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Apple genome sequenced


August 30, 2010
By Fruit & Vegetable

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August 30, 2010 – An international team of scientists from Italy, France, New
Zealand, Belgium and the U.S. has published a draft sequence of the domestic
apple genome in the current issue of Nature Genetics.

August 30, 2010 – An international team of scientists from Italy, France, New
Zealand, Belgium and the U.S. has published a draft sequence of the domestic
apple genome in the current issue of Nature Genetics.

The availability of a genome sequence for apple will allow
scientists to more rapidly identify which genes provide desirable
characteristics to the fruit and which genes and gene variants provide disease
or drought resistance to the plant. This information can be used to rapidly
improve the plants through more informed selective breeding.

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An organism’s genome is the total of all its genetic
information, including genes. Genes carry information that determines, among
other things, a plant's appearance, health, productivity and colour and taste
of the fruit.

The domestic apple is the main fruit crop of the world’s
temperate regions. Apple is a member of the plant family Rosaceae which
includes many other economically important species, including cherry, pear, peach,
apricot, strawberry, and rose, to name just a few.

Led by Washington State University horticultural genomicist
Amit Dhingra, the Washington-based team sequenced and analyzed a unique version
of the genome of the golden delicious apple in which all duplicated chromosomes
are genetically identical. This information was used to validate the sequence
of the more complicated “heterozygous” golden delicious apple (in which
duplicated chromosomes are not identical).

“Before genome sequencing, the best we could do was
correlate traits with genes. Now we can point to a specific gene and say, ‘This
is the one; this gene is responsible for this trait.’ That trait of interest
might be, for instance, a disease, which is why sequencing the human genome was
such an important milestone. Or the trait might be for something desirable,
like flavor in a piece of fruit. We are already working on finding
physiological solutions to issues like bitter pit in current apple varieties
with the gene-based information available to us and lay a foundation for
improved varieties in the future through generation of sports (mutations) and
breeding,” Dhingra said.

The Washington state contribution to the sequencing work was
a unique collaboration between the cross-state Apple Cup rivals of WSU and the
University of Washington.

Microbiologist Roger Bumgarner’s lab at the University of
Washington
provided the initial sequencing expertise and capability to the
project, which was later complemented and replaced by sequencing expertise in
the Dhingra genomics lab, who obtained the same DNA sequencing instrument used
in Dr. Bumgarner’s lab.

UW is a world leader in medical research and WSU is a world
leader in agricultural research,” said Bumgarner. “Technological advancements
and techniques initially used to study medically important genomes and problems
can be rapidly applied to genomes and problems of agricultural importance. We
both had something to contribute and to learn from one another. I think there
are many more opportunities for such collaborations to develop in the coming
years.”

After the sequencing was completed, WSU computational
biologist Ananth Kalyanaraman contributed to the analysis by comparing the
apple genome with that of pear, peach and grape to identify the differences and
commonalities that exist between these fruit crops.

While the apple genome provides a valuable resource for
future research, one pressing question answered by the international team's
paper in Nature Genetics was one of origin. Scientists have long wanted to know
– and have for years argued vehemently about – the ancestor of the modern
domesticated apple. The question is now settled: Malus sieversii, native to the
mountains of southern Kazakhstan, is the apple's wild ancestor. Now that that
question is settled, scientists will begin using the apple genome to help breed
apples with desirable new traits, including disease resistance and,
potentially, increased health-benefiting qualities.

“Having the apple genome sequence will greatly accelerate
our ability to define the differences between apple cultivars at the genetic
level,” said Kate Evans, an apple breeder based at the WSU Tree Fruit Research
and Extension Center
. “This will allow us to exploit these differences and
target areas of diversity to incorporate into the breeding program, resulting
in improved cultivars for the consumers that are also better suited for
long-term, sustainable production.”


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