Analysis of Rice Plant Type Using P-type Fourier Descriptors and the Search for Related Chromosomal Regions

The method of combining P-type Fourier Descriptors (PFDs) and principal component analysis (PCA) was effective for the quantitative evaluation of ordinal “plant type” of rice. The evaluation method involved plant type outlines from the 2, 3 and 4 leaves of the 5 leaf stage. These were extracted and described quantitatively with PFDs. In a previous study, it was possible to distinguish differences in plant type between rice cultivars “Koshihikari” and “Kasalath” with this method. In the current study, PFDs were applied to chromosome segment substitution lines (CSSLs), which have substituted a part of the Koshihikari chromosome with that of the Kasalath chromosome and allowed the estimation of chromosomal regions related to each rice plant type. The materials in this experiment consisted of 39 Koshihikari / Kasalath CSSLs from the Rice Genome Resource Center and the parental lines of “Koshihikari” and “Kasalath”. Eight individuals per line were used for the analysis. The curves of the 2, 3 and 4 leaves at the 5 leaf stage were extracted. The coefficients of the PFDs were calculated from the curves and summarized with PCA. The obtained PC scores were used to describe characteristics of plant type shape. To visualize the plant type shape, the curves were reconstructed from the PC scores using “Inverse Fourier Descriptors”. Plant type traits evaluated by each PC were identified from the reconstructed outlines. The t-test was used to assess mean differences between the Koshihikari and the CSSL component identified from the PC scores. These CSSLs were found to be statistically significant and facilitated the estimation of those chromosomal regions that are related to plant type including the gene(s) that may be involved.