What can we learn from grape berry ripening from transcriptomic data?
Claudio Moser, Department of Genetics and Molecular Biology, E. Mach Foundation - IASMA
Plenary Talk, Afternoon Session, 1 September (11th MGED Meeting, 1-4 September, 2008)
The grapevine berry ripening process
It takes 4 months to go from a flowering cluster to a fully-ripened cluster. The development of the grape is in three phases: 2 growing phases divided by a phase where the berry doesn't grow anymore. Berry formation followed by berry ripening. There are three major tissues: skin, pulp, seeds.
Why is it important?
Economics: It is the most important fleshy fruit from an economic point of view. There are 8 million hectares of vineyards worldwide with an annual turnover of more than 20 billion US $. There is increased interest in grape-derived anti-oxidant compounds. In Trentino, grapes and apples represent the two most relevant crops.
Biological relevance: The ancestor of the cultivated version climbed trees, reached the top of the canopy, and then flowered. Domestication has passed from separated-sex flowers (male flowers and female flower) to a hermaphrodite flower.
The grape transcriptome
Transcript profiles are studied to understand the molecular dynamics of berry ripening and regulation. Research can be done with the Affymetrix Vitis GeneChip. This chip contains 14,000 unigenes. Applications of the research improve management practices (via lower inputs, lower costs, and higher quality), use gene transfer to create new varieties or improve traditional ones. There are two ways of getting new genes in: gene transfer (direct) or marker-assisted selection.
They used pinot noir grapes, and sampled them at three different stages
of the life cycle, with 3 biological replicates for each time point,
then repeated the analysis in 3 different seasons. The 2003 data was
quite different - this can probably be explained by 2003 having a very
hot summer. Further, the analysis separated out the ripe berry time
point from the earlier two time points. They ended up with ~1800 genes
that will form the berry-ripening core set.
What have we learned about the biology?
9 GO classes were statistically significantly different from the affy chip, with 6 of those being overrepresented. Ripening is finely programmed before veraison and its transcriptional modulation reflects berry biochemical changes. In the first phase, the berry goes through a re-programming phase before moving on to the next growing phase. A consistent fraction of the isolated genes are devoted to the control of the developmental program. (This has also been found in tomatoes.) Major TF families include zinc finger, oxin-related, and others.
He looked more closely at genes related to ROS metabolism. Noticed there was a burst of hydrogen peroxide at the veraison phase. Seasonal influences produces changes that involve light signalling, ripening-related genes, and non-ripening-specific isoforms
Future directions
Wants to look into ethylene, as it is probably quite important in berry development. Exogenous ethylene application can modify the ripening curve. Endogenous ethylene can be measured just before veraison. Tried to measure these things on their pino noir grapes. They got some noisy data, but think they saw two peaks. In 2007 there were two different genome sequences of pinot noir grapes published. They found about 30,000 genes. They want to do more analysis on it.
These are just my notes and are not guaranteed to be correct. Please feel free to let me know about any errors, which are all my fault and not the fault of the speaker. :)
