Leveraging the Use of Historical Data Gathered During Seed Regeneration of an ex Situ Genebank Collection of Wheat

Abstract The paper presents the results of geobotanical studies on the distribution and resources of Aster tripolium L. and Plantago maritima L, two rare halophytes in Poland. The research was conducted in northern Poland, along the Baltic coast in 2013. The present distribution of the two species was compared with historical data and general trends of and threats to these two species were examined. In total, 33 sites of A. tripolium and 18 of P. maritima were found in the research area. The resources of both species have been perceptibly depleting during last 150 years, which is mostly due to human agencies (e.g. habitat devastation caused by growing urban areas and the change in management and/or habitat condition). In order to preserve both species, it may be necessary to start an ex situ conservation program.

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Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection

Scientific Data ◽

10.1038/sdata.2018.278 ◽

2018 ◽

Vol 5 (1) ◽

Cited By ~ 2

Author(s):

Maria Y. Gonzalez ◽

Stephan Weise ◽

Yusheng Zhao ◽

Norman Philipp ◽

Daniel Arend ◽

...

Keyword(s):

Genetic Resources ◽

Phenotypic Diversity ◽

Spring Barley ◽

Plant Genetic Resources ◽

Crop Improvement ◽

Model Organism ◽

Ex Situ ◽

Phenotypic Characterization ◽

Phenotypic Data ◽

Seed Regeneration

Abstract The scarce knowledge on phenotypic characterization restricts the usage of genetic diversity of plant genetic resources in research and breeding. We describe original and ready-to-use processed data for approximately 60% of ~22,000 barley accessions hosted at the Federal ex situ Genebank for Agricultural and Horticultural Plant Species. The dataset gathers records for three traits with agronomic relevance: flowering time, plant height and thousand grain weight. This information was collected for seven decades for winter and spring barley during the seed regeneration routine. The curated data represent a source for research on genetics and genomics of adaptive and yield related traits in cereals due to the importance of barley as model organism. This data could be used to predict the performance of non-phenotyped individuals in other collections through genomic prediction. Moreover, the dataset empowers the utilization of phenotypic diversity of genetic resources for crop improvement.

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Genebank Phenomics: A Strategic Approach to Enhance Value and Utilization of Crop Germplasm

Plants ◽

10.3390/plants9070817 ◽

2020 ◽

Vol 9 (7) ◽

pp. 817 ◽

Cited By ~ 3

Author(s):

Giao N. Nguyen ◽

Sally L. Norton

Keyword(s):

High Throughput ◽

Cost Effective ◽

Screening Tools ◽

Ex Situ ◽

Phenotypic Data ◽

Germplasm Collections ◽

Digital Phenotyping ◽

Seed Regeneration ◽

Novel Alleles ◽

Crop Germplasm

Genetically diverse plant germplasm stored in ex-situ genebanks are excellent resources for breeding new high yielding and sustainable crop varieties to ensure future food security. Novel alleles have been discovered through routine genebank activities such as seed regeneration and characterization, with subsequent utilization providing significant genetic gains and improvements for the selection of favorable traits, including yield, biotic, and abiotic resistance. Although some genebanks have implemented cost-effective genotyping technologies through advances in DNA technology, the adoption of modern phenotyping is lagging. The introduction of advanced phenotyping technologies in recent decades has provided genebank scientists with time and cost-effective screening tools to obtain valuable phenotypic data for more traits on large germplasm collections during routine activities. The utilization of these phenotyping tools, coupled with high-throughput genotyping, will accelerate the use of genetic resources and fast-track the development of more resilient food crops for the future. In this review, we highlight current digital phenotyping methods that can capture traits during annual seed regeneration to enrich genebank phenotypic datasets. Next, we describe strategies for the collection and use of phenotypic data of specific traits for downstream research using high-throughput phenotyping technology. Finally, we examine the challenges and future perspectives of genebank phenomics.

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Historical phenotypic data from seven decades of seed regeneration in a wheat ex situ collection

Scientific Data ◽

10.1038/s41597-019-0146-y ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 1

Author(s):

Norman Philipp ◽

Stephan Weise ◽

Markus Oppermann ◽

Andreas Börner ◽

Jens Keilwagen ◽

...

