virginia University

39 questions in TASSEL | Science topic

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In this study, a total of n = 3850 individuals were recruited between July 1998 and March 2003. A nested case‐control study of European ancestry severe angiographic CAD cases and angiographic normal controls were selected for genome‐wide genotyping.

39 questions in TASSEL | Science topic

A guide to genome‐wide association analysis and post ...

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こんばんわ。今日は以前の投稿でも取り扱ったGWASのcase-control studyで問題となり得る「集団の構造化(以下PF)」について書きます。今回は『Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Grou…

A guide to genome‐wide association analysis and post ...

GWAS カテゴリーの記事一覧 - 統計学と疫学と時々 …

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TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples. ... software for association mapping of complex traits. ... According to genome-wide association study (GWAS) based ...

GWAS カテゴリーの記事一覧 - 統計学と疫学と時々 …

TASSEL: Software for Association Mapping of Complex Traits ...

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1/1/2019 · In this study, four statistical models of GWAS analysis–PLINK 25, TASSEL 20, EMMAX 21, and GEMMA 22 –were used to predict loci significantly associated with grape berry quantitative traits.

TASSEL: Software for Association Mapping of Complex Traits ...

Genome-wide association study of berry-related traits in ...

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研究関係で役立つソフトの備忘録です。 私は主にWindows環境で使用していますが、一部にMacやLinux専用のソフトも含まれてい ...

Genome-wide association study of berry-related traits in ...

岩崎貴也のページ - 解析ソフトウェア

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Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has …

岩崎貴也のページ - 解析ソフトウェア

Genome-wide Association Studies in Maize: Praise and ...

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11/21/2016 · Genome-wide association study (GWAS), which is based on genetic linkage disequilibrium (LD) in a panel including a large number of genotypes representing broadly natural variations, has been used as an alternative approach for exploring the molecular basis and identifying SNPs of complex quantitative traits [27 – 30].

Genome-wide Association Studies in Maize: Praise and ...

Genome-wide association study (GWAS) reveals the genetic ...

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program TASSEL. Although genome-wide association studies (GWAS) have the poten-tial to pinpoint genetic polymorphisms underlying human diseases and agriculturally important traits, false discoveries are a major concern1 and can be partially attributed to spurious associations caused by population structure and unequal relatedness among

Genome-wide association study (GWAS) reveals the genetic ...

Mixed linear model approach adapted for genome-wide ...

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11/9/2016 · Results. An Upland cotton MAGIC population was developed through random-mating of 11 diverse cultivars for five generations. In this study, fiber quality data obtained from four environments and 6071 SNP markers generated via GBS and 223 microsatellite markers of 547 recombinant inbred lines (RILs) of the MAGIC population were used to conduct a genome wide association study (GWAS).

Mixed linear model approach adapted for genome-wide ...

A MAGIC population-based genome-wide association study ...

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In the recent years, in order to dissect complex quantitative traits and identify candidate genes affecting such traits, the association mapping approach has been widely used. This strategy relies on detecting linkage disequilibrium (LD) between genetic markers and genes controlling the phenotype of interest by exploiting the recombination events accumulating over many generations and thus ...

A MAGIC population-based genome-wide association study ...

Association mapping bioinformatics tools | GWAS analysis ...

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Multiple testing for GWAS in Tassel MLM Showing 1-3 of 3 messages. ... Which multiple testing correction method is appropriate for the MLM's p-valuse in GWAS? Could you help please? ... If a study is underpowered and fails to detect any real QTL, then the q-method can mislead one into accepting some tests (rejecting some null hypotheses) in ...

Association mapping bioinformatics tools | GWAS analysis ...

Multiple testing for GWAS in Tassel MLM - Google Groups

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1/10/2017 · Comparing GWAS analyses from PEPIS and TASSEL, we found consistent results for flowering traits with five overlapping peak regions significant for …

Multiple testing for GWAS in Tassel MLM - Google Groups

Development of a multiple-hybrid population for genome ...

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I think this is a correct answer. Age should not be a covariate because it is dependent on your response variable. An alternative could be to model a poisson regression on the age, instead of a logistic regression, which would give you how much each SNP status leads to an increase of one year of age (instead of categories centanarians/non centenarians).

