BackgroundTree peonies are great ornamental plants associated with a rich ethnobotanical history in Chinese culture and have recently been used as an evolutionary model. The Qinling Mountains represent a significant geographic barrier in Asia, dividing mainland China into northern (temperate) and southern (semi–tropical) regions; however, their flora has not been well analyzed. In this study, the genetic differentiation and genetic structure of Paeonia rockii and the role of the Qinling Mountains as a barrier that has driven intraspecific fragmentation were evaluated using 14 microsatellite markers.Methodology/Principal FindingsTwenty wild populations were sampled from the distributional range of P. rockii. Significant population differentiation was suggested (FST value of 0.302). Moderate genetic diversity at the population level (HS of 0.516) and high population diversity at the species level (HT of 0.749) were detected. Significant excess homozygosity (FIS of 0.076) and recent population bottlenecks were detected in three populations. Bayesian clusters, population genetic trees and principal coordinate analysis all classified the P. rockii populations into three genetic groups and one admixed Wenxian population. An isolation-by-distance model for P. rockii was suggested by Mantel tests (r = 0.6074, P<0.001) and supported by AMOVA (P<0.001), revealing a significant molecular variance among the groups (11.32%) and their populations (21.22%). These data support the five geographic boundaries surrounding the Qinling Mountains and adjacent areas that were detected with Monmonier's maximum-difference algorithm.Conclusions/SignificanceOur data suggest that the current genetic structure of P. rockii has resulted from the fragmentation of a formerly continuously distributed large population following the restriction of gene flow between populations of this species by the Qinling Mountains. This study provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of this species and for improving the genetic basis for breeding its cultivars.

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Genetic linkage maps, permitting the elucidation of genome structure, are one of most powerful genomic tools to accelerate marker-assisted breeding. However, due to a lack of sufficient user-friendly molecular markers, no genetic linkage map has been developed for tree peonies (Paeonia Sect. Moutan), a group of important horticultural plants worldwide. Specific-locus amplified fragment sequencing (SLAF-seq) is a recent molecular marker development technology that enable the large-scale discovery and genotyping of sequence-based marker in genome-wide. In this study, we performed SLAF sequencing of an F1 population, derived from the cross P. ostti ‘FenDanBai’ × P. × suffruticosa ‘HongQiao’, to identify sufficient high-quality markers for the construction of high-density genetic linkage map in tree peonies. After SLAF sequencing, a total of 78 Gb sequencing data and 285,403,225 pair-end reads were generated. We detected 309,198 high-quality SLAFs from these data, of which 85,124 (27.5%) were polymorphic. Subsequently, 3518 of the polymorphic markers, which were successfully encoded in to Mendelian segregation types, and were in conformity with the criteria of high-quality markers, were defined as effective markers and used for genetic linkage mapping. Finally, we constructed an integrated genetic map, which comprised 1189 markers on the five linkage groups, and spanned 920.699 centiMorgans (cM) with an average inter-marker distance of 0.774 cM. There were 1115 ‘SNP-only’ markers, 18 ‘InDel-only’ markers, and 56 ‘SNP&InDel’ markers on the map. Among these markers, 450 (37.85%) showed significant segregation distortion (P < 0.05). In conclusion, this investigation reported the first large-scale marker development and high-density linkage map construction for tree peony. The results of this study will serve as a solid foundation not only for marker-assisted breeding, but also for genome sequence assembly for tree peony.

The endangered species Paeonia rockii is the most important ancestral species of the cultivated tree peonies. These well-known ornamental plants are termed the 'King of Flowers' in China. In this study, we investigated the genetic diversity and phylogeographic structure of 335 wild samples from 20 populations throughout the entire distributional range of the species based on three chloroplast DNA sequences (petB-petD, rps16-trnQ and psbA-trnH). At those loci, high levels of genetic differentiation (G ST = 0.94) and low levels of genetic variation (h = 0.00185) were detected. The intraspecific phylogeny revealed four groups, the western group, the Taibai mountain group, the northern group and the eastern group, which closely coincided with the geographic distribution of the species. A phylogeographic structure of this kind could result from a number of integrated factors, such as allopatric fragmentation, climatic fluctuations, increased abortion and declining germination of seeds, or lack of gene flow among populations, especially across the geographic barrier of the high Qinling Mountains, and it could also result from adaptive evolution. For conservation purposes, each extant population of P. rockii should be recognized as a conservation-significant unit, and a more stringent conservation strategy should incorporate in situ and ex situ methods.

JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org.. The University of Chicago Press is collaborating with JSTOR to digitize, preserve and extend access to International Journal of Plant Sciences.In Paeonia, hybridization is an important path for both the development of new cultivars and species formation in nature, but the characterization of hybrids has long been a problem. To establish the relationship among Paeonia yananensis, P. jishanensis, and P. rockii, we sampled 159 individuals from 11 populations around the core population of P. yananensis. Samples were subjected to morphological analysis of 22 characters and molecular analysis of three chloroplast DNA (cpDNA) fragments and 14 microsatellites. Paeonia yananensis was distinguishable from the other two species on the basis of morphological characteristics. The phylogenetic tree based on three intergenic spacers in the chloroplast genome (petB-petD, rps16-trnQ, and psbA-trnH) demonstrated that P. yananensis was very closely related to P. jishanensis. However, analysis of 14 microsatellite loci revealed that P. yananensis shared a considerable number of alleles with both P. jishanensis and P. rockii. These results demonstrated that P. yananensis (¼P. 3 yananensis) is of hybrid origin, with P. jishanensis as a maternal parent and P. rockii as a paternal parent. Our success in documenting the hybrid origin of P. yananensis suggests that combined evidence from morphology, maternally inherited cpDNA, and biparentally inherited microsatellites could serve as a powerful tool in hybrid studies.

Tree peonies are important ornamental plants worldwide, but growing them can be frustrating due to their short and concentrated flowering period. Certain cultivars exhibit a reblooming trait that provides a valuable alternative for extending the flowering period. However, the genetic control of reblooming in tree peonies is not well understood. In this study, we compared the molecular properties and morphology of reblooming and non-reblooming tree peonies during the floral initiation and developmental processes. Using transcriptome sequencing technology, we generated 59,275 and 63,962 unigenes with a mean size of 698 bp and 699 bp from the two types of tree peonies, respectively, and identified eight differentially expressed genes that are involved in the floral pathways of Arabidopsis thaliana. These differentially regulated genes were verified through a detailed analysis of their expression pattern during the floral process by real time RT-PCR. From this combined analysis, we identified four genes, PsFT, PsVIN3, PsCO and PsGA20OX, which likely play important roles in the regulation of the reblooming process in tree peonies. These data constitute a valuable resource for the discovery of genes involved in flowering time and insights into the molecular mechanism of flowering to further accelerate the breeding of tree peonies and other perennial woody plants.

Tree peony (Paeonia Sect. Moutan) is an economically important ornamental plant, but little is known about the genetic architecture of important ornamental traits. To effectively improve ornamental value, we require a better understanding of genetic architecture in the complex traits of the tree peony. Association mapping is a powerful tool for detection of variation associated with traits. Thus, we examined the genetic diversity and the population structure of 462 unrelated cultivated P. rockii individuals, then performed association mapping to identify simple sequence repeat (SSR) markers associated with 12 floral traits. We observed a moderate level of genetic diversity (PIC = 0.459) and low linkage disequilibrium (LD) between markers, demonstrating that the potential value of an LD approach in elucidating the molecular basis of the quantitative variation in this species. An analysis of population structure revealed three subgroups in the association population. Subsequent single-marker association analysis identified 46 significant associations, involving the 11 traits with 37 SSRs. These loci explained a small proportion of the phenotypic variance, ranging from 2.68 to 23.97% (mean 5.50%). We also validated 15 of the 46 associations in a linkage mapping population of 159 individuals. Finally, five associations were further confirmed in the linkage mapping population, involving the four traits with four SSRs. These results can serve as a foundation for further analyses of the genetic architecture of floral traits, and the SSRs associated in this work have potential applications in marker-assisted breeding in tree peony.

An understanding of plant domestication history provides insights into general mechanisms of plant adaptation and diversification and can guide breeding programmes that aim to improve cultivated species. Cultivated tree peonies (genus Paeonia L.) are among the most popular ornamental plants in the world; yet, the history of their domestication is still unresolved. Here, we explored whether the domestication in China of historically cultivated peonies, that is, the common and flare cultivated tree peonies, was a single event or whether independent domestications occurred. We used 14 nuclear microsatellite markers and a comprehensive set of 553 tree peonies collected across China, including common tree peonies, flare tree peonies and the wild species or subspecies that are potential contributors to the cultivated tree peonies, that is, Paeonia rockii ssp. rockii, P. rockii ssp. atava, P. jishanensis and P. decomposita. Assignment methods, a principal component analysis and approximate Bayesian computations provided clear evidence for independent domestications of these common tree and flare tree peonies from two distinct and allopatric wild species, P. jishanensis and P. rockii ssp. atava, respectively. This study provides the first example of independent domestications of cultivated trees from distinct species and locations. This work also yields crucial insight into the history of domestication of one of the most popular woody ornamental plants. The cultivated peonies represent an interesting case of parallel and convergent evolution. The information obtained in this study will be valuable both for improving current tree peony breeding strategies and for understanding the mechanisms of domestication, diversification and adaptation in plants.