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 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 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.

Establishment of a cassava (Manihot esculenta Crantz) core collection based on agro-morphological descriptors

2012 ◽  
Vol 10 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Ranjana Bhattacharjee ◽  
Dominique Dumet ◽  
Paul Ilona ◽  
Soyode Folarin ◽  
Jorge Franco
Keyword(s):  
Manihot Esculenta ◽  
Core Collection ◽  
Phenotypic Diversity ◽  
Crop Improvement ◽  
International Institute ◽  
Environment Interaction ◽  
Manihot Esculenta Crantz ◽  
Linear Discriminant ◽  
The Core ◽  
Entire Collection

International Institute of Tropical Agriculture maintains 2544 cassava accessions (Manihot esculenta Crantz) from 28 countries in its field bank. Being vegetatively propagated, this poses challenges in maintenance in terms of cost as well as in labour requirements. A core collection representing the range of phenotypic diversity present in the entire collection would enhance the conservation aspects and increase the potential for its exploitation in crop improvement programmes. The present study aimed to establish a core collection using 40 agro-morphological traits evaluated at two locations using a different number of accessions in each location. To meet the challenges generated by the types of variables and include maximum diversity in the core collection, a sequential strategy based on five major concepts was used: hierarchical multiple factor analysis allowing the mixture of variables of different kinds; three-way analysis that included the effect of genotype × environment interaction in the clustering process; linear discriminant function to assign all those individuals who were included in one location but not in the other to the groups that were generated from the common number of accessions evaluated in both locations; and D-allocation method to select samples from each cluster. The representativeness of the core subset to the entire collection was further estimated by comparing means and variances, range, and distances between accessions. The established cassava core collection consisted of 428 accessions that conserved 15% higher phenotypic diversity with no redundancies. The phenotypic diversity represented in this core collection will be a guide to users of cassava germplasm in their crop improvement programmes.

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 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.

Establishment of the core collection of Ziziphus mauritiana Lam. from India

2013 ◽  
Vol 12 (1) ◽  
pp. 140-142 ◽  
Author(s):  
P. N. Sivalingam ◽  
D. Singh ◽  
Sarita Chauhan ◽  
H. K. Changal ◽  
Chander Bhan ◽  
...  
Keyword(s):  
Core Collection ◽  
Quantitative Traits ◽  
Diversity Index ◽  
Crop Improvement ◽  
Ziziphus Mauritiana ◽  
Mean Values ◽  
Phenotypic Characters ◽  
The Core ◽  
Significant Difference ◽  
Clustering Patterns

Ziziphus mauritiana Lam. is an important fruit crop of the Thar Desert of India. About 330 accessions and cultivars collected from various parts of India are currently being maintained at a farm in the Central Institute for Arid Horticulture. Utilization of such a large collection of germplasm for breeding and crop improvement is difficult. Therefore, in the present study, using a heuristic approach based on phenotypic characters, we identified 52 accessions that represented a core collection, with a coverage of 100% and a coincidence rate of 98.1%. No significant difference was observed with respect to either the Shannon–Weaver or the Nei diversity index for qualitative traits, mean values and ranges for quantitative traits or clustering patterns between the core and whole collections. The core collection represents the entire range of diversity with minimum redundancy and should be useful for the conservation and utilization of Z. mauritiana germplasm.

Imaging of ribosomal RNA-protein interactions by dark-field STEM

1989 ◽  
Vol 47 ◽  
pp. 250-251
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
S. Tumminia ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Nucleic Acid ◽  
16S Rrna ◽  
Dark Field ◽  
Radius Of Gyration ◽  
Central Domain ◽  
The Core ◽  
16S Rna ◽  
30S Subunit ◽  
Core Particles

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

Nauwkeurige methode voor de aanwasbepaling van het grondvlak met behulp van de Pressler-boor

1968 ◽  
Vol 12 ◽  
Author(s):  
R. Goossens
Keyword(s):  
Basal Area ◽  
Precise Determination ◽  
Maximum Diameter ◽  
Precise Method ◽  
Maximum Radius ◽  
The Core ◽  
Two Parameters

A precise method for the determination of the increment of the  basal area using the PressIer bore. Refering to  previous research showing that the basal area of the corsica pine could be  characterized by an ellips, we present in this paper a precise method for the  determination of the increment of the basal area. In this method we determine  the direction of the maximum diameter, we measure this diameter and we take a  core in one of the points of tangency of the caliper with the measured tree.  The determination of the diameter perpendicular to the maximum diameter  finishes the work wich is to be done in the forest. From the classical  measurements effectuated on the core and from the measured diameters we can  then determine the form (V) and the excentricity (e). Substituting these two  parameters in the formula 2 or 2', we can also calculate the error of a  radius measured on the core with respect to the representative radius, This  error with them allow us to correct the measured value of the minimum or the  maximum radius and we will be able to do a precise determination of the  increment.

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