scholarly journals Optimization of BSA-seq experiment for QTL mapping

2021 ◽  
Author(s):  
Likun Huang ◽  
Weiqi Tang ◽  
Weiren Wu
Keyword(s):  
Qtl Mapping ◽  
Population Size ◽  
Dominance Effect ◽  
Bulked Segregant Analysis ◽  
Design Tool ◽  
Web Based ◽  
Intrinsic Factors ◽  
Degree Of Dominance ◽  
Small Pool ◽  
Pool Proportion

Abstract Deep sequencing-based bulked segregant analysis (BSA-seq) has become a popular approach for quantitative trait loci (QTL) mapping in recent years. Effective statistical methods for BSA-seq have been developed, but how to design a suitable experiment for BSA-seq remains unclear. In this paper, we show in theory how the major experimental factors (including population size, pool proportion, pool balance, and generation) and the intrinsic factors of a QTL (including heritability and degree of dominance) affect the power of QTL detection and the precision of QTL mapping in BSA-seq. Increasing population size can improve the power and precision, depending on the QTL heritability. The best proportion of each pool in the population is around 0.25. So, 0.25 is generally applicable in BSA-seq. Small pool proportion can greatly reduce the power and precision. Imbalance of pool pair in size also causes decrease of the power and precision. Additive effect is more important than dominance effect for QTL mapping. Increasing the generation of filial population produced by selfing can significantly increase the power and precision, especially from F2 to F3. These findings enable researchers to optimize the experimental design for BSA-seq. A web-based program named BSA-seq Design Tool is available at http://124.71.74.135/BSA-seqDesignTool/ and https://github.com/huanglikun/BSA-seqDesignTool.

scholarly journals The Narrative Event Diagram

2009 ◽  
pp. 101-118
Author(s):  
Helyn Gould ◽  
Michael Hughes ◽  
Paul Maharg ◽  
Emma Nicol
Keyword(s):  
Professional Learning ◽  
Information Science ◽  
Further Education ◽  
Design Tool ◽  
Design History ◽  
Game Based Learning ◽  
Web Based ◽  
Design Iteration ◽  
The United Kingdom ◽  
Narrative Event

Game-based learning and simulation is a powerful mode of learning, used by industries as diverse as aviation and health sciences. While there are many generic Virtual Learning Environments available to further education and higher education in the United Kingdom, there is no widely available open-source Web-based simulation environment for professional learning. The SIMPLE (SIMulated Professional Learning Environment) project has designed, created, implemented and is in the process of evaluating such an environment in a range of disciplinary settings. The simulations that are being created place both undergraduates and postgraduates in a professional context where their work is, as it will be in the workplace, distributed between tools, colleagues, resources, anticipated, and unanticipated problems. One of the key tools that staff will use to create simulations is the “narrative event diagram”, a design tool as well as a means by which the narrative of the simulation is constructed. This chapter will describe the tool, its design history and context, its current use, and next design iteration. In particular it will show the interdisciplinary genesis of the tool’s design, arising from the confluence of computer science, information science, and narrative theory, and its power in designing professional educational simulations.

Web-Based Cad Tools for a Networked Manufacturing Service

1998 ◽  
Author(s):  
Fu-Chung F. Wang ◽  
Paul K. Wright
Keyword(s):  
New Product Development ◽  
Design Tool ◽  
Internet Technology ◽  
Machining Process ◽  
Global Network ◽  
The Internet ◽  
Distributed Design ◽  
Cad Tools ◽  
Web Based ◽  
Design And Manufacturing

Abstract New techniques in Information Technology are now changing not only our daily life, but also the professional practice of product design and manufacturing for new product development. Internet technology in particular opens up another domain for building future CAD/CAM environments. This environment will be a global, network-centric environment with various members providing different software tools, manufacturing facilities, and analysis services for distributed design and fabrication. In this paper, we first briefly describe a vision and current development in a distributed design and manufacturing environment. The paper then emphasizes how current CAD tools will evolve to facilitate the distributed design and fabrication process. In particular, the development of a set of Web-based design tools for fabricating parts using a machining process via the Internet is presented. Experiments on machining 2-1/2 D and freeform parts through this Java-based design tool have shown the feasibility for a networked machining service via the Internet.

scholarly journals Identification of a Major QTL (qRRs-10.1) That Confers Resistance to Ralstonia solanacearum in Pepper (Capsicum annuum) Using SLAF-BSA and QTL Mapping

2019 ◽  
Vol 20 (23) ◽  
pp. 5887 ◽  
Author(s):  
Heshan Du ◽  
Changlong Wen ◽  
Xiaofen Zhang ◽  
Xiulan Xu ◽  
Jingjing Yang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Capsicum Annuum ◽  
Ralstonia Solanacearum ◽  
Bulked Segregant Analysis ◽  
Severity Index ◽  
Clear Cut ◽  
Close Proximity ◽  
Specific Locus ◽  
Resistance Markers ◽  
Resistant Rootstock

The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt (BW), a major disease of pepper (Capsicum annuum). The genetic basis of resistance to this disease in pepper is not well known. This study aimed to identify BW resistance markers in pepper. Analysis of the dynamics of bioluminescent R. solanacearum colonization in reciprocal grafts of a resistant (BVRC 1) line and a susceptible (BVRC 25) line revealed that the resistant rootstock effectively suppressed the spreading of bacteria into the scion. The two clear-cut phenotypic distributions of the disease severity index in 440 F2 plants derived from BVRC 25 × BVRC 1 indicated that a major genetic factor as well as a few minor factors that control BW resistance. By specific-locus amplified fragment sequencing combined with bulked segregant analysis, two adjacent resistance-associated regions on chromosome 10 were identified. Quantitative trait (QTL) mapping revealed that these two regions belong to a single QTL, qRRs-10.1. The marker ID10-194305124, which reached a maximum log-likelihood value at 9.79 and accounted for 19.01% of the phenotypic variation, was located the closest to the QTL peak. A cluster of five predicted R genes and three defense-related genes, which are located in close proximity to the significant markers ID10-194305124 or ID10-196208712, are important candidate genes that may confer BW resistance in pepper.

