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July 24, 2009
 A
team of researchers from the
Chinese
Academy of Agricultural Sciences, the
China Agricultural University
and the United States
Department of Agriculture's Agricultural Research Service
(ARS) has produced the world's first integrated genetic and
cytogenetic map of the cucumber genome, an important resource
for scientists working to develop improved cucurbit crops.
"This map will facilitate whole genome sequencing and positional
cloning, enhance marker assisted selection (MAS), and provide
opportunities to investigate synteny among cucurbit species,"
wrote Sanwen Huang, a researcher at the Institute of Vegetables
and Flowers of the Chinese Academy of Agricultural Sciences, and
his colleagues in a paper published by PLoS One.
Cucumbers belong to the family Cucurbitaceae, which also
includes important vegetable and fruit crops such as melon,
watermelon, pumpkin and squash. Despite their commercial
importance, however, there are few genomic tools available for
cucurbits.
"Cucurbits are orphan crops. Before the map we published in PLoS
One, there are hardly any maps with more than 300 markers
mapped. There was very little knowledge on cytogenetics of
cucurbits either," said Dr. Huang. "Linkage groups of genetic
maps were not assigned to chromosomes. For comparative genetics,
there is no common language."
Dr. Huang further noted that compared to other agricultural
families such as Poaceae (grasses), Fabaceae (legumes), and
Solanaceae (potato, tomato and tobacco), the amount of DNA
sequences and ESTs (expressed sequence tags) of cucurbits in
public domains is scarce. For instance, the ESTs of all
cucurbits are less than 50,000, while rice has more than one
million.
Dr. Huang and his team identified 995 simple sequence repeat
(SSR) markers using whole genome shotgun sequences. These
markers were used to construct a high-density genetic map using
a segregating population with 77 recombinant inbred lines,
resulting in seven linkage groups. The team then used
fluorescence in situ hybridization (FISH) to assign the linkage
groups to seven cucumber chromosomes.
The researchers deliberately developed the SSR markers from the
gene-rich or euchromatic region of the cucumber genome.
"Sequences provide a good start for molecular marker
development, as shown in our case. We developed the ~1000 SSR
markers from the 3x Sanger sequences," commented Dr. Huang. "I
think the advantage of the approach is that we explore the power
of bioinformatics to develop appropriate markers for mapping."
The researchers found that around 65 percent of the SSR markers
were polymorphic in eleven inbred cucumber lines, suggesting
that they may be useful in marker assisted selection. The team
also proved that part of the SSR markers can be adopted for
melon and watermelon genetic studies. Among the 995 SSR markers,
49 percent and 26 percent were found to be conserved in melon
and watermelon, respectively.
On the average any gene or QTL can be located within a genetic
interval of < 1 cM using the map. According to Dr. Huang, this
is a critical step towards developing better cucumber varieties.
The team has shared the map to several colleagues working to
pinpoint agronomically important cucumber traits. Huang said
that his lab is now working to identify and map genes that
control bitterness, scab resistance, and sex determination. And
his team has also been successful in deciphering the whole
genome of cucumber, which is composed of 370 million bases. They
have also annotated some 26,000 cucumber genes.
Reference
Ren Y, Zhang Z, Liu J,
Staub JE, Han Y, et al. (2009)
An Integrated Genetic and Cytogenetic Map of the Cucumber
Genome
PLoS ONE 4(6): e5795.
http://dx.doi.org/10.1371/journal.pone.0005795
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