Genome-wide Association Studies On Key Traits Of Chrysanthemum Flower Type

Chrysanthemum(Chrysanthemum×morifolium Ramat.)has the highest floral variation among ornamental plants in the world.However,the genetic mechanism of its flower type has not been clarified,which restricts the directional breeding of chrysanthemum.The flower of chrysanthemum is actually a head consisting of outer ray flower and inner disc flower,and its petals include deformed ray flower and disc flower.In this study,morphological observation and quantitative definition were carried out on the flower-related traits of six germplasm resources of chinese traditional chrysanthemum,japanese chrysanthemum,cut chrysanthemum,open-ground small chrysanthemum,wild chrysanthemum and new varieties collected from the chrysanthemum germplasm resources garden of Beijing forestry university.Based on these,the variety classification was studied and typical samples were screened to construct associated populations;Genotyping-by-sequencing(GBS)and genome-wide association studies(GWAS)were performed on associated populations to locate molecular markers associated with flower type of chrysanthemum.The key markers or segments obtained were identified using published genomic data of wild chrysanthemum species.The following results were obtained:(1)For a total of 6 different types of more than 1200 varieties and strains for five consecutive years of observation,the material with 437 chrysanthemum three consecutive years of 16 flower character of observation data,through the study of the probability of the data classification and statistical analysis,the chrysanthemum flower type factor is defined as the petal morphology,petal number,petal orientation and petal arrangement and combination.According to the degree of deformation of disc flower and whether there was obvious difference between disc flower and ray flower,the flower type of chrysanthemum were divided into two types: anemone type and non-anemone type.According to the method of quantitative classification,the petal morphology was divided into four types:flat,spoon,tube and deformed.On this basis,the flower type of chrysanthemum were divided into four types: single type of anemone,compound type of anemone,single type of non-anemone and compound type of non-anemone,which were used as the first classification standard.There are four petal types under each type.Based on this,four categories and 16 types of chrysanthemum flower type classification systems were constructed.(2)Based on 4 kinds of 16 chrysanthemum flower type two-stage classification system,selected from 437 chrysanthemum samples with a single disc type designs are stable 300 chrysanthemum samples build associated population,distribution analysis method was used to study the quality traits in the associated population distribution,classification method using probability analysis of quantitative traits in the variation regularity of associated population.The results showed that all the quality traits of chrysanthemum flower type were included in the samples constructed from the associated population,and the quantitative traits were normally distributed in the associated population.(3)A total of 1,813.48 G of Raw＿Bases were obtained by GBS of 300 single type chrysanthemum materials from associated populations,of which Valid＿Bases reached1,775.79 G,the proportion of effective data was 97.9%,and the average Q30 value was89.6%.GC content reached 40.0%.SNP mutation detection was carried out by selecting the chrysanthemum nankingense as the reference genome,a total of 3,669,092 SNP markers(MAF>0.05).(4)Based on the genetic analysis of the flower-related SNP markers obtained above,the results of population structure analysis showed that when k = 3,the CV error value was the smallest,and the population was divided into three groups.The results of phylogenetic tree analysis showed that the open-ground small chrysanthemum and the wild chrysanthemum samples were grouped together,while the large Chrysanthemum samples were distributed in different groups.According to the results of principal component analysis,the first principal component and the second principal component can be clearly divided into three categories.All the three methods divided the related groups into three categories.(5)Genome-wide association studies of flower type of chrysanthemum was conducted by mixed linear model(MLM),and 56 loci or segments associated with flower type of chrysanthemum were screened out.Among them,7 SNPs were significantly correlated with petal morphology,31 SNPs were significantly correlated with petal number,13 SNPs were significantly correlated with petal orientation,and 5 SNPs were significantly correlated with petal arrangement and combination.A total of 118 genes related to the flower type of chrysanthemum were identified by sequence alignment with the genomes of chrysanthemum nankingense.Based on the above studies,the authors proposed that the flower type of chrysanthemum was determined by the morphology,number,orientation and arrangement of petals.Based on this,the flower type of chrysanthemum was divided into four categories and 16 types.A single petal type sample covering all the above traits was used to construct an association population,population genetic structure analysis,phylogenetic tree analysis and principal component analysis of 3,669,092 SNP markers(MAF>0.05)obtained by GBS simplified genome sequencing showed that the associated populations were divided into three groups.The open-ground small chrysanthemum and wild chrysanthemum samples were grouped into one group,while the large chrysanthemum samples were distributed in different groups.It further explains the complexity of the origin of Chrysanthemum cultivars.A total of 56 SNP markers and QTL regions associated with flower type were identified based on MLM genome-wide association analysis,and118 genes related to the above traits were identified.This study provides a new classification index and a new classification project for the definition and classification of chrysanthemum flower types.Through genome-wide association studies,molecular markers closely linked to chrysanthemum flower type were mined,which provided a new idea for molecular marker-assisted breeding of chrysanthemum flower type and directional breeding of improved chrysanthemum flower type.