| Xanthoceras sorbifolium is a deciduous shrub or small tree that belongs to the Sapindaceae family and the monotypic genus Xanthoceras,and widely distributed in arid and semiarid regions in northern China.It is one of the most important eco-functional species integrating of woody oil,ecological afforestation,landscaping,and medicines.So it has potential use at ecological civilization construction,rural revitalization and ensuring China’s edible oil security.But low yield and low benefit have become the major bottle-necks of X.sorbifolium industry development.Therefore,the protection and innovation of the germplasm resources and breeding of new cultivars are important and urgent to promote the development of X.sorbifolium industry.However,the systematic research of genetic background,construction of core collection,and precision breeding of X.sorbifolium is lack.In this study,119 accessions germplasm of X.sorbifolium were used as research object.Through the investigation and conduction of phenotypic traits and whole genome re-sequencing,the genetic diversity were analyzed both by phenotypic traits and SNP set;the core germplasms were conducted and a genome-wide association study(GWAS)of significant phenotypic traits was performed using the genome-wide SNP set;and new cultivars were selected.The main research conclusions are as follows:(1)Large variation and rich phenotypic diversity were found among and within germplasms of X.sorbifolium.The Shannon-Wiener information index(I)and Simpson genetic diversity index(D)for 19 qualitative traits among 119 germplasms ranged from 0.09to 1.35 and 0.03 to 0.71,respectively;and for 19 quantitative traits ranged from1.42 to 1.90and 0.16 to 0.85 respectively.The mean of coefficient of variation(CV)for 19 quantitative traits among119 germplasms was 24.06%.It varied from 20.83%to 40.39%,and ranked as follows:branch traits(40.39%)>fruit traits(26.56%)>inflorescence traits(26.06%)>leaf traits(20.93%)>seed traits(20.83%)>flower traits(17.98%).The mean phenotypic differentiation coefficient(Vst)among germplasms was 74.16%.Significant correlations were observed within and among most branch,leaf,inflorescence,flower,fruit,and seed traits.The cumulative contribution rate of the first six main principle components reached69.18%.The 119 germplasms were classified into three main groups and five subgroups according to their characteristics by Ward’s clustered method and reasonable utilization of each subgroup were suggested.(2)The re-sequence genome-wide SNP data of 119 X.sorbifolium germplasms were conducted,and after filtering,105,685,557 high-quality SNPs were identified.The results from the phylogenetic,population structure and principal component analyses were well in agreement,with 119 germplasms being classified into three main groups.The germplasms were not completely classified based on their geographical origins and flower colors;further,the genetic backgrounds of these germplasms were complex and diverse.The average Nei diversity index(H),Shannon-Wiener index(I),and polymorphsim information content(PIC)values for the three inferred groups by population structure and the six classified groups by flower color were 0.3018 and 0.3611;0.4624 and 0.4940;0.2445 and 0.2628,respectively,indicating a medium informative degree of genetic diversity among 119 germplasms.(3)A core collection containing 35(29.40%)out of the 119 X.sorbifolium germplasms was established using the Core Hunter software based on the re-sequence genome-wide SNP data.The gene coverage of the core collection was 99.80%.The core collection possesses the intact genetic diversity of the total collection;the observed heterozygosity(Ho),expected heterozygosity(He),Nei diversity index(H),Shannon-Wiener index(I)and polymorphsim information content(PIC)values of the core collection compared with the total collection were 107.40%,108.27%,109.33%,106.59%and 107.17%,respectively.The PCA plot of the first two components(PC1 and PC2)based on the core collection and total collection was consistent.These results showed that the core collection was well represented.(4)The genome-wide association study(GWAS)of 20 significant phenotypic traits was performed using the genome-wide SNP set.A total of 37 significant SNPs loci and 404genes were detected with 9 phenotypic traits,including tree vigor,hairy,base petal color,base petal size,petal fold,petal size,leaflets size,fruit weight and seed weight.These loci were distributed on all chromosomes of the genome.Functional annotation was performed on related genes and the most important candidate related genes were screened(still needs gene functional verification).The genes were functionally annotated as E3 ubiquitin-protein ligase BRE1-like,F-box protein,Protein ODORANT1,Zinc finger CCCH domain-containing protein,etc.(5)Two new landscaping varieties of X.sorbifolium with special flower colors were selected,by single plant selection.The distinctness,uniformity and stability test(DUS)of the two varieties were done and the new plant variety rights were obtained(identification number:20210512,and 20210513).Comparison tests of 13 clones were conducted.The heritability(H~2)of the evaluation traits were ranged from 0.31 to 0.99;and the genetic gain(G)were ranged from 3.60%to 34.96%.Fourteen evaluation traits(including single plant fruit number,single plant fruit weight,single plant seed weight,fruit weight,single fruit seed weight,seed percentage,seed weight,kernel weight,kernel percentage,seed 100-grain weigh,fat content,linoleic acid,oleic acid and nervonic acid)were used to make multiple-traits evaluation for 13 clones.Three clones(Smthg,N917 and Zs9)were selected as excellent clones which were suitable for fruit-based applications;and the clone N923 had the high seed yield and high unsaturated fatty acid which suitable for oil applications.In conclusion,this research revealed the genetic variation and diversity of X.sorbifolium from phenotypic and molecular levels;a core collection was development;significant SNPs loci and genes were detected by genome-wide association study;and landscaping new varieties and clones for fruit and oil application were selected.These findings will provide useful information for genetic improvement,preservation,and evaluation of X.sorbifolium germplasms. |
PDF Full Text Request