scholarly journals Establishment of a core collection of Cynodon based on morphological data

2020 ◽  
Vol 8 (3) ◽  
pp. 203-213
Author(s):  
C.Q. Huang ◽  
T. Long ◽  
C.J. Bai ◽  
W.Q. Wang ◽  
J. Tang ◽  
...  
Keyword(s):  
Mahalanobis Distance ◽  
Core Collection ◽  
Morphological Data ◽  
Phenotypic Traits ◽  
Optimal Sampling ◽  
Square Root ◽  
Sample Distribution ◽  
Core Collections ◽  
The Core ◽  
Preferential Sampling

In a field plot study conducted in Danzhou, Hainan province, China, a total of 537 wild Cynodon accessions from 22 countries and classified into 11 groups according to taxonomy and origin, were characterized in terms of 11 phenotypic traits in order to construct a core collection. For this, the optimal strategy was developed by screening within the following method levels: (i) 7 sampling proportions (5, 10, 15, 20, 25, 30 and 35%); (ii) 3 sampling methods (preferential sampling, deviation sampling and random sampling); (iii) 5 clustering methods [single linkage, completed linkage, median linkage, unweighted pair-group average (UPGMA) and Ward’s method]; (iv) 3 genetic distances (Euclidean distance, Mahalanobis distance and principal component distance); and (v) 3 sampling proportions within groups (simple, logarithmic and square root proportions). Mean difference percentage, variance difference percentage, coincidence rate of range and variation coefficient changing rate were the criteria adopted for evaluating how well the core collection represented the original collection. The correlation between the original and core collections was determined for comparison. The core collections were validated with the sample distribution diagram of the main components. Results showed that the optimal sampling method for constructing a Cynodon core collection was preferential sampling, the optimal sampling proportion being 20%. The optimal sampling proportion within groups was the square root proportion, the optimal genetic distance was Mahalanobis distance and the optimal clustering method was UPGMA. The proposed core collection of Cynodon is composed of 108 accessions; it was constructed following the optimal sampling strategy identified and retained the original collection´s phenotypic diversity, phenotypic trait correlations and phenotypic group structure. Thus, this collection could be considered a representative sample of the entire resource.

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 A Modified Roger’s Distance Algorithm for Mixed Quantitative–Qualitative Phenotypes to Establish a Core Collection for Taiwanese Vegetable Soybeans

2021 ◽  
Vol 11 ◽  
Author(s):  
Chung-Feng Kao ◽  
Shan-Syue He ◽  
Chang-Sheng Wang ◽  
Zheng-Yuan Lai ◽  
Da-Gin Lin ◽  
...  
Keyword(s):  
Core Collection ◽  
Dietary Habits ◽  
Phenotypic Traits ◽  
Variable Rate ◽  
Vegetable Soybean ◽  
Breeding Programs ◽  
The Core ◽  
Entire Collection ◽  
Redundant Accessions ◽  
High Diversity

Vegetable soybeans [Glycine max (L.) Merr.] have characteristics of larger seeds, less beany flavor, tender texture, and green-colored pods and seeds. Rich in nutrients, vegetable soybeans are conducive to preventing neurological disease. Due to the change of dietary habits and increasing health awareness, the demand for vegetable soybeans has increased. To conserve vegetable soybean germplasms in Taiwan, we built a core collection of vegetable soybeans, with minimum accessions, minimum redundancy, and maximum representation. Initially, a total of 213 vegetable soybean germplasms and 29 morphological traits were used to construct the core collection. After redundant accessions were removed, 200 accessions were retained as the entire collection, which was grouped into nine clusters. Here, we developed a modified Roger’s distance for mixed quantitative–qualitative phenotypes to select 30 accessions (denoted as the core collection) that had a maximum pairwise genetic distance. No significant differences were observed in all phenotypic traits (p-values > 0.05) between the entire and the core collections, except plant height. Compared to the entire collection, we found that most traits retained diversities, but seven traits were slightly lost (ranged from 2 to 9%) in the core collection. The core collection demonstrated a small percentage of significant mean difference (3.45%) and a large coincidence rate (97.70%), indicating representativeness of the entire collection. Furthermore, large values in variable rate (149.80%) and coverage (92.5%) were in line with high diversity retained in the core collection. The results suggested that phenotype-based core collection can retain diversity and genetic variability of vegetable soybeans, providing a basis for further research and breeding programs.

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 Genetic Diversity and Structure of Core Collection of Huangqi (Astragalus) Developed by Genomic Simple Sequence Repeat Markers

2022 ◽  
Author(s):  
Fanshu Gong ◽  
Yaping Geng ◽  
Pengfei Zhang ◽  
Feng Zhang ◽  
Xinfeng Fan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simulated Annealing ◽  
Core Collection ◽  
Phylogenetic Trees ◽  
Simulated Annealing Algorithm ◽  
Therapeutic Effects ◽  
Core Collections ◽  
The Core ◽  
Genetic Diversity And Structure ◽  
Annealing Algorithm

Abstract Huangqi (Astragalus) is a versatile herb that possesses several therapeutic effects against a variety of diseases, especially lung diseases. The aim of this study was to establish a core collection of Astragalus germplasm resources based on molecular 10 SSR markers. Based on 380 samples of Astragalus collected from different areas, five different methods were utilized to construct the core collection of Astragalus, including PowerCore-based M strategy, CoreFinder-based M strategy, Core Hunter-based stepwise sampling, PowerMarker-based simulated annealing algorithm based on allele maximization, and PowerMarker-based simulated annealing algorithm based on maximizing genetic diversity. Of the constructed Astragalus core collections, the CoreFinder-based M strategy was found to be the most suitable approach as it reserved all the alleles and most of the genetic diversity parameters were higher than those of the initial collection. Additional analyses demonstrated that the genetic diversity of the core collection matched the properties of the initial collection. Further, the phylogenetic trees indicated that the population structure of the core collection was similar to that of the initial collection. In addition, our results showed that the optimal grouping value of K was 2. The construction of a core collection is beneficial for the understanding, management, and utilization of Astragalus. Moreover, this study will act as a valuable reference for constructing core collections for other plants or fungi.

