Potato Genome Sequenced

The potato genome has just been published in the journal Nature.

The Potato Genome Sequencing Consortium (PGSC), an international team of scientists including some from Teagasc in Ireland, has published the "genetic blueprint" for the world's third most important food crop.

Scientists say the information will help plant scientists and breeders to improve yield, quality, nutritional value and disease resistance pf potato varieties. The PGSC say it should also allow potato breeders "reduce the 10-12 years currently needed to breed new varieties".

The potato genome is the first sequence of an Asterid to be published - a group of flowering plants encompassing around 25% of all known plant species.

The consortium published a draft sequence in 2009 after a meeting of the consortium in Oakpark, Carlow in Ireland to plan the final phases of the project. The most recent publication is a refined version covering approximately 95% of all the genes in the potato - around 39,000 genes that code for proteins.

Worldwide, it's estimated that a loss of about €3 billion per year in the potato crop arises from diseases such as late blight and potato cyst nematodes. These problems are still largely controlled by frequent applications of fungicides and nematicides.

An indepth knowledge of the genetics of the potato should allow scientists to develop new varieties which show high levels of resistance against these pests and diseases.

The potato genome has 12 chromosomes and an extimate 840 million base pairs.

Speaking on the release of the first draft, Professor Jimmy Burke, head of Teagasc Crops Research Centre and leader of the plant biotechnology programme said: “Research such as this is incredibly important to the future competitiveness of Irish agriculture and puts Teagasc at the forefront of exciting developments in science”.

Combining our expertise in plant breeding with cutting-edge biotechnology-based research is enhancing our ability to develop plant varieties suitable for Irish conditions and agricultural practices. We are pursuing similar projects in other species important to agriculture here in Ireland, including perennial ryegrass, white clover and wheat, and energy crops, and we expect similar successes in these species in the future”.


The Nature paper is available here.
The full sequence is available here.

Little water flea has big genome

Credit: Paul Hebert, University of Guelph

The little water flea used to have pride of place on the front cover of the Leaving Certificate Biology textbook when I was going to school. Little did we realise then that Daphnia would turn out to be so impressive!

Research just published in Science shows that the near-microscopic freshwater crustacean Daphnia pulex (the water flea) is the animal with most genes (about 31,000 in total).

"Daphnia's high gene number is largely because its genes are multiplying, creating copies at a higher rate than other species," said project leader and CGB (Centre for Genomics and Bioinformatics, Indiana University) genomics director John Colbourne.

"We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of humans."

Colbourne postulates that "since the majority of duplicated and unknown genes are sensitive to environmental conditions, their accumulation in the genome could account for Daphnia's flexible responses to environmental change."

Much of the media coverage has centred around the fact that the water flea outstrips humans in terms of gene number (humans have around 23,000 genes). This "paradox" known as the C-value enigma or C-value paradox is based on the fact that the genome size of an organism does not correlate with the complexity of the organism.

'Daphnia is an exquisite aquatic sensor, a modern version of the mineshaft canary' - James KlaunigIt's not a new idea - the term was first used in 1971 and the solution lies in the fact that lots of DNA in eukaryotes (i.e. non-bacteria) does not code for genes. For example, only about 1.5% of the human genome codes for genes. The wheat genome, for example, is five times larger than the human genome.

Daphnia have long been studied because they can be an indicator of environmental health in freshwater bodies. "Daphnia is an exquisite aquatic sensor, a potential high-tech and modern version of the mineshaft canary", says James Klaunig of Indiana University.

"With knowledge of its genome, and using both field sampling and laboratory studies, the possible effects of environmental agents on cellular and molecular processes can be resolved and linked to similar processes in humans."

