Phylogenetic Analysis Of High Latitude Weedy Rice And Its Genetic Basis Of Population Specificity

Crop weedization has been a major problem in the field of crop sciences since ancient times,especially the origin and evolution of weed rice(Oryza sativa f.spontanea),which has not yet been solved.Weedy rice is highly ecologically adaptable,but it is not very clear how the unique genetic characteristics of its population are gradually shaped.High-latitude weedy rice is a common type of paddy field weedy rice associated with japonica rice.It has typical weed invasion characteristics,such as strong reproductive ability,invasiveness,resource competition and high phenotypic plasticity.There is also a serious lack of herbicides that can be used for control.At the same time,weedy rice also has genetic characteristics similar to wild rice(Oryza rufipogon),such as seed shattering,red peel and black shell,which makes weedy rice an excellent model for studying rice domestication and adaptability.As technologies such as high-throughput sequencing and gene editing mature,this study applies it to population-specific population genetic studies and evolutionary analysis of weedy rice population.The main results are as follows:1.This study analyzes the phylogenetic status of high-latitude weedy rice and cultivated rice to weedy rice based on simplified genome sequencing.The results indicate that highlatitude weedy rice has a relatively independent phylogenetic status in the temperate japonica rice group.2.Compared with weedy rice and associated cultivated rice,the population has a smaller average gene diversity(?),but the selection characteristic parameter Tajima's D is relatively higher.This implies that compared with cultivated rice,high-latitude weedy rice genome may have some undomesticated sites.Based on the genetic sliding coefficient of the genome sliding window ?,Tajima's D population selection clearing analysis,further clarified the highlatitude weedy rice populations of the un-domestication genome region,and clearly identified the known functional genes in the un-domestication genome region.3.Identify the divergent regions of the genome of weedy rice and cultivated rice by the genetic differentiation coefficient Fst.At the same time,we conducted KEGG analysis and GO analysis for all genes of weedy rice and cultivated rice in the region.We have further determined that the grain-type genes have significant gene grouping characteristics by identifying different areas of weedy rice and cultivated rice.4.This study further investigated the grain types of 282 samples including weed rice.The results showed that the phenotypes of grain length and grain width of weed rice were significantly different from cultivated rice.The grain width ratio is narrower and the grain length is shorter than the associated weedy rice.Whole-genome association analysis further confirmed that the GW5 / GSE5 region contributed to the genetic differentiation of weedy rice and cultivated rice.Further use of CRISPR-case9 gene editing technology to knock out the weedy rice grain type gene GW5 / GSE5,and now we have obtained the T1 generation of gene editing,which provides further clarification of the contribution of the GW5 / GSE5 gene to the genetic differentiation of weedy rice and cultivated rice Important evidence.