At the end of the chapter, we describe the internal structure of qtl mapping data within r qtl. You can either simulate a data set or collect one yourself. Mapmaker qtl tutorial page 1 mapping genes controlling quantitative traits using mapmaker qtl table of contents. Ici mapping manual quantitative trait locus genetic. Use either winqtlcart online help or the pdf manual. It allows users to perform qtl mapping for continuous and discrete traits within the sas platform. Windows qtl cartographer maps quantitative trait loci qtl in cross populations from inbred lines. With r qtl, one may import data in several different formats by use of the function read.
Pdf a reference manual and tutorial for qtl mapping. The method has been implemented in qtl cartographer to facilitate its. Over the last two decades advances in genotyping technology, and the development of quantitative genetic analytical techniques have made it possible to dissect complex traits and link quantitative variation in traits to allelic variation on chromosomes or quantitative trait loci qtls. Click the link below to view the pdf manual in your browser. Citeseerx scientific documents that cite the following paper. Weir and zhaobang zeng program in statistical genetics department of. Qtl seq to rice recombinant inbred lines and f 2 populations and successfully identi. Software for mapping qtl with epistatic and qe interaction effects. Weir and zhaobang zeng program in statistical genetics bioinformatics research center department of statistics north carolina state university. The first phase in using qtl cartographer is to create some data.
Tutorial multiple qtl mapping mqm analysis for r qtl danny arends, pjotr prins, karl w. Campaign cartographer is all about helping you take the maps from your imagination and creating a visual representation of them. Qtl cartographer a reference manual and tutorial for qtl mapping christopher j. Before using genotype data, you should clean the data bad markers, monomorphic etc this will be in appendix process 1. Jansen october 27, 2014 1 1 introduction multiple qtl mapping mqm provides a sensitive approach for mapping quantititive trait loci qtl in experimental populations. In the present study, we report on finemapping of the minor qrfg2 that is located on chromosome 1 and account for 8.
Some data may need to be formatted manually before. Analysis of experimental crosses to identify genes called quantitative trait loci, qtls contributing to variation in quantitative traits. Since lander and botstein proposed the interval mapping method for qtl mapping data analysis in 1989, tremendous progress has been made in the last many years to advance new and powerful statistical methods for qtl analysis. Once r is installed, and provided that your computer has an internet connection, it is easiest to install r qtl by first invoking r and then typing the following. Methods and protocols, expert researchers in the field detail methods and. The development of this software as an addon to r allows us to take advantage of the basic mathematical and.
Pdf quantitative trait locus qtl analyses using qtl. Recent research progress has been focused on statistical methods and issues for mapping multiple qtl together. Andor, realtime loop closure in 2d lidar slam, in robotics and automation icra, 2016 ieee international conference. It is contained within the distribution for each platform in a sudirectory doc pdf or the folder pdf inside the folder doc. If you use cartographer for your research, we would appreciate it if you cite our paper.
An adobe portable document format pdf version is available with the distribution of. This file can be printed or viewed using acrobat reader. Weir and zhaobang zeng program in statistical genetics. Wang s, basten cj, zeng zb 2012 windows qtl cartographer 2. The manual for qtl cartographer is written in project on digestive system of human body pdf latex2e. The qtl were identified by composite interval mapping cim using windows qtl cartographer version 2. Composite interval mapping and multiple interval mapping. The genomic region associated with the expression of a quantitative trait is referred to as quantitative trait locus qtl, which may contain one or more genes. Composite interval mapping by a scheme from qtl cartographer. Stalk rot is one of the most devastating diseases in maize worldwide. Manual the manual for qtl cartographer is written in latex2e.
Background about the algorithms developed for cartographer can be found in the following publication. Qtl mapping data into r qtl, we describe some of the example data sets that will be considered further in later chapters, and we demonstrate how one may simulate qtl mapping data in r qtl. Program in statistical genetics bioinformatics research center department of statistics. The manual for qtl cartographer is written in latex2e. Qtl analysis was performed using windows qtl cartographer 2. Windows qtl cartographer is a user friendly version of qtl cartographer. Welcome to the wonderful world of fantasy mapmaking. Tutorial multipleqtl mapping mqm analysis for rqtl.
Algorithms and programs for mapping quantitative trait. This file can be printed or viewed using acrobat reader, available through the adobe website. An adobe portable document format pdf version is available with the distribution of the. Qtl phenotypeexpression, eqtl, candidate gene and association data gwas, and copy number variations cnv mapped to livestock animal genomes, in order to facilitate locating and comparing discoveries within and between species. Finemapping of qrfg2, a qtl for resistance to gibberella. Rcross uses the general genetic model developed by cockerham 1954.
A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. This manual is the guide to get you started with that process. A practical example of tomato qtl mapping using a ril. Simulation study showed that qtl seq is able to detect qtls over wide ranges of. During these pages i will try to give to the skills and knowledge to. One will contain the information on a genetic linkage map marker order, chromosome assignment and recombination. Qtl cartographer manual pdf exporting source data to qtl cartographer. Mapping quantitative trait loci qtl is important for studying the genetic basis. Check the qtl cartographer manual whether and how it may facilitate this.
It has a gui interface and runs under microsoft windows. Winqtlcart includes a powerful graphic tool for presenting mapping results and can import and export data in a variety of formats. Weir and zhaobang zeng program in statistical genetics bioinformatics research center department of statistics. The 95% threshold level for calling qtl was determined by. Shuyu liu presents for the fall 20 tcap graduate student seminar series. How can one do qtl analysis in the qtl cartographer with the. In our previous study, two qtls, a major qrfg1 and a minor qrfg2, were identified in the resistant inbred line 1145 to confer resistance to gibberella stalk rot. To troubleshoot this problem, open one of winqtlcarts sample files in notepad and compare it to the file you specified. Improving quantitative trait loci mapping resolution in. An adobe portable document format pdf version is available with the distribution of the programs. Winqtlcart includes a powerful graphic tool for presenting and summarizing mapping results and can import and export data in a. Detection of qtl epistsasis and qtl by environment. Mapping genes controlling quantitative traits using. Write an easily understood user manual for both qtl cartographer and windows qtl cartographer to help novice users to navigate through the program, to understand the analysis methods, and to interpret output results.
The internal data structure used by r qtl is rather complicated, and is described in the help. It is implemented as an addon package for the freely available and widely used statistical languagesoftware r see the r project homepage. Quantitative trait locus qtl analyses using qtl cartographer. Proc qtla sas procedure for mapping quantitative trait loci. State university, bioinformatics research center windows qtl cartographer 2. Rqtl is an extensible, interactive environment for mapping quantitative trait loci qtl in experimental crosses. In this chapter, we provide an introduction of composite interval mapping and multiple interval mapping methods for mapping qtl from inbred line crosses and also detailed instructions to perform the analyses in windows qtl cartographer. The qtl cartographer manual explains some other crosses that are possible. Tutorial for mapmaker qtl 7 getting data into mapmaker qtl 8 starting mapmaker qtl 10 preliminary examination of the trait data 12 scanning the genome for putative qtls 16. Proc qtl is a userdefined sas procedure for mapping quantitative trait loci qtl.