Unlocking historical phenotypic data from an ex situ collection to enhance the informed utilization of genetic resources of barley (Hordeum sp.)

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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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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Best practices for setting up a repository of phenotypic data for European germplasm holdings

Biodiversity Information Science and Standards ◽

10.3897/biss.2.25223 ◽

2018 ◽

Vol 2 ◽

pp. e25223

Author(s):

Stephan Weise ◽

Markus Oppermann

Keyword(s):

Best Practices ◽

Genetic Resources ◽

Rating Scales ◽

Plant Genetic Resources ◽

Wild Relatives ◽

Ex Situ ◽

Phenotypic Data ◽

Meta Information ◽

Passport Data ◽

Selection Of

The European Search Catalogue for Plant Genetic Resources, EURISCO, provides information about more than 1.9 million accessions of crop plants and their wild relatives, preserved ex situ by almost 400 institutes in Europe and beyond (Weise et al. 2017). EURISCO, which is being maintained on behalf of the European Cooperative Programme for Plant Genetic Resources, is based on a network of National Inventories of 43 member countries. It represents an important effort for the preservation of the world’s agrobiological diversity by providing information about the large genetic diversity kept by the collaborating institutions. Besides the classical passport data, in 2016, EURISCO started to additionally collect phenotypic data about the documented germplasm accessions. The selection of genebank material for both research and breeding purposes is increasingly carried out through the selection of specific phenotypic values, e.g. flowering time or plant height. Thus, these data are of high importance to users of plant genetic resources (PGR) since they determine the value of the respective germplasm. However, because there are no commonly agreed standards existing within the genebank community, this kind of data is very difficult to handle. In this context, the challenges range from synonymous/homonymous descriptor names over different rating scales to different/insufficient amounts of meta information, thus hampering both integration and cross-experiment comparison of data. The presentation will illustrate the approach followed within EURISCO, together with the challenges resulting therefrom. Using this as a solid basis for a discussion about the utilization of this kind of data, the presentation shall be regarded as a call for cooperation.

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Ex-situ conservation of medicinal plant genetic resources managed by national agrobiodiversity center of Korea

Planta Medica ◽

10.1055/s-0032-1320321 ◽

2012 ◽

Vol 78 (11) ◽

Author(s):

JS Sung ◽

CW Jeong ◽

YY Lee ◽

HS Lee ◽

YA Jeon ◽

...

Keyword(s):

Medicinal Plant ◽

Genetic Resources ◽

Ex Situ Conservation ◽

Plant Genetic Resources ◽

Ex Situ

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Diversity and Relationships among Neglected Apricot (Prunus armeniaca L.) Landraces Using Morphological Traits and SSR Markers: Implications for Agro-Biodiversity Conservation

Plants ◽

10.3390/plants10071341 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1341

Author(s):

Giandomenico Corrado ◽

Marcello Forlani ◽

Rosa Rao ◽

Boris Basile

Keyword(s):

Prunus Armeniaca ◽

Ex Situ ◽

Skin Colour ◽

Maintenance Breeding ◽

Prunus Armeniaca L ◽

Ex Situ Collection ◽

Loss Of Diversity ◽

Ssrs Markers ◽

On Farm ◽

Simple Sequence

Apricot (Prunus armeniaca L.) is an economically important tree species globally cultivated in temperate areas. Italy has an ample number of traditional varieties, but numerous landraces are abandoned and at risk of extinction because of increasing urbanization, agricultural intensification, and varietal renewal. In this work, we investigated the morphological and genetic diversity present in an ex-situ collection of 28 neglected varieties belonging to the so-called “Vesuvian apricot”. Our aim was to understand the level of diversity and the possible link between the promotion of specific fruit types (e.g., by public policies) and the intraspecific variation in apricot. The combination of five continuous and seven categorical traits allowed us to phenotypically distinguish the varieties; while fruit quality-related attributes displayed high variation, both apricot size and skin colour were more uniform. The twelve fluorescent-based Simple Sequence Repeats (SSRs) markers identified cultivar-specific molecular profiles and revealed a high molecular diversity, which poorly correlated with that described by the morphological analysis. Our results highlighted the complementary information provided by the two sets of descriptors and that DNA markers are necessary to separate morphologically related apricot landraces. The observed morphological and genetic differences suggest a loss of diversity influenced by maintenance breeding of specific pomological traits (e.g., skin colour and size). Finally, our study provided evidence to recommend complementary strategies to avoid the loss of diversity in apricot. Actions should pivot on both the promotion of easily identified premium products and more inclusive biodiversity-centred on-farm strategies.

