Genetic diversity in the endangered terrestrial orchid Cypripedium japonicum in East Asia: Insights into population history and implications for conservation

Phylogenetic relationships and genetic diversity of the Korean endemic Phedimus latiovalifolius (Crassulaceae) and its close relatives

Phedimus latiovalifolius (Y.N.Lee) D.C.Son & H.J.Kim is exclusively distributed in the high mountains in the Korean Peninsula, mainly along the Baekdudaegan mountain range. Despite its morphological and distributional distinction from other Phedimus Raf. species, its taxonomic identity and phylogenetic relationship with congeneric species remain unclear. This study employs genotyping-by-sequencing-derived genome-wide single nucleotide polymorphisms to establish the monophyly of P. latiovalifolius and its relationship with closely related species. Genetic diversity and population differentiation of P. latiovalifolius are also assessed to provide baseline genetic information for future conservation and management strategies. Our phylogenetic analyses robustly demonstrate the monophyletic nature of P. latiovalifolius, with P. aizoon (L.) 't Hart identified as its closest sister lineage. There is no genetic evidence supporting a hybrid origin of P. latiovalifolius from P. aizoon involving either P. ellacombeanus (Praeger) 't Hart or P. kamtschaticus (Fisch.) 't Hart. Population genetic analyses reveal two major groups within P. latiovalifolius. A higher genetic variation is observed in P. ellacombeanus than in the congeneric species. Notably, most of the genetic variation exists within P. latiovalifolius populations. Given its distribution and the potential role of Baekdudaegan as an East Asian Pleistocene refugia, P. latiovalifolius could be considered rare and endemic, persisting in the refugium across glacial/interglacial cycles.

Population genetics and genetic variation of Pomacea canaliculata (Gastropoda: Ampullariidae) in China revealed by sequence analyses of three mitochondrial genes

The Golden apple snail, Pomacea canaliculata, is one of the world's 100 worst invasive alien species that is best known for its damage to wetland agriculture. It also acts as an intermediate host of some zoonotic parasites such as Angiostrongylus cantonensis, posing threats to human public health and safety. Despite is being an important agricultural pest, the genetic information and population expansion history of this snail remains poorly understood in China. In this study, we analyzed the genetic variation and population genetics of P. canaliculata populations in seven regions of China based on molecular markers of three mitochondrial (mt) genes. A total of 15 haplotypes were recognized based on single mt cox1, nad1, and nad4, and eight haplotypes were identified using the concatenated genes. High haplotype diversity, moderate nucleotide diversity, low gene flow, and high rates of gene differentiation among the seven P. canaliculata populations were detected. Shanghai and Yunnan populations showed higher genetic flow and very low genetic differentiation. The results of Tajima's D, Fu's F s, and mismatch distribution showed that P. canaliculata did not experience population expansion in China. Genetic distance based on haplotypes suggested that nad1 gene was more conserved than cox1 gene within P. canaliculata. The phylogenetic analyses showed there may be two geographical lineages in the Chinese mainland. The present study may provide a new genetic marker to analyze P. canaliculata, and results support more evidence for studying the genetic distribution of P. canaliculata in China and contribute to a deeper understanding of its population genetics and evolutionary biology.

Genetic diversity and structure in two epiphytic orchids from the montane forests of southern Ecuador: The role of overcollection on Masdevallia rosea in comparison with the widespread Pleurothallis lilijae

Ecuador has a high diversity of orchids, but little is known about levels of genetic diversity for the great majority of species. Understanding how orchids might adapt to changes is crucial as deforestation and fragmentation of forest ecosystems threaten the survival of many epiphytic orchids that depend on other species, such as fungi and their host trees, for germination, growth, and establishment. Overcollection and the illegal trade are also major concerns for the survival of wild populations of orchids. Despite increasing awareness, effective interventions are often limited by a lack of data concerning the impacts that overexploitation might have. To fill this gap, we tested the effects of overcollection in the genetic diversity and structure of Masdevallia rosea, a narrow distributed epiphytic orchid historically collected in Ecuador, in comparison with the widely distributed Pleurothallis lilijae. Genotyping based on AFLPs showed reduced levels of diversity in wild populations but most especially in the overcollected, M. rosea. Overall, genetic admixture was high in P. lilijae segregating populations by altitude levels while fewer genetic groups were found in M. rosea. Genetic differentiation was low in both species. A spatial genetic structure was found in P. lilijae depending on altitude levels, while no spatial genetic structure was found in M. rosea. These results suggest different scenarios for the two species: while gene flow over long distance is possible in P. lilijae, the same seems to be unlikely in M. rosea possibly due to the low levels of individuals in the known populations. In situ and ex situ conservation strategies should be applied to protect the genetic pool in these epiphytic orchid species, and to promote the connectivity between wild populations. Adopting measures to reduce overexploitation and to understand the impacts of harvesting in wild populations are necessary to strengthen the legal trade of orchids.

