Abstract Background An introgression library is a family of near-isogenic lines in a common genetic background, each of which carries one or more genomic regions contributed by a donor genome. Near-isogenic lines are powerful genetic resources for the analysis of phenotypic variation and are important for map-base cloning genes underlying mutations and traits. With many thousands of distinct genotypes, querying introgression libraries for lines of interest is an issue. Results We have created IView, a tool to graphically display and query near-isogenic line libraries for specific introgressions. This tool incorporates a web interface for displaying the location and extent of introgressions. Each genetic marker is associated with a position on a reference map. Users can search for introgressions using marker names, or chromosome number and map positions. This search results in a display of lines carrying an introgression at the specified position. Upon selecting one of the lines, color-coded introgressions on all chromosomes of the line are displayed graphically. The source code for IView can be downloaded from <url>http://xrl.us/iview</url>. Conclusions IView will be useful for those wanting to make introgression data from their stock of germplasm searchable. </p

Christopher A Bottoms

LD Stein

MD McMullen

Michael D McMullen

Sherry Flint-Garcia

TJ Hubbard

English

PubMed

Abstract Background An introgression library is a family of near-isogenic lines in a common genetic background, each of which carries one or more genomic regions contributed by a donor genome. Near-isogenic lines are powerful genetic resources for the analysis of phenotypic variation and are important for map-base cloning genes underlying mutations and traits. With many thousands of distinct genotypes, querying introgression libraries for lines of interest is an issue. Results We have created IView, a tool to graphically display and query near-isogenic line libraries for specific introgressions. This tool incorporates a web interface for displaying the location and extent of introgressions. Each genetic marker is associated with a position on a reference map. Users can search for introgressions using marker names, or chromosome number and map positions. This search results in a display of lines carrying an introgression at the specified position. Upon selecting one of the lines, color-coded introgressions on all chromosomes of the line are displayed graphically. The source code for IView can be downloaded from http://xrl.us/iview. Conclusions IView will be useful for those wanting to make introgression data from their stock of germplasm searchable. </p

