The steps of the constitution of a core collection

Preliminary step: check of files

The input files could be rapidly controlled by building up a core collection of a small size. Errors are printing in a file (See details previously given). Use the description mode to control the presence of missing data and the description of variables.

1st step: study of the collection

The Tcl interface allows to view graphs of richness against the number of individuals in the core. Two plots are produced: random and M curves. The random curve indicates the extent of potential redundancy in the collection. A convex relationship indicates redundancy whereas a linear relationship indicates zero redundancy in the collection. The choice of variables defining richness and the number of classes in the variables influence the expected amount of redundancy.


The choice of active variables and the number of classes in variables could be done on two criterions: the shape of the curve of richness against the number of individuals in the core and the response on ‘target’ variables. With a nearly linear curve, the sample which optimises the richness will be difficult to find. With a very convex curve, the optimal sample will have a very small size and beyond this size, various samples will satisfy the optimum of richness. The choice of variables and number of classes could also be defined on the response on other variables. Higher will be the response on target variables; higher will be probably the response on other loci.

After the choice of variables and the number of classes in the variables, the inflection point of the M curve provides the optimal size for a core collection.


2nd step: Core collection constitution

Several samples are obtained according to the requested number of replicates. The final core collection could be chosen on the response on target variables.

To define a final core collection, you can ask a great number of replicates and retain in the final core collection the accessions which are sampled a great number of times.


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