scholarly journals Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis

2021 ◽  
Author(s):  
Uyen Vu Thuy Hong ◽  
Muluneh Tamiru-Oli ◽  
Bhavna Hurgobin ◽  
Christopher R Okey ◽  
Artur R. Abreu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North Africa ◽  
Crop Improvement ◽  
Strong Association ◽  
Geographic Origin ◽  
Genotyping By Sequencing ◽  
Papaver Somniferum ◽  
Opium Poppy ◽  
Germplasm Management ◽  
Sequencing Analysis

Opium poppy (Papaver somniferum) is one of the world's oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the level of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations. Although the accessions were from geographically diverse regions, no strong association was detected between geographic origin and subpopulation at regional and sub-regional levels. However, most accessions obtained from the same country were grouped together as genetically distinct, likely a consequence of the restriction on movement of poppy germplasm. Phylogenetic analysis identified clades that were largely consistent with the subpopulations detected. Clades could be differentiated broadly based on capsule dehiscence, plant stature and seed weight, traits believed to be associated with poppy domestication. Our study determined that the genetically diverse collection was likely composed of both wild and cultivated forms. This has direct implications for germplasm management and utilization of the available diversity for genetic improvement of poppy.

scholarly journals Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Uyen Vu Thuy Hong ◽  
Muluneh Tamiru-Oli ◽  
Bhavna Hurgobin ◽  
Christopher R. Okey ◽  
Artur R. Abreu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Crop Improvement ◽  
Genotyping By Sequencing ◽  
Opium Poppy ◽  
Sequencing Analysis ◽  
Genetic Groups ◽  
Genebank Management ◽  
Core Sets ◽  
Definition Of ◽  
Number Of Branches

AbstractOpium poppy (Papaver somniferum) is one of the world’s oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop.

scholarly journals Assessment of Genetic Diversity among Indian and Exotic Genotypes of Brassica juncea using Phenotypic Evaluation

2020 ◽  
Author(s):  
Vivek K. Singh ◽  
Ram Avtar ◽  
Mahavir . ◽  
Nisha Kumari ◽  
Manjeet . ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Brassica Juncea ◽  
Crop Improvement ◽  
Morphological Characters ◽  
Germplasm Management ◽  
Dissimilarity Matrix ◽  
High Genetic Diversity ◽  
Early Maturity ◽  
Mean Values ◽  
Dissimilarity Coefficients

Background: Rapeseed-mustard is one of the most important oilseed crops in India, however, its genetic diversity is barely known. A better understanding on this topic is essential for the proper utilization of genotypes in crop improvement. Methods: Present study was carried out to determine the genetic diversity among 95 diverse genotypes of Brassica juncea (L.) in paired rows of 4 m length with a spacing of 30 x 10-15 cm (row × plant). Data were recorded on 11 different agro-morphological characters. Result: All the 95 genotypes were grouped into five distinct clusters based on Manhattan dissimilarity coefficients. Amongst the five clusters, cluster V and IV had the maximum number of genotypes (35 and 23 genotypes respectively) and cluster II with least number of genotypes (three). The Manhattan dissimilarity coefficients ranged from 0.741 to 8.299. Based on the genetic dissimilarity matrix, the maximum dissimilarity (8.299) was observed between the genotypes, DRMRIJ-15-133 and M 62. Cluster III recorded for medium plant height with medium early maturity and cluster I, had maximum mean values for most of the agro-morphological traits. The present work indicated the presence of high genetic diversity among genotypes, which can be used in future breeding programmes for developing mustard cultivars and germplasm management purposes.

scholarly journals Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics

2016 ◽  
Author(s):  
Juan José Martínez ◽  
Pablo Melgarejo ◽  
Pilar Legua ◽  
Francisco García ◽  
Francisca Hernández
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Plant Material ◽  
Phenotypic Variability ◽  
Geographical Area ◽  
Geographic Origin ◽  
Germplasm Management ◽  
Morphometric Characteristics ◽  
Germplasm Bank ◽  
Improvement Programs

Background . Miguel Hernandez University ( Spain ) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the juice’s acidity and pH had the highest power of discrimination, and were, therefore, the most useful for genetic characterization of this pomegranate germplasm banks. This is opposed to leaf and flower characteristics, which had a low power of discrimination. This germplasm bank, more specifically, was characterized by its considerable phenotypic (and presumably genetic) diversity among pomegranate accessions, with a greater proximity existing among the varieties from the same geographical area, suggesting that over time, there had not been an exchange of plant material among the different cultivation areas. In summary, knowledge on the extent of the genetic diversity of the collection is essential for germplasm management. In this study, these data may help in developing strategies for pomegranate germplasm management and may allow for more efficient use of this germplasm in future breeding programs for this species.