Flint-Garcia Sherry

Bottoms Christopher A

McMullen Michael D

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BMC Bioinformatics

IView: introgression library visualization and query tool

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PROCEEDINGS Open Access
IView: introgression library visualization and
query tool
Christopher A Bottoms1*, Sherry Flint-Garcia1,2, Michael D McMullen1,2
From Seventh Annual MCBIOS Conference. Bioinformatics: Systems, Biology, Informatics and Computation
Jonesboro, AR, USA. 19-20 February 2010
Abstract
Background: An introgression library is a family of near-isogenic lines in a common genetic background, each of
which carries one or more genomic regions contributed by a donor genome. Near-isogenic lines are powerful
genetic resources for the analysis of phenotypic variation and are important for map-base cloning genes
underlying mutations and traits. With many thousands of distinct genotypes, querying introgression libraries for
lines of interest is an issue.
Results: We have created IView, a tool to graphically display and query near-isogenic line libraries for specific
introgressions. This tool incorporates a web interface for displaying the location and extent of introgressions. Each
genetic marker is associated with a position on a reference map. Users can search for introgressions using marker
names, or chromosome number and map positions. This search results in a display of lines carrying an
introgression at the specified position. Upon selecting one of the lines, color-coded introgressions on all
chromosomes of the line are displayed graphically.
The source code for IView can be downloaded from http://xrl.us/iview.
Conclusions: IView will be useful for those wanting to make introgression data from their stock of germplasm
searchable.
Background
Near isogenic lines (NILs) are lines derived from a parti-
cular parental line (i.e. the recurrent parent) that carry
genomic regions of another line (i.e. the donor parent).
An introgression library is a family of NILs with com-
mon recurrent and donor parents. The NILs are created
by crossing the donor and recurrent parents, and back-
crossing the F1 and subsequent generations with the
recurrent parent, thereby reducing the amount of donor
genome in each generation. The resulting offspring are
then self-pollinated several generations to produce the
NILs. The genomes of the NILs are primarily that of the
recurrent parent, with one or more regions of the gen-
ome originating from the donor parent genome (i.e.
introgressions). Each NIL in a family will contain differ-
ent combinations of introgressions.
Introgression libraries are useful for testing the pheno-
typic effects of donor introgressions and as the starting
material for map-based cloning populations. Since NILs
are genetically similar to the recurrent parent except for
the genomic region of interest, they can be used to test
the phenotypic effects of the donor region. Fine map-
ping studies are initiated by choosing a NIL with the
smallest introgression surrounding a given region of the
genome. Being able to quickly query an introgression
library for introgressions of interest facilitates their use
in genetic studies.
Implementation
IView is a Perl-based web application. Prior to setting
up the web interface, users provide input files that allow
determining introgressions. Data are stored in a MySQL
database. Template Toolkit templates are used for the
web pages. IView is currently configured to run using
the “Plack” server that is automatically installed along1Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
Full list of author information is available at the end of the article
Bottoms et al. BMC Bioinformatics 2010, 11(Suppl 6):S28
http://www.biomedcentral.com/1471-2105/11/S6/S28
© 2010 Bottoms et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.
with the source code. IView has been tested and works
well on 64-bit Debian Lenny Linux.
Installation
Installation on Debian Linux
A Debian Linux-specific installation bash script can be
downloaded from http://xrl.us/iviewdebbsh. This script
can be used to install everything that is needed to run
IView. If you do not have super-user privileges, then
contact the system administrator to ensure that the fol-
lowing packages are installed: mysql-server-5.0, make,
gcc, and libgd2-xpm-dev. Otherwise, the installation
script will ask for the “sudo“ password so that it can
install these automatically.
To use the installation script, first open a terminal
window. To do so, click on “Applications”, then “Acces-
sories”, and then “Terminal”. Please remember that
Linux is case sensitive. Type the following commands,
pressing <ENTER> after each one (commands are in the
font Courier New).
wget http://xrl.us/iviewdebbsh
chmod u+x iview-deb.bsh
./iview-deb.bsh
The script will install the MySQL relational database
management system, if it is not already installed. During
installation of MySQL, a window will open that will
request that you create a password for the MySQL root
user. Note that this is distinct from the system root.
Enter the password that you wish to create and then
press <ENTER>. As is usual when creating passwords,
you will then be asked to re-enter the new password.
After entering it again, press <ENTER>. Please keep
