Genome-wide Association Mapping Of Water Logging Traits In Brassica Napus L.

Rapeseed(Brassica napus L.),as a crucial oil crop,is widely planted around the world.It is also one of the major oil crops in China.However,the yield and quality of rapeseed are significantly affected by water logging.Though there have been many researches on water logging of rapeseed,mostly aimed to research its mechanism and physiological reaction,and only a few of them related to genes of water logging.In present study,a total of 246 diverse accessions,including cultivated species and inbred lines,were used to construct a research population.Firstly,population structure,relative kinship,and linkage disequilibrium(LD)of research population were assessed based on the 60 K Brassica single nucleotide polymorphism(SNP)array.Then 24062 SNPs combined with eight growth-index traits(shoot fresh weight,root fresh weight,fresh rootshoot ratio,shoot dry weight,root dry weight,dry root-shoot ratio,green leaf number,plant water content)and five physiological traits(malondialdehyde content,soluble sugar content,soluble protein content,superoxide dismutase activity,peroxidase activity)were used for genome-wide association study.Candidate genes were identified according to regions of significantly-associated SNP and genome function annotation.The main results were summarized as follows:1.Phenotypic analysis of water logging related traits in Brassica napus L.: In the present study,all these 13 traits,which showed characteristic of typical quantitative trait,existed widely phenotypic variation.Under water logging stress,the average value of root fresh weigh,root dry weight,root-shoot ratio,peroxidase activity,soluble sugar content and malondialdehyde content increased,while the average value of other traits showed various extent of decrease.2.Population structure and relative kinship analysis: 246 accessions were divided into two populations(P1 and P2).P1 contained 111 accessions,accounting for 45% of all the accessions.In the association panel,about 56.16% kinship between any two accessions were equal to 0,and about 20% ranged from 0 to 0.1.These results indicated that most of the accessions had no kinship or had a weak kinship,which caused the little influence on association mapping.3.Linkage disequilibrium analysis: The LD value(r2)of both the whole genome and each subgenome declined rapidly as the physical distance increased.However,the extent of LD decay is different.The LD decay of C-subgenome was slower than Asubgenome.When the threshold value of r2 was set to 0.2,the LD decay in the whole genome was about 600 kb,300 kb of A-subgenome,and approximately 800 kb in Csubgenome.4.Genome-wide association mapping of water logging traits: After compared the results of each model in Quantile-quantile plot,a best model was chosen to conduct associated loci detection.In total,15 SNP loci were detected,which distributed on different chromosomes,and could explain about 10% of the phenotypic variation.Among them,two loci were associated with malondialdehyde content,peroxidase activity,and root dry weight,respectively.No SNP was detected in soluble protein content.For the other nine traits,all were detected only one SNP.5.Prediction of candidate genes of water logging traits: The LD region of all the detected significantly-related SNP loci were compared with French Brassica napus L.genome.Then,genes were annotated according to the genome informations of Arabidopsis thaliana.Thirty-seven genes were chosen to be candidate genes of water logging traits according to previous function annotation of genome.There were six genes associated with the balance adjustment of plant endogenous hormones and twelve genes induced stress protein.Nine genes were involved in the active oxygen metabolic pathway,while ten genes were transcription factors.