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 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.

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 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.

scholarly journals Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8572 ◽  
Author(s):  
Suzhen Niu ◽  
Hisashi Koiwa ◽  
Qinfei Song ◽  
Dahe Qiao ◽  
Juan Chen ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Genetic Relationships ◽  
Genotyping By Sequencing ◽  
Leaf Size ◽  
Snp Markers ◽  
Multiple Traits ◽  
Core Collections ◽  
The Core ◽  
High Quality Snps ◽  
Core Set

An accurate depiction of the genetic relationship, the development of core collection, and genome-wide association analysis (GWAS) are key for the effective exploitation and utilization of genetic resources. Here, genotyping-by-sequencing (GBS) was used to characterize 415 tea accessions mostly collected from the Guizhou region in China. A total of 30,282 high-quality SNPs was used to estimate the genetic relationships, develop core collections, and perform GWAS. We suggest 198 and 148 accessions to represent the core set and mini-core set, which consist of 47% and 37% of the whole collection, respectively, and contain 93–95% of the total SNPs. Furthermore, the frequencies of all alleles and genotypes in the whole set were very well retained in the core set and mini-core set. The 415 accessions were clustered into 14 groups and the core and the mini-core collections contain accessions from each group, species, cultivation status and growth habit. By analyzing the significant SNP markers associated with multiple traits, nine SNPs were found to be significantly associated with four leaf size traits, namely MLL, MLW, MLA and MLSI (P < 1.655E−06). This study characterized the genetic distance and relationship of tea collections, suggested the core collections, and established an efficient GWAS analysis of GBS result.

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 &gt; 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 Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Debjani Roy Choudhury ◽  
Ramesh Kumar ◽  
Vimala Devi S ◽  
Kuldeep Singh ◽  
N. K. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Core Collection ◽  
Tamil Nadu ◽  
East Coast ◽  
Snp Markers ◽  
The Core ◽  
Core Set ◽  
Population Structure Analysis ◽  
The Mean

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.

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.

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 Comparison of Single Linkage, Complete Linkage, and Average Linkage Methods on Community Welfare Analysis in Cities and Regencies in East Java

2021 ◽  
Vol 18 (1) ◽  
pp. 130-140
Author(s):  
Yanuwar Reinaldi ◽  
Nurissaidah Ulinnuha ◽  
Moh. Hafiyusholeh
Keyword(s):  
Hierarchical Clustering ◽  
National Development ◽  
Clustering Methods ◽  
Single Linkage ◽  
Complete Linkage ◽  
Average Linkage ◽  
Linkage Methods ◽  
Silhouette Index ◽  
Linkage Method ◽  
Index Value

Community welfare is one of the important points for a region and is also the essence of national development. The welfare of the people in Indonesia is fairly unequal, especially in East Java. To be able to map an area to the welfare of its people in East Java, one way that can be used is to use clustering. The hierarchical clustering method is one of the clustering methods for grouping data. In hierarchical clustering, single linkage, complete linkage, and average linkage methods are suitable methods for grouping data, which will compare the best method to use. The results of the calculation show that the average linkage method with three clusters is the best calculation with a silhouette index value of 0.6054, with the 1st cluster there are 23 regions, namely the city/district with the highest community welfare, the 2nd cluster there are 11 regions, namely cities/districts with moderate social welfare, and in the third cluster there are 4 regions, namely cities/districts with the lowest community welfare.

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