scholarly journals The walnut genetic resources of INRA: chronological phenotypic data and ontology

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Anthony Bernard ◽  
Teresa Barreneche ◽  
Marine Delmas ◽  
Sophie Durand ◽  
Cyril Pommier ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Agricultural Research ◽  
Juglans Regia ◽  
Germplasm Collection ◽  
Phenotypic Characterization ◽  
Climate Data ◽  
Phenotypic Data ◽  
Nut Production ◽  
Data Files

Abstract Objectives Persian walnut (Juglans regia L.), the walnut species cultivated for nut production, is grown worldwide in temperate areas. In this work, chronological phenotypic data have been collected regarding a part of the walnut genetic resources of the French National Institute for Agricultural Research (INRA) of Bordeaux. Using a well described ontology, these data have been collected in order to assess the phenotypic variations among the accessions, and to better manage the germplasm collection. These data can also be helpful for any breeding program as they provide a clear phenotypic characterization of the main cultivars. Data description This paper introduces a dataset collected for 150 J. regia accessions for a period from 1965 to 2016, and for 3 observation sites, released as comma separated value spreadsheet. It includes observations about phenological traits (e.g. flowering dates), traits related to in-shell walnut (e.g. weight and size), and traits related to kernel (e.g. color). It can be used by other researchers particularly for multi-site phenological studies in the context of climate change since climate data files are also available. In addition, a complete walnut ontology was deposited in this repository and can assist to standardize the management of any walnut germplasm collection.

scholarly journals Towards Development, Maintenance, and Standardized Phenotypic Characterization of Single‐Seed‐Descent Genetic Resources for Lupins

2021 ◽  
Vol 1 (7) ◽  
Author(s):  
Magdalena Kroc ◽  
Magdalena Tomaszewska ◽  
Katarzyna Czepiel ◽  
Elena Bitocchi ◽  
Markus Oppermann ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Phenotypic Characterization ◽  
Single Seed Descent ◽  
Single Seed

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.

Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 357-365 ◽  
Author(s):  
Gilda Rose S. Amaral ◽  
Graciela M. Dias ◽  
Michiyo Wellington-Oguri ◽  
Luciane Chimetto ◽  
Mariana E. Campeão ◽  
...  
Keyword(s):  
Phenotypic Characterization ◽  
Whole Genome ◽  
Genome Sequences ◽  
Diagnostic Features ◽  
Phenotypic Data ◽  
Content Type ◽  
Ecological Relationships ◽  
Phenotypic Information ◽  
Specific Proteins

Vibrios are ubiquitous in the aquatic environment and can be found in association with animal or plant hosts. The range of ecological relationships includes pathogenic and mutualistic associations. To gain a better understanding of the ecology of these microbes, it is important to determine their phenotypic features. However, the traditional phenotypic characterization of vibrios has been expensive, time-consuming and restricted in scope to a limited number of features. In addition, most of the commercial systems applied for phenotypic characterization cannot characterize the broad spectrum of environmental strains. A reliable and possible alternative is to obtain phenotypic information directly from whole genome sequences. The aim of the present study was to evaluate the usefulness of whole genome sequences as a source of phenotypic information. We performed a comparison of the vibrio phenotypes obtained from the literature with the phenotypes obtained from whole genome sequences. We observed a significant correlation between the previously published phenotypic data and the phenotypic data retrieved from whole genome sequences of vibrios. Analysis of 26 vibrio genomes revealed that all genes coding for the specific proteins involved in the metabolic pathways responsible for positive phenotypes of the 14 diagnostic features (Voges–Proskauer reaction, indole production, arginine dihydrolase, ornithine decarboxylase, utilization of myo-inositol, sucrose and l-leucine, and fermentation of d-mannitol, d-sorbitol, l-arabinose, trehalose, cellobiose, d-mannose and d-galactose) were found in the majority of the vibrios genomes. Vibrio species that were negative for a given phenotype revealed the absence of all or several genes involved in the respective biochemical pathways, indicating the utility of this approach to characterize the phenotypes of vibrios. The absence of the global regulation and regulatory proteins in the Vibrio parahaemolyticus genome indicated a non-vibrio phenotype. Whole genome sequences represent an important source for the phenotypic identification of vibrios.

scholarly journals Karakterisasi Plasma Nutfah Kangkung

2016 ◽  
Vol 12 (1) ◽  
pp. 30
Author(s):  
Yenni Kusandriyani ◽  
NFN Luthfy
Keyword(s):  
Genetic Resources ◽  
Germplasm Collection ◽  
Dry Season ◽  
Breeding Program ◽  
Stable Manure ◽  
High Yielding Varieties ◽  
Program Description ◽  
Research Institute