scholarly journals Genomic Analysis of Spanish Wheat Landraces Reveals Their Huge Potential for Breeding

2019 ◽  
Author(s):  
Laura Pascual ◽  
Magdalena Ruiz ◽  
Matilde López-Fernández ◽  
Helena Pérez-Peña ◽  
Elena Benavente ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Durum Wheat ◽  
Bread Wheat ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Geographic Origin ◽  
Local Conditions ◽  
Reference Set ◽  
Wheat Landraces

Abstract Background One of the main goals for the XXI century breeding is the development of crop cultivars that can maintain current yields under unfavorable environments. Landraces that have been grown under varied local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research (CRF-INIA) holds a wide collection of wheat landraces. These accessions, locally adapted to a really wide diversity of eco-climatic conditions, represent a highly valuable material for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping. Results DArTseq GBS approach generated 10K SNPs and 40K DArT high-quality markers that were mapped against the currently available bread wheat reference genome. The markers with known location were distributed in all the chromosomes, having a relatively well-balanced genome-wide coverage. The genetic analysis showed that Spanish wheat landraces are clustered in different groups, thus representing genetic pools capable to provide different allelic variation. The subspecies had a major impact on the population structure of durum wheat landraces, identifying three different clusters that corresponded to subsps. durum, turgidum and dicoccon. The population structure of bread wheat landraces was more biased by geographic origin. Conclusions The results showed a wider genetic diversity in landraces when compared to a reference set that included commercial varieties, and a higher divergence between landraces and the reference set in durum wheat than in bread wheat. Some genomic regions with patterns of variation that differ between landraces and reference varieties could be detected, pointing out loci under selection during crop improvement that could help to target breeding efforts. The results obtained from this work will be highly valuable for future GWAS analysis.

scholarly journals Molecular genetic diversity and population structure analyses of rutabaga accessions from Nordic countries as revealed by single nucleotide polymorphism markers

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhiyu Yu ◽  
Rudolph Fredua-Agyeman ◽  
Sheau-Fang Hwang ◽  
Stephen E. Strelkov
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Seed Quality ◽  
Leaf Shape ◽  
Crop Improvement ◽  
Geographic Origin ◽  
Nordic Countries ◽  
Group Method ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Abstract Background Rutabaga or swede (Brassica napus ssp. napobrassica (L.) Hanelt) varies in root and leaf shape and colour, flesh colour, foliage growth habits, maturity date, seed quality parameters, disease resistance and other traits. Despite these morphological differences, no in-depth molecular analyses of genetic diversity have been conducted in this crop. Understanding this diversity is important for conservation and broadening the use of this resource. Results This study investigated the genetic diversity within and among 124 rutabaga accessions from five Nordic countries (Norway, Sweden, Finland, Denmark and Iceland) using a 15 K single nucleotide polymorphism (SNP) Brassica array. After excluding markers that did not amplify genomic DNA, monomorphic and low coverage site markers, the accessions were analyzedwith 6861 SNP markers. Allelic frequency statistics, including polymorphism information content (PIC), minor allele frequency (MAF) and mean expected heterozygosity ($$ \overline{H} $$ H ¯ e) and population differentiation statistics such as Wright’s F-statistics (FST) and analysis of molecular variance (AMOVA) indicated that the rutabaga accessions from Norway, Sweden, Finland and Denmark were not genetically different from each other. In contrast, accessions from these countries were significantly different from the accessions from Iceland (P < 0.05). Bayesian analysis with the software STRUCTURE placed 66.9% of the rutabaga accessions into three to four clusters, while the remaining 33.1% constituted admixtures. Three multivariate analyses: principal coordinate analysis (PCoA), the unweighted pair group method with arithmetic mean (UPGMA) and neighbour-joining (NJ) clustering methods grouped the 124 accessions into four to six subgroups. Conclusion Overall, the correlation of the accessions with their geographic origin was very low, except for the accessions from Iceland. Thus, Icelandic rutabaga accessions can offer valuable germplasm for crop improvement.

scholarly journals Interactions between genetics and environment shape Camelina seed oil composition

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jordan R. Brock ◽  
Trey Scott ◽  
Amy Yoonjin Lee ◽  
Sergei L. Mosyakin ◽  
Kenneth M. Olsen
Keyword(s):  
Genetic Diversity ◽  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Acid Composition ◽  
Seed Oil ◽  
Crop Improvement ◽  
Genotyping By Sequencing ◽  
Oilseed Crop ◽  
Environmental Niche ◽  
Oil Composition

