| Weedy rice generally accompanies the cultivated rice with strong competition against the later.And it causes serious harmfulness due to impacting on rice yield and quality.Weedy rice has widely distributed in rice growing areas worldwide.Because of the high similarity of morphological and genetic background between weedy rice and cultivated rice,effective but economic way to control weedy rice has not been available yet.Hence,studies on origin and evolution of weedy rice will provide theoretic basis for exploring new control techniques against this weed.At present,a large amount of research work has been done on origin and evolution of weedy rice.It may be generalized that three hypotheses have been suggested:a wild rice parallel evolution with cultivated rice;a cross between wild rice and cultivated rice;wide hybridization between different cultivated rice caused atavistic mutation.Because of the different materials and methods,the researchers drew different conclusions on the origin.Therefore,the real origin and evolution of weedy rice will still be disputed.Based on the characteristics of the matrilineal inheritance,the origin and evolution patterns of weedy rice revealed by genetic diversity of weedy rice chloroplast were studied by the method of gene sequencing.The results of this study were given as follows.The development of chloroplast molecular marker In order to obtain high-frequency mutations in chloroplast genome of weedy rice,13 homologous chloroplast genomes were obtained by blast on NCBI database through a nipponbare chloroplast genome sequence as template.Through further comparing and analyzing the article 13 of the reference genome sequence,13 mutation sites were found in three high-frequency mutation areas,which identified before.Then the primers were designed to amplify target gene fragments,and a good result was made.Those three chloroplast gene fragments were used to sequence 12 weedy rice samples collected nationwide in our laboratory in order to verify the effect of the molecular markers.The result showed that weedy rice chloroplast genome had polymorphism in these area and those weedy rice samples could be classified well by the three molecular markers.This indicates that the chloroplast genome of the weedy rice may potentially be used to study the genetic diversity.Genetic diversity of weedy rice based on chloroplast genome The 545 samples including 83 accessions of cultivated rice,18 accessions of wild rice and 440 accessions of weedy rice were sequenced based on the 3 chloroplast gene fragments.Those sequenced products were spliced into a total of 1981 bp sequence.There were 40 mutation loci which included 18 SNPs and 22 InDels in total 1981 bp length.There were 30 haplotypes in the 454 samples and the haplotype diversity was 0.7196.The total variation sequence length was 52bp with 3.5%of the total 1981bp.It indicates that there were rich variations in counting with 35 mutation loci each 1000bp.Class,evolution and distribution of weedy rice haplotype According to the network analysis,all of cultivated rice,weedy rice and wild rice were classified into 6 main haplotypes.Specific haplotype was not found in weedy rice.The wild rice had the rich haplotype diversity,and was not closely related to any cultivated rice and weedy rice accessions.H6 was a rare haplotype.In this haplotype,weedy rice and cultivated rice had the same rare InDel site,which the chloroplast of weedy rice in this haplotype sourced from the cultivated rice.Classification of haplotypes showed the close relationship was found between weedy rice and cultivated rice.Study on the relationship of the geographical distribution among weedy rice,cultivated rice and wild rice showed that the indica type and japonica type of weedy rice were almost associated with those of cultivated rice.The wild rice mainly distributes in the southern provinces to the Yangtze River.This indicates that weedy rice had no direct relationship to wild rice but closely correlated to cultivated rice.Distribution of weedy rice was significantly related to the temperature and latitude.The japonica-like weedy rice distributed in the growing area with the growing average temperature between 18° and 27° and the latitude between 22°N and 50°N.And the indica-like weedy rice distributed in the area with the growing average temperature between 24° and 30° and the latitude between 18°N and 35°N.Male sterile gene evidence The detection of sterility genes among weedy rice samples showed that the weedy rice in haplotype H7 had sterility gene which was used in three-line hybrid rice.And sterility gene was detected among the cultivated rice belonging to three-line hybrid rice.It indicates that there were direct gene exchanges between the weedy rice and three-line hybrid rice.The weedy rice pollen drift on hybrid rice could produce hybrid offspring with the weedy rice traits.Diversity of weedy rice in Jiangsu Province The study on weedy rice in Jiangsu Province showed that most of weedy rice samples were indica-like type.However,there were significant differences in indica and japonica between phenotype and chloroplast gene type of some weedy rice samples.This indicates that they might be offspring of indica and japonica hybrid.Therefore,RC gene was detected among the weedy rice and cultivated rice samples collected in 3 doubted areas in Jiangsu Province using RC marker in rice.The result showed that the weedy rice samples were highly heterozygous sharing with heterozygous RC gene,and RC gene which came from weedy rice introgressed into accompanied cultivated rice with heterozygous RC gene.And it further indicates that there were direct gene exchange between the weedy rice and cultivated rice,and the hybrid progenies sharing with weedy rice traits evolved.Those explained why some weedy rice accessions had the heterotype between phenotype and chloroplast gene type..The above results showed that hybridization occurred between weedy rice and accompanied cultivated rice and there was a spread pathway in geographic distribution.The essence of weedy rice evolution was the consequence through interaction of weedy rice spread and gene flow with cultivated rice.It is supposed that weedy rice spread to the destination,then crossed with local cultivated rice and got the local cultivated rice gene rapidly.So the weedy rice kept the weedy characteristics,but improved the adaptability in the local habitat.In the evolutionary process the spread of weedy rice was the prerequisite,while the gene exchange was the optimal way driving weedy rice rapid adaptive evolution.This was the direct reason that why previous studies showed that weedy rice and cultivated rice always had similar genetic background.Moreover,it may also be the reason that why weedy rice is difficult to be controlled by chemical method in molecular level.The homology of chloroplasts between weedy rice and cultivated rice reflected that weedy rice may directly originate from cultivated rice.Mode of origin may be hybrid with cultivated rice as female parent and other rice(wild rice and distant strains of cultivated rice)as male parent.At least cultivated rice surely participated in the evolutionary process of weedy rice. |
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