<p>Characterization of Ipomoea reptans germplasm collection were done in order to describe the accessions and to utilize as working collection materials for breeding program. Description was aimed to identify the new collections of 15 accessions I. reptans which were taken from IVEGRI (Indonesia Vegetable Goverment Research Institute) germplasm collection. The experiment was carried out in Subang station (100 m asl) in dry season 2002. Each accession were planted 40 plant per plot of I. reptans with plant distance 20 x 30 cm. The plants of were fertilized with stable manure 20 t/ha and NPK (15 : 15 : 15) 500 kg/ha. The result of the study was a description of genetic resources that will be exchanged and utilized in breeding for high yielding varieties of I. reptans with better quality.</p><p> </p><p><strong>Abstrak</strong></p><p>Karakterisasi plasma nutfah kangkung dilakukan untuk mendapatkan deskripsi sifat tanaman dan sebagai bahan working collection yang akan digunakan sebagai bahan dalam program pemuliaan. Penelitian mencakup 15 nomor aksesi kangkung di Kebun Percobaan Subang (100 m dpl) Jawa Barat pada musim kemarau 2002, tiap nomor dari masing-masing aksesi ditanam sebanyak 40 tanaman. Tanaman diberi pupuk kandang domba dengan takaran 20 t/ha dan NPK (15 : 15 : 15) 500 kg/ha. Hasil penelitian ini menghasilkan deskripsi plasma nutfah tanaman kangkung untuk pertukaran informasi mengenai sumber genetik yang akan digunakan dalam pemuliaan untuk mendapatkan varietas unggul dengan kualitas yang lebih baik.</p>

scholarly journals Phenotypic characterization of naturalized swine breeds in Brazil, Uruguay and Colombia

2010 ◽  
Vol 53 (3) ◽  
pp. 583-591 ◽  
Author(s):  
Concepta McManus ◽  
Samuel Rezende Paiva ◽  
Alva Vanessa Rezende Silva ◽  
Luci Sayori Murata ◽  
Helder Louvandini ◽  
...  
Keyword(s):  
Sexual Dimorphism ◽  
Analysis Of Variance ◽  
Coefficient Of Determination ◽  
Phenotypic Characterization ◽  
Morphometric Data ◽  
Morphometric Measurements ◽  
Phenotypic Data ◽  
Material Information ◽  
On Farm

Morphometric data was collected on 859 naturalized swine in Brazil (Piau, Tatu, Nilo, Caruncho, Casco de Burro, Moura, Monteiro and Rabo de Peixe), Colombia (Criolla Zungo, Sanpedreño and Casco de Mula) and Uruguay (Mamellado), both on farm and in published material. Information was collected on breed, sex and age, as well as various morphometric measurements. Analysis of variance was carried out using PROC MIXED of SAS ® on phenotypic data. The coefficients of variance varied between 11.50 and 83.81%, and the coefficient of determination was medium to high. Females were in general smaller for most measurements than males, showing sexual dimorphism. The Moura was the closest naturalized breed to the commercial breeds, followed by the Piau, while the Monteiro was the furtherest. The dendrogram obtained from morphological information showed a division of the pigs into three groups. Characterization was possible using morphological and morphometric data.

Root phenotypic characterization of lesquerella genetic resources

2014 ◽  
Vol 62 ◽  
pp. 130-139 ◽  
Author(s):  
Von Mark V. Cruz ◽  
Louise H. Comas ◽  
David A. Dierig
Keyword(s):  
Genetic Resources ◽  
Phenotypic Characterization

scholarly journals Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single‐Seed‐Descent Genetic Resources for Common Bean

2021 ◽  
Vol 1 (5) ◽  
Author(s):  
Gaia Cortinovis ◽  
Markus Oppermann ◽  
Kerstin Neumann ◽  
Andreas Graner ◽  
Tania Gioia ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Common Bean ◽  
Phenotypic Characterization ◽  
Single Seed Descent ◽  
Single Seed

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

2018 ◽  
Vol 5 (1) ◽  
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.

Population and quantitative genomic properties of the USDA soybean germplasm collection

2018 ◽  
Vol 16 (6) ◽  
pp. 513-523 ◽  
Author(s):  
Alencar Xavier ◽  
Rima Thapa ◽  
William M. Muir ◽  
Katy Martin Rainey
Keyword(s):  
Genetic Resources ◽  
Agronomic Traits ◽  
Snp Array ◽  
Genetic Material ◽  
Germplasm Collection ◽  
Effective Population ◽  
Department Of Agriculture ◽  
Soybean Germplasm ◽  
National Plant Germplasm System

AbstractThis study is the first assessment of the entire soybean [Glycine max (L.) Merr] collection of the United State Department of Agriculture National Plant Germplasm System (USDA) reporting quantitative and population genomic parameters. It also provides a new insight into soybean germplasm structure. Germplasm studies enable plant breeders to incorporate novel genetic resources into breeding pipelines to improve valuable agronomic traits. We conducted comprehensive analyses on the 19,652 soybean accessions in the USDA-ARS germplasm collection, genotyped with the SoySNP50 K iSelect BeadChip SNP array, to elucidate the quantitative properties of existing subpopulations inferred through hierarchical clustering performed with Ward's D agglomeration method and Nei's standard genetic distance. We found the effective population size to be approximately 106 individuals based on the linkage disequilibrium of unlinked loci. The cladogram indicated the existence of eight major clusters. Each cluster displays particular properties with regard to major quantitative traits. Among those, cluster 3 represents the tropical and semi-tropical genetic material, cluster 5 displays large seeds and may represent food-grade germplasm, and cluster 7 represents the undomesticated material in the germplasm collection. The average FST among clusters was 0.22 and a total of 914 SNPs were exclusive to specific clusters. Our classification and characterization of the germplasm collection into major clusters provides valuable information about the genetic resources available to soybean breeders and researchers.

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