Abstract:
Diversity Arrays Technology (DArT)
provides a high-throughput whole-genome genotyping
platform for the detection and scoring of hundreds
of polymorphic loci without any need for prior
sequence information. The work presented here
details the development and performance of a DArT
genotyping array for apple. This is the first paper on
DArT in horticultural trees. Genetic mapping of
DArT markers in two mapping populations and their
integration with other marker types showed that
DArT is a powerful high-throughput method for
obtaining accurate and reproducible marker data,
despite the low cost per data point. This method
appears to be suitable for aligning the genetic maps of
different segregating populations. The standard complexity reduction method, based on the methylation-
sensitive PstI restriction enzyme, resulted in a
high frequency of markers, although there was 52–54%
redundancy due to the repeated sampling of highly
similar sequences. Sequencing of the marker clones
showed that they are significantly enriched for lowcopy,
genic regions. The genome coverage using the
standard method was 55–76%. For improved genome
coverage, an alternative complexity reduction method
was examined, which resulted in less redundancy and
additional segregating markers. The DArT markers
proved to be of high quality and were very suitable for
genetic mapping at low cost for the apple, providing
moderate genome coverage.