track of this password, as it will be needed later.
For all other questions that occur during installation,
the user can choose to accept the defaults by simply
pressing <ENTER>.
This command will start installation of multiple pro-
grams and takes about twenty minutes.
Setting up the program with the sample data set
These instructions should work equally well for users
wanting to view their own introgression data. These
instructions pick up at the end of the installation
instructions. As part of the installation process, the
directory “IView” should have been created. To change
to this directory and run the sample, type the following
two commands, pressing <ENTER> after each one:
cd IView
perl setup_site.pl sample.cfg
This last command processes a sample dataset. You
will be asked for the MySQL root password (that you
created earlier) so that a dummy user can be created for
accessing the sample database.
To start the web server, type the following commands,
pressing <ENTER> after each one:
cd cgi-bin
plackup sample.psgi
Now, please minimize the terminal window, since it is
now tied up by output from the web server. When you
need to stop the web server, click in this terminal win-
dow and press the <Ctrl> key at the same time as the
<C> key.
Now open another terminal and type the following
and then press <ENTER>:
firefox http://localhost:5000/sample
A web browser should now open to the IView search
page, similar to Figure 1.
Type “ PZA00832.1” in the first “Include” box and
press <ENTER>.
You should now see a page similar to the one shown
in Figure 2. Click on one of the lines listed to see a NIL
Introgression Summary page, similar to the one shown
in Figure 3. Scroll down for the legend.
Input files
Processing and viewing data with IView requires gener-
ating several input files beforehand: a reference map file,
relationships file, a raw data file, and a configuration
file. We cannot overemphasize the need to format these
files correctly. If you encounter any difficulties with pre-
paring these files or running IView, please do not hesi-
tate to contact us.
reference map file
A reference genetic map provides a common framework
within which to compare single nucleotide polymorph-
ism (SNP) data. Reference map data include the SNP
name, the chromosome on which it is located, and the
genetic position on the chromosome. In Table 1 is a
representation of the first few lines of a reference map
file. This is a tab-delimited file with the following col-
umns: marker name, chromosome number, and marker
position. The headers should not be included, but are
only included in Table 1 to help clarify what each col-
umn represents.
relationships file
The first line contains headers and the remaining lines
contain tab-delimited fields in the following order: sam-
ple id, sample name, group name, recurrent parent,
donor parent, sample id for a sample that this is a repli-
cate of, sample id for the F1 of the recurrent and donor
parents. If any of the last four fields are not applicable,
they can be left blank. However, being blank when they
are applicable will result in failure of the program to
analyze the data properly. See Table 2 for a representa-
tion of this file.
Bottoms et al. BMC Bioinformatics 2010, 11(Suppl 6):S28
http://www.biomedcentral.com/1471-2105/11/S6/S28
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Figure 1 Initial Search Page. Queries identify NILs having (or not having) specified donor regions in the genome. Regions can be defined by
marker names or by chromosome numbers and map positions corresponding to those of the reference map. This example uses the current
maize nested association map[12] as the reference map.
Bottoms et al. BMC Bioinformatics 2010, 11(Suppl 6):S28
http://www.biomedcentral.com/1471-2105/11/S6/S28
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raw-data file
This file contains data in a matrix format in which rows
represent genotypes at individual markers and columns
represent each sample. The file has up to four parts, the
last three of which are relevant to processing data with
IView:
(1) Header section. The beginning of the file can be
any text as long as it does not contain the string
“[Data]”.
(2) End of Header indicator. The line just before the
sample IDs must contain the text “[Data]”.
(3) Sample ID line. This line contains a tab character
followed by tab-delimited sample IDs. These sample IDs
correspond to columns of data in the subsequent lines.
Sample IDs in this line must be represented in the rela-
tionships file in order to be processed.
(4) The remaining lines contain the name of the mar-
ker in the first field and data in the remaining fields.
See Table 3 for a representation of this file.
configuration file
See Table 4 for an example configuration file with
explanations. The configuration file is arranged as
name/value pairs separated by whitespace (tabs and/or
spaces).
Results and discussion
GBrowse [1] and Ensembl [2] are two of the most popu-
lar web-based genome browsers available. After consid-
ering these browsers, we decided to create a tool that
required less configuration and initial setup for uses spe-
cific for displaying introgression lines. Another program
related to our problem domain is CSSL Finder, a desk-
top application for managing introgression data.[3]
