scholarly journals Comparison of structure analyses and core collections for the management of walnut genetic resources

2020 ◽  
Vol 16 (5) ◽  
Author(s):  
Anthony Bernard ◽  
Teresa Barreneche ◽  
Armel Donkpegan ◽  
Fabrice Lheureux ◽  
Elisabeth Dirlewanger
Keyword(s):  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Allelic Diversity ◽  
Germplasm Collection ◽  
Germplasm Management ◽  
Core Collections ◽  
Construction Methods ◽  
Genetic Resources Management ◽  
Starting Point ◽  
Key Steps

Abstract The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods based on different algorithms (“maximum length subtree” and “entry-to-nearest-entry” methods). We showed that core collections based on few SSR markers are able to capture at least 99.5% of the SNP allelic diversity, irrespective of the construction method used. Then, core collections based on each marker type are highly similar, using both construction methods. All these steps are crucial to identify the suitable tools and methods to improve plant genetic resources management.

scholarly journals Management of a Walnut Germplasm Collection: Which of SSR or SNP Markers Are Most Suitable to Preserve Biodiversity?

2019 ◽  
Author(s):  
Anthony Bernard ◽  
Teresa Barreneche ◽  
Armel Donkpegan ◽  
Lheureux Fabrice ◽  
Elisabeth Dirlewanger
Keyword(s):  
Snp Array ◽  
Allelic Diversity ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Germplasm Management ◽  
Core Collections ◽  
Construction Methods ◽  
Genetic Resources Management ◽  
Starting Point ◽  
Genomics Tools

AbstractThe preservation of the maximum of diversity within the smallest number of accessions is one of the challenges of germplasm management. To construct core-collections, the assessment of the population structure and the relationships between the accessions represents a key step and the choice of suitable molecular markers is the starting point. Since the expansion of available SNP-based genomics tools, a debate has emerged regarding the usefulness of the widely used microsatellites (SSRs) markers. In this study, we analysed a part of the INRAE walnut germplasm collection of 150 accessions, unique in Europe for walnut biodiversity conservation, by comparing the power of both types of marker. We found that the first level of structure is equally detected using 13 SSRs or the Axiom™ J. regia 700K SNP array, and is in relation with the geographical origin of the accessions. For K=2, there was no exchange of accession between the two groups when both markers were compared. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to SSRs in Principal Coordinate Analysis (PCoA). The neighbor-joining trees constructed were also consistent between both types of marker. The main differences lied in the upper levels of structure from K=3 to K=6, more powerful using the SNPs, and in the percentage of the explained variation in PCoA for K=2, higher using SSRs. We then constructed core-collections of 50 accessions, a crucial step in genetic resources management to reduce the costs and preserve the allelic diversity. Using two different construction methods, both SSR and SNP markers were suitable and able to keep at least 88.57% of the alleles. 32/50 accessions were in common between the two markers, for both methods. We concluded that the use of either marker is dependent on the researcher’s goal.

scholarly journals Characterization of Nutritional Quality Traits of a Common Bean Germplasm Collection

Foods ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1572
Author(s):  
Ester Murube ◽  
Romina Beleggia ◽  
Deborah Pacetti ◽  
Ancuta Nartea ◽  
Giulia Frascarelli ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Common Bean ◽  
Extreme Values ◽  
Plant Genetic Resources ◽  
Germplasm Collection ◽  
Growth Conditions ◽  
Phenotypic Characterization ◽  
Quality Traits ◽  
Societal Challenges ◽  
Food Legumes

Food legumes are at the crossroads of many societal challenges that involve agriculture, such as climate change and food sustainability and security. In this context, pulses have a crucial role in the development of plant-based diets, as they represent a very good source of nutritional components and improve soil fertility, such as by nitrogen fixation through symbiosis with rhizobia. The main contribution to promotion of food legumes in agroecosystems will come from plant breeding, which is guaranteed by the availability of well-characterized genetic resources. Here, we analyze seeds of 25 American and European common bean purified accessions (i.e., lines of single seed descent) for different morphological and compositional quality traits. Significant differences among the accessions and superior genotypes for important nutritional traits are identified, with some lines showing extreme values for more than one trait. Heritability estimates indicate the importance of considering the effects of environmental growth conditions on seed compositional traits. They suggest the need for more phenotypic characterization in different environments over different years to better characterize combined effects of environment and genotype on nutritional trait variations. Finally, adaptation following the introduction and spread of common bean in Europe seems to have affected its nutritional profile. This finding further suggests the relevance of evolutionary studies to guide breeders in the choice of plant genetic resources.

