Genetic Analysis And Gene Mining Of Rice Rooting Ability,Grain Size And Quality

Rice is an important staple food in China.As we all known,rice grain quality influences the taste and commodification of rice.The grain size of rice is related to the rice yield by influencing the grain weight.The vigorous root helps plant to absorb and utiliz the nutrients and water which helps to enhance the biomass per plant and has an advantage on yield increasing.It has a great significance to analyze the genetic basis and regulatory mechanism of these traits for rice high yield and good quality breeding.At present,only a few major genes related to rice quality have been identified and there are only several QTL have been identified in the researches related to rice rooting ability.Though there are many genes have been cloned for grain shape,more genes are needed to elucidate the precise regulation mechanism.Based on this,in the research,we analyzed the genetic basis and obtained the candidated SNP for rice,rice rooting ability at the seedling stage,rice grain size and quality these three important agronomic traits by genome-wide association study.Through the linkage disquilibrium analysis,expression profile and DNA sequencing,et al,some candidate genes were identyfied and we also cloned a gene GW3 which can regulate rice grain width.The main results obtained are as follows:1.Using the method of hydroponics by nutrient solution,the rooting-related traits of 145 rice varieties at the seedling stage were evaluated and the genetic structure was also analyzed.The results showed that the indica-japonica subgroups of this population spring up the new roots by different establishing of root morphology.Japonica tends to grow longer roots,while indica tends to grow more roots.In addition,the genome-wide association analysis was performed in the full,indica and japonica populations.And three candidate genes which may regulate rice rooting ability were obtained.One is related to the number of new roots(LOC_Os05g11810),and the other two genes(LOC_Os04g09900 and LOC_Os04g10060)are related to root length.In addition,it also found that the significant SNP loci obtained from the indica and japonica subgroups had less overlap,which may imply the different genetic basis for the rooting ability beteween the indica and japonica.2.We analyzed the genetic structure of a natural population with abundant grain size variation,and measured the traits related to the grain size in this population with different environment for many years.Firstly,two groups seperatedly contained 231 accessions and 223 accessions obtained by combining the accessions from the large natural population were used for association analysis.Then,linkage disequilibrium analysis,haplotype analysis and expression profile analysis were performed based on the results of genome-wide association study of these two populations.Next,one gene GW3 that regulates grain width located on chromosome 3 was finally cloned,and transgenic experiment was also performed to verify the function of GW3.Overexpression of GW3 resulted in narrow grain width.While the gene-edited mutant plants with single base insertion showed a wide grain width.GW3 encodes a transcription factor with a zinc finger domain.The expression signal of GW3 could be detected in every growth stage and tissue of rice,and the panicle has the highest expression level among these tissues.Among the differential expressed genes detected by transcriptome sequencing and qRT-PCR,it was found that the genes involved in ubiquitin,cell cycle and cell expansion may be induced by GW3,GW3 can negatively regulate the rice grain width by affecting the number and area of the cell in the outer parenchyma of the glume,and it has transcriptional autoactivation activity.3.The genetic and pedigree analysis of the 200 japonica rice varieties from the northeastern of China found that genetic basis of northeastern japonica rice was narrow and the breeding parents of these varieties were concentrated and the utilization of these parents has regional differences.Through the genome-wide association study for three traits related to eating and cooking quality as well as summaryzing candidate genes' expression profiles information,we identyfied four possible candidate genes(LOC_Os02g29980,LOC_Os02g30300,LOC_Os02g3O470 and LOC_Os02g30600).In addition,from the DNA sequencing results,we found that ALK gene was not fixed during the japonica rice breeding process in northeast China.The Wxb allele of the Wx gene is widely used in most northeastern japonica varieties.