Germplasm Acquisition Research Articles

Seeing the Forest for the Trees: Threats, Vulnerabilities, and Opportunities for Woody Landscape Plant Genetic Resources

Genetic resources are the foundation of American agriculture’s ongoing success—the diversity, security, health, and genetic integrity of these resources must be safeguarded. However, in contrast to other crops, protecting, managing, and using collections of woody landscape plant genetic resources present significant challenges. These include conservation of at-risk populations that have high genetic diversity, evaluation of taxa with an unknown potential to invade, and management of large specimens that have long generation times and often recalcitrant or difficult-to-store seeds. The wide diversity of taxa and the limited number of specialist curators and scholars present further challenges. Thus, effective collection, preservation, evaluation, and distribution of woody landscape plant germplasm require substantial and specialized resources. The most fundamental challenge is simple: too many built landscapes have low taxonomic diversity and are often dominated by a single taxon, or monoculture. In turn, these taxonomically and genetically depauperate landscapes are vulnerable to a host of biotic and abiotic threats and are less likely to provide ecosystem and societal services for which they were designed. To develop more resilient landscapes, there is an urgent need to expand taxonomic diversity, which requires the horticultural community to effectively acquire, curate, evaluate, distribute, and use diverse woody landscape plant genetic resources. The role of the US Department of Agriculture-Agricultural Research Service (USDA-ARS) National Plant Germplasm System (NPGS) Woody Landscape Plant Crop Germplasm Committee (WLPCGC) is to identify vulnerabilities and threats that compromise WLP crops in the United States and make recommendations for prioritization of germplasm acquisition, evaluation, research, and management priorities through regular interaction with stakeholders. Due to the breadth of genera and shifting plant genetic resource needs of the nursery industry, it is impractical to list specific threatened or priority genera in a broadly applicable crop vulnerability statement. Instead, the WLPCGC has identified themes of threats and vulnerabilities providing a foundation upon which to support prioritization as threats to specific genera emerge.

Germplasm Acquisition and Distribution by CGIAR Genebanks.

The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization’s global system of conservation and use of PGRFA. They also play an important supportive role in realizing Target 2.5 of the Sustainable Development Goals. This paper analyzes CGIAR genebanks’ trends in acquiring and distributing PGRFA over the last 35 years, with a particular focus on the last decade. The paper highlights a number of factors influencing the Centers’ acquisition of new PGRFA to include in the international collections, including increased capacity to analyze gaps in those collections and precisely target new collecting missions, availability of financial resources, and the state of international and national access and benefit-sharing laws and phytosanitary regulations. Factors contributing to Centers’ distributions of PGRFA included the extent of accession-level information, users’ capacity to identify the materials they want, and policies. The genebanks’ rates of both acquisition and distribution increased over the last decade. The paper ends on a cautionary note concerning the potential of unresolved tensions regarding access and benefit sharing and digital genomic sequence information to undermine international cooperation to conserve and use PGRFA.

A tale of two genera: exotic Eucalyptus and Acacia species in China. 1. Domestication and research

In China a substantial plantation industry, including 5.4 M ha of eucalypts and up to 50,000 ha of acacias, has been built on a foundation of R&D and germplasm acquisition for exotic eucalypt and acacia species over the past 40 years. From the 1980s through to the early 2000s a suite of Chinese-Australian collaborative R&D projects made major contributions to domestication, genetic improvement, silviculture and other aspects of plantation eucalypts and acacias in southern China. Even today, germplasm derived from earlier projects still provides the majority of planting stock deployed in China's current eucalypt plantations. For eucalypts, improvements in plantation productivities have been achieved through solid, well managed R&D programs. For acacias, despite work done in past decades to develop breeding populations and production capacities for improved seeds, genetic resources of acacias in China have deteriorated greatly in recent years. Factors affecting domestication and genetic improvement of both genera in China are reviewed in this report along with the research undertaken for both genera over the past 40 years.

Higher Effectiveness of New Common Bean (Phaseolus vulgaris L.) Germplasm Acquisition by Collecting Expeditions Associated with Molecular Analyses

A remarkable portion of crop genetic diversity is represented by landraces and obsolete cultivars, that have not yet been integrated into the collections of genetic resources in genebanks. Fortunately, they are still maintained by small farmers in rural areas. Their acquisition is an important goal for collecting expeditions, followed by the evaluation of their genetic background. Molecular markers are powerful tools to evaluate the effectiveness of acquisition of new genetic variants. This approach was used for common bean landraces, that were collected through expeditions in the Slovak and Ukrainian Carpathians. In this study, microsatellite markers, developed from expressed sequence tags, were used for genotyping the collected materials. The sub-population of collected landraces contained higher total and average number of different alleles in comparison to equally large sub-populations of already-maintained cultivars. The same was true for the Shannon’s information index, observed heterozygosity, and expected heterozygosity. Both sub-populations showed the presence of private alleles: Average values of 0.500 and 0.833 private alleles per genotype were detected in landraces, and cultivars, respectively. Obtained results emphasized the importance of collecting expeditions to specific regions where landraces are cultivated, even at the present time. The effectiveness of the acquisition of new genetic variability can be determined by molecular tools, as confirmed by microsatellite markers in this study.

