Differentiation of Indica-Japonica Rice Revealed by Insertion/deletion Fragments Obtained from Comparative Genomic Study of DNA Sequences between 93-11 (Indica) and Nipponbare (Japonica)

DNA polymorphisms resulted in nucleotide Insertion/Deletions in genomic sequences are the basis for developing InDel molecular markers.In order to validate the InDel primer pairs designed based on the comparative genomic study of DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare,in identifying Indica and Japonica rice varieties, and studying wild Oryza species,49 Indica,43 Japonica and 24 wild rice accessions from 10 Asian countries using 45 InDel primer pairs were studied.The results indicated that of the 45 InDel primer pairs,41 can accurately identify Indica or Japonica rice varieties with the reliability over 80%.The scatter plotting data of the principal component analysis(PCA) indicated that(i) the InDel primer pairs can easily distinguish between Indica and japonica rice varieties,and indicate their genetic differentiation;(ii) the AAgenome wild rice species showed a close genetic relationship with the Indica rice varieties;and(iii) the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types.It is concluded from the study that the InDel primer pairs based on 93-11 and Nipponbare can be useful for identifying Indica and Japonica rice varieties,and for studying genetic relationships of wild rice species,particularly related to the Indica-Japonica differentiation.