Effect of geographic isolation on genetic variation and population structure of Euphrasia nankotaizanensis, a threatened endemic alpine herb in Taiwan

Euphrasia nankotaizanensis (Orobanchaceae) is a rare alpine herb that is endemic to Taiwan. Only four small populations remain in Xue, Nanhu, and Cilai Mountains of Taiwan. The distribution of alpine herbs is severely threatened by climate change, which influences genetic variation and population structure. In this study, we investigated the effects of the natural isolation of alpine habitats on the genetic diversity and geographic structure of populations of E. nankotaizanensis using chloroplast (cp) and nuclear DNA (nrDNA) markers. We found lower levels of genetic diversity in E. nankotaizanensis than in other alpine plants and little to no genetic variation within populations, which could be mainly attributed to the small population size and genetic drift. Only one nrDNA haplotype was present in each population. The lack of monophyly of the four populations in cpDNA probably resulted from lineage sorting or occasional long-distance seed dispersal. Phylogeographic analysis suggested that Nanhu Mountain was probably a refugium over the glacial maxima, agreeing with the potential refugia in central Taiwan. The STRUCTURE and AMOVA analyses revealed significant genetic differentiation in nrDNA among the mountains, which resulted from geographical isolation among these mountains. Estimates of the effective population size (Ne) and demography reflected lower Ne values and a recent population decline, probably implying a greater extinction risk for E. nankotaizanensis. We observed genetic depletion and considerable genetic differentiation among mountain populations, which should be considered in future conservation efforts for this species. In addition, this study provides important insights into the long-term potential of alpine herbs in Taiwan, which are useful for a better prediction of their responses to future climate change.

Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.

Advances and prospects of orchid research and industrialization

Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.

Cytological Study of Cypripedium japonicum Thunb. (Orchidaceae Juss.): An Endangered Species from Korea

Changes in chromosome number and karyotype evolution are important to plant diversification, as they are both major drivers of speciation processes. Herein, chromosome number, karyotype, and genome size of the Korean lady's slipper orchid Cypripedium japonicum Thunb., an endangered species, were investigated in natural populations. Furthermore, all cytological data from this species are reported herein for the first time. The chromosome number of all investigated C. japonicum plants was diploid (2n = 2x = 22), with x = 11 as base chromosome number, whereby the species can now be clearly distinguished from the Japanese lady's slipper orchid. The karyotypes of all studied individuals were of similar length, symmetrical, and rather unimodal. Flow cytometry of the C. japonicum revealed that the genome size ranged from 28.38 to 30.14 pg/1C. Data on chromosome number and karyotypes were largely consistent with previous results indicating that Korean (x = 11) populations of C. japonicum are more closely related to Chinese populations (x = 11) compared to Japanese (x = 10) populations. These comprehensive cytological results will benefit the efforts to discriminate the geographically isolated and endangered Eastern Asian (China, Japan, and Korea) lady's slipper orchid species.

Modelling the Effects of Climate Change on the Distribution of Endangered Cypripedium japonicum in China

Cypripedium japonicum is an endangered terrestrial orchid species with high ornamental and medicinal value. As global warming continues to intensify, the survival of C. japonicum will be further challenged. Understanding the impact of climate change on its potential distribution is of great significance to conserve this species. In this study, we established an ensemble species distribution model based on occurrence records of C. japonicum and 13 environmental variables to predict its potential distribution under current and future climatic conditions. The results show that the true skill statistic (TSS), Cohen’s kappa statistic (Kappa), and the area under the receiver operating characteristic curve (AUC) values of the ensemble model were 0.968, 0.906, and 0.995, respectively, providing more robust predictions. The key environmental variables affecting the distribution of C. japonicum were the precipitation in the warmest quarter (Bio18) and the mean temperature in the driest quarter (Bio9). Under future climatic conditions, the total suitable habitat of C. japonicum will increase slightly and tend to migrate northwestward, but the highly suitable areas will be severely lost. By 2070, the loss of its highly suitable habitat area will reach 57.69–72.24% under representative concentration pathway (RCP) 4.5 and 8.5 respectively, and the highly suitable habitats in Zhejiang and Anhui will almost disappear. It is noteworthy that the highly suitable habitat of C. japonicum has never crossed the Qinba mountainous area during the migration process of the suitable habitat to the northwest. Meanwhile, as the best-preserved area of highly suitable habitat for C. japonicum in the future, the Qinba mountainous area is of great significance to protect the wild germplasm resources of C. japonicum. In addition, we found that most of the changes predicted for 2070 will already be seen in 2050; the problem of climate change may be more urgent than it is believed.

