Development of core subset for the collection of Chinese cultivated eggplants using morphological-based passport data

2008 ◽  
Vol 6 (1) ◽  
pp. 33-40 ◽  
Author(s):  
Mao Weihai ◽  
Yi Jinxin ◽  
Darasinh Sihachakr
Keyword(s):  
Core Collection ◽  
Solanum Melongena ◽  
Sampling Strategy ◽  
Sampling Strategies ◽  
Numerical Classification ◽  
Clustering Methods ◽  
Single Linkage ◽  
The Core ◽  
Pair Group ◽  
Passport Data

A total of 1968 accessions of cultivated eggplants, belonging to Solanum melongena and Solanum aethiopicum and procured from the IVC/JAAS (Nanjing) and IVC/ZAAS (Hangzhou), China, were examined for 23 morphological traits, such as characteristics of plant, stems, leaves, flowers, fruits and original geographic information. A comprehensive numerical classification methodology, including two types of genetic distance, viz. Mahalanobis (Ma) distance and Euclidean (Eu) distance; four clustering methods, viz. unweighted pair group average (UPGA), Ward's (W), complete linkage (CL) and single linkage (SL) methods; three sampling strategies, viz. random (R), preferred (P) and deviation (D); and four sampling sizes (10, 15, 20 and 30% of initial collection), was used to divide all accessions into main groups and subgroups for the establishment of candidate collections. The evaluation of these candidate collections showed that a combination of Eu distance, UPGA clustering method, and R or P sampling strategy with sampling size at 15–20% was suitable for establishing the core collection, providing an adequate and representative genetic diversity of the initial collection of the cultivated eggplants.

scholarly journals Comparing the efficiency of sampling strategies to establish a representative in the phenotypic-based genetic diversity core collection of orchardgrass (Dactylis glomerata L.)

2013 ◽  
Vol 49 (No. 1) ◽  
pp. 36-47 ◽  
Author(s):  
M. Studnicki ◽  
W. Mądry ◽  
J. Schmidt
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Dactylis Glomerata ◽  
Sampling Strategy ◽  
Sampling Strategies ◽  
Core Collections ◽  
The Core ◽  
Entire Collection ◽  
The Mean ◽  
Dactylis Glomerata L

Establishing a core collection that represents the genetic diversity of the entire collection with a minimum loss of its original diversity and minimal redundancies is an important problem for gene bank curators and crop breeders. In this paper, we assess the representativeness of the original genetic diversity in core collections consisting of one-tenth of the entire collection obtained according to 23 sampling strategies. The study was performed using the Polish orchardgrass Dactylis glomerata L. germplasm collection as a model. The representativeness of the core collections was validated by the difference of means (MD%) and difference of mean squared Euclidean distance (d‒D%) for the studied traits in the core subsets and the entire collection. In this way, we compared the efficiency of a simple random and 22 (20 cluster-based and 2 direct cluster-based) stratified sampling strategies. Each cluster-based stratified sampling strategy is a combination of 2 clusterings, 5 allocations and 2 methods of sampling in a group. We used the accession genotypic predicted values for 8 quantitative traits tested in field trials. A sampling strategy is considered more effective for establishing core collections if the means of the traits in a core are maintained at the same level as the means in the entire collection (i.e., the mean of MD% in the simulated samples is close to zero) and, simultaneously, when the overall variation in a core collection is greater than in the entire collection (i.e., the mean of d‒D% in the simulated samples is greater than that obtained for the simple random sampling strategy). Both cluster analyses (unweighted pair group method with arithmetic mean UPGMA and Ward) were similarly useful in constructing those sampling strategies capable of establishing representative core collections. Among the allocation methods that are relatively most useful for constructing efficient samplings were proportional and D2 (including variation). Within the Ward clusters, the random sampling was better than the cluster-based sampling, but not within the UPGMA clusters.

scholarly journals Construction of the Core Collection of Catalpa fargesii f. duclouxii (Huangxinzimu) Based on Molecular Markers and Phenotypic Traits

