Genome-Wide Association Study And Candidate Gene Excavation On The Key Agronomic Traits Of Xanthoceras Sorbifolium

Xanthoceras sorbifolium Bunge is a unique oil tree species in northern China.It is an economic tree species with great development potential and promotion value in China by its highly resistant,ecological and economic value.But the genetic background for many of the drought tolerance,yield,and quality traits of yellowhorn is not known.In this study,we performed whole genome sequencing of yellowhorn.Based on this,48 agronomic trait of 208 germplasm resources were investigated and whole-genome resequencing were carried out to excavate SNP loci and candidate genes that are closely related to the trait.The results of these studies will provide a data base for further analysis of the genetic mechanisms of important traits in yellowhorn and the selection of drought-resistant,high-yielding and high-quality varieties.The main results are as follows.1.Whole Genome Sequencing of yellowhornIn this study,the whole genome sequencing of yellowhorn drought-tolerant and productive new variety "Zhong Shi 4" was completed using Pacbio sequencing technologies.The length of the final yellowhorn genome assembly was 504.2 Mb with a Contig N50 size of1.04 Mb and heterozygosity 0.77%.Genome annotation revealed that 68.67% of the yellowhorn genome was composed of repetitive elements.Gene modelling predicted 24,672protein-coding genes.By comparing orthologous genes,the divergence time of yellowhorn and its close sister species longan(Dimocarpus longan)was estimated at ～33.07 million years ago.Gene cluster and chromosome synteny analysis demonstrated that the yellowhorn genome shared a conserved genome structure with its ancestor in some chromosomes.2.Genome-wide association analysis and candidate gene miningWe performed phenotyping and analysis of 48 agronomic traits for 208 germplasm resources.The results shown that,these traits are extremely variable,with coefficients of variation ranging from-0.03(δ13C)to 15.59(δ15N),and multiple traits having coefficients of variation greater than 0.9.Correlation analysis showed that significant correlation between multiple pairs of traits,such as δ13C and specific leaf weight,δ13C and leaf relative water content,leaf freshness and specific leaf weight,leaf freshness and wax thickness.A total of1.24 million high-quality SNPs were obtained from 208 germplasm resources by whole-genome resequencing with a sequencing depth of about 13 X and multiple quality control.10762 SNPs filtered from LD prunes were used for population structure analysis,PCA analysis and phylogenetic tree analysis,and no significant stratification of this natural population was found.The 1.24 million high-quality SNP markers were correlated with 48 agronomic traits and screened for potential candidate SNPs by correlating FDR-corrected values of significance(P-value).A total of 545 significant SNPs loci and 83 genes localized to14 traits,including leaf moisture content.The genes were functionally annotated and found to function primarily as: ubiquinone-cytochrome C reductase,serine/threonine receptor kinase,and ASIL2,b HLH85,R2R3-MYB family transcription factors.