Causes and evolutionary consequences of primordial germ-cell specification mode in metazoans

In animals, primordial germ cells (PGCs) give rise to the germ lines, the cell lineages that produce sperm and eggs. PGCs form in embryogenesis, typically by one of two modes: a likely ancestral mode wherein germ cells are induced during embryogenesis by cell–cell signaling (induction) or a derived mechanism whereby germ cells are specified by using germ plasm—that is, maternally specified germ-line determinants (inheritance). The causes of the shift to germ plasm for PGC specification in some animal clades remain largely unknown, but its repeated convergent evolution raises the question of whether it may result from or confer an innate selective advantage. It has been hypothesized that the acquisition of germ plasm confers enhanced evolvability, resulting from the release of selective constraint on somatic gene networks in embryogenesis, thus leading to acceleration of an organism’s protein-sequence evolution, particularly for genes expressed at early developmental stages, and resulting in high speciation rates in germ plasm-containing lineages (denoted herein as the “PGC-specification hypothesis”). Although that hypothesis, if supported, could have major implications for animal evolution, our recent large-scale coding-sequence analyses from vertebrates and invertebrates provided important examples of genera that do not support the hypothesis of liberated constraint under germ plasm. Here, we consider reasons why germ plasm might be neither a direct target of selection nor causally linked to accelerated animal evolution. We explore alternate scenarios that could explain the repeated evolution of germ plasm and propose potential consequences of the inheritance and induction modes to animal evolutionary biology.

Chickpea Genetic Resources Regeneration and Safety Duplication in Georgia

A set of most released 46 chickpea accessions maintained in the collection of the Legume’s Genebank of the Agrarian University of Georgia (AUG) was regenerated using advance growing technology of seed pilling and nano herbicides. For AUG grain legumes are mandatory crops in the frame of country regulations. The level of genetic diversity and the affectivity of new germplasm acquisition for the collection enrichment were evaluated. All of them, safety duplicated 6 years ago, needed regular regeneration for future breeding works, as well as for sending to genebanks of our collaborators and breeder in abroad in accordance with international agreements. A new material was obtained from all the accessions special pilot plots of chickpea. Recently acquired new germplasm contributed all of new entire collection, i.e. almost 100% of collected diversity originated from the recently obtained accessions. Remarkable is also, that all accession carries a unique germination, not present in the remaining collection. Field and lab analysis revealed the importance of collecting missions for the enrichment of collections of genetic resources. They will be used locally and sent to international scientific institutions.

Biobanking genetic resources: challenges and implementation at the USDA National Animal Germplasm Program.

There is adequate infrastructure in the US to identify and acquire germplasm from the major beef and dairy cattle and swine breeds. However, when we venture outside these species, the same tasks become more difficult because of a lack of breed associations, databases that include genotypic and phenotypic data and low numbers of animals. Furthermore, acquisition of germplasm from non-cattle and non-swine species can be difficult because these animals are often not located near the National Animal Germplasm Program, which makes collection and preservation of the samples in a timely manner that much more complicated. This problem is compounded because not all preservation protocols are optimised for field collection conditions or for all types of germplasm. Since 1999, the USDA National Animal Germplasm Program has worked to overcome these obstacles by developing policies, procedures and techniques in order to create a germplasm repository for all agricultural species (wild and domesticated) in the US. Herein, we describe these activities and illustrate them via a case study on how our efforts collecting Navajo-Churro sheep have created a secure backup of germplasm and how we specifically overcome these issues as they relate to rare and minor breeds of agricultural species.

Acquisition of germ plasm accelerates vertebrate evolution.

Primordial germ cell (PGC) specification occurs either by induction from pluripotent cells (epigenesis) or by a cell-autonomous mechanism mediated by germ plasm (preformation). Among vertebrates, epigenesis is basal, whereas germ plasm has evolved convergently across lineages and is associated with greater speciation. We compared protein-coding sequences of vertebrate species that employ preformation with their sister taxa that use epigenesis and demonstrate that genes evolve more rapidly in species containing germ plasm. Furthermore, differences in rates of evolution appear to cause phylogenetic incongruence in protein-coding sequence comparisons between vertebrate taxa. Our results support the hypothesis that germ plasm liberates constraints on somatic development and that enhanced evolvability drives the evolution of germ plasm.