scholarly journals Composite core set construction and diversity analysis of Iranian walnut germplasm using molecular markers and phenotypic traits

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248623
Author(s):  
Razieh Mahmoodi ◽  
Mohammad Reza Dadpour ◽  
Darab Hassani ◽  
Mehrshad Zeinalabedini ◽  
Elisa Vendramin ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Genetic Variability ◽  
Core Collection ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Phenotypic Variability ◽  
Juglans Regia ◽  
Phenotypic Traits ◽  
Core Collections ◽  
Shannon’S Diversity Index

Iran is a center of origin and diversity for walnuts (Juglans regia L.) with very good potential for breeding purposes. The rich germplasm available, creates an opportunity for study and selection of the diverse walnut genotypes. In this study, the population structure of 104 Persian walnut accessions was assessed using AFLP markers in combination with phenotypic variability of 17 and 18 qualitative and quantitative traits respetively. The primers E-TG/M-CAG, with high values of number of polymorphic bands, polymorphic information content, marker index and Shannon’s diversity index, were the most effective in detecting genetic variation within the walnut germplasm. Multivariate analysis of variance indicated 93.98% of the genetic variability was between individuals, while 6.32% of variation was among populations. A relatively new technique, an advanced maximization strategy with a heuristic approach, was deployed to develop the core collection. Initially, three independent core collections (CC1–CC3) were created using phenotypic data and molecular markers. The three core collections (CC1–CC3) were then merged to generate a composite core collection (CC4). The mean difference percentage, variance difference percentage, variable rate of coefficient of variance percentage, coincidence rate of range percentage, Shannon’s diversity index, and Nei’s gene diversity were employed for comparative analysis. The CC4 with 46 accessions represented the complete range of phenotypic and genetic variability. This study is the first report describing development of a core collection in walnut using molecular marker data in combination with phenotypic values. The construction of core collection could facilitate the work for identification of genetic determinants of trait variability and aid effective utilization of diversity caused by outcrossing, in walnut breeding programs.

Presize: an approach for precise estimation of core collection size using the Similarity Elimination (SimEli) method

2014 ◽  
Vol 13 (3) ◽  
pp. 282-285
Author(s):  
R. Ramesh Krishnan ◽  
B. B. Bindroo ◽  
V. Girish Naik
Keyword(s):  
Genetic Distance ◽  
Core Collection ◽  
Crop Improvement ◽  
Genetic Distances ◽  
Core Collections ◽  
Elimination Process ◽  
The Core ◽  
Precise Estimation ◽  
Rare Alleles

Core collections are the integral part of biotechnology-aided modern-day crop improvement programmes and utilized for a variety of applications including conventional plant breeding, association mapping, resequencing, among others. Since their advent, determination of core collection size has been based on the size of the whole collection. In this study, we precisely estimated the size of the core collection based on the diversity of the whole collection using the Similarity Elimination method. For each of the elimination cycle, allele retention and pairwise and mean genetic distances were calculated and used as the criteria for the precise estimation of the core collection size. We sampled a coconut core collection with 266 entries by retaining the diversity of the whole collection. During the elimination process, accessions with very rare alleles were eliminated first when compared with those having rare and common alleles. Therefore, our results support the hypothesis that the less frequent alleles seldom contribute to the genetic distance when compared with common alleles. In conclusion, presize can be efficiently utilized in any crop for the precise estimation of core collection size.

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.

Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 884-898 ◽  
Author(s):  
Jianjun Zhao ◽  
Anna Artemyeva ◽  
Dunia Pino Del Carpio ◽  
Ram Kumar Basnet ◽  
Ningwen Zhang ◽  
...  
Keyword(s):  
Association Mapping ◽  
Flowering Time ◽  
Brassica Rapa ◽  
Core Collection ◽  
Field Experiments ◽  
Research Centre ◽  
Candidate Gene Approach ◽  
Core Collections ◽  
Genome Wide ◽  
Using Data

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

scholarly journals Phenotyping plants: genes, phenes and machines

2012 ◽  
Vol 39 (11) ◽  
pp. 813 ◽  
Author(s):  
Roland Pieruschka ◽  
Hendrik Poorter
Keyword(s):  
Structural Information ◽  
Plant Phenotyping ◽  
Phenotypic Traits ◽  
Special Issue ◽  
Non Invasive ◽  
The Core ◽  
The Relationship ◽  
Non Destructive ◽  
Major Progress ◽  
Meaningful Data

No matter how fascinating the discoveries in the field of molecular biology are, in the end it is the phenotype that matters. In this paper we pay attention to various aspects of plant phenotyping. The challenges to unravel the relationship between genotype and phenotype are discussed, as well as the case where ‘plants do not have a phenotype’. More emphasis has to be placed on automation to match the increased output in the molecular sciences with analysis of relevant traits under laboratory, greenhouse and field conditions. Currently, non-destructive measurements with cameras are becoming widely used to assess plant structural properties, but a wider range of non-invasive approaches and evaluation tools has to be developed to combine physiologically meaningful data with structural information of plants. Another field requiring major progress is the handling and processing of data. A better e-infrastructure will enable easier establishment of links between phenotypic traits and genetic data. In the final part of this paper we briefly introduce the range of contributions that form the core of a special issue of this journal on plant phenotyping.

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