Statistical Techniques for Defining Reference Sets of Accessions and Microsatellite Markers
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Date
2011
Journal Title
Journal ISSN
Volume Title
Publisher
Crop science
Abstract
Exploitation of the available genetic resources
around the world requires information about
the relationships and genetic diversify present
among gene bank collections. These relations
can be established by defining for each crop a
small but informative set of accessions, together
with a small set of reliable molecular markers,
that can be used as reference material. In this
study, various strategies to arrive at small but
informative reference sets are discussed. For
selection of accessions, we proposed genetic
distance optimization (GDOpt) method, which
selects a subset of accessions that optimally
represent the accessions not included in the
core collection. The performance of GDOpt was
compared with Core Hunter, an advanced stochastic
local search algorithm for selecting core
subsets. For the selection of molecular markers,
we evaluated (i) the backward elimination
(BE) method and (ii) methods based on principal
component analysis (PCA). We examined
the performance of the proposed methodologies
using five real datasets. Relative to average
distance between an accession and the nearest
selected accession (repressiveness),
GDOpt outperformed Core Hunter. However,
Core Hunter outperformed GDOpt with respect
to allelic richness. The BE performed much better
than other methods in selecting subsets of
markers. Methods based on PCA showed that,
for practical purposes, the inclusion of the first
few (two or three) principal components (PCs)
was often sufficient. To obtain robust and high qualify
reference sets of accessions and markers
we advise a combination of GDOpt (for
accessions) and BE or methods based on PCA
using a few PCs (for subsets of markers).
Description
Keywords
Techniques, Reference Sets, Accessions, Microsatellite Markers
Citation
Odong, T. L., van Heerwaarden, J., Jansen, J., van Hintum, T. J., & van Eeuwijk, F. A. (2011). Statistical techniques for defining reference sets of accessions and microsatellite markers. Crop science, 51(6), 2401-2411.