Development of best practices for ex situ conservation of radish germplasm in the context of the crop genebank knowledge base

Information about crop-specific best practices for ex situ conservation of plant genetic resources has been difficult to find until recently. The CGIAR, together with national and regional partners, started to fill that gap by publishing best practices on the crop genebank knowledge base (CGKB -http://cropgenebank.sgrp.cgiar.org/), a website specifically developed and officially launched in 2010 to provide easy access to knowledge about all aspects of ex situ conservation of specific crops to genebank managers and ex situ conservation researchers. A collaborative study, undertaken by Bioversity International with eight national and international genebanks, utilized the framework provided by the CGKB to develop and publish radish conservation best practices. This paper focuses on two aspects of this study: (1) Differences in procedures and practices in radish conservation currently applied in five key genebank activities, namely, acquisition of germplasm, viability testing and monitoring, seed drying, seed storage, and regeneration. While in a few cases genebanks agreed on a specific best practice to recommend, in others it was not desirable to identify one practice as superior to another, therefore a range of existing practices is described as a variety of equivalent options. The results highlight the importance of proactive genebank management aimed at meeting the standards within the specific context in which a genebank operates. (2) The framework and template provided by the CGKB in guiding the development of genebank best practices, and the CGKB as an excellent resource to widely and freely share best practices with the global community to support the effective management of crop genebanks.

Genetic resources collections of leafy vegetables (lettuce, spinach, chicory, artichoke, asparagus, lamb’s lettuce, rhubarb and rocket salad): composition and gaps

Lettuce, spinach and chicory are generally considered the main leafy vegetables, while a fourth group denoted by ‘minor leafy vegetables’ includes, amongst others, rocket salad, lamb’s lettuce, asparagus, artichoke and rhubarb. Except in the case of lettuce, central crop databases of leafy vegetables were lacking until recently. Here we report on the update of the international Lactuca database and the development of three new central crop databases for each of the other leafy vegetable crop groups. Requests for passport data of accessions available to the user community were addressed to all known European collection holders and to the main collection holders located outside Europe. Altogether, passport data of 17,530 accessions from a total of 129 collections were collected. The four separate databases were made available on line via a common entry page accessible at http://documents.plant.wur.nl/cgn/pgr/LVintro/ . Based on a literature study, an analysis of the gene pool structure of the crops was performed and an inventory was made of the distribution areas of the species involved. The results of these surveys were related to the contents of the newly established databases in order to identify the main collection gaps. Priorities are presented for future germplasm acquisition aimed at improving the coverage of the crop gene pools in ex situ collections.

Characterization of the genetic structure of mango ginger (Curcuma amada Roxb.) from Myanmar in farm and genebank collection by the neutral and functional genomic markers

A preliminary characterization was undertaken to describe genetic structure of mango ginger ( Curcuma amada ) acquired from farmers and ex situ genebank in Myanmar using neutral (rice SSR based RAPDs) and functional genomic (P450 based analog) markers. The high polymorphism (> 91%) depicted has displayed existence of genetic variability in the germplasm investigated. Large number of source-specific alleles (neutral-markers = 78, functional-markers = 63) was amplified which revealed that neutral regions of the mango ginger were more variable compared with the functional regions. The major fraction of the molecular variance (neutral-markers = 85%, functional-markers = 93%) was explained within germplasm acquisition sources and this tendency was also supported by the estimate of gene diversity. The genebank accessions have shown comparatively more genetic variability than farmers' accessions. The variability observed in mango ginger may possibly be associated with the long history of its cultivation under diverse ecological conditions. The two marker systems elucidated their high resolving power which detected variability even in fewer genotypes assayed. As the target sites of these markers are different, therefore, the variability detected is believed to cover diverse part of the genome together with neutral and functional regions. We found the concurrent use of the different types of molecular markers valuable to comprehend a dependable variability pattern in the germplasm assayed.

Options and legal requirements for national and regional animal genetic resource collections

The contraction of animal genetic resources on a global scale has motivated countries to establish gene banks as a mechanism to conserve national resources. Gene banks should establish a set of policies that ensure they are complying with national laws. The two primary areas of consideration are how gene banks interact with the owners of the livestock from which they are collecting samples and the relevant national or international health standards. With respect to dealing with livestock breeders for the purpose of germplasm acquisition, private property rights are the most common legal issue that will come into consideration while building collections and distributing stored material. National animal health standards may determine which animals may or may not be collected and to what extent the germplasm can be used. Internationally, the country's overall health status will determine the type of testing necessary before, during and after collection to ensure the movement of germplasm across international boundaries and through the normal protocols of animal germplasm transfer. Policy-makers will need to evaluate if the current structure of the World Organization for Animal Health (OIE) regulations will allow the development of bilateral backup collections or if waivers should be given to facilitate the genetic security afforded through gene banking.