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Conservation of animal genetic resources: approaches and technologies for in situ and ex situ conservation

Animal Genetic Resources Information ◽

10.1017/s1014233900002571 ◽

2008 ◽

Vol 42 ◽

pp. 71-85 ◽

Cited By ~ 8

Author(s):

J.A. Woolliams ◽

O. Matika ◽

J. Pattison

Keyword(s):

Rural Communities ◽

Genetic Resources ◽

Large Scale ◽

Production Systems ◽

Regional Distribution ◽

Livestock Production ◽

Ex Situ ◽

Animal Genetic Resources ◽

The Face ◽

Livestock Products

SummaryLivestock production faces major challenges through the coincidence of major drivers of change, some with conflicting directions. These are:1. An unprecedented global change in demands for traditional livestock products such as meat, milk and eggs.2. Large changes in the demographic and regional distribution of these demands.3. The need to reduce poverty in rural communities by providing sustainable livelihoods.4. The possible emergence of new agricultural outputs such as bio-fuels making a significant impact upon traditional production systems.5. A growing awareness of the need to reduce the environmental impact of livestock production.6. The uncertainty in the scale and impact of climate change. This paper explores these challenges from a scientific perspective in the face of the large-scale and selective erosion of our animal genetic resources, and concludes thai there is a stronger and more urgent need than ever before to secure the livestock genetic resources available to humankind through a comprehensive global conservation programme.

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Low effective population size and high spatial genetic structure of black poplar populations from the Oder valley in Poland

Annals of Forest Science ◽

10.1007/s13595-021-01055-2 ◽

2021 ◽

Vol 78 (2) ◽

Author(s):

Błażej Wójkiewicz ◽

Andrzewj Lewandowski ◽

Weronika B. Żukowska ◽

Monika Litkowiec ◽

Witold Wachowiak

Keyword(s):

Genetic Structure ◽

Genetic Resources ◽

Population Size ◽

Effective Population Size ◽

Spatial Genetic Structure ◽

Demographic History ◽

River Valley ◽

Ex Situ ◽

Effective Population ◽

Black Poplar

Abstract Context Black poplar (Populus nigra L.) is a keystone species of European riparian ecosystems that has been negatively impacted by riverside urbanization for centuries. Consequently, it has become an endangered tree species in many European countries. The establishment of a suitable rescue plan of the remaining black poplar forest stands requires a preliminary knowledge about the distribution of genetic variation among species populations. However, for some parts of the P. nigra distribution in Europe, the genetic resources and demographic history remain poorly recognized. Aims Here, we present the first study on identifying and characterizing the genetic resources of black poplar from the Oder valley in Poland. This study (1) assessed the genetic variability and effective population size of populations and (2) examined whether gene flow is limited by distance or there is a single migrant pool along the studied river system. Methods A total of 582 poplar trees derived from nine black poplar populations were investigated with nuclear microsatellite markers. Results (1) The allelic richness and heterozygosity level were high and comparable between populations. (2) The genetic structure of the studied poplar stands was not homogenous. (3) The signatures of past bottlenecks were detected. Conclusion Our study (1) provides evidence for genetic substructuring of natural black poplar populations from the studied river catchment, which is not a frequent phenomenon reported for this species in Europe, and (2) indicates which poplar stands may serve as new genetic conservation units (GCUs) of this species in Europe. Key message The genetic resources of black poplar in the Oder River valley are still substantial compared to those reported for rivers in Western Europe. On the other hand, clear signals of isolation by distance and genetic erosion reflected in small effective population sizes and high spatial genetic structure of the analyzed populations were detected. Based on these findings, we recommend the in situ and ex situ conservation strategies for conserving and restoring the genetic resources of black poplar populations in this strongly transformed by human river valley ecosystem.