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1518
Author(s):  
Huifen Xue ◽  
Xiaochi Yu ◽  
Pengyue Fu ◽  
Bingyang Liu ◽  
Shen Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Core Collection ◽  
Snp Markers ◽  
Rate Of Change ◽  
Phenotypic Traits ◽  
Clustering Methods ◽  
Single Linkage ◽  
Core Collections ◽  
The Core ◽  
Linkage Method

To promote the conservation and utilization of Catalpa fargesii f. duclouxii (Huangxinzimu) germplasm resources, a total of 252 accessions were used to construct a preliminary core collection according to phenotypic traits and single nucleotide polymorphism (SNP) markers. In this study, 24 phenotypic traits, namely, 9 quantitative traits and 15 qualitative traits, were investigated. The core collection of C. fargesii f. duclouxii (Huangxinzimu) was constructed to remove redundant samples from the collected materials. First, the phenotypic core collection, with a sample proportion of 30, consisting of 24 clones, was constructed according to two genetic distances (Euclidean distance and Mahalanobis), four system clustering methods (the unweighted pair-group average method, Ward’s method, the complete linkage method, and the single linkage method), and three sampling methods (random sampling, deviation sampling, and preferred sampling). The best construction strategies were selected for further comparison. Three core collections (D2C3S3-30, D2C3S3-50, and D2C3S3-70) were constructed according to the optimal construction strategy at three sampling proportions. The core collection D2C3S3-30 with the best parameters was evaluated by using six parameters: the mean difference percentage (MD), variance difference percentage (VD), periodic rate of range (CR), changeable rate of the coefficient of variation (VR), minimum rate of change (CRMIN), and maximum rate of change (CRMAX). Three core collections (M-30, M-50, and M-70) were constructed by molecular markers, and the optimal core collection M-30 was selected by using five parameters, namely, Ho, He, PIC, MAF, and loci. The combination of D2C3S3-30 and M-30 was used to construct the final core collection DM-45, 45 samples representing the complete range of phenotypic and genetic variability. In this study, phenotypic traits combined with molecular markers were used to construct core collections to effectively capture the entire range of trait variation, effectively representing the original germplasm and providing a basis for the conservation and utilization of C. fargesii f. duclouxii (Huangxinzimu).

scholarly journals Selection of Core Collection from Jesso-Balam Rice (Oryza sativa L.) Accessions Using Quantitative, Qualitative and Molecular Characters-A Review

2017 ◽  
Vol 15 (1) ◽  
pp. 170-181
Author(s):  
MS Ahmed ◽  
Khandakar Md. Iftekharuddaula
Keyword(s):  
Oryza Sativa ◽  
Core Collection ◽  
Oryza Sativa L ◽  
Hierarchical Cluster ◽  
Genetic Distances ◽  
Sampling Strategies ◽  
The Core ◽  
Rice Genotypes ◽  
Molecular Characters ◽  
Selection Of

Genetic improvement of rice (Oryza sativa L.) for yield is important for increasing demand of the growing population and the changing climate of the world. Recent studies showed that backcrossing twice using modern varieties as receptor and mini core collection as doner, most of the undesirable traits could be improved remarkably and in other words its maximum allele diversity could be brought back into rice fields. Core collection is defined as a subset chosen to represent the most genetic diversity of an initial collection with a minimum of redundancies. The objective of the present study was to review the selection of core collection of Jesso-Balam group of rice genotypes through quantitative, qualitative and molecular characters. Earlier, the same germplasms were characterized for agro-morphological, physico-chemical and molecular characters and grouped into different clusters by different methods at Bangladesh Rice Research Institute during 2009-12. Finally, the core collection was selected by reviewing the above characterized data and using the hierarchical cluster analysis. Moreover, the selection processes of core collection were improved by applying composite evaluation methods; such as agro-morphological traits, biochemical characters and so on, through sampling strategies based on genotypic values, predicted genotypic value, comparing different genetic distances, cluster methods and sampling strategies methods, molecular characterization or SSR marker base data. As a result, the selected core germplasm of Jesso-Balam rice accessions were JBPL1, JBPL8, JBPL9, JBPL10, JBPL13, JBPL15, JBPL16, JBPL17, JBPL19, JBPL20, JBPL21, JBPL23, JBPL25 and JBPL26. In conclusion, the core collection  need to be considered as the ‘working collection’ of Jesso-Balam rice genotypes for their easy and safe conservation and effective utilization in Gene bank.The Agriculturists 2017; 15(1) 170-181