scholarly journals Training in Plant Genetic Resources Management: A Way Forward

Crop Science ◽  
2019 ◽  
Vol 59 (3) ◽  
pp. 853-857 ◽  
Author(s):  
Gayle M. Volk ◽  
Deana Namuth-Covert ◽  
Patrick F. Byrne
Keyword(s):  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Resources Management ◽  
Genetic Resources Management

Distribution of genetic diversity in wild European populations of prickly lettuce (Lactuca serriola): implications for plant genetic resources management

2010 ◽  
Vol 8 (2) ◽  
pp. 171-181 ◽  
Author(s):  
C. C. M. van de Wiel ◽  
T. Sretenović Rajičić ◽  
R. van Treuren ◽  
K. J. Dehmer ◽  
C. G. van der Linden ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Crop Wild Relatives ◽  
Population Variation ◽  
Lactuca Serriola ◽  
Genetic Resources Management ◽  
Nbs Profiling ◽  
The Uk

Genetic variation in Lactuca serriola, the closest wild relative of cultivated lettuce, was studied across Europe from the Czech Republic to the United Kingdom, using three molecular marker systems, simple sequence repeat (SSR, microsatellites), AFLP and nucleotide-binding site (NBS) profiling. The ‘functional’ marker system NBS profiling, targeting disease resistance genes of the NBS/LRR family, did not show marked differences in genetic diversity parameters to the other systems. The autogamy of the species resulted in low observed heterozygosity and high population differentiation. Intra-population variation ranged from complete homogeneity to nearly complete heterogeneity. The highest genetic diversity was found in central Europe. The SSR results were compared to SSR variation screened earlier in the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN). In the UK, practically only a single SSR genotype was found. This genotype together with a few other common SSR genotypes comprised a large part of the plants sampled on the continent. Among the ten most frequent SSR genotypes observed, eight were already present in the CGN collection. Overall, the CGN collection appears to already have a fair representation of genetic variation from NW Europe. The results are discussed in relation to sampling strategies for improving genebank collections of crop wild relatives.

Next-generation genebanking: plant genetic resources management and utilization in the sequencing era

2014 ◽  
Vol 12 (3) ◽  
pp. 298-307 ◽  
Author(s):  
Rob van Treuren ◽  
Theo J. L. van Hintum
Keyword(s):  
Genetic Resources ◽  
Strategic Alliances ◽  
Plant Genetic Resources ◽  
Production Costs ◽  
New Developments ◽  
User Community ◽  
Sequencing Technologies ◽  
Genetic Resources Management ◽  
Management Procedures ◽  
Research Populations

Advances in sequencing technologies have made it possible to analyse large amounts of germplasm against low production costs, which has opened the door to screen genebank collections more efficiently for DNA sequence variation. The present study explores how these developments may affect the operations of genebanks and, consequently, how genebank agendas may change. It is argued that the new developments are more likely to have an impact on the user-oriented activities than the housekeeping operations of genebanks. To better facilitate the user community, genebanks may have to strengthen their core business, in particular, by improving quality management procedures and by providing access to a wider diversity of a crop's gene pool. In addition, genebanks may have to provide novel services, such as the introduction of specific user-oriented collection types, including research populations and genetically purified lines, and the development of novel information services, including plant genetic resources portals that should guide users to the information and materials of specific interest. To improve their user-oriented services, genebanks need to increase their communication and collaboration with the user community and to develop strategic alliances with this sector.

Morphological diversity in brinjal (Solanum melongena L.) germplasm accessions

2008 ◽  
Vol 6 (3) ◽  
pp. 232-236 ◽  
Author(s):  
Gunjeet Kumar ◽  
B. L. Meena ◽  
Ranjan Kar ◽  
Shailesh K. Tiwari ◽  
K. K. Gangopadhyay ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Solanum Melongena ◽  
Morphological Diversity ◽  
National Bureau ◽  
Starting Point ◽  
Wide Range ◽  
Breeding Programmes ◽  
Improvement Programme

Brinjal (Solanum melongena L.) is an important solanaceous vegetable in many countries of Asia and Africa. It is a good source of minerals and vitamins in the tropical diets. Assessment of genetic resources is the starting point of any crop improvement programme. In India, the National Bureau of Plant Genetic Resources is the nodal institute for management of germplasm resources of crop plants and holds more than 2500 accessions of brinjal in its genebank. In the present study, morphological diversity in a set of 622 accessions, comprising 543 accessions from indigenous sources and 79 accessions of exotic origin, was assessed. Wide range of variations for 31 descriptors, 13 quantitative and 18 qualitative, were recorded. The wide regional variations for plant, flower and fruit descriptors revealed enough scope for improvement of yield characters by selection. The genetic differences among the landraces are potentially relevant to breeding programmes in that the variability created through hybridization of the contrasting forms could be exploited.

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