Field Assessment of Anthracnose Disease Response for the Sorghum Germplasm Collection from the Mopti Region

Problem statement: Sorghum anthracnose (Colletotrichum sublineolum) is a highly variable pathogen and new sources of host plant resistance are required for the development of resistant sorghum varieties. Germplasm collections are an important source of host plant resistance and screening germplasm will be essential to identify new sources of resistance. Approach: The sorghum (Sorghum bicolor) collection from the Mopti region of Mali was inoculated with Colletotrichum sublineolum and evaluated for foliar anthracnose disease response in Isabela, Puerto Rico during the 2004 and 2005 growing seasons using a partially balanced lattice design with three replications. Results: A resistant response was observed for 45 of the 97 accessions in the collection and mean infection severity for the 52 susceptible accessions was 27.6%. An association was observed between resistance and the administrative district where the germplasm was collected. More than 50% of the accessions from the Bandiagara and Bankass districts showed a resistant response. The lowest frequency of resistant germplasm was observed for the Mopti district with 25% of the accessions showing a resistant response. The susceptible accessions from the Mopti district, however, showed the lowest mean infection severity. Approximately 44% of the accessions from the Douentza district showed a resistant response with the susceptible accessions showing the highest mean infection severity. These results suggest an association between annual rainfall and anthracnose resistance, with sorghum accessions from drier regions showing greater susceptibility. Anthracnose resistance also showed an association with sorghum race classification and race guinea accessions were more frequently resistant as compared to accessions classified as race durra or durra-bicolor. Conclusion: The results indicated that anthracnose resistant sorghum germplasm is frequent in the Mopti region of Mali and that ecogeographic origin and sorghum characterization information can be used to aid in germplasm selection or germplasm acquisition to identify anthracnose resistant sources.

An empirical assessment of the effects of the 1994 In Trust Agreements on IRRI Germplasm Acquisition and Distribution

An empirical assessment of the effects of the 1994 In Trust Agreements on IRRI Germplasm Acquisition and Distribution

An empirical assessment of the effects of the 1994 In Trust Agreements on IRRI Germplasm Acquisition and Distribution

The objective of this paper is to assess the possible influence of the 1994 In Trust Agreements (ITAs) on acquisition and distribution of germplasm held by the International Research Rice Institute (IRRI) genebank. The agreements, legally affirmed the ‘public good’ status of the collections that were placed ‘In Trust’ for the benefit of the world community under agreements with FAO. They initiated a formal system of multilateral access to CGIAR-held ex situ genetic resources. The hypothesis that the consequences of the ITAs lead to an enhancement of CGIAR germplasm utilization is tested here using a basic conceptual framework to infer on factors determining the distribution of germplasm. Subsequently a Bayesian empirical model is applied to IRRI accessions distribution’s time-series to provide formal evidence to the hypothesis. Results show that there is a discernible ‘change’ point that would support a significant drop in germplasm distribution followed by a new growing trend around the establishment of the ITAs. This had followed a period beginning around 1989 and leading up to the establishment of the ITAs of a large number of requests for restoration of germplasm back to countries of origin and a reduction in acquisitions. As a result the number of accessions held by IRRI reached a low point around 1994. The number of accessions might not have been built back up without the establishment of a stable policy environment that was provided by the ITAs.

Enrichment of chickpea genetic resources collection monitored by microsatellites

A set of 49 chickpea accessions maintained in the collection of the Genebank of the Slovak Republic was analyzed using microsatellite markers. The level of genetic diversity and the effectivity of new germplasm acquisition for the collection enrichment were evaluated. Five primer pairs used generated 50 different amplified alleles. Four of them, TA2, TA5, TR1, and TR7, containing a long TAA-tandem repeat, were polymorphic with 11–13 alleles per locus. A single fragment was obtained from all the accessions with the primer pair CATPER flanking a small microsatellite repetition in the mRNA sequence of chickpea cationic peroxidase. The genetic diversity was expressed as a diversity index (DI) and polymorphic information content (PIC) with values in the range from 0.885 to 0.904 and from 0.972 to 0.991, respectively. Recently acquired new germplasm contributed 13 new alleles to the entire collection, i.e. almost 70% of microsatellite diversity originated from the recently acquired accessions. Remarkable is also, that one accession carries a unique allel, not present in the remaining collection. Microsatellite analysis revealed the importance of collecting missions for the enrichment of collections of genetic resources.

