A Study Of Identifying Weedy Rice From Cultivated Rice In Shanghai

Weedy rice (Gramineae), often growing in paddy fields, is similar to the Asiancultivated rice. Weedy rice and Asian cultivated rice share same Latin name, namely,Oryza sativa. The weedy rice, however, also have some similar morphologicalfeatures with the wild rice, such as grain of strong shattering, red pericarp, etc.Because of their strong root system, weedy rice populations could compete with thoseof cultivated rice for sunshine, water, and soil nutrient, thus affect growth ofcultivated rice and reduce rice production. In recent years, with spreading of broadcasttechnology in paddy fields, the weedy rice has become a serious harm to thecultivated rice. However, it is rather difficult for us to separate the weedy rice fromcultivated rice in fields, which is an important problem to be solved. In the presentwork, we collected a total of98samples from Shanghai, which included cultivate riceand weedy rice, then apply the indices including morphological traits, ISSR markers,and genes (ITS2, trnH-psbA, rbcL, matK) to identify weedy rice from cultivated rice.The main results are as follows:1. A total of98samples including weedy rice and cultivated rice was collectedfrom the paddy fields of the suburb of Shanghai. The morphological data includingindividual height, grain length and width, and their ratio, spikelet length, awn length,and grain colors were determined. Based on the above data, clustering analysis,Principal Component Analysis, and Non-matric Multidimentional Scaling(Non-matric MDS) were applied to quantitatively analyze the phonetic similarityamong these98samples. The results showed that these samples could be divided intothree groups, including57and33and8samples, respectively. Based on seedshattering trait, spike shape, seed coat colors and the data of their maturity, Group1 and Group2were identified as weedy rice and cultivated rice, respectively, whileGroup3as the samples with transitional characteristics between the weedy rice andcultivated rice. Analysis of variance on the phonetic data between Group1and Group2showed that the grain length, grain width, grain length/width, and the spikelet lengthof the weedy rice are significantly greater than those of the cultivated rice, whileindividual height and awn length had no significant difference between them.2. ISSR markers were applied to analyze weedy rice and cultivated rice samplesgathered from the suburb of Shanghai. A total of74amplified fragments and27polymorphic fragments were detected by applying6ISSR primers screened from32primers. The polymorphic fragment percentage was36.49%. And the amplifiedfragments were all between150-2000bp. The primer881has two fragments that candistinguish the samples into two groups. After applying the method of clustering andordination methods, the weedy rice and cultivated rice can be effectivelydistinguished by using five primer-couples (881-827，881-818，827-818，827-825，827-840). The clustering and ordination based on the ISSR data were simple andeffective in the identification of weedy rice from cultivated rice in their seedingstages.3. According to the results based on morphological and ISSR markers, wedivided experimental materials into two groups, the weedy rice group and thecultivated rice group. We randomly selected seven samples from each group, andchoose seven genes including ITS2, trnH-psbA, rbcL, matK as DNA markers toidentifying the weedy rice from the cultivated rice. After PCR amplification andsequencing, and alignment of the sequences in NCBI Gene Bank, as well as analysesby using MEGA5.0, we calculated genetic distance within and between groups. Ourstudy showed that the distance between the two groups resulting from ITS2is thebiggest, while those from matK and atpFH’s are zero. A phylogenetic tree based onITS2gene sequence was produced by using maximum likelihood method (maximumlikelihood, ML). The tree showed that the seven weedy rice samples formed one largeclad, while the seven cultivated rice samples formed five small clads. The14samplesin the phylogenetic tree based on trnG gene sequence was directly divided into two clads, corresponding to two weedy rice and cultivated rice, respectively.