Can you imagine how much easier it would be to get funding if you too worked on panda biology?

Nature just released a pre-publication copy of a paper detailing the sequencing of the panda genome. The genome was sequenced and assembled using entirely 2nd generation sequencing technologies (specifically the Illumina sequencer) which produced reads that averaged only 53 basepairs long.*

The panda they chose was a three year old female, and they got such resolution (the average individual base pair was sequenced 73 times!) they were even able to identify individual changes in sequence between her two copies of each chromosome.** From this they were able to estimate a difference in the DNA sequence (called a SNP***) occur once every 740 bases which is almost twice the rate of humans.

Having so much genetic diversity is surprising in a species as endangered as Giant Pandas with only 2500-3000 remaining in the wild, with a few hundred more in captive breeding programs like the one where the panda whose genome was sequenced is kept.

Imagine from a friend who spent a summer in China working on panda genetics a couple of years ago

Much of the comparative analysis of the panda genome used the dog genome for comparison as dogs are currently the best sequenced carnivora**** species (last I heard, the cat genome was only 2x coverage). By including data from the human and mouse genomes, the authors were able to conclude that mutations accumulated more slowly in the genome of giant pandas than in any of the other three lineages (human, mouse, and dog), which just makes the high level of diversity within pandas even more interesting.

That wraps up my initial thoughts on the panda genome. Here are a couple of links for further reading:

• The Nature paper itself.
• AFP article on the publication of the genome
• If you’re interested, here’s the site where you can download the panda genome itself. Edit: The site appears to be down, I imagine they’re getting hammered with traffic today.
• And of course, we couldn’t have a post on giant pandas without at least one panda youtube video (only 20 seconds long)

In closing, consider that the pandas don’t seem very motivated to survive as a species considering all the work we humans (specifically the Chinese government) are putting into trying to keep them around (quote from the AFP article linked above):

The animals’ notoriously low libidos have frustrated efforts to boost their numbers. Breeders have resorted to tactics such as showing them “panda porn” videos of other pandas mating, and putting males through “sexercises” aimed at training up their pelvic and leg muscles for the rigours of copulation.

*For perspective, the epic novel War and Peace contains approximately 5 million letters in its english translation. Assembling the Panda genome is the equivalent of piecing together a novel 500 times as long using random fragments of text such as:

nglish ambassador’s? Today is Wednesday. I must put

adron of varicolored horsemen. Two of them rode side

I am impressed.

**Normally to avoid issues created by the fact most organisms contain to equivalent but slightly different copies of each chromosome, the first draft of an organism is created using an inbred line, where both copies of each chromosome are essentially identical after many generations of selfing, or mating siblings. I know this was the case with the mouse genome, as well as many of the currently sequenced plant genomes (arabidopsis, rice, sorghum, maize, brachy). I’m not sure how the issue was dealt with in the human genome, since creating a highly inbred human for sequencing would be both unethical and impractical (human generation times are so long it’d take as much as a century to create someone appropriately inbred).

***SNP stands for single nucleotide polymorphism.

If my DNA reads:

ATGCACGTGTAG

and at the same position yours reads:

ATGCATGTGTAG

A single nucleotide has changed between us. That site is a SNP. For humans differences like that will occur, on average, once in every 1500 base pairs.

****Carnivora doesn’t mean all carnivores (although that is where the name comes from) but is, rather, an group of related species, many of them carnivores, including cats, dogs, weasels, bears, raccoons, and even seals and walruses.

From the article:

China produces 31 percent of the world’s rice and 20 percent of its corn, U.S. Department of Agriculture data show. …[China] uses 7 percent of the world’s arable land to feed a quarter of its population.

China has only 7% of the world’s farmland yet feeds more than 1.3 billion people (and still growing). No wonder they’re investing so heavily in crop/plant science.

Another one I recently read (if it was you, sorry for not attributing it properly, the comparison just stuck in my head) was that India and Argentina are about the same size (India is about a quarter bigger) yet India must feed 30 times as many people!*

*Of course this isn’t quite a fair comparison since Argentina exports so much food to Western Europe, since those countries can afford to buy food abroad instead of focusing on increasing local production, and China and India must

China is also in a unique position when it comes to commercializing any form of genetically engineered rice, as the world’s largest producer of rice, but only a small next exporter*** China stands to benefit from any improvements to rice, and is largely immune to pressure from food importing countries such as the members of the European Union. China has also invested (and continues to invest) billions of dollars in developing their own, publicly-funded, domestic crop research and breeding which has kept their per acre crop yields trending upwards, and now means they’re prepared to make the leap to genetically engineered food crops (they’ve had bt cotton for some time) with home-grown technology, killing any narrative about this being western tech foisted off on the developing world.

Whatever bad things you can say about the current government in China (and there definitely are bad things to say), it’s at least clear they’re pulling out all the stops to make sure their people stay fed, but today and in decades to come. Clearly it’s in their own self interest to do so.

When the people are hungry, governments have a way of falling often with bad consequences to those formerly in power (see: The French Revolution). Plenty of societies throughout history have seen problems on the scale of those China will face (feeding a population of 1.3 billion that continues to grow) coming have closed their eyes rather than do everything they can do develop solutions before it was too late.

We’ll have to wait and see if this story is confirmed before much more can be said.

*Even if the routers story pans out, and that’s not assured in a story based solely on anonymous sources, the bt rice is still a couple of years away from large scale planting.

**Since this strain was developed by the government, which I assume isn’t developing genetically engineer traits for a profit, the cost of farmers of buying the new seeds may be quite low. China is also one of the countries that is already producing and using a hybrid rice seed and as a result China farmers are already using purchased seeds.

***China’s rice exports are expected to keep shrinking as demand for rice grows along with the growth of their population.

Anyway, two new developments seem to have prompted this article. First, Monsanto and Syngenta have been sending signs that they’re both interested in restarting their programs to develop new wheat traits using genetic engineering. Views about among wheat farmers have begun to shift, partly as they see the acreage devoted to wheat shrinking as more and more land is converted to corn production, but also because of the second development.

Wheat growers in the US, Canada, and Australia have banded together to push for a simultaneous adoption of future genetically engineered wheat traits. That’s significant, because those three countries are some of the biggest wheat exporting nations in the world.* US farmers were worried that if genetically engineered wheat was introduced in America, rich wheat importing countries (basically Japan and the EU) would stop buying US wheat and wheat prices would fall in the US. But if more countries switch at the same time, it’s less likely any of them will get cut off.

It’s the same logic as a union. If a big company decides to fire me without cause, there isn’t much I can do about it, there are plenty of other people they can hire to replace me (or pay a little more to many of their current employees to work overtime and cover my job). But they can’t replace all their employees at once, so a union has more bargaining power than individual employees. Wheat farmers in Australia, Canada, and the United States are banding together to increase their freedom to adopt new technologies with less fear of retaliation from countries that are less food self-sufficient. Although I’ll admit it does violate the violate the cliche about the customer always being right. But then again we already knew it wasn’t.

h/t to Amy for pointing out the great article in Nature Biotechnology, and Mr_Subjunctive to the final link.

*India and China are actually the two biggest producers of wheat, but their production is consumed domestically, which means that #1 they’ve got even more interest in increasing yield since for them its a question of feeding their people, not making more or less money on the world market #2 they don’t have to worry about they acceptance of their crops in other countries. The article I linked to above suggests China is much closer to the commercial production of a range of genetically engineered traits in wheat than anything in the research pipelines of western biotech companies, which after all are only just restarting after turned completely off for years.