Brainfood: Seed viability double, Forest reserves, Biodiversity value, Hunter-gatherers, Seed concentration, Past CC, Hot lablab, Mungbean adoption, Climate smart impacts, Tree threats, Chicken domestication, Top sorghum, Ancient wines, Plant extinctions

Extinct crop wild relatives

You may have seen coverage of a recent paper in Nature in which Kew researchers quantified the rate of plant extinction over the last 250 or so years. The headline number is about 3 species have been going extinct per year, which is about 500 times the background rate. But I know that what you really want to know is how many of these are crop wild relatives. Well, my friends at CIAT worked their database magic, and came up with the following list of extinct species which are classified by at least one source as a crop wild relative:

Diplotaxis siettiana
Franklinia alatamaha
Helianthus praetermissus
Hutchinsia tasmanica
Ilex gardneriana
Isatis arnoldiana
Lepidium drummondii
Lepidium obtusatum
Mangifera casturi
Musa fitzalanii
Piper collinum
Potentilla multijuga
Rorippa coloradensis
Solanum bauerianum
Solanum cajamarquense
Solanum ruvu
Syzygium balfourii
Syzygium microphyllum
Syzygium palghatense

Which means about 1 per decade or thereabouts. But that, clearly, is just a minimum.

Perhaps I’ll try to map where these plants were last seen.

The art of seed storage research

Dr Christina Walters, Supervisory Plant Physiologist at the National Laboratory for Genetic Resource Preservation (NLGRP), Fort Collins, Colorado, kindly agreed to share her reaction to the recent paper Seeds and the Art of Genome Maintenance. If you leave a question or comment here, I’ll make sure to pass it on, and I’m sure Christina will respond.

I thought I would take a few moments to interpret this paper in the context of what we in Fort Collins do for the National Plant Genetic System effort (at least in terms of orthodox seeds, as is the topic of the Waterworth et al. review). Many of you are collaborating with us on studies of seed germination or longevity, and it would be interesting to know work happening independent of Fort Collins and how you interpret this paper relative to your own work.

Frontiers caters to a general plant biology audience, and so the Waterworth et al. review might not emphasize the critical distinction between seed germination and longevity that is needed for seed bank practitioners. Germination reflects a transition from dry seed to hydrated seedling. This is what our seed analysts measure upon receipt of seeds and during seed storage. Longevity, on the other hand, is a time or a rate parameter; how long can a seed be stored and still maintain its ability to germinate? Crudely speaking, seed germination tells us if the accession is dead yet. But, the more useful information — for NLGRP and maybe for you — is when the accession will die so we can warn you that the accession needs to be regenerated soon. Like climate change, seed longevity is either a prediction or something that can be described after-the-fact. Curve-fitting routines that describe decay after it has occurred might contribute to making predictive models if we can understand how variables contribute to the shape. What we really need are models that reliably predict longevity or describe how much error we can expect beyond the limits of inference of the model. To that end, many of us are seeking to answer (1) why do preserved seeds lose viability? and (2) what causes the high variation in seed longevity among species, individuals and even tissues within seeds? Some focus these questions further into what lesion(s) lead to mortality and whether these are general or specific. Waterworth and colleagues are known for their research on oxidative damage to the genome and subsequent repair, and so we’d expect them to show a little bias about the primary role of DNA damage and repair in lost viability. However, these authors do not make any direct cause-effect conclusions that specifically link accumulated DNA damage and failure to germinate, nor do they attempt to relate longevity differences (a comparison of time or rate) to this metabolic function.

The paper importantly acknowledges that repair only occurs in hydrated cells — after imbibition. This counters a 10-15 year body of work that assumed repair occurs in dry (i.e., preserved) cytoplasm, which had implications beyond the seed longevity context. The acknowledgement points to the discreet metabolism of dry biological systems. Once again, we see that a basic criterion for ‘aliveness’ (i.e., the ability to repair damaged molecules) is not demonstrated in dried seeds, even though they are alive — making seeds a fascinating experimental system to study grey area of alive but not apparently living. The study of recovery and repair after preservation is important to future work on embryo rescue, recalcitrant-seed “therapies” as well as improved viability assessments.

To accomplish NLGRP mission, we focus our work on the speed of damaging reactions within preserved cytoplasm, which is a bit removed from the Waterworth et al. review. We feel that understanding the speed at which damage accumulates can lead us to (a) better storage methods that limit damage (hence reduced need for metabolic repair) and (b) better models to predict when damage accumulates beyond repair (which we presume is a cause of mortality). We might find our work intersecting with Waterworth’s in terms of the contribution of DNA damage to cell mortality. One of the hardest aspects of our research is the inability to correlate damage or repair with mortality and viability. That is because we are studying change before seeds die (we call it the asymptomatic period of seed ageing) and we are studying it in a system that doesn’t show typical signs of life until you wet it up (I like to call it discreet discrete).

Ricing to the challenge of climate change

There’s a nice feature on the BBC on preparing rice cultivation for climate change. I’ve taken the liberty of dissecting out the bit about the IRRI genebank and the breeding work of Haiyan Xiong. Mainly because I found all the scrolling so annoying.

Farmers in China are acutely aware of the impact of water shortages. Population growth, increasing urbanisation and industrial water use are all making water shortages more common in China, says Haiyan Xiong, a postdoctoral researcher in plant sciences at the University of Cambridge. Water distribution is geographically uneven, with limited rainfall in northern China and seasonal droughts in southern China.

Much of China’s variable water supply is going to a single crop: rice. About 4,000 litres of water are needed to produce just one kilogram of rice, according to Xiong. Other estimates vary between about 2,500 and 5,000 litres. In China, irrigation for the crop accounts for about 70% of the total agricultural water use.

One response to this problem has been to look for types of rice that use less water. To this end, thousands of rice varieties are being preserved at the world’s largest rice gene bank, in the Philippines. These include enhanced varieties such as ‘scuba rice’, which can withstand flooding, and the drought-tolerant Sahod Ulan varieties being used by some Filipino farmers.

Xiong and her colleagues hope to combine genome editing with traditional breeding methods to create new drought-resistant varieties. But this is a challenge. “Due to the complexity of the genetic mechanism…not much progress has been made in improving rice drought resistance in China,” she says. “Very few genes can be used in actual production to improve the rice drought resistance.”

Yet the team have identified a single gene in upland rice, known as OsLG3, that’s linked to the length of rice grains as well as drought tolerance. Upland regions, which are dry and hilly, are a much harder environment to grow rice in than lowland paddy fields, and upland rice is usually of lower quality. So introducing the upland drought-tolerance gene into the more widely cultivated lowland rice could allow for the best of both worlds.

Another new type of rice bred for challenging conditions is known as Green Super Rice.

Chinese soil, especially in coastal provinces, naturally contains high amounts of salt, which can become even more concentrated in areas with low rainfall and high evaporation. When there’s too much salt in the soil, plants experience something known as osmotic stress. A large amount of water exits the plant’s cells, causing them to shrink suddenly. The process limits plant growth and productivity.

As with Xiong’s drought-tolerant upland-lowland rice, researchers have found genetic traits in rice varieties that can help Green Super Rice withstand high salt levels and osmotic stress. This often involves backcross breeding, in which genes associated with a desirable trait are bred into a second variety by hybridisation. So far, Green Super Rice appears to produce a high yield in addition to having a high salt tolerance. The hope is that this could open up coastal or other high-salt areas to rice growing.