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agriculture Feeding the world Fun With Numbers Life in Academia

The Growth of Plant Science Research In China (2009-2021)

The world changes fast. Once we form perceptions about the way the world is or works, we tend to be a bit too slow to update those perceptions in response to new data.

Last week I posted some analysis of where the scientists who publish in the most selective plant science journals work and live. The short version for those who don’t want to re-read that post:

40% of the papers published in The Plant Cell had a corresponding author based in China, 28% from the European Union plus the United Kingdom, 16% from the United States and 16% from the rest of the world (Japan and Korea are particularly well represented in this last category).

I also said that I was really surprised when I actually read through a year’s worth of issues and counted up the numbers. I would have guessed closer to one quarter of the papers came from scientists in the United States and another quarter from China. There are lots of potential reasons to explain why my gut was wrong, but a big one is that just in the length of my scientific career things have changed a lot and my perception is struggling to catch up with the current facts on the ground.

Tracking the changes in authorship of papers at The Plant Cell between 2009 and 2021. Data was only collected from odd numbered years and only from papers listed under the “Research Article” category.

I started graduate school in the fall of 2008. My first full year as a “professional” plant scientist* was 2009. At that time 7% of papers in The Plant Cell were published by authors working in China, 28% by authors working in the USA, 37% by authors working in the EU and 28% by authors working in the rest of the world. In the 12 years since that, China’s share grew to 40%, almost a 6x increase.

So what happened in that 12 year time frame? I don’t have good insight into Chinese policy and funding decisions. But at various points I’ve run into people who have told me that in China, human health research and agricultural research are treated as roughly equal priorities. And China invests a lot in funding plant science, including plenty of dedicated funding for institutes and professors. In the United States plant science is a very small slice of the research our country funds**, and much more of the funding we do have goes out as part of 3-5 year grants for specific projects. Here’s a great visualization of US federal government R&D spending from back when I was a grad student.

Anyway, I’m not sure what the key takeaways are here. I guess 1) It is possible for a country to take big steps forward in scientific discovery and innovation but only if we’re willing to pay for it 2) If you happen to live in the USA, like me, your subconscious may still be assuming that we play a much bigger role in the global plant science research community than we actually do.

The world changes. It is easy to fall behind.

*I was getting paid a bit more than $2,000/month to do plant science. It felt very adult at the time.

**Two big sources of funding for plant science when I started graduate school were the Arabidopsis 2010 project and the Plant Genome Research Program, both run through US National Science Foundation. As you might guess from the name, the Arabidopsis 2010 project ended a decade ago. Plant Genome Research is still around. However, it used to receive dedicated line item funding from congress to conduct research into agriculturally and economically relevant crop plants and the program is now funded at the discretion of the director of NSF.

Categories
agriculture Dryland Genetics Feeding the world

Proso millet interview with 1010 KSIR Farm Radio

If you want to become more self conscious about your own vocal fillers, sentence fragments and the general nonsense that comes out of your mouth, ask a really good transcriptionist to write out an interview you did.

Click “Read More” to view the full transcript
Categories
Dryland Genetics Feeding the world Plant breeding

It turns out genetics (and plant breeding) actually work

So I did a thing. For those who don’t want to click the link, it describes the results farmers are seeing in their first year of growing two new varieties of proso millet developed by a company called Dryland Genetics. Many farmers are getting 20% more grain from the same land as they did with the varieties they grew in the past. Since proso millet is grown in close to half a million acres in the USA (two hundred thousand hectares or three million mu (亩) for those of you reading internationally), that means these new varieties have the potential to produce a lot more calories from the same land, using the same water and the same nitrogen.

I helped found Dryland Genetics in 2014. At the beginning that meant reading a lot. Then writing a business plan. Then pitching that business plan. Winning over investors. Wrangling logistics. Hiring a full time breeder. Crunching numbers and datasets. Losing sleep over logistics and seed processing and cleaning and inspections and sales. More recently hiring more people who take over the job of wrangling and lose sleep over logistics and seed processing and cleaning and inspections and sales.

Categories
Genetics genomics Genotyping Plant breeding

Resequencing the sorghum association panel

A really nice thing about many crop plants is that through natural self pollination it is possible to create true breeding inbred lines. Inbred lines plants that are homozygous across all or nearly all of their genomes. If the same inbred plant is the used as the mother and father to produce new seeds, all those seeds will be genetically identical to the parent plant. Just like identical twins. And like identical twins, inbred lines make it possible to understand a LOT more about the interplay of genetics and environment since we have a chance to see how different or similar the characteristics of genetically identical individuals turn out to be.

Categories
agriculture biofortified Genetics Plants

Where the superpowers of superweeds come from

Superman had the yellow sun of earth, spiderman had a radioactive spider-bite, but what about superweeds, where does their super power (surviving application of Round-up/glyphosate) come from?

To understand how superweeds survive, we first have to understand why normal weeds (the Jimmy Olsens and Lois Lanes of the plant world) die. <– last superhero reference of this post I promise.

Categories
agriculture Genetics Plants

Don’t judge the genetic diversity of a species by its cover

Photo: ekpatterson, flickr (click photo to see in original context)

There are more differences in the genomes of two unrelated corn plants than between the genomes of a human and a chimpanzee (two species separated by 3.5 million years of evolution).

