Evaluation Of Important Horticultural Traits And SNP Association Analysis Of Renanthera Philippinensis

Renanthera coccinea Lour.Belongs to the Orchidaceae family.It is mainly distributed in Hainan,Guangxi and other areas in China.Renanthera coccinea prefers high temperature and high humidity climate,likes to climb on the trunk of trees and rocks at the edge of ditches or in the sparse forests.Because of its bright color and special Chinese-red color,flowers and peculiar shape,it is now widely used for cut flowers and potted flower plants,etc.and holds great market value.In this study,we studied the phenotypic traits of Ren.philippinensis in two consecutive flowering seasons from September 2020 to May 2021.we investigated 26phenotypic traits of 204 Ren.philippinensis germplasm accessions and statistically analyzed phenotypic trait data.Subsequently,we conducted phenotypic diversity analysis,correlation analysis,principal component analysis and cluster analysis,and the genetic diversity of the germplasm population was verified by using ISSR markers.A subset of the germplasm population were subjected to genome wide association analysis to identify the superior phenotypic traits of Ren.philippinensis and related genes by simplified genome sequencing of individuals genome of the germplasm accessions.This study has enriched the fundamental genetic information in relation to phenotypic traits of Ren.philippinensis The results can provide references for effective use of genetic diversity to carry out Ren.philippinensis varieties development and high-quality Ren.Philippinensis local germplasm resources development.（1）The results of phenotypic diversity analysis showed that the genetic diversity index of 7 morphological traits were 1.85.The coefficients of variation ranged from 8.71to 20.44,except for the coefficient of variation of leaf length which was 8.71,the coefficients of variation of the other six traits were all greater than 10%,which indicated that there were large genetic diversity among individual accessions.The results showed that the genetic diversity index of 19 quantitative traits of flower part were 1.87.The coefficients of variation ranged from 6.25 to 181.02,and again all the traits showed large diversity among accessions.Preliminary results from the phenotypic data analysis showed that these 204 Renanthera philippinensis had large phenotypic diversities and very rich variation indicated this germplasm population had great potential for variety improvements.（2）The correlation analysis showed that there were 148 pairs of highly significant correlations among the traits,of which 132 pairs were positively correlated and 16 pairs were negatively correlated.A total of 20 pairs of traits were significantly correlated with each other,including 11 pairs of positive correlations and 9 pairs of negative correlations.The length of flower branches was highly correlated with most of the traits,and was also significantly correlated with the number of leaves,etc.（P<0.05）,and was significantly negative correlated with the thickness of flower petals,etc.,and was also significantly negative correlated with the width of the stamens,thus showing significant or highly significant correlations between most of the traits in this germplasm population.（3）Through principal component analysis,7 principal components were extracted,and found the cumulative contribution rate reached 67.887%.Among them,the main traits that represent the differences among Ren.philippinensis germplasm accessions were selected:whether all flower branches were on the same surface,petal thickness,lateral branch length,middle calyx width,stamen column length,number of leaves,number of side branches,etc.（4）Based on the data of phenotypic traits,cluster analysis was performed,and 204Ren.philippinensis germplasm accessions were divided into 5 groups,the group I consisted of 78 accessions,the individuals in this group have more number of leaves than the individuals of other groups.The groupⅡcontains 11 accessions,,member of this group showed the more number of flower branches and the more number of flowers than others.TheⅢgroup contains 31 germplasm accessions,and members of this group were characterized by longer length from the base to the first flower branch,and have shorter the leaf length than those of other groups.GroupⅣcontains 70 germplasm accessions,the individuals in this group have smaller stamen column（smaller in length and width）than those of other groups.GroupⅤcontains 14 germplasm accessions,the individuals of this group was characterized by having larger pedicel diameter and wider calyx than other groups.（5）ISSR markers were also used to analysis the genetic diversity of Renanthera philippinensis germplasm population.Cluster analysis also formed by ISSR markers,17polymorphic bands were amplified by 2 pairs of primers on 24 accessions of Ren.philippinensis germplasm,On average there were 8.5 polymorphic bands amplified by each pair of primers.Cluster analysis results showed germplasm accessions can be divided into five groups,which indicated the genetic variations had taken place at the molecular level.（6）In this study,116 accessions of Renanthera philippinensis were sequenced with5X genome coverage,274,727 SNP were obtained after fitlering,Log₁₀（P₁）was used as the threshold line to find significantly associated variants for 26 phenotypic traits.Ten of these traits had significantly different loci of 414,while no significant loci were identified for the remaining 16 traits.These included 1 gene associated with the labellum width trait,12 genes associated with the number of lateral branches;1 gene associated with the number of flower forks,317 genes associated with petal thickness;2 genes associated with the number of flowers;3 genes associated with pedicel diameter;23 genes associated with branch length;2 genes associated with whether all branches were on the same side;28genes associated with the number of dehiscence and 25 genes associated with mid-calyx width.Subsequently,the functions of these genes were further analyzed,and 8 genes with important functions were screened:MADS50,SOC1,rps12,rps2,RMND1,and MADS9associated with petal thickness;rps10 associated with mid-calyx width and CB5＿LOCUS22476 associated with pedicel diameter,and the remaining genes currently have no function annotated,are putative proteins but may also have the function of control plant-related traits and to be potential genes.