Exploring genetic variations in threatened medicinal orchids using start codon targeted (SCoT) polymorphism and marker-association with seed morphometric traits

We aimed to study the genetic diversity and population structure of eight Iranian terrestrial orchid species, including Anacamptis coriophora (L.) R. M. Bateman, Pridgeon and M. W. Chase, Dactylorhiza umbrosa (Kar. & Kir.) Nevski, Himantoglossum affine (Boiss.) Schltr., Orchis collina Banks and Solander, Orchis mascula (L.) L., Orchis simia Lam., Ophrys schulzei Bornm. and Fleischm., and Ophrys straussii H. Fleischm. and Bornm. using start target codon markers (SCoT) and finding markers associated with seed morphometric traits. A total of 254 reproducible SCoT fragments were generated, of which 248 fragments were polymorphic (average polymorphism of 96.18%). The SCoT markers showed a narrow range of polymorphism information content (PIC) varied from 0.397 for S9 primer to 0.499 for S11 and S20 primers. Based on the population analysis results, the Orchis simia accessions collected from Paveh region (Os.P) represented the lowest observed number of alleles (Na) (1.13) and effective number of alleles (Ne) (1.09). At the same time, the highest Na (1.29) and Ne (1.18) values were obtained in O. schulzei collected from Javanrood (Oyst.JA). Shannon's information index (I) was ranged from 0.03 for D. umbrosa accessions collected from Marivan (Du.M population) to 0.263 for Ha.Ja population (H. affine accessions collected from Javanrood). The UPGMA dendrogram obtained with the Jaccard similarity coefficient (r = 0.97295) divided 97 studied terrestrial orchid accessions into eight groups mainly based on species type and geographical origin. Based on the Bayesian statistical index, the highest probability of the data was achieved when accessions were divided into eight groups (K = 8). Multiple association analysis (MRA) revealed significant associations between some of SCoT bands with seed morphometric traits. Our findings can be useful for germplasm characterization, conservation, and improvement of Iranian terrestrial orchid species.

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The online version contains supplementary material available at 10.1007/s12298-021-00978-4.

Molecular characterization of endangered Iranian terrestrial orchids using ISSR markers and association with floral and tuber-related phenotypic traits

We aimed to study the genetic diversity, population structure, and phylogeny of Iranian orchids using inter-simple sequence repeat (ISSR) markers to find markers associated with phenotypic traits. Based on the phenotypic analysis, the inflorescence length and the flower number of studied accessions ranged from 3.92 to 27.13 cm and 5 to 50, respectively. On the other hand, the tuber length ranged from 1.80 to 9.35 cm. A total of 310 reproducible ISSR fragments with a size range of 150 to 3000 bp were amplified. ISSR primers provided an average polymorphism information content of 0.391, varied from 0.488 for UBC-876 to 0.351 for UBC-842. Os.J population showed the lowest genetic diversity (H = 0.057 and I = 0.075), while Oyst.JA population showed the highest genetic diversity (H = 0.114 and I = 0.158). At species level, the average coefficient of genetic differentiation (G ST) ranged from 0.265 for Orchis simia to 0.587 for Himantoglossum affine. Gene flow (Nm) varied from 1.38 (O. simia) to 0.756 (Anacamptis collina). The UPGMA genetic similarity dendrogram using Jaccard coefficients (r = 0.973) revealed six main clusters. Based on the Bayesian clustering method, the highest probability of the data was achieved when accessions were divided into eight groups. Floral and tuber-related phenotypic traits represented high correlations together, and they were associated with some ISSR bands based on the multiple association analysis. Altogether, ISSR markers proved to be useful for discrimination and clarification of the relationships among species and populations collected from geographically different locations. Furthermore, it could identify the polymorphism among accessions within each population and species.

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The online version of this article (10.1007/s12298-020-00920-0) contains supplementary material, which is available to authorized users.

Population genetic variation characterization of the boreal tree Acer ginnala in Northern China

