Meta-analysis of genetic representativeness of plant populations under ex situ conservation in contrast to wild source populations

Capturing and managing genetic diversity in ex situ collections of threatened tropical trees: A case study in Karomia gigas

Premise

Although ex situ collections of threatened plants are most useful when they contain maximal genetic variation, the conservation and maintenance of genetic diversity in collections are often poorly known. We present a case study using population genomic analyses of an ex situ collection of Karomia gigas, a critically endangered tropical tree from Tanzania. Only ~43 individuals are known in two wild populations, and ex situ collections containing 34 individuals were established in two sites from wild-collected seed. The study aimed to understand how much diversity is represented in the collection, analyze the parentage of ex situ individuals, and identify efficient strategies to capture and maintain genetic diversity.

Methods

We genotyped all known individuals using a 2b-RADseq approach, compared genetic diversity in wild populations and ex situ collections, and conducted parentage analysis of the collections.

Results

Wild populations were found to have greater levels of genetic diversity than ex situ populations as measured by number of private alleles, number of polymorphic sites, observed and expected heterozygosity, nucleotide diversity, and allelic richness. In addition, only 32.6% of wild individuals are represented ex situ and many individuals were found to be the product of selfing by a single wild individual.

Discussion

Population genomic analyses provided important insights into the conservation of genetic diversity in K. gigas, identifying gaps and inefficiencies, but also highlighting strategies to conserve genetic diversity ex situ. Genomic analyses provide essential information to ensure that collections effectively conserve genetic diversity in threatened tropical trees.

Ex situ conservation of two rare oak species using microsatellite and SNP markers

Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.

Genome-wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of golden Camellia tunghinensis

Whether ex situ populations constructed in the limited nursery resources of botanical gardens can preserve enough genetic diversity of endangered plants in the wild remains uncertain. Here, a case study was conducted with Camellia tunghinensis, which is one of the species with the lowest natural distribution area in the sect. Chrysantha (golden camellia) of the family Theaceae. We investigated the genetic diversity and population structure of 229 samples from wild and ex situ populations using genotyping by sequencing (GBS). Core germplasm was constructed from these samples. The results showed that wild C. tunghinensis exhibited high genetic diversity, with observed heterozygosity of 0.257-0.293 and expected heterozygosity of 0.247-0.262. Compared with wild populations, the genetic diversity of ex situ populations established by transplanting wild seedlings was close to or even higher. However, the genetic diversity of those established by seed or cuttings of a few superior trees was lower. The Admixture analysis revealed that the structure of the ex situ populations derived from seeds and cuttings was relatively simple compared with the ex situ populations derived from transplanted wild seedlings and wild populations. These results suggested that direct transplanting of wild seedlings was more conducive to preserving the genetic diversity of endangered plants in the wild. In addition, wild populations demonstrated a small differentiation (mean F ST = 0.044) among themselves, possibly due to long-term and frequent gene flow between the wild populations. In contrast, moderate differentiation (mean F ST > 0.05) was detected among ex situ populations and between ex situ and wild populations. This may be the combined result of the absence of gene flow pathways and strong selection pressure in various ex situ environments. Finally, 77 core germplasms were extracted from 229, likely representing the genetic diversity of C. tunghinensis. This study provides future strategies for the ex situ conservation and management of the golden camellia species and other rare and endangered plants.

Limited genetic changes observed during in situ and ex situ conservation in Nordic populations of red clover (Trifolium pratense)

Introduction

In situ and ex situ conservation are the two main approaches for preserving genetic diversity. The advantages and disadvantages of the two approaches have been discussed but their genetic effects have not been fully evaluated.

Methods

In this study we investigate the effects of the two conservation approaches on genetic diversity in red clover. Seed samples collected from wild populations in Sweden and Norway in 1980, their subsequent generations created during seed regeneration at the gene bank and samples recollected from the same location as the original samples, were analyzed with microsatellite markers, alongside reference samples from cultivars.

Results

Overall, there was a differentiation between cultivars and the wild material and between wild material from Sweden and Norway. In general, the original collections clustered together with the later generations of the same accession in the gene bank, and with the recollected samples from the same location, and the level of diversity remained the same among samples of the same accession. Limited gene flow from cultivated varieties to the wild populations was detected; however, some wild individuals are likely to be escapees or affected by gene flow.

