Identification of Indica-Japonica Attribute for Breeding Materials Using InDel Markers in Rice

It is greatly significant to identify indica or japonica accurately and efficiently for exploring the heterosis of indica-japonica inter-subspecies in rice breeding.In this paper,forty eight rice varieties including indica,japonica and intermediate type which commonly used in rice breeding were analyzed by 19 pairs of insertion/deletions(InDel) molecular markers,which were designed on the base of the comparative genomic DNA sequences between indica variety 9311 and japonica variety Nipponbare.Indica-japonica attribute of each rice variety was identified by calculating indica and japonica gene frequencies at the 19 InDel sites of each DNA sample,together with cluster analysis and principal component analysis(PCA).Compared with the results of the Cheng's index method the effectiveness of using InDel molecular markers to identify indica japonica in rice was verified.Results showed that the coincidence rate between InDel molecular marker method and traditional Cheng's index method is 89.58% in identifying indica or japonica for all the tested materials,and 100% for the typical indica or japonica varieties.It hinted that InDel molecular marker method is more accurate than Cheng's index method for the intermediate type materials with complicated genetic background.The results indicated that the InDel molecular marker method has higher resolution and accuracy compared with the traditional one,and the new method can be completely used to identify indica-japonica and genetic differentiation research in rice.