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Genomic prediction models trained with historical records enable populating the German ex situ genebank bio-digital resource center of barley (Hordeum sp.) with information on resistances to soilborne barley mosaic viruses

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03815-0 ◽

2021 ◽

Author(s):

Maria Y. Gonzalez ◽

Yusheng Zhao ◽

Yong Jiang ◽

Nils Stein ◽

Antje Habekuss ◽

...

Keyword(s):

Genetic Resources ◽

Mosaic Virus ◽

Genomic Prediction ◽

Prediction Models ◽

Ex Situ ◽

Yellow Mosaic Virus ◽

Plant Responses ◽

Resource Center ◽

Digital Resource ◽

Best Linear Unbiased

AbstractKey messageGenomic prediction with special weight of major genes is a valuable tool to populate bio-digital resource centers.AbstractPhenotypic information of crop genetic resources is a prerequisite for an informed selection that aims to broaden the genetic base of the elite breeding pools. We investigated the potential of genomic prediction based on historical screening data of plant responses against theBarley yellow mosaic virusesfor populating the bio-digital resource center of barley. Our study includes dense marker data for 3838 accessions of winter barley, and historical screening data of 1751 accessions forBarley yellow mosaic virus(BaYMV) and of 1771 accessions forBarley mild mosaic virus(BaMMV). Linear mixed models were fitted by considering combinations for the effects of genotypes, years, and locations. The best linear unbiased estimations displayed a broad spectrum of plant responses against BaYMV and BaMMV. Prediction abilities, computed as correlations between predictions and observed phenotypes of accessions, were low for the marker-assisted selection approach amounting to 0.42. In contrast, prediction abilities of genomic best linear unbiased predictions were high, with values of 0.62 for BaYMV and 0.64 for BaMMV. Prediction abilities of genomic prediction were improved by up to ~ 5% using W-BLUP, in which more weight is given to markers with significant major effects found by association mapping. Our results outline the utility of historical screening data and W-BLUP model to predict the performance of the non-phenotyped individuals in genebank collections. The presented strategy can be considered as part of the different approaches used in genebank genomics to valorize genetic resources for their usage in disease resistance breeding and research.

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THE GEOGRAPHICAL DISTRIBUTION OF ALLELIC DIVERSITY, A PRACTICAL MEANS OF PRESERVING AND USING MINOR ROOT CROP GENETIC RESOURCES

Experimental Agriculture ◽

10.1017/s0014479705002875 ◽

2005 ◽

Vol 41 (4) ◽

pp. 475-489 ◽

Cited By ~ 21

Author(s):

VINCENT LEBOT ◽

ANTON IVANCIC ◽

KUTTOLAMADATHIL ABRAHAM

Keyword(s):

Genetic Resources ◽

Geographical Distribution ◽

Allelic Diversity ◽

Core Sample ◽

Ex Situ ◽

Breeding Strategies ◽

Current Conservation ◽

Crop Genetic Resources ◽

Root Crop

This paper addresses the preservation and use of minor root crop genetic resources, mostly aroids and yams. Conservation is fraught with difficulty: ex situ collections are expensive to maintain and methods for on-farm conservation have not been studied. Conventional breeding strategies present serious limitations when applied to these species. Furthermore, the evaluation and distribution of improved material are as problematical as its conservation. The similarities shared by these species regarding their domestication, breeding constraints and improvement strategies as well as farmers' needs, are briefly reviewed. Based on these biological constraints, we propose a practical alternative to current conservation and breeding strategies. This approach focuses on the geographical distribution of allelic diversity rather than localized ex situ and/or in situ preservation of genotypes. The practical steps are described and discussed. First, a core sample representing the useful diversity of the species is assembled from accessions selected for their diverse and distant geographic origins, wide genetic distances, quality, agronomic performances and functional sexuality. Second, the geographical distribution of this core sample, in vitro via a transit centre, allows the direct use of selected genotypes by farmers or for breeding purposes. Third, the distribution of genes is realized in the form of clones resulting from segregating progenies and, fourth, farmers select clones with local adaptation.

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