Discussion

In conclusion, there were examples of genetic changes within individual accessions both in situ and ex situ, as is also to be expected in any living population. However, we observed only limited genetic changes in both in situ and ex situ conservation over the generations included in this study and with the relatively large populations used in the ex situ conservation in the gene bank at NordGen.

Identification of the Efficacy of Ex Situ Conservation of Ammopiptanthus nanus Based on Its ETS-SSR Markers

Ammopiptanthus possesses ancestral traits and, as a tertiary relict, is one of the surviving remnants of the ancient Mediterranean retreat and climate drought. It is also the only genus of super xerophytic, evergreen, broad-leaved shrubs. Ammopiptanthus nanus, one of the two species in this genus, is predominantly found in extremely arid and frigid environments, and is increasingly threatened with extinction. Study of the species' genetic diversity is thus beneficial for its survival and the efficacy of ex situ conservation efforts. Based on transcriptome data, 15 pairs of effective EST-SSR were screened to evaluate A. nanus genetic diversity. In all, 87 samples from three populations were evaluated, the results of which show that ex situ conservation in the Wuqia region needs to be supplemented. Conservation and breeding of individual A. nanus offspring should be strengthened in the future to ensure their progeny continue to exhibit high genetic diversity and variation.

Monitoring Genetic Erosion of Aromatic and Medicinal Plant Species in Alentejo (South Portugal)

The main goal of this work was to study the genetic erosion risk of plants with aromatic, medicinal and gastronomic applications in Portugal, particularly in the Alentejo region. The target species were coriander (Coriandrum sativum L.), hart's pennyroyal (Mentha cervina L.) and pennyroyal (Mentha pulegium L.). The methodology involved direct observations and surveys (2002/2003 and 2011). The GE formula applied in Hammer's studies was used to estimate genetic erosion. The main factors causing genetic erosion were the primary drivers of biodiversity loss: habitat loss, invasive species, and overexploitation influenced by human intervention such as the clearing of watercourses, vegetation control, grazing and desertification. The results indicate a reduction in individuals per species in Alentejo, with a net erosion loss of 11% for M. pulegium, 32% for M. cervina and 33% for C. sativum. The overall loss of accessions (genetic erosion risk) was higher in cultivated accessions (33%) than in wild accessions (11%), with an annual genetic erosion rate of 3.7% and 1.2%, respectively. The annual risk of genetic erosion for M. pulegium accessions collected in a natural habitat was 0.6%, which is much lower than the 3.7% for M. cervina. These results consolidate the importance of collecting and conserving genetic resources.

Conservation of rare and endangered plant species in China

Rare and endangered plant species (REPs) are facing high danger of extinction, yet a comprehensive and up-to-date review on their conservation in China is still lacking. This paper systematically collected studies and achievements on REPs conservation, including species surveys and monitoring, cause of endangerment, in situ conservation, ex situ conservation, reintroduction, propagation, conservation legislation, public participation, progress in conservation of wild plant with extremely small populations, and progress in China's implementation of the Convention on Biological Diversity. Although enormous advances have been made in conservation policies and legislations, protection systems, and research, as well as public education and international collaborations, the conservation efficiency is still restricted largely by the conflict between economic growth and biodiversity conservation in China. In order to meet its commitments to the new Post-2020 Global Biodiversity Framework, more work on basic investigation and long-term observation, as well as advanced technologies and application-oriented research on REPs should be carried out.