scholarly journals Port Governance and Cruise Tourism

2021 ◽  
Vol 13 (9) ◽  
pp. 4877
Author(s):  
Alejandro Vega-Muñoz ◽  
Guido Salazar-Sepúlveda ◽  
Nicolás Contreras-Barraza ◽  
Lorena Araya-Silva
Keyword(s):  
Core Collection ◽  
Web Of Science ◽  
Selection Process ◽  
Meta Analysis ◽  
Eligibility Criteria ◽  
The Core ◽  
Cruise Ships ◽  
Governance Model ◽  
Cruise Tourism ◽  
Governance Models

Cruise activities, until 2020, have presented a significant increase in revenue, as well as number of cruises and passengers transported, and it has become a challenge for ports to respond to this demand for services. In response to this, the world’s ports have implemented different governance models. In this context, in this paper, we aim to review the different governance models, as well as port cooperation, competition, and stakeholders. For this purpose, using science metric meta-analysis, an article set is extracted that strictly refers to the governance model of two databases integrated into the Core Collection Web of Science, whose selection process is polished with the PRISMA guidelines, establishing the eligibility criteria of studies using PICOS tool, to which a qualitative meta-analysis is applied. A limited studies set is identified, that includes governance model implementations, private strategies and internalization patterns in the port sector and cruise ships, patterns of port cooperation and governance, governance models in cruise ports, structures and strategies, and changes in the cruise market. Finally, various governance model forms are determined, all documented in the scientific research worldwide, discussing the various components of study topics.

scholarly journals Genotype Heterogeneity in Accessions of a Winter Barley Core Collection Assessed on Postulated Specific Powdery Mildew Resistance Genes

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 513
Author(s):  
Antonín Dreiseitl
Keyword(s):  
Resistance Genes ◽  
Core Collection ◽  
Powdery Mildew Resistance ◽  
Gene Bank ◽  
Winter Barley ◽  
The Core ◽  
Genotype Identification ◽  
Environmentally Safe ◽  
Mla Locus ◽  
Resistance Tests

Gene bank accessions are necessary for implementing many research and breeding projects. However, a great number of accessions are contaminated or confused. If such accessions are used, the results obtained from these projects are inaccurate and non-reproducible. There are methods that allow almost perfect genotype identification; nevertheless, they are relatively recent and results cannot be compared with the characteristics of the original accessions. Growing resistant cultivars is an environmentally safe and cheap way of disease management and knowledge of diverse resistance genes and their combinations can be used to identify varieties and verify their authenticity and homogeneity. For this purpose, all 172 accessions of the core collection (CC) of the Czech winter barley (Hordeum vulgare) gene bank, originating from 35 countries, were studied. For resistance tests, 51 reference isolates of Blumeria graminis f. sp. Hordei, collected in all nonpolar continents over a period of 63 years and representing the global virulence/avirulence diversity of the pathogen, were used. Only 25 barley accessions were homogeneous (genetically uniform), whereas 147 accessions were heterogeneous due to presence of different genotypes. In total, 17 resistance genes were found singly or in combinations; 76.3% of accessions with identified resistance genes carried alleles at the Mla locus. To purify the CC, progenies of individual plants must be multiplied and authenticity and homogeneity of the seed should be confirmed with resistance tests, and subsequently can be studied with more advanced methods.

