Genome-Wide Association Studies Of Important Economic Traits In Camellia Oleifera Abel

Camallia oleifera Abel.is a unique woody edible oil tree grown in China,which belongs to one of the four woody oil tree species in the world.It is widely distributed in 15 provinces(cities and districts)in China,such as Hunan,Jiangxi and Guangxi.It has the characteristics of strong adaptability,long continuous income period,high product value and good comprehensive benefit.The breeding goal of C.oleifera is high yield,high quality and stable production.However,due to the long differential growth cycle,complex genetic background and ploidy of C.oleifera,the genome is very large and the development of markers is difficult.Therefore,most of the current researches on C.oleifera focus on conventional breeding based on phenotype selection,while lack of genetic structure resolution on important yield traits and genome-wide selective breeding.The genome-wide selective breeding remains to be further at the same time.In this study,610 free pollination progeny collected from 61 individuals with different genotypes were choosed as the research object to conduct this experiment.Firstly,the seed phenotype and oil quality of C.oleifera were analyzed,and then single nucleotide polymorphism markers were developed in the whole genome level,and the genetic diversity of the population were evaluated.Finally,the genome-wide association analysis were carried with the economic traits of C.oleifera,and combined with fruit transcriptome analysis for validation.The main research conclusions are as follows:(1)The important economic traits of 610 progenies of C.oleifera with the open pollination were determined and analyzed.The results showed that most of the traits of seed phenotype(seed weight,volume,length,width,thickness,coat thickness,kernel weight and coat weight)and oil quality(palmitic acid,stearic acid,oleic acid,linoleic acid,eicosenoic acid and oil content of dried kernel)showed significant normal distribution(P<0.01).The genetic variation coefficient were higher than0.11,and the same type of traits had strong genetic and phenotypic correlation,but the correlation between seed phenotype and oil traits was weak,indicating that the population had high diversity of important economic traits.Through principal component analysis,combined with eigenvector and comprehensive ranking,the top three lines for oil content of dried kernel were XL31,XL109 and XL51,and for palmitic acid and linoleic acid,XL15 ranked first and XL31 ranked second,which could provide materials for targeted quality breeding of C.oleifera.(2)Based on the RAD sequencing,205609 SNPs were obtained after quality control and filtration,which could cover the whole genome.Through the analysis of genetic structure and genetic relationship,the population could be divided into three subgroups.The proportion of non-genetic relationship was66%,and the population differentiation coefficient Fst was 0.028.According to the analysis of molecular variance,the genetic differences of the population were mainly derived from the different individuals of the whole population,accounting for 87% of the total variance variance,while the genetic variance of different subpopulations was only 2%.This indicates that the population differentiation was very weak,and it was conducive to improving the accuracy of subsequent genome-wide association analysis.(3)The genome-wide combined effect analysis of C.oleifera revealed 461 seed phenotypic markers,among which the heritability of seed length marker was 41%,and the rest was lower than 32%;145 oil quality significant markers were found,of which the heritability of eicosenoic acid marker was47%,and the rest was lower than 35%.The epistatic interaction model across the whole genome of C.oleifera detected 134 pairs epistatic interactions for seed phenotypic traits,contributing heritability between 8.7%-24.3%.There were 65 pairs of oil quality traits,and the contribution heritability ranged from 1.1% to 19.9%.To some extent,it makes up for the missing heritability of some phenotypes.Functional annotation of significant markers revealed that Snp58876,snp58878 and snp58881 were three synonymous mutations in css0049619.1,and WRKY DNA binding protein 33 isoform 1 may be an important candidate gene.(4)Fourteen lipid metabolism-related genes were screened out based on transcriptome difference analysis,time series analysis and phenotypic-gene correlation analysis of C.oleifera seeds at different developmental stages.q RT-PCR showed that most of the gene expression patterns were consistent with the transcriptional sequencing,which proved that the sequencing accuracy was high.The co-mapping of QTL and transcriptome with significant yield traits revealed that 32 genes were closely related to seed,oil and other traits,and most of them were expressed continuously,which could be used as important candidate genes.Based on the analysis of the population’s important economic traits,the SNP covering the whole genome of C.oleifera were obtained by RAD high-throughput sequencing technology.The genetic mechanism of yield characters of C.oleifera were deeply explored by the co-effect and epistatic interaction models.Through the genome-wide association and fruit development transcriptome analysis,the genetic mechanism of the yield traits thoroughly explored,and the genes related to the yield traits were discovered.This study laid a foundation for genome-wide selection breeding of C.oleifera and the mining and verification of functional genes related to yield traits.