Variations in genetic diversity in cultivated Pistacia chinensis

Identification of the evolution history and genetic diversity of a species is important in the utilization of novel genetic variation in this species, as well as for its conservation. Pistacia chinensis is an important biodiesel tree crop in China, due to the high oil content of its fruit. The aim of this study was to uncover the genetic structure of P. chinensis and to investigate the influence of intraspecific gene flow on the process of domestication and the diversification of varieties. We investigated the genetic structure of P. chinensis, as well as evolution and introgression in the subpopulations, through analysis of the plastid and nuclear genomes of 39 P. chinensis individuals from across China. High levels of variation were detected in the P. chinensis plastome, and 460 intraspecific polymorphic sites, 104 indels and three small inversions were identified. Phylogenetic analysis and population structure using the plastome dataset supported five clades of P. chinensis. Population structure analysis based on the nuclear SNPs showed two groups, clearly clustered together, and more than a third of the total individuals were classified as hybrids. Discordance between the plastid and nuclear genomes suggested that hybridization events may have occurred between highly divergent samples in the P. chinensis subclades. Most of the species in the P. chinensis subclade diverged between the late Miocene and the mid-Pliocene. The processes of domestication and cultivation have decreased the genetic diversity of P. chinensis. The extensive variability and structuring of the P. chinensis plastid together with the nuclear genomic variation detected in this study suggests that much unexploited genetic diversity is available for improvement in this recently domesticated species.

Continuous inbreeding affects genetic variation, phenology, and reproductive strategy in ex situ cultivated Digitalis lutea

PREMISE

Ex situ cultivation is important for plant conservation, but cultivation in small populations may result in genetic changes by drift, inbreeding, or unconscious selection. Repeated inbreeding potentially influences not only plant fitness, but also floral traits and interactions with pollinators, which has not yet been studied in an ex situ context.

METHODS

We studied the molecular genetic variation of Digitalis lutea from a botanic garden population cultivated for 30 years, a frozen seed bank conserving the original genetic structure, and two current wild populations including the source population. In a common garden, we studied the effects of experimental inbreeding and between-population crosses on performance, reproductive traits, and flower visitation of plants from the garden and a wild population.

RESULTS

Significant genetic differentiation was found between the garden population and the wild population from which the seeds had originally been gathered. After experimental selfing, inbreeding depression was only found for germination and leaf size of plants from the wild population, indicating a history of inbreeding in the smaller garden population. Moreover, garden plants flowered earlier and had floral traits related to selfing, whereas wild plants had traits related to attracting pollinators. Bumblebees visited more flowers of outbred than inbred plants and of wild than garden plants.

CONCLUSIONS

Our case study suggests that high levels of inbreeding during ex situ cultivation can influence reproductive traits and thus interactions with pollinators. Together with the effects of genetic erosion and unconscious selection, these changes may affect the success of reintroductions into natural habitats.

A Model-Based Assessment for the Ability of National Nature Reserves to Conserve the Picea Species in China under Predicted Climate Conditions

Climate change has a profound impact on the conservation and management of the Picea species, and establishing more nature reserves would be an effective way to conserve wild species in general. Based on a novel computational method using ecological niche modeling to predict the potential geographical distribution of species and a spatial decision support system, the planning process could predict the future distribution of the Picea species and thus select appropriate nature reserves. In this research, we utilized systematic conservation planning to define priority conservation areas for the Picea species in China according to future climate predictions. We hypothesized that: (1) the distribution of the Picea species could be changed under predicted climate conditions in China; (2) the current national nature reserves had sufficient capacity to conserve Picea species under predicted climate conditions in China; and (3) there were still deficiencies in the planned conservation for the Picea species based on predicted climate predictions in China. The results of a spatial analysis showed that the predicted climate would have an impact on the area of distribution of the Picea species. Current nature reserves have a strong potential to conserve the Picea species. However, the conservation of the Picea species in the existing nature reserves was not adequate. There were still many Picea specimens outside the reserve that would be threatened. This research systematically improved the research on the Picea species, and it also scientifically identified the suitable growth and conserved areas of the Picea species in China to provide an empirical basis for the conservation and management of the Picea species.

Overcoming biotic homogenization in ecological restoration

Extensive evidence shows that regional (gamma) diversity is often lower across restored landscapes than in reference landscapes, in part due to common restoration practices that favor widespread species through selection of easily-grown species with high survival and propagation practices that reduce genetic diversity. We discuss approaches to counteract biotic homogenization, such as reintroducing species that are adapted to localized habitat conditions and are unlikely to colonize naturally; periodically reintroducing propagules from remnant populations to increase genetic diversity; and reintroducing higher trophic level fauna to restore interaction networks and processes that promote habitat heterogeneity. Several policy changes would also increase regional diversity; these include regional coordination amongst restoration groups, financial incentives to organizations producing conservation-valued species, and experimental designations for rare species introductions.