Keyword(s):

Ex Situ ◽

Phenotypic Data ◽

Seed Regeneration ◽

Ex Situ Collection

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Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks

10.1101/238840 ◽

2017 ◽

Cited By ~ 1

Author(s):

Eltohamy A. A. Yousef ◽

Thomas Müller ◽

Andreas Börner ◽

Karl J. Schmid

Keyword(s):

Genetic Diversity ◽

Missing Data ◽

Genetic Differentiation ◽

Brassica Oleracea ◽

Principal Component ◽

Genotyping By Sequencing ◽

Ex Situ ◽

Nucleotide Polymorphisms ◽

Phenotypic Differences ◽

Seed Regeneration

AbstractCauliflower (Brassica oleracea var. botrytis) is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS). They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs) with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (<1%) of SNPs that are highly differentiated between the two genebanks, which indicates that selection during seed regeneration is not a major cause of differentiation between genebanks. Seed regeneration procedures of both genebanks do not result in different levels of genetic drift and loss of genetic variation. We therefore conclude that the composition and type of accessions mainly influence the level of genetic diversity and explain the strong genetic differentiation between the two ex situ collections. In summary, GBS is a useful method for characterizing genetic diversity in cauliflower genebank material and our results suggest that it may be useful to incorporate routine genotyping into accession management and seed regeneration to monitor the diversity present in ex situ collections and to reduce the loss of genetic diversity during seed regeneration.

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Combination of high resolution melting (HRM) analysis and SSR molecular markers speeds up plum genotyping: case study genotyping the Greek plum GeneBank collection

Plant Genetic Resources ◽

10.1017/s1479262116000022 ◽

2016 ◽

Vol 15 (4) ◽

pp. 366-375 ◽

Cited By ~ 5

Author(s):

Georgios Merkouropoulos ◽

Ioannis Ganopoulos ◽

Athanasios Tsaftaris ◽

Ioannis Papadopoulos ◽

Pavlina Drogoudi

Keyword(s):

High Resolution ◽

High Resolution Melting ◽

Cost Effective ◽

Ex Situ ◽

Hrm Analysis ◽

Prunus Salicina ◽

Genebank Collection ◽

Of Greece

AbstractIn a germplasm bank collection the conservation and characterization of genetic resources is a prerequisite in order to use the material in breeding projects aiming the creation of new cultivars. In the present study, 54 Prunus salicina domestica and Prunus domestica genotypes (including seven Greek cultivars), maintained in the ex situ National Genebank Collection of Greece, were classified using microsatellite (simple sequence repeat, SSR) markers on high resolution melting (HRM) analysis. The SSR primer pairs were chosen from the published literature as originally designed on Prunus species. This combined approach was used to genotype all plum accessions of the collection highlighting the benefits of either method (HRM and SSRs) for cultivar identification. Dendrograms for P. domestica and P. salicina and a combined one with all the genotypes assayed were produced. A total of 15 from the 19 P. domestica accessions analysed, including all the Greek accessions but ‘Avgati Skopelou’, were grouped into the same clade in the combined dendrogram, whereas the remaining four were dispersed into the P. salinica clades. Bayesian structure analysis confirmed that ‘Avgati Skopelou’ differs from the rest of the Greek plum cultivars since it was not grouped into the same cluster. The combination of HRM and SSRs, provided a considerably faster, cost-effective, closed-tube microsatellite genotyping method for molecular characterization of plum cultivars.

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An in situ and ex situ TEM study of the formation of thin cobalt silicide films by molecular beam epitaxy on the silicon (100) surface

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010010648x ◽

1988 ◽

Vol 46 ◽

pp. 884-885

Author(s):

D. Loretto ◽

J. M. Gibson ◽

S. M. Yalisove ◽

R. T. Tung

Keyword(s):

Molecular Beam Epitaxy ◽

Molecular Beam ◽

Defect Density ◽

High Vacuum ◽

Ultra High Vacuum ◽

Ex Situ ◽

Metal Base ◽

In Situ Experiments ◽

Potential Applications

The cobalt disilicide/silicon system has potential applications as a metal-base and as a permeable-base transistor. Although thin, low defect density, films of CoSi2 on Si(111) have been successfully grown, there are reasons to believe that Si(100)/CoSi2 may be better suited to the transmission of electrons at the silicon/silicide interface than Si(111)/CoSi2. A TEM study of the formation of CoSi2 on Si(100) is therefore being conducted. We have previously reported TEM observations on Si(111)/CoSi2 grown both in situ, in an ultra high vacuum (UHV) TEM and ex situ, in a conventional Molecular Beam Epitaxy system.The procedures used for the MBE growth have been described elsewhere. In situ experiments were performed in a JEOL 200CX electron microscope, extensively modified to give a vacuum of better than 10-9 T in the specimen region and the capacity to do in situ sample heating and deposition. Cobalt was deposited onto clean Si(100) samples by thermal evaporation from cobalt-coated Ta filaments.

