Friday, January 29, 2021

Field Wars: Revenge of the Rogue Rice

from Wikipedia

Humanity's rise as an intelligent species, and one that today dominates the world, would not have been possible without the grasses. Not only did our species develop in the savannahs those traits that mark us as Homo sapiens during the time when grasslands spread throughout the world, but our very civilization would not be possible without the domestication of various grass species, including wheat, maize (corn), and rice.

The latter of this Big Three directly feeds more than half the people on earth, and was thought to have been domesticated twice, once as Oryza sativa in the Yangtze Valley of China more than 9000 years ago (Molina et al, 2011), and another time  in Africa in the inland delta of the Upper Niger River as Oryza glaberrima between 2000-3000 years ago (Linares, 2002). Amazingly, there is now recent evidence that rice (as a wild Oryza sp) was domesticated in a THIRD continent about 4000 years ago, this time by the mid-Holocene residents of the Monte Castelo shell mound in the Amazon regions in South America (Hilbert et al, 2017)!

Such a tight relationship between humanity and this grass genus would surely mean both benefit greatly from the association, and in fact its mutualistic relationship with people has made rice one of the most common plants in the world. But you would be mistaken to think that all rice has become soft and meek and domesticated.

There are rebels in the midst of the rice paddies, and their effect on the productivity of the Empire of Man is surprisingly substantial. Some estimates put crop losses due to this rebellion at more than 90% in some fields, and in the USA up to 30% of rice fields can be compromised, leading to more than $50 million in annual losses.

These weedy rice have characteristics that differentiate them from their still-domesticated brethren. For example, domesticated rice has non-shattering seedheads, which simply means that the grains do not have a tendency to break off from the plant and scatter. This makes it easier to harvest and prevent significant losses of the crop. In the case of the weedy rice, easy shattering of the seedheads means the rice gets to disperse its seeds, which is obviously the usual goal of any species. 

Another example of a trait that these rebellious rice have gotten is seed dormancy, which allows them to stay dormant in the soil until conditions are optimal for seedling growth. Such a trait has been taken out of their more domesticated compatriots because farmers tend to collect the seeds of plants that don't have dormancy.

Lin-Feng et al, 2017

One interesting thing about these rebellious rice is that not only were they derived from different varieties of rice, but that they arose during different periods of the domestication and improvement history of rice. The way researchers discovered when each weedy rice broke off from being domesticated was by looking at what types of genes they have in common with the domesticated type (Lin-Feng et al, 2017).

How does that work?

Well, remember that as rice developed over the centuries and millennia, it acquired various domestication genes (e.g. genes for non-shattering seedheads), followed by various improvement genes (e.g. popcorn taste, nice aroma, etc). So for example, if rebel rice #1 has the genes for domestication, but not the improvement genes, whereas rebel #2 has both genes for domestication and some improvement genes, then the researchers can deduce that rebel #1 broke off earlier than rebel #2 during the history of rice. In the image above, the BHA (black hull awned) weedy rice diverged earlier in the process than the SH (straw hull) weed.

"But wait!" You might ask. "If they still have the domestication and improvement genes, then how were they able to get all those weedy traits?"

It turns out that these weeds modified other genes to re-acquire the weedy traits  (such as re-enabling shattering of seedheads), and these genes are not scattered throughout the genome but tend to cluster into genomic islands. These genomic islands that re-create similar weedy characteristic are completely different for each weed type, which means that each rice weed evolved the weedy traits independently using different methods.

Amazingly, it seems rice has a tendency to rebel against domestication, and it repeatedly evolves gene islands that allow it to break from its "chains of slavery"! 

How totally ungrateful! *smh*

Literature Cited

Hilbert, L., Neves, E.G., Pugliese, F. et al. Evidence for mid-Holocene rice domestication in the Americas. Nat Ecol Evol 1, 1693–1698 (2017).

Lin-Feng Li, Ya-Ling Li, Yulin Jia, Ana L Caicedo, Kenneth M Olsen. Signatures of adaptation in the weedy rice genome. Nature Genetics, 2017; DOI: 10.1038/ng.3825

Linares, Olga F. (2002-12-10). "African rice (Oryza glaberrima): History and future potential". Proceedings of the National Academy of Sciences. 99 (25): 16360–16365. 

Molina, J., Sikora, M., Garud, N., Flowers, J. M., Rubinstein, S., Reynolds, A., Huang, P., Jackson, S., Schaal, B. A., Bustamante, C. D., Boyko, A. R., & Purugganan, M. D. (2011). Molecular evidence for a single evolutionary origin of domesticated rice. Proceedings of the National Academy of Sciences of the United States of America, 108(20), 8351–8356.

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