Next-generation sequencing-based bulked segregant analysis for QTL mapping in the heterozygous species Brassica rapa

2019 ◽  
Vol 132 (10) ◽  
pp. 2913-2925 ◽  
Author(s):  
Noriaki Itoh ◽  
Tenta Segawa ◽  
Muluneh Tamiru ◽  
Akira Abe ◽  
Shota Sakamoto ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Qtl Mapping ◽  
Brassica Rapa ◽  
Bulked Segregant Analysis ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Simulation of Ecological and Evolutionary Interactions of Darwin's Finches—A Multimedia Learning Tool

HortScience ◽  
1997 ◽  
Vol 32 (6) ◽  
pp. 983b-983
Author(s):  
R.D. Quinn
Keyword(s):  
Population Size ◽  
Pilot Project ◽  
Early Summer ◽  
Initial Population ◽  
Introductory Biology ◽  
Web Based ◽  
Darwin's Finches ◽  
Darwin’S Finches ◽  
Large Numbers ◽  
Bill Morphology

Dr. Quinn is one of a team of six biology professors from six different CSU campuses collaborating on this pilot project. EvolvelT is a web-based method for students to learn the fundamentals of natural selection and speciation by simulating natural processes. The simulation will be modeled on the evolution of Darwin's Finches in the Galapagos Islands. Learners will manipulate variables such as initial population size, variability and heritability of bill morphology, and quantity and quality of seeds, and then observe changes with time in population size and bill morphology. The interactive model will allow variables to be changed and simulations to be repeated, producing results that can be graphed and statistically analyzed. The Integrated Technology Strategy (ITS) of the California State University System (CSU) is using the Internet to create new and more flexible learning opportunities. Recently the ITS brought together biologists from several CSU campuses to explore ways to use technology to improve learning in introductory biology laboratories for non-science students. These laboratories were chosen because they affect large numbers of students at all campuses. Development criteria include applicability across the CSU, improvement in learning quality, accessibility to large numbers of students, and measurable success. We selected evolution as a topic for web-based learning because it is a central concept of biology, and it is relatively difficult to teach in conventional introductory biology laboratories. Our development team will work with multimedia design specialists to insure that the web presentation promotes scientifically sound and efficient learning. We are collaborating via e-mail and occasional video conferences and face-to-face meetings. We will work on the actual teaching materials via a web page. The initial prototype will be ready by early summer 1997 and will be tested, modified, and released for beta testing by summer's end.

scholarly journals PAVOOC: Designing CRISPR sgRNAs using 3D protein structures and functional domain annotation

2018 ◽  
Author(s):  
Moritz Schaefer ◽  
Dr. Djork-Arné Clevert ◽  
Dr. Bertram Weiss ◽  
Dr. Andreas Steffen
Keyword(s):  
Gene Editing ◽  
State Of The Art ◽  
Protein Structures ◽  
Design Tool ◽  
Protein Crystal ◽  
Functional Domain ◽  
Web Based ◽  
Domain Annotation ◽  
Sgrna Design ◽  
Processing Steps

AbstractSummary: sgRNAs targeting the same gene can significantly vary in terms of efficacy and specificity. PAVOOC (Prediction And Visualization of On- and Off-targets for CRISPR) is a web-based CRISPR sgRNA design tool that employs state-of-the art machine learning models to prioritize most effective candidate sgRNAs. In contrast to other tools, it maps sgRNAs to functional domains and protein structures and visualizes cut sites on corresponding protein crystal structures. Furthermore, PAVOOC supports HDR template generation for gene editing experiments and the visualization of the mutated amino acids in 3D.Availability and Implementation: PAVOOC is available under https://pavooc.me and accessible using current browsers (Chrome/Chromium recommended). The source code is hosted at github.com/moritzschaefer/pavooc under the MIT License. The backend, including data processing steps, and the frontend is implemented in Python 3 and ReactJS respectively. All components run in a simple Docker environment.Contact: [email protected]

BRM: a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing

2019 ◽  
Vol 36 (7) ◽  
pp. 2150-2156 ◽  
Author(s):  
Likun Huang ◽  
Weiqi Tang ◽  
Suhong Bu ◽  
Weiren Wu
Keyword(s):  
Confidence Interval ◽  
Qtl Mapping ◽  
Statistical Method ◽  
Deep Sequencing ◽  
Multiple Testing ◽  
Bulked Segregant Analysis ◽  
Supplementary Information ◽  
Multiple Testing Correction ◽  
Significance Threshold ◽  
Trait Locus

Abstract Motivation Bulked segregant analysis by deep sequencing (BSA-seq) has been widely used for quantitative trait locus (QTL) mapping in recent years. A number of different statistical methods for BSA-seq have been proposed. However, determination of significance threshold, the key point for QTL identification, remains to be a problem that has not been well solved due to the difficulty of multiple testing correction. In addition, estimation of the confidence interval is also a problem to be solved. Results In this paper, we propose a new statistical method for BSA-seq, named Block Regression Mapping (BRM). BRM is robust to sequencing noise and is applicable to the case of low sequencing depth. Significance threshold can be reasonably determined by taking multiple testing correction into account. Meanwhile, the confidence interval of QTL position can also be estimated. Availability and implementation The R scripts of our method are open source under GPLv3 license at https://github.com/huanglikun/BRM. Supplementary information Supplementary data are available at Bioinformatics online.

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