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The use of transmission and analytical electron microscopy in studying reactions and phase transformations in thin film

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100150046 ◽

1993 ◽

Vol 51 ◽

pp. 842-843

Author(s):

K. Barmak

Keyword(s):

Thin Film ◽

Thin Films ◽

Phase Transformations ◽

Analytical Electron Microscopy ◽

Ex Situ ◽

Multilayer Thin Films ◽

Absolute Concentration ◽

Analytical Electron ◽

Deposition Step

Generally, processing of thin films involves several annealing steps in addition to the deposition step. During the annealing steps, diffusion, transformations and reactions take place. In this paper, examples of the use of TEM and AEM for ex situ and in situ studies of reactions and phase transformations in thin films will be presented.The ex situ studies were carried out on Nb/Al multilayer thin films annealed to different stages of reaction. Figure 1 shows a multilayer with dNb = 383 and dAl = 117 nm annealed at 750°C for 4 hours. As can be seen in the micrograph, there are four phases, Nb/Nb3-xAl/Nb2-xAl/NbAl3, present in the film at this stage of the reaction. The composition of each of the four regions marked 1-4 was obtained by EDX analysis. The absolute concentration in each region could not be determined due to the lack of thickness and geometry parameters that were required to make the necessary absorption and fluorescence corrections.

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Transmission Electron Microscopy of Epitaxial silicides grown by ultra high vacuum deposition

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100154287 ◽

1989 ◽

Vol 47 ◽

pp. 462-463

Author(s):

D. Loretto ◽

J. M. Gibson ◽

S. M. Yalisove

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Electron Diffraction ◽

High Vacuum ◽

High Energy ◽

Energy Electron ◽

Ultra High Vacuum ◽

Ex Situ ◽

Transmission Electron

The silicides CoSi2 and NiSi2 are both metallic with the fee flourite structure and lattice constants which are close to silicon (1.2% and 0.6% smaller at room temperature respectively) Consequently epitaxial cobalt and nickel disilicide can be grown on silicon. If these layers are formed by ultra high vacuum (UHV) deposition (also known as molecular beam epitaxy or MBE) their thickness can be controlled to within a few monolayers. Such ultrathin metal/silicon systems have many potential applications: for example electronic devices based on ballistic transport. They also provide a model system to study the properties of heterointerfaces. In this work we will discuss results obtained using in situ and ex situ transmission electron microscopy (TEM).In situ TEM is suited to the study of MBE growth for several reasons. It offers high spatial resolution and the ability to penetrate many monolayers of material. This is in contrast to the techniques which are usually employed for in situ measurements in MBE, for example low energy electron diffraction (LEED) and reflection high energy electron diffraction (RHEED), which are both sensitive to only a few monolayers at the surface.

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Interfacial properties of GaSb/InAs superlattices

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100149969 ◽

1993 ◽

Vol 51 ◽

pp. 826-827

Author(s):

M. E. Twigg ◽

B. R. Bennett ◽

J. R. Waterman ◽

J. L. Davis ◽

B. V. Shanabrook ◽

...

Keyword(s):

Gaas Substrate ◽

Molecular Beam ◽

Infrared Detector ◽

Interfacial Properties ◽

Ex Situ ◽

X Ray Diffraction ◽

Absorption Coefficients ◽

X Ray ◽

Short Period ◽

High Optical Absorption

Recently, the GaSb/InAs superlattice system has received renewed attention. The interest stems from a model demonstrating that short period Ga1-xInxSb/InAs superlattices will have both a band gap less than 100 meV and high optical absorption coefficients, principal requirements for infrared detector applications. Because this superlattice system contains two species of cations and anions, it is possible to prepare either InSb-like or GaAs-like interfaces. As such, the system presents a unique opportunity to examine interfacial properties.We used molecular beam epitaxy (MBE) to prepare an extensive set of GaSb/InAs superlattices grown on an GaSb buffer, which, in turn had been grown on a (100) GaAs substrate. Through appropriate shutter sequences, the interfaces were directed to assume either an InSb-like or GaAs-like character. These superlattices were then studied with a variety of ex-situ probes such as x-ray diffraction and Raman spectroscopy. These probes confirmed that, indeed, predominantly InSb-like and GaAs-like interfaces had been achieved.

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