BioResource newsletter BioResource Now!
  October 2013
Vol.9 No.10
PDF download
 Hot News <No. 43>
CIMMYT wheat breeding and Japan's contribution to world wheat production
Read more >>>

 Ongoing Column <No.84>
Easy and free mapping of NGS data to genomic data  ∼Part 1∼

 Database of This Month National BioResource Project


Bioresources information is available at the following URLs

 Hot News <No. 43>

CIMMYT Wheat Breeding and Japan's Contribution to World Wheat Production

Masahiro Kishii, Head of Global Wheat Program
(International Maize and Wheat Improvement Center)

The International Maize and Wheat Improvement Center (CIMMYT; located in Mexico; Photo 1) is an international breeding center aiming to improve living standards of poor farmers in the world by providing better wheat and maize varieties. One of the achievements of the institute is a pioneer work on the development of semi-dwarf wheat varieties headed by Dr. Norman Borlaug that led to the Green Evolution. Since then, many of the wheat varieties produced in CIMMYT have been not only directly released to developing countries where their own breeding capacity has not been sufficient but also utilized as breeding materials in many industrialized counties.

As predicted by a report that the world population will increase to 10.9-16.6 billion by the end of this century (UN DESA 2013;, it is necessary to keep releasing higher yield wheat varieties to satisfy increasing food demand.  But in recent years it has become more difficult to catch up this mandate because of global climate change that would cause many abiotic stresses such as drought and heat.

To overcome these difficulties, CIMMYT wheat-breeding program has been utilizing any kind of key methodologies that would be able to facilitate for releasing higher yield and stress resistance varieties, including molecular technique, bioinformatics (such as genomic selection), transgenic, physiological approaches, F1 hybrid wheat, improved agronomical practices and, of course, use of genetic resources (landraces, wheat ancestor and alien species).

  Photo 1
Photo 1: CIMMYT headquarter in Mexico
Photo: Dr. Kishii in front of the Genebank Building

It is not known by many Japanese people that Japan has been hugely helping the works of CIMMYT by providing infrastructures including its Genebank building (Photo 2).  Much less people are aware of the more important fact that hundreds of accessions of wheat ancestor species (namely Aegilops tauschii) originally coming from NBRP-Wheat (or Kyoto University prior to the start of NBRP project) have been used to produce new synthetic bread wheats (man-made new bread wheat by crossing durum and Aegilops tauschii; Photo 3) for improvement of drought and other stresses (Photo 4).  It is certain that many of additional genetic resources in NBRP-Wheat will contribute to world wheat production in the future.

Photo 2
Photo 2: The front of the Genebank building in CIMMYT
Photo 3
Photo 3: New synthetic wheat (right; green color as resistance for rust disease) and non-resistant wheat variety (left)
Photo 4
Photo 4: Drought tolerance test in Obregon field.
The right side is for drought condition, and the left is for control with irrigation. 
"This article is written in English by author."

 Ongoing Column  <No.84>

Easy and Free Mapping of NGS Data to Genomic Data    ∼Part 1∼

Advances in next-generation sequencing (NGS) methods and their wide availability have led to a greater number of sequence databases, making it easier to acquire NGS data in recent years. I will introduce techniques for mapping NGS data to genome sequences and viewing the results using a genome viewer. The article is split into two parts, with Part 1 being presented this month.

Although examples in this article use Windows (validated in Windows 7 and 8), the software being introduced also supports Mac and Linux operating systems.  

Mapping sequence data to genomes
A tool called Bowtie2 will be used for mapping sequence data.

  In the example below, a folder called "test" is created directly under the C:\ drive. Downloaded zip files as well as unzipped files are stored in this folder. Please use an appropriate tool for extracting the contents of the downloaded archives.  

  Obtaining the software
You can download Bowtie2 from the following URL:

Download for 64-bit OS or 32 for 32-bit OS) and extract the contents to a folder.
Open [Control Panel → System → Advanced System Settings] and click on [Environmental Variables]. Click on the "Path" variable within [System variables] and click on [Edit]. Add a semicolon (";") at the end of the input field and add the path to the unzipped content (Fig. 1). Please do not make changes to any of the existing path information.

Fig. 1: Editing system variables
  Preparing the data
You will need a reference genome (in FASTA format) and sequence data (in FASTQ or FASTA format). In the example below, we will use the genome data of Brassica rapa. This can be obtained from URL : by clicking on v1.5/ and downloading the file, "Brapa_sequence_v1.5.fa."
The sequence data can be obtained from the DNA Data Bank of Japan (DDBJ): access DRASearch (, enter "ERX014878" in the "Accession" field, and click on [Search]. Click on the "FASTQ" link at the top of the page, which will take you to an FTP site. Download the file "ERR037339.fastq.bz2" and extract its contents. Place the extracted fastq file in the test folder created previously.

  Mapping using Bowtie2
 Click on the [Start] button, enter "cmd" in the search box, and execute "cmd.exe" or "command prompt." Type the command given in Table 1-1 and press [Enter]. Next, execute the command given in Table 1-2 in order to create an index. After the indexing has completed, execute the command given in Table 1-3 to commence mapping. The results will be displayed after a while and a file in SAM format will be generated. A SAM-format file comprises a header section starting with "@" followed by a standard set of fields.

       Table 1. Commands      (␣: a space)
Table 1

The generated SAM file is very large: please use a viewer that can handle large files. The standard fields in the SAM file are given below in Table 2.

          Table 2. The contents of a SAM file
  Table 2
In Part 2 of this article, I will introduce Integrative Genome Viewer (IGV), which can be used to visualize the mapping results contained in the generated SAM file.
(Shunsuke Maeda, Genetic Resource Center)  

Database of This Month

National BioResource Project  "Zebrafish"

 Number of strains: 357
(as of October 2013)   
DB name: NBRP Zebrafish
Language: Japanese, English
Contents: Zebrafish strain resources for research
(wild, mutant, and transgenic strains)
Useful information on zebrafish
(zebrafish-related sites, protocols, seminars, and laboratories)
Features: You can order resources from this database.
Direct link with the Zebrafish Model Organism Database (ZFIN) enables you to obtain zebrafish-related information.
Cooperative DB: ZFIN, zTRAP
DB construction group: NBRP Zebrafish, NBRP Information
Management organization: Genetic Resource Center, NIG
Year of first DB publication: 2004   Year of last DB update: 2013

Comment from a developer : Although the NBRP Zebrafish is a small and simple database in terms of the amount of data and information items, the database can provide sufficient information to users, in cooperation with ZFIN. The database is managed by the Center for Genetic Resource Information, National Institute of Genetics. Since information on zebrafish is managed by NBRP Zebrafish, the latest information can be provided. In the future, we will add research papers from users of our resources to the database. Please feel free to use the database, and do not hesitate to send us your comments, questions, or opinions via Contact Us on the left-hand side menu.