Indica-Japonica Typing Technology Of Weedy Rice Based On InDel Molecular Marker

Weedy rice(Oryza sativa L.f.spontanea),as a special weed associated with cultivated rice,has become one of the most serious weeds in the paddy field.Previous studies found that weedy rice in China is rich in diversity,including indica and japonica types.However,because there are limited techniques available for indica and japonica classification,only Cheng index method has been applied to classify indica and japonica of weedy rice.It remains unclear about the indica and japonica types and distribution pattern of weedy rice in China.This is disadvantageous to lay down control strategy for weedy rice and utilize this weed as germplasm resources.Therefore,it is necessary to develop the indica-japonica classification technique of weedy rice and carry out the classification of weedy rice types.Indica and japonica are two common types of rice and weedy rice.Lu Baorong et al.tried to use 45 specific(insertion/deletion)loci which were obtained by comparing the whole genome DNA sequences of Nipponbare and 93-11 as the control to detect the molecular markers of 44 typical indica and japonica rice varieties.It was found that 34 InDel loci played a major role in them,which could clearly judge the indica and japonica types of the samples and establish the "InDel molecular marker technique".Chen Xiaofeng et al.successfully applied 34 molecular marker primers at these 34 InDel loci to the classification of Chinese weedy rice indica and japonica.However,all 34 pairs of InDel primers were used to identify a large number of weedy rice,and the work is still huge.In this technology,can InDel molecular marker primers be further simplified?There is still a need for in-depth technical research.Here,japonica rice Nipponbare and indica rice 93-11 were used as the control,and 1189 weedy rice samples collected from 24 provinces,municipalities directly under the Central Government and the autonomous region were identified by 34 pairs of InDel molecular marker primers.Their indica and japonica distribution patterns were studied by geographic information processing technique.Arcgis analysis reveals that there is obvious north-south distribution characteristics of weedy rice in China.The Yellow River is the boundary line between the north and the south of China.For the geographical distribution indica-japonica type,the area in the south of the Yellow River is mainly of the type of indica and indicaclinous,and the north of the Yellow River is dominated by the types of japonica and japonica-clinous.By comparing with the known distribution law of indica and japonica rice,it is found that the distribution of indica and japonica rice in longitude and latitude is consistent,and it is speculated that the way of producing miscellaneous grass rice may exist in indica and japonica hybrid rice,and the phenomenon that weed rice and cultivated rice can carry out natural outcrossing may also aggravate the evolution process of weed rice and make it more adaptable.Then,using 34 pairs of primers,indica and japonica typing and cluster analysis were carried out on weed rice in China,and three groups were divided into three groups by Euclidean distance cluster analysis:group 1(Indica group:typical indica,indica and indica-clinous),group 2(Japonica-clinous group:japonica-clinous)and group 3(Japonica group:typical japonica,japonica).Further,the InDel loci,which play a more key role,were identified.It is found that these 23 pairs of primers certainly play an important role in the typing results.Finally,the optimized 23 pairs of primers were used for clustering analysis.It is indicated that the conclusion of the two clustering results is the Euclidean distance changed.It is concluded that these 34 pairs of InDel primers can be optimized to 23 pairs of primers.Therefore,the technique of typing weedy rice by InDel molecular markers can be optimized.Based on the 23 key InDel loci identified in this study,it is expected to develop a new,more efficient and suitable typing technique for weed rice.