1. Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi.

    1. Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi.

      1. Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi.

        1. ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, Tamil Nadu.

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Overview

A core collection is a “limited set of accessions representing, with minimum repetitiveness, the genetic diversity of a crop species and its wild relatives”(Frankel, 1984).

In case of several large and unwieldy germplasm collections conserved in genebanks, development of several such core collections has facilitated increasing the efficiency of their characterisation and in turn the utilisation.

There are different criteria available for evaluating the core collections by comparing with the original collections from which they have been sampled. The choice of the suitable evaluation criteria should be dictated by the objectives of the core collection. Several such criteria including the distance based metrics described in Odong et al. (2013) have been implemented in EvaluateCore and this document shows how to use them. This document assumes a basic knowledge of R programming language.

Installation

The package can be installed using the following functions:

# Install from CRAN
install.packages('EvaluateCore', dependencies=TRUE)

# Install development version from Github
devtools::install_github("aravind-j/EvaluateCore")

Then the package can be loaded using the function


--------------------------------------------------------------------------------
Welcome to EvaluateCore version 0.1.3.9000


# To know whats new in this version type:
  news(package='EvaluateCore')
  for the NEWS file.

# To cite the methods in the package type:
  citation(package='EvaluateCore')

# To suppress this message use:
  suppressPackageStartupMessages(library(EvaluateCore))
--------------------------------------------------------------------------------

Version History

The current version of the package is 0.1.3. The previous versions are as follows.

Table 1. Version history of EvaluateCore R package.

Version Date
0.1.1 2020-06-03
0.1.2 2021-06-12

To know detailed history of changes use news(package='EvaluateCore').

Table 2 : Core evaluation methods implemented in EvaluateCore.

Metric Criteria/Method Function Type of Variable Type of Core Type of comparison Reference
Genetic distance Average entry-to-nearest-entry distance (EENE-EN) dist.evaluate.core Quantitative & Qualitative CC–I Multivariate Odong et al. (2013)
Genetic distance Average accession-to-nearest-entry distance (AENA-EN) dist.evaluate.core Quantitative & Qualitative CC–X Multivariate Odong et al. (2013)
Genetic distance Average entry-to-entry distance (EEE-E) dist.evaluate.core Quantitative & Qualitative CC–X Multivariate Odong et al. (2013)
Mean Student-Newman-Keuls test snk.evaluate.core Quantitative CC–D Univariate Newman (1939); Keuls (1952)
Median Wilcoxon rank sum test or Mann-Whitney-Wilcoxon test or Mann-Whitney U test wilcox.evaluate.core Quantitative CC–D Univariate
Mean Student’s t test ttest.evaluate.core Quantitative CC–D Univariate
Mean and Variance Sign test signtest.evaluate.core Quantitative CC–D Multivariate
Variance Levene’s test levene.evaluate.core Quantitative CC–D Univariate
Variability Interquartile range iqr.evaluate.core Quantitative CC–D Univariate
Range Coincidence rate of range cr.evaluate.core Quantitative CC–D Multivariate
Variance Variable rate of coefficient of variation vr.evaluate.core Quantitative CC–D Multivariate
Probability distribution Quantile-quantile plots qq.evaluate.core Quantitative CC–D Univariate
Probability distribution Kullback-Leibler distance pdfdist.evaluate.core Quantitative CC–D Univariate
Probability distribution Kolmogorov-Smirnov distance pdfdist.evaluate.core Quantitative CC–D Univariate
Probability distribution Anderson-Darling distance pdfdist.evaluate.core Quantitative CC–D Univariate
Probability distribution Box-and-whisker plot box.evaluate.core Quantitative CC–D Univariate
Mean Percentage of significant differences of mean percentdiff.evaluate.core Quantitative CC–D Multivariate
Variance Percentage of significant differences of variance percentdiff.evaluate.core Quantitative CC–D Multivariate
Mean Average of absolute differences between means percentdiff.evaluate.core Quantitative CC–D Multivariate
Variance Average of absolute differences between variances percentdiff.evaluate.core Quantitative CC–D Multivariate
Euclidean distance Percentage difference between the mean squared Euclidean distance percentdiff.evaluate.core Quantitative CC–D Multivariate
Probability distribution Principal component analysis pca.evaluate.core Quantitative CC–D Multivariate
Frequency distribution Bar plot bar.evaluate.core Qualitative CC–D Univariate
Frequency distribution Chi-squared test for homogeneity chisquare.evaluate.core Qualitative CC–D Univariate
Frequency distribution Class coverage coverage.evaluate.core Qualitative CC–I Univariate
Diversity Shannon-Weaver diversity index shannon.evaluate.core Qualitative CC–I Univariate
Diversity Maximum Shannon-Weaver diversity index shannon.evaluate.core Qualitative CC–I Univariate
Diversity Shannon Equitability index shannon.evaluate.core Qualitative CC–I Univariate
Phenotypic correlation Pearson correlation coefficients corr.evaluate.core Quantitative & Qualitative CC-D Multivariate
Correlation matrix Mantel correlation coefficient corr.evaluate.core Quantitative & Qualitative CC-D Multivariate
Frequency distribution Stacked frequency distribution histogram freqdist.evaluate.core Quantitative & Qualitative CC-D Univariate

References

Frankel, O. H. (1984). “Genetic perspective of germplasm conservation,” in Genetic Manipulations: Impact on Man and Society, eds. W. Arber, K. Limensee, W. J. Peacock, and P. Stralinger (Cambridge University Press: Cambridge, UK), 161–170.
Keuls, M. (1952). The use of the „studentized range” in connection with an analysis of variance. Euphytica 1, 112–122. doi:10.1007/BF01908269.
Newman, D. (1939). The distribution of range in samples from a normal population, expressed in terms of an independent estimate of standard deviation. Biometrika 31, 20–30. doi:10.1093/biomet/31.1-2.20.
Odong, T. L., Jansen, J., Eeuwijk, F. A. van, and Hintum, T. J. L. van (2013). Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation. Theoretical and Applied Genetics 126, 289–305. doi:10.1007/s00122-012-1971-y.