Genetic Differentiation Among Rosa Rugosa Populations Of Different Provenances Based On Transcriptome Sequencing

Rosa rugosa is a shrub species distributing on temperate sandy beaches,dunes or hill slopes of coastal areas.It is an important germplasm resource species for breeding of oil and ornamental Rosa cultivars.Since the 1990s,the distrbution area of wild R.rugosa in China has been continuously shrinked and fragmented,therefore it had been included in the list of rare and endangered plants of China(category II)However,the introduced R.rugosa from East Asia to Europe was successfully escaped to natural habitats from gardens in the early 18th century.This species had been considered as an invasive species by some countries around the North Sea and the Baltic Sea.Based on transcriptome sequencing,studies on the morphological and genetic differentiation of R.rugosa populations of different provenances in common gardens with similar climate and environment conditions can help to reveal the adaptive evolution pattern of R.rugosa genome and functional genes,as well as the potential driving factors by eliminating the influences of phenotypic plasticity.The results are expected to provide a new insight into the evolutionary patterns,field management and gene exploration of R.rugosa.The totally thirteen sampled R.rugosa populations of different provenances have been cultivated in three common gardens with similar climate and environment conditions in central Shandong province for more than three years.Rosa davurica was used as an outer group.The genetic differentiation pattern of thirteen R.rugosa populations from four Chinese wild populations(CWR group),three European wild populations(EWR group)and 6 Chinese cultivated R.rugosa varieties(CCR group)were studied.Nested ANOVA(Analysis of variance),multiple comparisons.correlation analysis,cluster analysis etc.were used to uncover the phenotypic variation pattern among populations.The next generation transcriptome sequencing was used to study the adaptive differentiation pattern of functional genes and expression differences among populations and groups of different provenances.The significant enrichment analysis of differentially expressed genes was carried out.and the candidate genes related cold tolerance of R.rugosa were sorted and the relationships between these genes and temperature factors.Phenotypic analysis showed that the phenotypic traits of R.rugosa had higher variability.Most of these traits were significantly different within and among three groups.The average differentiation coefficient among three groups was 40.6%and the average differentiation coefficient within groups was 59.4%.The average coefficient of variation of 22 phenotypic traits was 24.0%.Among them,the phenotypic variation coefficient of flower traits was 15.8%,which was much smaller than that of the leaf and fruit phenotypic traits.The average coefficient of variation of the European wild R.rugosa group was 28.2%,which was much larger than that of the other two groups.The multiple phenotypic traits of leaves in the wild R.rugosa populations were significantly correlated with some ecological factors such as the frost-free period and the average highest temperature in July in the provenance sites of these populations(p<0.05).The temperature conditions associated with these factors may be one of the dominant factors affecting the variation of rose leaf traits.A total of 101,083 Unigenes were gained from the R.rugosa transcriptome De novo sequencing assembly and de-redundant,and a total of 81.20%of these genes were annotated.There were 53,717 genes differentially expressed between any two groups,accounting for 53.14%.By combining the clustering dendrogram based on phenotypic differentiation and the phylogenetic tree based on unigenes diffrentiation.we found that the differentiation pattern among the thirteen R.rugosa populations was very complex.The European wild R.rugosa populations were associated with both of the Chinese wild R.rugosa populations and the Chinese cultivated R.rugosa populations.The Skane(SKA)population from Sweden and the Rongcheng(RON)population of China were closer in the phenotypic traits and the transcriptome sequences implicating potentially similar phenotypic and genetic adaptation characteristics.The Langeog(LAN)R.rugosa population and the Chinese cultivated R rugosa group had higher similarity in phenotypic traits and transcriptome sequences meaning closer genetic relationship.The Hunchun(HCH)population was less similar to the other populations.The photosynthesis-antenna protein pathway was significantly enriched in the differentially expressed genes of thirteen R.rugosa populations(Qvalue<0.05),while the ribosomal components in the wild R.rugosa groups of CWR and EWR were significantly enriched(Qvalue<0.05).In the SKA population and the MUP population with large latitude differences,the cellular components of the chloroplast stroma,chloroplast envelope,and the porphyrin and chlorophyll metabolism pathways were significantly enriched in up-regulated DEGs(Qvalue<0.05),sucrose synthase activity and the sucrose metabolism process was significantly enriched in down-regulated DEGs(Qvalue<0.05).Totally twelve candidate genes associated with latitude were sorted from the genes related cold and drought regulated proteins,of which the expression levels of four genes were significantly correlated with some ecological factors in the provenance sites of the wild populations(p<0.05).The results reflected a potential geographical pattern of temperature adaptation in wide distributed R.rugosa populations.Therefore,the annual average temperatures,especially the the average lowest temperature might affect the adaptive evolution pattern of R.rugosa by affecting the expression levels of genes related to photosynthesis,glucose metabolism and cold and drought regulating proteins.Overall,there were high variability within and between groups of different provenance R.rugosa populations.European wild and Chinese wild R.rugosa populations showed geographical adaptation patterns related to latitude and temerature factors of provenance sites,and the expression levels of some cold-tolerant related candidate genes may be affected by the annual average temperatures.The effects of such factors need to be further studied.