Unlike IView, it is dependent on Microsoft Excel and is
not readily configured for displaying its data on the web.
In comparison with the genome- browsers, IView can
easily be installed and used by biologists with minimal
computer skills (see Installation section). Our testing
volunteer, who has no experience using or installing
Perl programs, successfully installed and used IView.
Figure 2 Query Results. Links for each of the NILs matching the
query result are shown. Each link leads to a NIL Introgression
Summary page.
Figure 3 NIL Introgression Summary. Introgression information
for a NIL is displayed by graphically and in a table.
Table 1 Representation of a reference map file
Marker Name Chromosome Marker position
PZA01271.1 1 0
PZA03613.1 1 9
PZA02129.1 1 37
PZA02032.1 1 51
Bottoms et al. BMC Bioinformatics 2010, 11(Suppl 6):S28
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Before being able to display introgression data, intro-
gressions must be determined. Given SNP genotype data
for recurrent, donor, and NIL lines, IView can be used
to determine the locations of introgressions.
Introgressions can be displayed and queried via
IView’s web interface, which comprises three web-pages.
First is the initial search page that allows the user to
identify NILs that have, or that lack, introgressions in
specific locations (Figure 1). On the initial search page,
there are two sets of search boxes: one for searching by
marker names and the other for searching by chromo-
some name and reference map position. Next, the
Query Results page displays all of the lines matching the
query (Figure 2), and allows the user to choose a speci-
fic NIL. After choosing a specific NIL, the NIL Intro-
gression Summary page summarizes all of the
introgressions in the chosen line, both graphically and
in tabular form (Figure 3).
So far, IView has only been used in-house for display-
ing and querying Teosinte introgressions in maize NILs.
We look forward to seeing it used for introgression lines
in others species as well.
Conclusions
We have found this tool useful in our own work and
expect it to be useful to others working with near-iso-
genic introgression lines.
Availability and requirements
Project name: IView: Introgression library and visualiza-
tion tool
Project home page:http://sourceforge.net/projects/
iviewer/
Operating system(s): Debian Linux
Programming language: Perl
Other requirements:
GD Graphics Library [4]
MySQL [5]
Major Perl module dependencies (will be auto-
matically installed, if needed)
CGI::Application [6]
CGI::Application::Plugin::TT [7]
File::Slurp [8]
GD [9]
Template [10]
Plack [11]
License: Perl license
List of abbreviations
CGI: common gateway interface; NIL: near-isogenic line; SNP: single
nucleotide polymorphism.
Competing interests
The author declare that they have no competing interests.
Authors’ contributions
CAB contributed to design, performed programming, and prepared the
manuscript. SFG contributed design ideas for the program. MDM
contributed design ideas and supervised the project. All authors have read
and approved the final version of the manuscript.
Table 2 Representation of a relationships file
Sample ID Sample name Group Recurrent Parent Donor Parent Replicate of F1 ancestor
1 B73 Control
2 B73 Control 1
3 B73 Control 1
4 Mo17 Control
5 Mo17 Control 4
6 Mo17 Control 4
7 M0021 IBM 1 4
8 B73xZ100 F1 1
9 TIP Z Inbred 1 8
Table 3 Representation of a raw-data file
[DATA] sample IDs
marker 1 2 3 4 5 6 7 8
SNP1 AA AA AA AA AA AG GG GG
SNP2 AA AA AA AA AA AT AA AA
SNP3 CC CC CT CC CC CC CC CC
SNP4 GG GG GG GG GG AG – –
SNP5 GG GG GG GG GG AG AG AG
SNP6 AA AA – – – AC CC CC
SNP7 AA AA AA AA AA AG TT TT
SNP8 TT GG CC CC CC CC CC CC
Table 4 Sample configuration file
Key-Value pairs (i.e. file contents) Explanation
DB_NAME sample Name for the new database to
be created.
RAW_DATA sample_data.tab Data file containing genotype
data.
REF_MAP sample_ref_map.tab Reference map file.
RELATIONSHIPS sample_relationships.
tab
Relationships file.
Bottoms et al. BMC Bioinformatics 2010, 11(Suppl 6):S28
http://www.biomedcentral.com/1471-2105/11/S6/S28
Page 5 of 6
Acknowledgements
This project was supported by National Science Foundation Plant Genome
Program Grant DBI-0820619 and funds from USDA-ARS to SFG and MDM.
We would like to thank Marcella Bottoms for testing our software.
This article has been published as part of BMC Bioinformatics Volume 11
Supplement 6, 2010: Proceedings of the Seventh Annual MCBIOS
Conference. Bioinformatics: Systems, Biology, Informatics and Computation.
The full contents of the supplement are available online at
http://www.biomedcentral.com/1471-2105/11?issue=S6.
Author details
1Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
2Plant Genetics Research Unit, USDA-Agricultural Research Service, Columbia,
MO 65211, USA.
Published: 7 October 2010
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doi:10.1186/1471-2105-11-S6-S28
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E: Ensembl 2007. Nucleic Acids Res

ES: Genetic properties of the maize nested association mapping population. Science

Lewis S: The generic genome browser: a building block for a model organism system database. Genome Res

Template Toolkit.

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