Ecophysiological Leaf Traits of Forty-Seven Woody Species under Long-Term Acclimation in a Botanical Garden

Ex situ conservation plays an important role in the conservation and utilization of plant resources. In recent years, botanical gardens have greatly improved the ex situ conservation of plants, and research has mainly focused on morphological characteristics, reproduction technology, and conservation value. There are few studies on the ecophysiological traits of plants after conservation. Forty-seven plants that are frequently used in North China and were grown in the Beijing Botanic Garden were selected to measure their photosynthetic traits, light-use efficiency (LUE), water–use efficiency (WUE), specific leaf area (SLA), relative chlorophyll content (SPAD), and leaf water potential (φ). An analysis of variance showed that there were significant differences in the ecophysiological traits of the leaves of 47 woody species. The light saturation point (LSP), net photosynthetic rate at light saturation (Pnmax), φ, and SLA had significant differences among different plant life forms. The SLA and SPAD of leaves were significantly different among the families. The LUE of all species reached its maximum under a low light intensity, and species with a large difference between the light saturation point and light compensation point had larger Pnmax values. This research further adds to the understanding of the adaptation mechanisms of plants to the environment under the conditions of a botanical garden as well as the environmental fitness in a long-term ex situ domestication and then helps with scientifically setting up artificial management conditions.

Banana seed genetic resources for food security: Status, constraints, and future priorities

Storing seed collections of crop wild relatives, wild plant taxa genetically related to crops, is an essential component in global food security. Seed banking protects genetic resources from degradation and extinction and provides material for use by breeders. Despite being among the most important crops in the world, banana and plantain crop wild relatives are largely under‐represented in genebanks. Nevertheless, banana crop wild relative seed collections are in fact held in different countries, but these have not previously been part of reporting or analysis. To fill this gap, we firstly collated banana seed accession data from 13 institutions in 10 countries. These included 537 accessions containing an estimated 430,000 seeds of 56 species. We reviewed their taxonomic coverage and seed storage conditions including viability estimates. We found that seed accessions have low viability (25% mean) representing problems in seed storage and processing. Secondly, we surveyed 22 institutions involved in banana genetic resource conservation regarding the key constraints and knowledge gaps that institutions face related to banana seed conservation. Major constraints were identified including finding suitable material and populations to collect seeds from, lack of knowledge regarding optimal storage conditions and germination conditions. Thirdly, we carried out a conservation prioritization and gap analysis of Musaceae taxa, using established methods, to index representativeness. Overall, our conservation assessment showed that despite this extended data set banana crop wild relatives are inadequately conserved, with 51% of taxa not represented in seed collections at all; the average conservation assessment showing high priority for conservation according to the index. Finally, we provide recommendations for future collecting, research, and management, to conserve banana and plantain crop wild relatives in seed banks for future generations.

New developments in the field of genomic technologies and their relevance to conservation management

Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.

Plant Diversity Conservation Challenges and Prospects-The Perspective of Botanic Gardens and the Millennium Seed Bank

There is a pressing need to conserve plant diversity to prevent extinctions and to enable sustainable use of plant material by current and future generations. Here, we review the contribution that living collections and seed banks based in botanic gardens around the world make to wild plant conservation and to tackling global challenges. We focus in particular on the work of Botanic Gardens Conservation International and the Millennium Seed Bank of the Royal Botanic Gardens, Kew, with its associated global Partnership. The advantages and limitations of conservation of plant diversity as both living material and seed collections are reviewed, and the need for additional research and conservation measures, such as cryopreservation, to enable the long-term conservation of 'exceptional species' is discussed. We highlight the importance of networks and sharing access to data and plant material. The skill sets found within botanic gardens and seed banks complement each other and enable the development of integrated conservation (linking in situ and ex situ efforts). Using a number of case studies we demonstrate how botanic gardens and seed banks support integrated conservation and research for agriculture and food security, restoration and reforestation, as well as supporting local livelihoods.

Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives

BACKGROUND

Conservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were M. acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16-20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples from different individuals and 16 seed samples from one infructescence ('bunch') were analysed for each population.

RESULTS

Allelic richness of seeds compared to populations was 51, 81 and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (> 15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch.

CONCLUSIONS

We demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.