Effects of age and food source on secondary chemistry of larvae of Lymantria species (Lepidoptera: Lymantriidae)

2004 ◽  
Vol 94 (2) ◽  
pp. 137-143 ◽  
Author(s):  
R. Deml
Keyword(s):  
Secondary Metabolites ◽  
Developmental Stages ◽  
Secondary Compounds ◽  
Food Plants ◽  
Gas Chromatography Mass Spectrometry ◽  
Chemical Compositions ◽  
Clustering Methods ◽  
Single Linkage ◽  
Secondary Chemistry ◽  
Dissimilarity Coefficients

AbstractHaemolymph and osmeterial secretions of caterpillars of Lymantria monacha (Linnaeus) and L. concolor Walker were analysed by gas chromatography/mass spectrometry for low molecular weight secondary metabolites. The similarities of their chemical compositions were determined by means of cluster analysis techniques in order to characterize possible chemical variations related to developmental stage or food of the larvae. For this purpose, two dissimilarity coefficients (Euclidean distances, Canberra metrics) and four clustering methods (UPGMA, WPGMA, WPGMC, single linkage) were combined. The patterns of secondary compounds obtained from the haemolymph and osmeterial secretions studied did not differ statistically significantly between two groups of L. monacha larvae fed with either larch, Larix decidua Mil., or Norway spruce, Picea abies (L.), indicating no relevant influence of plant chemistry. However, haemolymph of penultimate instar larvae of L. concolor fed on Rhododendroncontained a mixture of compounds differing statistically significantly from that of last instar caterpillars. The total compositions of the corresponding gland secretions were statistically identical though the presence/amounts of individual compounds varied. This suggested that the haemolymph composition reflected changing physiological requirements of the successive instars, whereas the composition of the defensive mixtures remained comparatively constant, possibly due to a constant spectrum of potential enemies. A more pronounced age-dependence of larval chemistry was shown by a similar analysis of data from various developmental stages of L. dispar (Linnaeus) and one of its food plants. This analysis suggested plant composition affected the secondary chemistry of early larval instars of L. dispar. The results are discussed in terms of the roles of secondary metabolites in defence against natural enemies.

scholarly journals Guidelines for depth data collection in rivers when applying interpolation techniques (kriging) for river restoration

2007 ◽  
Vol 4 (3) ◽  
pp. 1069-1094
Author(s):  
M. Rivas-Casado ◽  
S. White ◽  
P. Bellamy
Keyword(s):  
River Restoration ◽  
Sampling Strategy ◽  
Spatial Dimension ◽  
Sampling Strategies ◽  
Depth Data ◽  
Cyclic Patterns ◽  
Efficient Sampling ◽  
Before And After ◽  
Geostatistical Techniques ◽  
River Site

Abstract. River restoration appraisal requires the implementation of monitoring programmes that assess the river site before and after the restoration project. However, little work has yet been developed to design effective and efficient sampling strategies. Three main variables need to be considered when designing monitoring programmes: space, time and scale. The aim of this paper is to describe the methodology applied to analyse the variation of depth in space, scale and time so more comprehensive monitoring programmes can be developed. Geostatistical techniques were applied to study the spatial dimension (sampling strategy and density), spectral analysis was used to study the scale at which depth shows cyclic patterns, whilst descriptive statistics were used to assess the temporal variation. A brief set of guidelines have been summarised in the conclusion.

Interviews with Whom?

2020 ◽  
pp. 45-65
Author(s):  
Kathleen Gerson
Keyword(s):  
Sampling Strategy ◽  
Snowball Sampling ◽  
The Core ◽  
Theoretical Sampling ◽  
Good Sample ◽  
Selection Of

Chapter 3 considers the principles underlying the selection of an appropriate sample for depth interviewing and the range of strategies available to identify and recruit participants in that sample. Rather than claiming representativeness, as a quantitative researcher might, a depth interviewer aims to select a sample capable of yielding theoretically generalizable insights—an approach called theoretical sampling. Theoretical sampling focuses on finding a variety of participants who are well positioned to reveal the practices, mechanisms, and relationships the research seeks to explain. The chapter then looks at the range of strategies for finding a good sample and deciding whom to include and whom to exclude. Whether the sampling strategy involves recruiting randomly selected participants, snowball sampling, seeking volunteers, or some combination, a good sample contains both the core controls and the built-in comparisons needed to answer the study questions and develop an explanation for the outcomes.