Abstract Background Camelina sativa (gold-of-pleasure) is a traditional European oilseed crop and emerging biofuel source with high levels of desirable fatty acids. A twentieth century germplasm bottleneck depleted genetic diversity in the crop, leading to recent interest in using wild relatives for crop improvement. However, little is known about seed oil content and genetic diversity in wild Camelina species. Results We used gas chromatography, environmental niche assessment, and genotyping-by-sequencing to assess seed fatty acid composition, environmental distributions, and population structure in C. sativa and four congeners, with a primary focus on the crop’s wild progenitor, C. microcarpa. Fatty acid composition differed significantly between Camelina species, which occur in largely non-overlapping environments. The crop progenitor comprises three genetic subpopulations with discrete fatty acid compositions. Environment, subpopulation, and population-by-environment interactions were all important predictors for seed oil in these wild populations. A complementary growth chamber experiment using C. sativa confirmed that growing conditions can dramatically affect both oil quantity and fatty acid composition in Camelina. Conclusions Genetics, environmental conditions, and genotype-by-environment interactions all contribute to fatty acid variation in Camelina species. These insights suggest careful breeding may overcome the unfavorable FA compositions in oilseed crops that are predicted with warming climates.

scholarly journals Genetic diversity and GWAS of agronomic traits using an ICARDA lentil (Lens culinaris Medik.) Reference Plus collection

2021 ◽  
pp. 1-10
Author(s):  
Karthika Rajendran ◽  
Clarice J. Coyne ◽  
Ping Zheng ◽  
Gopesh Saha ◽  
Dorrie Main ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lens Culinaris ◽  
Agronomic Traits ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Phenotypic Data ◽  
Reference Set ◽  
Genome Wide

Abstract Genotyping of lentil plant genetic resources holds the promise to increase the identification and utilization of useful genetic diversity for crop improvement. The International Center for Agriculture Research in the Dry Areas (ICARDA) lentil reference set plus collection of 176 accessions was genotyped using genotyping-by-sequencing (GBS) and 22,555 SNPs were identified. The population structure was investigated using Bayesian analysis (STRUCTURE, k = 3) and principal component analysis. The two methods are in concordance. Genome-wide association analysis (GWAS) using the filtered SNP set and ICARDA historical phenotypic data discovered putative markers for several agronomic traits including days to first flower, seeds per pod, seed weight and days to maturity. The genetic and genomic resources developed and utilized in this study are available to the research community interested in exploring the ICARDA reference set plus collection using GWAS.

Biochemistry, Genetics, and Genomics of Opium Poppy ( Papaver somniferum ) for Crop Improvement

2019 ◽  
pp. 1177-1219
Author(s):  
Muluneh Tamiru‐Oli ◽  
Shirmila D. Premaratna ◽  
Anthony R. Gendall ◽  
Mathew G. Lewsey
Keyword(s):  
Crop Improvement ◽  
Papaver Somniferum ◽  
Opium Poppy ◽  
Genetics And Genomics

scholarly journals Genetic diversity assessment of ancient mulberry (Morus spp.) in Lebanon using morphological, chemical and molecular markers (SSR and ISSR)

2021 ◽  
Vol 35 (3) ◽  
pp. 243-253
Author(s):  
Aline Kadri ◽  
Shoaib Saleh ◽  
Ahmad Elbitar ◽  
Ali Chehade
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Crop Improvement ◽  
Germplasm Management ◽  
Diversity Assessment ◽  
Geographical Regions ◽  
Relative Separation ◽  
Morus Spp ◽  
High Level ◽  
Issr Primers

Lebanon has ancient mulberry trees which are the remnants of the abundant orchards that dominated its lands during the nineteenth century. Lebanese mulberry germplasm has not been assessed yet. This study aims to collect local old rainfed mulberry accessions from different geographical regions and assess their diversity by using morphological and molecular markers (SSR and ISSR). Genetic diversity of 70 accessions of mulberry were evaluated by using 27 morphological traits. The dendrogram based on the morphological attributes showed a relative separation of the different accessions based on fruits color and taste. Molecular analysis was performed for the accessions by using selected SSR and ISSR primers. The primers marked a high discriminating power (0.7 to 0.89). The dendrogram constructed on the base of UPGMA method showed 13 different groups. The clustering patterns indicated no location nor local name specificity among mulberry accessions. The combination of SSR and ISSR primers was informative for estimating the extent of mulberry genetic diversity. It can be concluded that there is a high level of genetic diversity within mulberry trees in Lebanon. These results will be useful for mulberry germplasm management in terms of biodiversity protection and as a valuable source of gene pool for crop improvement.

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