Phenotypic Traits Evaluation And Genome-wide Association Analysis Of Oncidium Germplasm Resources

Oncidium hybridum belongs to the genus Orchidaceae.It is mainly distributed in Hai nan,Yun nan,Guang dong,Taiwan and other regions of China.It likes a humid and semi-dark growth environment.At present,Hainan mainly sells fresh cut flowers.The main varieties are’Boda No.1’,’Lime Green’,’Golden No.2’,etc.The flower colors are all yellow at the top with brown spots at the base,single color and no fragrance.Oncidium and interspecific hybridization can produce offspring,but due to the poor affinity of the parents,its seed setting rate is much lower than other orchid plants such as Phalaenopsis and Dendrobium,so the production of new varieties is relatively slow.In this study,106oncidium germplasm resources were used as the research population to analyze their main phenotypic traits,and through the association analysis of their genomic data,the purpose was to find out the excellent phenotypic traits of oncidium and screen out the first Related genes are used to promote the selection and breeding of fine varieties of Oncidium.In this study,25 phenotypic traits of 106 oncidium germplasm resources were collected for two consecutive years from 2018.10 to 2019.12,and genetic diversity analysis,correlation analysis,principal component analysis and cluster analysis were performed.（1）The results of genetic diversity analysis show that the value range of the coefficient of variation of quantitative traits is between 15.30%and 82.23%,the average value of the coefficient of variation is 45.74%,and the coefficient of variation greater than10%indicates that there are large differences between varieties.The value of genetic diversity index（H′）varies from 1.38 to 3.42,and the average value of H′is 2.04.The wide variation of the diversity index further illustrates the large differences between breeds.Preliminary data phenotyping data analysis shows that the 106 oncidium germplasm resources have significant differences in appearance and have obvious development potential.（2）Correlation analysis shows that there are 139 pairs of traits that are extremely significantly correlated,of which are positively correlated and 26 pairs are negatively correlated.There are 24 pairs of traits that are significantly correlated,of which are positively correlated and 3 pairs are negatively correlated.And most of the values are negatively significant,reaching more than 90%.The length and width of the main characters in flowers are mainly negatively correlated,and most of the characters show significant and extremely significant correlations.It can be seen that most of the 22quantitative traits of Oncidium are most of the traits.There are significant or extremely significant correlations between them,and the relationships among various traits are close and complex.（3）Through principal component analysis,a total of 5 main feature vectors,including the width of the middle calyx,the width of the pseudobulb,the number of branches,the length of the lateral calyx,and the hardness of the pedicel were screened out.These five feature vectors include the main characteristics of the whole oncidium such as flower,pseudobulb,flower branch,etc.,and provide important information for the selection and breeding of new varieties of oncidium.（4）Cluster analysis of 106 oncidium phenotypic traits divided them into 5 categories.Among them,the the first group contain 81 samples.The main outstanding features of them are the relatively soft diameter of the pedicel,the large number of flowers and the fragrance,such as the’chocolate’and’mengxiang’series.These,varieties are suitable for development as office potted plants.Group two is mainly composed of‘Kniphofia versicolor’and‘Triple-lip petals’,both of which belong to mini Oncidium,suitable for office mini potted plants.The third group contains 15 varieties,this group fresh cut flower varieties,such as’Boda No.1’,’Lime Green’and so on.In this study,106 samples of Oncidium were sequenced with 5X simplified genome,105,907 SNP were obtained after fitlering,and the association analysis was applied to the oncidium population for the first time.This study is based on Emmax’s Q+K mixed linear model for genome-wide association analysis,using log₁₀（P₁）（P1=0.05/105907）as the threshold to identify associated SNPs with 25 phenotypic traits.There are 14 of 25 traits are identified associated with SNPs.By annotating the high significance locus of Oncidium in the Ref Seq Non-redundant Proteins（NR）database and the Shenzhen pseudolan annotation file,177 genes genes were selected as the candidate genes to floral traits.Among them,among 23 genes related to flower number traits,48 genes related to petals,34 genes related to central calyx,71 genes related to lateral calyx,1 gene related to floral fragrance,and 1 gene related to leaf width,38 genes related to plant height.Through further analysis of the functions of these genes,a total of 23 genes with important functions were chose.Among them,the genes that may be related to the number of flowers are CALS12,JMJ14,and ABCC2.The genes that may be related to petal length are ADNT1,HOS1,SPA1,and UVH6.There are 5 genes that may be related to petal width,namely TRPA1,ABCB19,POL2A,B3GALT11 and DAR2,the genes that may be related to the length of the central calyx are ATPK1,the genes that may be related to the length of the lateral calyx are mainly 6 genes such as ccm B,FRS11,and FRS6,and the genes that may be related to the floral fragrance are mainly CUL4,which is related to plant height.The genes are mainly E2FB and FFC.The main gene related to pedicel stiffness is CPSF73-I.Some of the 177 genes screened out are hypothetical proteins with no functional annotations.These genes are also potential genes that controling related traits.