https://github.com/simhayn/basil_mapping

Script and data assosiated with basil genetic mapping for QTL analysis
https://github.com/simhayn/basil_mapping

genetic-mapping machine-learning plant-disease rqtl rstudio

Last synced: about 21 hours ago
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Script and data assosiated with basil genetic mapping for QTL analysis

• Host: GitHub
• URL: https://github.com/simhayn/basil_mapping
• Owner: simhayn
• License: mit
• Created: 2024-06-03T10:01:39.000Z (5 months ago)
• Default Branch: main
• Last Pushed: 2024-06-16T10:12:09.000Z (5 months ago)
• Last Synced: 2024-06-17T06:35:33.897Z (5 months ago)
• Topics: genetic-mapping, machine-learning, plant-disease, rqtl, rstudio
• Language: R
• Homepage:
• Size: 125 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Basil Genetic Mapping and QTL Analysis

Welcome to the Basil Genetic Mapping and QTL Analysis repository! This project focuses on the genetic mapping and analysis of quantitative trait loci (QTL) in basil (Ocimum basilicum).

## Table of Contents

- [Overview](#overview)

- [Thesis Information](#thesis-information)

- [Usage](#usage)

- [Data](#data)

- [Contributing](#contributing)

- [License](#license)

- [Contact](#contact)

## Overview

This repository contains code and data for performing genetic mapping and QTL analysis in basil. The goal is to identify genetic regions associated with important traits in basil, such as disease resistance and red coloring.

## Thesis Information

This project was conducted as part of my master's thesis at Bar Ilan University. The research was aimed at advancing our understanding of the genetic basis of key traits in basil, with potential applications in breeding and agriculture.

- **Student**: Nataly Yakobov

- **University**: Bar Ilan University

- **Department**: Ecology

- **Year**: 2021

- **Traits Studied**: Downy Mildew and Fusarium resistance, Cold tolerance, Anthocyanin accumulation (Red Color Intensity) on Leaves, Stems and Flowers, in Young and mature plants in Greenhouse or Field environments. 

## Usage

The repository includes a markdown file [basil-genetics.md](basil-genetics.md) of genetic mapping and QTL analysis. The results are found in the folder [results](results). Here is the outline:

1. **Data Preprocessing** 

2. **Genetic Map Construction**

3. **Map Evaluation**

   

4. **Exploratory Data Analysis**

5. **QTL Analysis**

6. **QTL Visualization on the Map using LinkageMapView**

## Data

The fictive data used in this project includes genotypic and phenotypic data for F2 population of basil. The original data is private.

## Contributing

I welcome contributions to this project! If you have suggestions, bug reports, or improvements, please open an issue or submit a pull request.

1. **Fork the repository.**

2. **Create a new branch.**

3. **Make your changes.**

4. **Submit a pull request.**

Please follow the [Contributor Covenant Code of Conduct](https://www.contributor-covenant.org/version/2/0/code_of_conduct/).

## License

This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.

## Contact

For any questions or inquiries, please contact Nataly Yakobov at [[email protected]](mailto:[email protected]).

Thank you for your interest in the Basil Genetic Mapping and QTL Analysis project!

"# Basil-Genetics"