I was lucky enough to get to visit CYMMIT, which is a breeding center for maize and wheat.   They also have a massive genebank with some 130,000 wheat accessions and 24,000 maize. The seed vault itself is tucked away in the center or the complex behind a few sets of impressive stainless steel doors.

Behind these doors are two stories of rows of shelves of seed. This picture is Maize (aka corn) but they have teosinte as well as a large number of other wild grasses.

One of the most exciting things is what they have planned for all this material. The Seeds of Discovery project (poor online presence for this project, unless anyone knows of some), which they are just starting, is going to involve phenotyping and genotyping all of the accessions in the entire genebank! Needless to say this is a multimillion dollar mutli year project. I can’t wait to see what they learn, it is going to be an amazing set of data.

Maybe it contains genes that could improve the nutrient uptake of the cultivated sunflower. As you can see, this does not look at all like the big single headed cultivated sunflower. In order to assess how this organism’s genes will act in the cultivated sunflower, we must move them into a cultivar’s genome: a process some call “Pre-breeding”. This is accomplished with a series of controlled crosses between wild and the domesticated sunflowers. In sunflowers there are cultivars that do not produce pollen (you may know some from non-allergenic pollen free types in seed catalogues), so you can make crosses by rubbing pollen from H. exilis onto a male sterile domesticated line. The seed from this cross is called ‘F1′, its genome contains one set of H. exilis chromosomes (from its father) and one set of domesticated chromosomes (from its mother). Such a plant looks some what intermediate: it is branching, has flowers that are bigger than the flowers of H. exilis, and is intermediate in terms of size and structure (pictured below).

Some F1 hybrids are quite happy, suggestive of future usefulness. Others, let’s just say are not as happy. At this stage we cannot really tell how useful the wild genes will be or which genes are responsible for any of the exciting traits we see. This is because this plant’s genome contains one whole complement of wild genes. The wild genes need to be separated from each other. This is accomplished with backcrossing, in which the F1 plant is crossed to another domesticated line. The seed from this cross will contain 25% wild genome and 75% domesticated. Importantly, each seed will have a different 25% of the wild genome and should have a different phenotype. It is this generation, which will be grown up this summer, that will give us a better idea of what the different parts of the wild genome do.

A square (well, polygon) going from Toronto to Ottawa to Portland (Maine) to Philadelphia would just fit all of 2010s Sunflowers with a little room to spare for a few roads in between (assuming you could plant all of Lake Ontario). Something to think about if you are ever on a long road trip, like the 5 hour drive from Toronto to Ottawa. 

The Hiseq 2000, which can be upgraded to this machine, is already a data fire hose. This upgrade promises an option to turn data out even faster, 120GB in a day! Also longer reads (but at a lower density?) are going to be possible. Its quickly getting to the point (if its not already there) where library prep is going to be the limiting step for data generation, especially if one is dealing with non-standard libraries or with multiplexing.  From an analysis perspective this will mean new challenges and opportunities.

I found the narration very extreme, so be warned that 1) some things are not as bad as it make them seem and 2) although breeding is going to be absolutely crucial to feeding people its not a stand alone magic bullet.

The documentary makes it appear that collection trip only yielded a chick peas at a single site, whether or not thats the actual case it made me think about ownership issues surrounding germplasm. A small increase in yield of any major crop can quickly add up to millions of dollars of value. If it is the case that ultra valuable chick pea land races, collected at single village, will change chick pea production globally shouldn’t the village or farmers who grew and protected them for generations get something? What about wild relatives? If countries can make money from germplasm there would be incentive to protect and/or collect them. Leave a comment and let me know what you think!

You can order the DVD from the official site, or you maybe be able to rent it or get it at a library. Its also broken into parts on youtube.

*new to me

Now, to enter a screen command first press Ctrl+a now the next letter you type will do something with screen. Here are the ones I use:

c # Creates a new screen
n # Next screen
d # Detach
k # kill

So, to continue our example, you could do “Ctrl+a”, “c” to create a new screen, start R in it and “Ctrl+a”, “n” as many times as you want to toggle between R and top. Once you have your the computer hard at work you can do “Ctrl+a”, “d”. Now you are back to where you were before you started the screen.

# exit the computer you are ssh’d to
>exit
# close your terminal on your computer
>exit
# go home have dinner etc. etc… want to check you program?
# open a terminal (on any computer)
>ssh Greg@myIP
# Re attach, (if you don’t do the -r you will start another screen!)
>screen -r

There are your processes now just use the “Ctrl+a” commands. When you are all done you can kill your screens with “Ctrl+a”, “k” and “y”.

There are over 5000 accessions of Helianthus (Sunflowers) in the gene banks of the USDA. Using data available from GRIN, a simple perl script* and google earth we can look at the distribution of all the collections on the globe. You can toggle species on and off. Clicking an accession gives you more information. You can take a look for yourself just download this kml file* change the .txt to .kml and open it (should open with google earth).

*Wordpress security features are preventing me from uploading things with their proper extensions, I will work this out in the future.

• 38% of earths ice free land is used for farming (68% of which is for pasture).
• Major crop yields have increased 20% between 1985 and 2005, not the often cited 47%.
• Food production will need to double by 2050.
• 35% of our crops (by weight) globally go to animal feed.
• Global fertilizer use is up 500% in the last 50 years.
• 30-35% of global greenhouse gas emissions are from agriculture.

They nicely articulate the fact that agricultural improvement often comes at an environmental cost and that environmentalist strategies often ignore our species appetite. Given agriculture is such a big part of our environment, food production and environmental health are two faces of the same issue.

There is also an interesting section on yield gaps; locations where productivity does not reach theoretical yield potentials. Closing these gaps (or at least 95% of them) would result in a 58% increase in global yields. Its here that the authors call for the adoption of modern varieties as well as continued (genetic) crop improvement, improvement of orphan crops and protection of crop diversity. The remainder of the strategies include increasing water and fertilizer efficiency,  changing diets, reducing waste and stopping the expansion of agriculture. I would have very much liked to see (and think that this may have been within the scope of the data and analysis carried out here) the relative potential of each of these strategies.

Jonathan A. Foley et al., “Solutions for a cultivated planet,” Nature advance online publication (October 12, 2011), http://dx.doi.org/10.1038/nature10452.

*gold star if you can figure out where this was taken

Thousands of years ago in the eastern United States people started a process that continues to this day. Seeds from wild sunflowers, Helianthus annuus, were harvested for their oil and protein. This ritual of collection resulted in conscious and unconscious selection and sunflowers which were more useful to humans. Sunflowers have made some changes. Here you can see a wild flower head on top of a head of a maturing modern cultivar. The difference in head and seed size is drastic. Now sunflowers are an extremely important source of fat and calories in over 70 countries. Researchers and plant breeders continue to improve sunflowers, although now it is done in a very conscious manner.

via The Economist

Right now the horn of Africa is experiencing its worst drought in 60 years. Whether climate change or La Nina are responsible is not yet clear. The resulting food shortage is affecting millions. Staple foods have more than tripled in price. Thousands are fleeing. A massive influx of food aid is needed immediately.

Whether this crisis could have been avoided we will never know. Working towards food security for this planet’s inhabitants is one of the most complicated problems we are faced with as a society. It will require efforts from many disciplines. Better crop technologies will be paramount to this process. The science of improving our crop plants, as well as various satellite issues, will be the focus of this weblog.