Abstract:
Marker-trait association studies in tomato have
progressed rapidly due to the availability of several populations
developed between wild species and domesticated
tomato. However, in the absence of whole genome
sequences for each wild species, molecular marker methods
for whole genome comparisons and Wne mapping are
required. We describe the development and validation of a
diversity arrays technology (DArT) platform for tomato
using an introgression line (IL) population consisting of
wild Solanum pennellii introgressed into Solanum lycopersicum
(cv. M82). A tomato diversity array consisting of
6,912 clones from domesticated tomato and twelve wild
tomato/Solanaceous species was constructed. We successfully
bin-mapped 990 polymorphic DArT markers together
with 108 RFLP markers across the IL population, increasing
the number of markers available for each S. pennellii
introgression by tenfold on average. A subset of DArT
markers from ILs previously associated with increased levels
of lycopene and carotene were sequenced, and 44%
matched protein coding genes. The bin-map position and
order of sequenced DArT markers correlated well with
their physical position on scaVolds of the draft tomato
genome sequence (SL2.40). The utility of sequenced DArT
markers was illustrated by converting several markers in
both the S. pennellii and S. lycopersicum phases to cleaved
ampliWed polymorphic sequence (CAPS) markers. Genotype
scores from the CAPS markers conWrmed the genotype
scores from the DArT hybridizations used to construct
the bin map. The tomato diversity array provides additional
“sequence-characterized” markers for Wne mapping of
QTLs in S. pennellii ILs and wild tomato species.
