scholarly journals Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0250786
Author(s):  
Hwang-Bae Sohn ◽  
Su-Jeong Kim ◽  
Su-Young Hong ◽  
Sin-Gi Park ◽  
Dong-Ha Oh ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Genetic Identification ◽  
Ex Situ ◽  
Tartary Buckwheat ◽  
Reference Sequence ◽  
Fagopyrum Tataricum ◽  
Indel Markers ◽  
Pcr Products ◽  
User Friendly ◽  
Modern Breeding

Tartary buckwheat (Fagopyrum tataricum Gartn.) is a highly functional crop that is poised to be the target of many future breeding efforts. The reliable ex situ conservation of various genetic resources is essential for the modern breeding of tartary buckwheat varieties. We developed PCR-based co-dominant insertion/deletion (InDel) markers to discriminate tartary buckwheat genetic resources. First, we obtained the whole genome from 26 accessions across a superscaffold-scale reference genome of 569.37 Mb for tartary buckwheat cv. “Daegwan 3–7.” Next, 171,926 homogeneous and 53,755 heterogeneous InDels were detected by comparing 26 accessions with the “Daegwan 3–7” reference sequence. Of these, 100 candidate InDels ranging from 5–20 bp in length were chosen for validation, and 50 of them revealed polymorphisms between the 26 accessions and “Daegwan 3–7.” The validated InDels were further tested through the assessment of their likelihood to give rise to a single or a few PCR products in 50 other accessions, covering most tartary buckwheat genome types. The major allele frequencies ranged from 0.5616 at the TB42 locus to 0.9863 at the TB48 locus, with the average PIC value of 0.1532 with a range of 0.0267–0.3712. To create a user-friendly system, the homology of the genotypes between and among the accessions were visualized in both one- (1D) and two-dimensional (2D) barcode types by comparing amplicon polymorphisms with the reference variety, “Daegwan 3–7.” A phylogenetic tree and population structure of the 76 accessions according to amplicon polymorphisms for the 50 InDel markers corresponded to those using non-synonymous single nucleotide polymorphism variants, indicating that the barcode system based on the 50 InDels was a useful tool to improve the reliability of identification of tartary buckwheat accessions in the germplasm stocks.

scholarly journals Pangenome of white lupin provides insights into the diversity of the species

2020 ◽  
Author(s):  
Bárbara Hufnagel ◽  
Alexandre Soriano ◽  
Jemma Taylor ◽  
Fanchon Divol ◽  
Magdalena Kroc ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Nutritional Value ◽  
Lupinus Albus ◽  
Reference Sequence ◽  
White Lupin ◽  
Plant Protein Sources ◽  
Modern Breeding ◽  
Recent Sequencing ◽  
Core Genes ◽  
Comprehensive Reference

ABSTRACTBackgroundWhite lupin is an old crop with renewed interest due to its seed high protein content and high nutritional value. Despite a long domestication history in the Mediterranean basin, modern breeding efforts have been fairly scarce. Recent sequencing of its genome has provided tools for further description of genetic resources but detailed characterization is still missing.ResultsHere, we report the genome sequencing of several accessions that were used to establish a white lupin pangenome. We defined core genes that are present in all individuals and variable genes that are absent in some and may represent a gene pool for stress adaptation. We believe that the identification of novel genes, together with a more comprehensive reference sequence, represents a significant improvement of the white lupin genetic resources. As an example, we used this pangenome to identify selection footprints and to provide a candidate gene for one of the main QTLs associated with late flowering in Ethiopian lupin types. A 686 nucleotide deletion was identified in exon 3 of the LaFTa1 (Lupinus albus Flowering Time a1) gene that suggests a molecular origin for this trait of importance, defining the need for vernalization in some lupins.ConclusionsThe white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability amongst this crop. It will be of major importance for breeders to select new breeding traits and incorporate them into new, more efficient and robust cultivars in order to face a growing demand for plant protein sources, notably in Europe.

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

Planta Medica ◽  
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

Development of Rutin-rich Noodles Using Trace-rutinosidase Variety of Tartary Buckwheat (Fagopyrum Tataricum Gaertn.) ‘Manten-Kirari’

2019 ◽  
Vol 25 (6) ◽  
pp. 915-920
Author(s):  
Tatsuro Suzuki ◽  
Toshikazu Morishita ◽  
Shigenobu Takigawa ◽  
Takahiro Noda ◽  
Koji Ishiguro
Keyword(s):  
Tartary Buckwheat ◽  
Fagopyrum Tataricum

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

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

2008 ◽  
Vol 42 ◽  
pp. 71-85 ◽  
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.

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

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.

scholarly journals 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

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.

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

2005 ◽  
Vol 41 (4) ◽  
pp. 475-489 ◽  
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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