Institute of Crop Science, NARO

Breeding Informatics Research Unit

Detailed genomic information has now been clarified in various crops such as rice, wheat, soybean, etc. In addition, gene expression data, various omics data such as proteome and metabolome are also collected vigorously. Regarding crop trait data as well, efforts are under way to efficiently measure the phenotype of large numbers of individuals, and a large amount of data is accumulated, including data collected in previous breeding projects. The rapid increase in amount of data related to breeding, and the efficiency of extracting knowledge useful for breeding and by analysis of enormous breeding data have led to continuous advancement of breeding strategies.

We analyze the genome sequence of various crop species and pursue bioinformatics research such as elucidation of genomic structure and marker development, and genome related to phenotype using data of phenotype data and genome information. We are developing statistical methods for identifying agronomically important regions, and modeling methods for predicting phenotypes with high accuracy based on the genomic information. In addition, in order to make full use of the genetic composition of crops in agricultural productivity, it is necessary to develop a breeding method that takes the cultivation environment into account, and to clarify the relationships between crop environmental response and genome information. Towards this goal, we are constructing mathematical models describing the phenotypic change that occurs in response to various environments and analyzing the relationships between the parameters of the model estimated for each variety and genomic information. We are also conducting research to elucidate differences between seed varieties at the genetic level. In addition, we compare and analyze gene expression profile of several rice varieties as measured in real-time. We also develop and publish databases of diverse and large amount of data related to breeding and other useful information for breeding.


Unit Leader


Unit Members

Research Topics
Hiroshi TSUNEMATSU Principal Researcher Data base for crop genetics
Daisuke HORYU Principal Researcher Construction of agricultural ontology
Tsuyoshi TANAKA Principal Researcher Bioinformatics
Yoshihiro KAWAHARA Senior Researcher Bioinformatics
Shiori YABE Researcher Statistical genetics

Research Publications

  • S. Yabe, M. Yamasaki, K Ebana, T Hayashi, H Iwata (2016) Island-model genomic selection for long-term genetic improvement of autogamous crops. doi:10.1371/journal.PLoS One .0153945