Development of a multiple-hybrid population for genome ...

GWAS: when is it appropriate to add covariates?

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10/10/2016 · Results. We performed a genome-wide association study (GWAS) in PRT including 15 cases and 29 controls and found a statistically strong signal in the genomic region on dog chromosome 38 (CFA38) where KCNJ10 is located. We tested the CAPN1:c.344G > A and KCNJ10:c.627C > G (Transcript XM_545752.4) mutations in a sample of 77 PRT and 9 JRT from Germany as well as …

GWAS: when is it appropriate to add covariates?

Genome-wide association study for hereditary ataxia in the ...

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11/1/2018 · Increasing popularity of high-throughput phenotyping technologies, such as image-based phenotyping, offer novel ways for quantifying plant growth and morphology. These new methods can be more or less accurate and precise than traditional, manual measurements. Many large-scale phenotyping efforts are conducted to enable genome-wide association studies (GWAS), but it is unclear exactly …

Genome-wide association study for hereditary ataxia in the ...

Comparing Genome-Wide Association Study Results from ...

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11/29/2018 · This article introduces the concept of association mapping and the related concepts of linkage disequilibrium (LD), kinship, and population structure. An accompanying tutorial and sample data provide instruction for association mapping using General Linear Model (GLM) and Mixed Linear Model (MLM) procedures in TASSEL software.

Comparing Genome-Wide Association Study Results from ...

Association Mapping Using TASSEL Software - eXtension

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Linking these genomic variants to phenotypes is the main goal in running genome‐wide association studies (GWAS). SNPs can be discovered and called using different technologies and methods, and subsequent quality control must be performed taking into account the …

Association Mapping Using TASSEL Software - eXtension

Genome‐Wide Association Studies in Plants

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Genome-wide association study (GWAS) is widely known to be an important approach for genetic dissection on complex traits. This approach is better than interval mapping in terms of higher resolution, utilization of historic recombination's, a large number of allele mining, and less time consuming (no need to develop mapping population), etc.

Genome‐Wide Association Studies in Plants

Genome-wide association study (GWAS) delineates genomic ...

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3/6/2017 · Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has been made in …

Genome-wide association study (GWAS) delineates genomic ...

Genome-wide Association Studies in Maize: Praise and ...

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2/5/2015 · Corn borers are the primary maize pest; their feeding on the pith results in stem damage and yield losses. In this study, we performed a genome-wide association study (GWAS) to identify SNPs associated with resistance to Mediterranean corn borer in a maize diversity panel using a set of more than 240,000 SNPs. Twenty five SNPs were significantly associated with three resistance traits: 10 …

Genome-wide Association Studies in Maize: Praise and ...

Genome-wide association study reveals a set of genes ...

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1/8/2013 · Linkage Disequilibrium and Recombination Rates. Characterizing patterns of linkage disequilibrium (LD) is critical for the design of association studies (21, 22), interpretation of association peaks (), and the transfer of alleles in marker-assisted selection ().To characterize the mapping resolution for genome scans and GWAS, we quantified the average extent of LD decay and localized patterns ...

Genome-wide association study reveals a set of genes ...

Population genomic and genome-wide association studies of ...

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2/10/2016 · Genome-Wide Association Study. The GWAS revealed a single area of highly significant association (FDR < 0.05) with MP and 4 less significant areas (0.05 < FDR < 0.1), with 10 total significant SNPs. ... TASSEL: software for association mapping of complex traits in diverse samples.

Population genomic and genome-wide association studies of ...

Genome-Wide Association Study in Arabidopsis thaliana of ...

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3.3 Case study 2: Medicago truncatula data. Kang et al. published GWAS results for leaf size and shoot biomass weight traits with a Medicago truncatula HapMap population consisting of 220 accessions with 1 810 466 SNPs using TASSEL (Supplementary Material B). We re-analyzed the same dataset using GWASpro and TASSEL and compared their results.

Genome-Wide Association Study in Arabidopsis thaliana of ...
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