Genetic diversity and differentiation are revealed particularly through spatio-temporal environmental heterogeneity. Acer ginnala, as a deciduous shrub/small tree, is a foundation species in many terrestrial ecosystems of Northern China. Owing to its increased use as an economic resource, this species has been in the vulnerability. Therefore, the elucidations of the genetic differentiation and influence of environmental factors on A. ginnala are very critical for its management and future utilization strategies. In this study, high genetic diversity and differentiation occurred in A. ginnala, which might be resulted from its pollination mechanism and species characteristics. Compared with the species level, relatively low genetic diversity was detected at the population level that might be the cause for its vulnerability. There was no significant relationship between genetic and geographical distances, while a significant correlation existed between genetic and environmental distances. Among nineteen climate variables, Annual Mean Temperature (bio1), Mean Diurnal Range (bio2), Isothermality (bio3), Temperature Seasonality (bio4), Precipitation of Wettest Month (bio13), Precipitation Seasonality (bio15), and Precipitation of Warmest Quarter (bio18) could explain the substantial levels of genetic variation (> 40%) in this species. The A. ginnala populations were isolated into multi-subpopulations by the heterogeneous climate conditions, which subsequently promoted the genetic divergence. Climatic heterogeneity played an important role in the pattern of genetic differentiation and population distribution of A. ginnala across a relatively wide range in Northern China. These would provide some clues for the conservation and management of this vulnerable species.

First Report of Gray Mold Disease on Endangered Species Cypripedium japonicum

Cypripedium japonicum is known to be the indigenous plant to Korea, Japan, and China. However, C. japonicum represents the most critically endangered plant species in South Korea. The plant is esthetically pleasing due to its flower, which is larger than any other orchidaceous species. Disease symptoms relating to gray mold were observed on C. japonicum in May 2019. The suspected pathogen was successfully isolated from the symptomatic leaf tissue and conducted a pure culture of the fungi. The conidia formed consisted of a colorless or light brown single cell, which was either egg or oval-shaped with a size of 7.1 to 13.4 × 5.2 to 8.6 μm. Molecular phylogenetic relationship analysis was also confirmed that the pathogen concerned belonging to the family of Botrytis cinerea. Therefore, the findings confirmed that the pathogen isolated from C. japonicum was consistent with the unique properties of B. cinerea.

Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India

10 primers each of random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), inter primer binding site (iPBS) and start codon targeted (SCoT) were used to analyze genetic polymorphism and relationship between 50 genotypes of 5 economical important native bamboos (Bambusa cacharensis, B. mizorameana, Dendrocalamus manipureanus, D. hamiltonii and D. sikkimensis) of North-East India. The 40 different primers generated 111, 115, 116 and 138 polymorphic bands for RAPD, ISSR, iPBS and SCoT markers respectively. The comparative analysis of 4 marker systems based on polymorphic information content (PIC), effective multiplex ratio (EMR) and marker index (MI) values showed SCoT to be more informative with higher discriminating power than the other three markers. The correlation value (r) as determined by the Mantel test ranged from 0.60 (SCoT and RAPD) to 0.83 (iPBS and ISSR) indicating a high positive correlation between the markers. The close correspondence between the genetic matrices of RAPD, ISSR, iPBS and SCoT markers revealed the effectiveness of each marker system in determining the genetic relationship between bamboos. UPGMA (Unweighted Pair Group Arithmetic Mean Method) dendrograms generated from DNA marker analysis demonstrated species-specific clustering of different bamboo genotypes. Except for RAPD, the dendrograms of ISSR, iPBS and SCoT markers also showed a close association of bamboo genotypes based on geographical origin. Principal coordinate analysis (PCoA) revealed the distribution of different bamboo genotypes in accordance with the cluster analysis. The cluster grouping based on phytochemical study not only discriminated the different bamboo species but also illustrated a location-specific grouping of the genotypes. The bamboo clustering pattern derived from phytochemical analysis matched closely with the dendrograms generated by the DNA markers. The present investigation established the possibility of using a combined molecular and phytochemical marker approach to determine the genetic relationship between 5 native bamboos of North-East India with high precision.

Using high-throughput sequencing to investigate the factors structuring genomic variation of a Mediterranean grasshopper of great conservation concern

Inferring the demographic history of species is fundamental for understanding their responses to past climate/landscape alterations and improving our predictions about the future impacts of the different components of ongoing global change. Estimating the time-frame at which population fragmentation took place is also critical to determine whether such process was shaped by ancient events (e.g. past climate/geological changes) or if, conversely, it was driven by recent human activities (e.g. habitat loss). We employed genomic data (ddRAD-Seq) to determine the factors shaping contemporary patterns of genetic variation in the Iberian cross-backed grasshopper Dociostaurus crassiusculus, an endangered species with limited dispersal capacity and narrow habitat requirements. Our analyses indicate the presence of two ancient lineages and three genetic clusters resulted from historical processes of population fragmentation (~18-126 ka) that predate the Anthropocene. Landscape genetic analyses indicate that the limits of major river basins are the main geographical feature explaining large-scale patterns of genomic differentiation, with no apparent effect of human-driven habitat fragmentation. Overall, our study highlights the importance of detailed phylogeographic, demographic and spatially-explicit landscape analyses to identify evolutionary significant units and determine the relative impact of historical vs. anthropogenic factors on processes of genetic fragmentation in taxa of great conservation concern.