[For our Irish Readers: Does anyone have an image of the front cover of the Leaving Certificate Biology Textbook with Daphnia ? If so, let me know and I'll add it to the post]

Reference
Colbourne, J., Pfrender, M., Gilbert, D., Thomas, W., Tucker, A., Oakley, T., Tokishita, S., Aerts, A., Arnold, G., Basu, M., Bauer, D., Caceres, C., Carmel, L., Casola, C., Choi, J., Detter, J., Dong, Q., Dusheyko, S., Eads, B., Frohlich, T., Geiler-Samerotte, K., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J., Muller, J., Pangilinan, J., Patwardhan, R., Pitluck, S., Pritham, E., Rechtsteiner, A., Rho, M., Rogozin, I., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y., Yamagata, H., Yamada, T., Ye, Y., Shaw, J., Andrews, J., Crease, T., Tang, H., Lucas, S., Robertson, H., Bork, P., Koonin, E., Zdobnov, E., Grigoriev, I., Lynch, M., & Boore, J. (2011). The Ecoresponsive Genome of Daphnia pulex Science, 331 (6017), 555-561 DOI: 10.1126/science.1197761

Wheat and Apple genomes provide hope for food security

The recent sequencing of two major crop genomes is good news for plant protection and for food security.

With the full genetic sequence now available for wheat and apple, scientists will have more information at their fingertips for the improvement of these crops to fight plant diseases and to ensure that growing human populations have adequate food resources in the future.

On the 26th of August last, a team of researchers in the UK released the 'first draft' of the wheat genome. While further work needs to be done to produce a fully annotated genome, the work is a major step forward for plant science.

The team of researchers responsible for the the wheat genome publication were funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and come from the University of Liverpool, the University of Bristol and the John Innes Centre.

The first draft (basically the raw data from the sequencing work) will need to be further annotated and assembled into the individual chromosomes and is based on a reference wheat variety called Chinese Spring. Information on this reference variety will be key to unlocking the genetic information behind other commercial varieties of wheat.

Prof. Mike Bevan from the John Innes Centre says that "The sequence coverage will provide an important foundation for international efforts aimed at generating a complete genome sequence of wheat in the next few years".

The information should lead to improvements in current wheat varieties to ensure that high yields can be maintained in the face of changing environmental conditions and an increased threat from a variety of plant pathogens.

'By understanding the genetic differences between varieties with different traits we can start to develop new types of wheat' - Prof. Anthony HallProf. Anthony Hall of the University of Liverpool hopes that the new information will allow scientists to probe differences between wheat varieties with different characteristics: "By understanding the genetic differences between varieties with different traits we can start to develop new types of wheat better able to cope with drought, salinity or able to deliver higher yields. This will help to protect our food security".

Meanwhile, just this week, an international team of scientists announced that they had published a draft sequence of the domestic apple genome. The genome was published in the current issue of Nature Genetics.

Apple is the main fruit crop of the world's temperate regions and is a member of the plant family Rosaceae which includes many other important species including cherry, pear, peach, apricot, strawberry, and rose.

Much like with the wheat genome, this new information will allow scientists to identify genes which provide desirable characteristics to the crop such as higher yields and disease or drought resistance.

The work by scientists from Italy, France, New Zealand, Belgium and the US was based on the well-known golden delicious apple.

'the scientists were also able to delve into the apples mysterious past'As well as looking to the future of apple production, the scientists were also able to delve into the apples mysterious past. For years they have argued about where the domestic apple came from and now they know. The data published this week shows that the ancestor of the modern apple in Malus sieversii, a plant native to the mountains of southern Kazakhstan.

Prof. Doug Kell, Chief Executive of the BBSRC, who funded the wheat project, points out that "The best way to support our food security is by using modern research strategies to understand how we can deliver sustainable increases in crop yields, especially in the face of climate change. Genome sequencing of this type is an absolutely crucial strategy.

"Knowledge of these genome sequences will now allow plant breeders to identify the best genetic sequences to use as markers in accelerated breeding programmes" said Prof. Kell.

Both the apple and wheat genome work have been made possible by huge advances in sequencing technology. As Prof. Hall of University of Liverpool notes: "Sequencing the human genome took 15 years to complete, but with huge advances in DNA technology, the wheat genome took only a year. The information we have collected will be invaluable in tackling the problem of global food shortage".