scholarly journals Constructing a Core Collection of the Medicinal Plant Angelica biserrata Using Genetic and Metabolic Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Man Liu ◽  
Xin Hu ◽  
Xu Wang ◽  
Jingjing Zhang ◽  
Xubing Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Medicinal Plant ◽  
Core Collection ◽  
Polymorphic Information Content ◽  
Sampling Strategy ◽  
Market Demand ◽  
Conservation Assessment ◽  
Information Index ◽  
Ssr Loci ◽  
Metabolic Data

Angelica biserrata is an important medicinal plant in Chinese traditional medicine. Its roots, which are known as Duhuo in Chinese, are broadly applied to treat inflammation, arthritis, and headache. With increasing market demand, the wild resources of A. biserrata have been overexploited, and conservation, assessment of genetic resources and breeding for this species is needed. Here, we sequenced the transcriptome of A. biserrata and developed simple sequence repeat (SSR) markers from it to construct a core collection based on 208 samples collected from Changyang-related regions. A total of 132 alleles were obtained for 17 SSR loci used with the polymorphic information content (PIC) ranging from 0.44 to 0.83. Abundant genetic diversity was inferred by Shannon’s information index (1.51), observed (0.57) and expected heterozygosity (0.72). The clustering analysis resulted into two sample groups and analysis of molecular variance (AMOVA) showed only 6% genetic variation existed among populations. A further metabolic analysis of these samples revealed the main coumarin contents, such as osthole and columbianadin. According to the genetic and metabolic data, we adopted the least distance stepwise sampling strategy to construct seven preliminary core collections, of which the 20CC collection, which possessed 42 A. biserrata individuals accounting for 90.20% of the genetic diversity of the original germplasm, represented the best core collection. This study will contribute to the conservation and management of A. biserrata wild germplasm resources and provide a material basis for future selection and breeding of this medicinal plant.

scholarly journals Performance and uncertainties of TSS stormwater sampling strategies from online time series

2018 ◽  
Vol 78 (6) ◽  
pp. 1407-1416
Author(s):  
Santiago Sandoval ◽  
Jean-Luc Bertrand-Krajewski ◽  
Nicolas Caradot ◽  
Thomas Hofer ◽  
Günter Gruber
Keyword(s):  
Time Series ◽  
Suspended Solids ◽  
Sampling Strategy ◽  
Sampling Strategies ◽  
Sampling Errors ◽  
Time Step ◽  
Sewer System ◽  
Time Intervals ◽  
Combined Sewer ◽  
One Year

Abstract The event mean concentrations (EMCs) that would have been obtained by four different stormwater sampling strategies are simulated by using total suspended solids (TSS) and flowrate time series (about one minute time-step and one year of data). These EMCs are compared to the reference EMCs calculated by considering the complete time series. The sampling strategies are assessed with datasets from four catchments: (i) Berlin, Germany, combined sewer overflow (CSO); (ii) Graz, Austria, CSO; (iii) Chassieu, France, separate sewer system; and (iv) Ecully, France, CSO. A sampling strategy in which samples are collected at constant time intervals over the rainfall event and sampling volumes are pre-set as proportional to the runoff volume discharged between two consecutive sample leads to the most representative results. Recommended sampling time intervals are of 5 min for Berlin and Chassieu (resp. 100 and 185 ha area) and 10 min for Graz and Ecully (resp. 335 and 245 ha area), with relative sampling errors between 7% and 20% and uncertainties in sampling errors of about 5%. Uncertainties related to sampling volumes, TSS laboratory analyses and beginning/ending of rainstorm events are reported as the most influent sources in the uncertainties of sampling errors and EMCs.

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