Use of GIS for Optimizing a Collecting Mission for a Rare Wild Pepper (Capsicum flexuosum Sendtn.) in Paraguay

This paper presents an effective method for prioritizing areas within a country for acquisition of germplasm of a crop gene pool for ex situ conservation. The method was applied to the rare wild pepper species, Capsicum flexuosum Sendtn., in south-east Paraguay. A model to prioritize areas for collecting germplasm was constructed by combining (1) a prediction of the species' geographic distribution based on the climate at previous collection points, (2) the distribution of forest margins (the species' natural habitat) and (3) areas accessible by road. The model was then tested in the field by visiting 20 sites having both high and low predicted probability of occurrence of C. flexuosum. Six new populations were found, representing a significant improvement over two previous collecting missions for the species in the same region, undertaken without the use of GIS targeting. Using the most optimistic analysis of model performance, C. flexuosum was found at five out of seven points predicted to harbour the species and not found at four of five points predicted not to harbour the species. The model was then improved by the use of higher resolution climate surfaces. It is recommended that future explorers use more recent and higher resolution satellite images to locate suitable habitats. The method is replicable for different species in different geographic regions and is offered as a means of optimizing efficiency in financially constrained, national plant genetic resources programs.

Germplasm Acquisition from Conception to Products

Germplasm Acquisition from Conception to Products

An Overview of the U.S. National Plant Germplasm System's Exploration Program

The Plant Exploration Program was established by USDA in 1898, several decades before the emergence of the US National Plant Germplasm System (NPGS), and continues to support international and domestic plant explorations for germplasm acquisition. These explorations are designed to fill collection gaps identified by the crop curators of the NPGS and the 40 Crop Germplasm Committees that counsel the NPGS. About 15 explorations are conducted annually under the auspices of this program. Although plant explorations to remote areas are often still the only means of acquiring unique new germplasm, the focus and methods applied by modern plant explorers have changed significantly in recent years in response to evolving germplasm needs and the new opportunities presented by recent technological advances. Modern explorations are characterized by the targeting of specific taxa and traits. New exploration techniques and tools, including geographic information systems and improved methods of data collection, are being applied to locate, document, and assess plant genetic diversity. During the past decade, legal obstacles faced by the Program have increased due to restrictive laws implemented in germplasm donor countries that exercise their national sovereignty over genetic resources, replacing the free and open access to genetic resources that prevailed before the ratification of the Convention on Biological Diversity in 1993. The NPGS has responded to these regulatory challenges with a flexible approach that includes nonmonetary benefit sharing and increased partnerships with host countries.

Geographic origin and taxonomic status of the invasive Privet, Ligustrum robustum (Oleaceae), in the Mascarene Islands, determined by chloroplast DNA and RAPDs.

Information concerning the area of origin, genetic diversity and possible acquisition of germplasm through hybridisation is fundamental to understanding the evolution, ecology and possible control measures for an introduced invasive plant species. Among the most damaging of alien plants that are invading and degrading native vegetation in the Mascarene Islands of the Indian Ocean is the Tree Privet, Ligustrum robustum. Exact information about the geographic source of introduced material of this species is lacking, in part because Ligustrum is a taxonomically difficult genus. Native material of L. robustum ssp. walkeri from Sri Lanka, L. robustum ssp. robustum from northeastern India, and the closely related L. perrottetii from southern India was compared with introduced material from La Réunion and Mauritius using chloroplast DNA RFLP markers and random amplified polymorphic DNA (RAPDs). Sri Lankan and introduced material was monomorphic for the same cpDNA haplotype that was absent from south and northeast Indian Ligustrum. Sri Lankan and introduced material was also clearly distinguished from Indian Ligustrum by RAPDs. It was concluded that material introduced and established in the Mascarene Islands is derived from the Sri Lankan subspecies L. robustum ssp. walkeri. No geographic structuring of genetic variation within Sri Lanka was detected for this taxon, so the location(s) within Sri Lanka from which introduced material is derived could not be pinpointed. RAPDs indicate that L. robustum ssp. walkeri in Sri Lanka is more similar to south Indian L. perrottetii than to northeast Indian L. robustum ssp. robustum. Moreover, RAPDs showed that introduced material in La Réunion has undergone little or no loss of genetic diversity since introduction. However, there was no evidence that it is introgressed with germplasm from two other alien Ligustrum species present on La Réunion.