On the other hand, two unrelated human beings, members of the same species, have more than four times as many genetic differences as two unrelated heirloom tomatoes.

Genetic Diversity:

Corn vs. Corn > Human vs. Chimpanzee >> Human vs. Human >> Heirloom Tomato vs. Heirloom Tomato

Now the fact that any two human beings are more closely related to each other than either is to a chimpanzee should be obvious to anyone who gives it a moments thought.

I plan to poll my sections tomorrow to see how many of them would put corn and heirloom tomatoes in the opposite positions, but many have figured out my feelings about corn, so they’ll probably guess it’s a trap.

Categories
agriculture Feeding the world Link Posts

BBC on drought tolerant maize/corn

There’s a new episode of BBC’s Discovery: Feeling the World out this morning. It’s only 26 minutes long, and the full piece is definitely worth a listen, but if you don’t have 26 minutes, the meat of the post can be summarized in 8 minutes:

3:20-7:54: Introducing the subject, developing drought tolerant varieties of maize in Africa, and the fact that the researchers working on it as using conventional breeding, marker assisted breeding and a genetically engineered trait Monsanto. When battling starvation, you use any tool that comes to hand.

18:40-21:20: This part is almost hard to listen to. You can hear the raw emotion in the researcher’s voice as the reporter keeps trying to make genetic engineering sound, at best, like a last resort. Couldn’t they just try irrigating more crop land she suggests?

25:10-end. Conclusion. I also thought this part was very powerful.

A few complaints:

Categories
Genetics Plant breeding Plants

The Most Studied Genes of Maize (and why we love kernel phenotypes)

Unique citations determined from papered linked to from MaizeGDB gene locus pages. Images of c1 and y1 segregating years by Gerald Neuffer and made available through MaizeGDB.

* = tied for number of citations

** = some mutant alleles have kernel phenotypes.

If you want to become one of the famous mutant corn genes, it helps if you have an effect that is visible in corn kernels instead of only from fully grown plants.

And here is why:

  • A geneticist could determine that the version of c1 that creates yellow kernels is recessive to the version that creates purple kernels just from looking at the ear of corn on left.
  • Furthermore, they could tell you that both the male parent (the plant that provided the pollen) and the female parent (the plant on which the ear of corn grew) were both heteryzygous for the c1 genes (they each had one dominant version of the genes and one recessive version), and therefore the corn kernels the parent plants were grown from were both purple.
  • They would know with certainty that all of the yellow kernels contain two recessive versions of the c1 gene.
  • While they couldn’t predict with absolute certainty whether a specific purple corn kernel on that ear carried two dominant versions of the c1 gene or one dominant and one recessive version, they would know there was a 1/3 chance that kernel has two dominant copies, and a 2/3 chance it had one dominant and one recessive copy.
  • That geneticist could make all sorts of predictions about what ears would look like in future generations depending on what colors of corn kernels were planted and which plants were mated with each other.

All this from a single picture of an ear of corn. For a phenotype seen in corn plants but not in kernels (like Knotted1), a geneticist would have to plant a row or more of corn seeds from an ear and examine the growing plants to get the same quantity of information.

And that is why mutations with kernel phenotypes have been so popular over a century of maize genetics research.

Categories
Feeding the world food Plant breeding

The Color of Corn and Cultural Values

MAT_kinase has sparked an interesting discussion about the associations people have with corn of different colors. I’d previously heard that yellow corn (where pre-vitamin A carotenoids are produced in the kernels) isn’t popular in Africa, with the reason usually being given as its association with American food aid.* If yellow corn comes predominantely from food aid, it eventually becomes associated with being poor and/or starving, so that when people have a choice they eat other varieties of corn. I can’t find where I read it, but I vividly remember reading an interview with a woman who talked about the shame of eating yellow food-aid corn, knowing that it had originally been intended to feed livestock in the US, not people.

MAT points out another more pragmatic reason yellow corn may not be favored in Africa that I hadn’t heard of before. Apparently the extra carotenoids make yellow corn more susceptiable to spoilage than white corn varieties, a very pertenent issue in areas without access to the kinds of storage facilities we take for granted in American agriculture.

Jeremy at the Agricultural Biodiversity Weblog picked up the torch, highlighting a number of their own previous posts relevant to the discussion, including one by fellow blogger Luigi that relates the reaction of his own wife, originally from Kenya, on ordering polenta** at a restuarant and receiving a yellow dish.

Fortunately breeds of corn that contain even more beta carotene (the carotenoid most easily converted into vitamin A by our bodies) aren’t even yellow all the time. Although I wasn’t able to find a freely available picture, sometimes they’re ORANGE.*** While it turns out the correlation between color and beta carotene content isn’t perfect****, there’s still reason to hope varieties bred for the highest pre-vitamin A content will end up a striking orange color. For a visual examples of how orange corn can get, check out check out Dr. Rocheford’s lab website.

Will the distinction between orange and yellow***** be enough to get over the Africa’s lack of enthusiasm for yellow corn? Will the benefits of a diet with more vitamin A be enough to outweight the issues with yellow corn going “off” if stored improperly? I certainly hope the answers to both these questions are yes, but we won’t know for sure until we try. And there are some hopeful signs. For example this segment in a story from NPR:

Categories
agriculture Feeding the world Politics

India and Bt Brinjal/Eggplant

India has delayed the introduction of their insect resistant eggplants.

Read about it in: