National BioResource Project of Japan II : DNA resource of Wheat

Yasunari Ogihara, Kanako Kawaura, Kazuko Umeda

Kihara Institute for Biological Research, Yokohama City UniversityMaioka-cho 641-12, Yokohama 244-0813, Japan 

Corresponding author: Yasunari Ogihara (E-mail: yogihara@yokohama-cu.ac.jp)

The second phase of the National BioResource Project of Japan “Komugi - wheat in Japanese” has been over in 2011.  DNA resource team of “Komugi” has continuously collected, maintained and supplied for cDNA clones of common wheat.  In total, 55 cDNA libraries were constructed with the RNAs from stressed tissues as well as various normal tissues.  The scheme for DNA resource of wheat is shown in Fig. 1.  Several thousands of cDNA clones were picked up from each of 55 libraries, and one-path sequencing had been carried out from both ends of the inserts (ESTs).  In the second phase, about 0.9 million EST data were obtained.  These ESTs were bioinfomatically classified into certain contigs (Manickavelu et al. 2012).  By counting the number of ESTs in each contig, we displayed gene expression patterns of their tissues in silico (Virtual Display; VD).  VD allows us to trace the global gene expression profiles of interest (Manickavelu et al. 2010), and it is opened from the “KOMUGI” site of National Institute of Genetics, Mishima, Japan.  By applying these cDNA sequence data, we constructed the Agilent oligo-DNA microarray harboring 38K gene probes (Kawaura et al. 2008).  The wheat oligo DNA microarray is available from the Agilent Co. Ltd.

     In addition to ordinary cDNA libraries of common wheat, we had constructed the wheat full length cDNA library.  We extracted total RNAs from 13 tissues and/or stress-treatments.  These RNAs were mixed, and supplied for construction of the full length cDNA library with the CAP-trapper method.  After subtraction of the clones against the previous clones (6162 clones), 10,645 additional novel clones were selected to complete the entire sequencing of inserts (Kawaura et al. 2009).

During the second phase of activity, 765 clones from 29 institutions inside and outside of Japan were supplied in response to their requests.

     Furthermore, we had constructed the genomic library of Chinese Spring wheat with the transformation-competent artificial chromosome (TAC vector).  This TAC library covers ca. three times of the Chinese Spring wheat genome to be proven the selection of single copy gene from the library.  In response to user’s request, we selected positive clones against the special targets.

      These lines of activities indicate that DNA resources of common wheat are substantial and useful, and are required to complete their line-ups in the next stage (Fig. 2).

References

Kawaura K, Mochida K, Ogihara Y (2008) Genome-wide analysis for identification of salt-responsive genes in common wheat. Funct Integr Genomics 8: 277-286.

Kawaura K, Mochida K, Enju A, Totoki Y, Toyoda A, Sakaki Y, Kai C, Kawai J, Hayashizaki Y, Seki M, Shinozaki K, Ogihara Y (2009) Assessment of adaptive evolution between wheat and rice as deduced from the full-length cDNA sequence data and the expression patterns of common wheat.  BMC Genomics E Pub 10: 271.

Manickavelu A, Kawaura K, Oishi K, Shin-I T, Kohara Y, Yahiaoui N, Keller B, Suzuki A, Yano K, Ogihara Y (2010) Comparative gene expressin analysis of susceptible and resistant near-isogenic lines in common wheat infected by Puccinia triticina. DNA Res 17: 211-222.

Manickavelu A, Kawaura K, Oishi K, Shin-I T, Kohara Y, Yahiaoui N, Keller B, Abe R, Suzuki A, Nagayama T, Yano K, Ogihara Y (2012) Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum). DNA Res 19: 165-177.