Domestication of African rice

by Jeremy on March 28, 2011 · 0 comments

Is this thing still on? Excellent. A big meeting is scheduled for next week in St Petersburg, Russia, to consider new discoveries about some of the holdings at the Pavlovsk Experiment Station and, perhaps, the station’s future, so it seemed like a good idea to make sure that this site was up and running and ready to broadcast whatever intelligence it might receive. As ever, it’s easy to make contact. Rather than just clearing my throat, though, here’s some substance.

African rice, Oryza glaberrima, differs in many respects from Asian rice, O. sativa. Yields are lower, partly because the seeds shatter more easily from the plant, although African rice is better able to withstand stress. The grains are often coloured red rather than white. And it may well be more nutritious, partly because it is harder to polish than Asian rice, and polishing removes essential micronutrients. Certainly average protein levels are higher. [1] And Africans say it fills them up properly, which might indicate a lower glycemic index (not that the official glycemic index contains anything as useful as either O. glaberrima or African Rice among its entries).

African rice has of course been crossed with Asian rice to create the wildly successful NERICA (NEw RICe for Africa) varieties, and some might think that it’s game over for pure African rice, but there’s still a lot to be learned.

The history of its domestication has been confused. [2] Jack Harlan originally suggested that it was domesticated by selection from O. barthii, the wild ancestor, at many places across its wide range. Archaeological evidence suggested a more circumscribed area, around the Middle Niger delta in what is now Mali, although given the relatively late date of the remains found there — around 500 years BCE — the possibility remains that it had been introduced from elsewhere.

ResearchBlogging.org A new DNA study by Chinese scientists confirms that African rice was domesticated in the Middle Niger delta and that the original selection may have taken place just once. [3] The scientists sequenced DNA from 20 samples of O. glaberrima and 20 samples of O. barthii, looking at the detailed sequence of 14 unlinked genes. While there was some variation in the diversity of the individual genes, overall the wild relative samples were about four times more diverse than the cultivated samples. That said, the actual diversity of both species is very low indeed, lower than all previously sampled crops and their wild relatives.

An obvious explanation for the low genetic diversity of O. glaberrima would be a genetic bottleneck during its domestication from a small initial population of O. barthii. … [T]he extremely low nucleotide diversity in African rice can be explained by severe bottleneck during domestication, with high value of the bottleneck intensity … which is consistent with its single origin in west Africa.

O. barthii and O. glaberrima are both largely self-pollinating, which would also account for the low genetic diversity. As for the place of domestication, there were 7 O. barthii samples that were clustered closely with all the O. glaberrima samples. All 7 were from previously postulated centres of domestication, three from the Middle Niger delta and two each from brackish mangrove areas of Guinea and the upland areas between Sierra Leone and Ivory Coast. There was no evidence for the kind of multiple domestication proposed by Harlan. More extensive sampling, the authors say, might reveal the precise place where O. glaberrima originated.

Quite apart from the satisfaction of knowing a little more about the origin and domestication of an important crop, this research is also important because in revealing the lack of genetic diversity within African rice and its wild progenitor, it provides insights into how best to conserve the diversity of both species and also suggests that the wild relative might still be able to donate important characteristics to African rice and, perhaps, to NERICA varieties too.

Notes:
  1. Kennedy, G., & Burlingame, B. (2003). Analysis of food composition data on rice from a plant genetic resources perspective Food Chemistry, 80 (4), 589-596 DOI: 10.1016/S0308-8146(02)00507-1 [↩]
  2. Linares OF (2002). African rice (Oryza glaberrima): history and future potential. Proceedings of the National Academy of Sciences of the United States of America, 99 (25), 16360-5 PMID: 12461173 [↩]
  3. Li ZM, Zheng XM, & Ge S (2011). Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik PMID: 21400109 [↩]

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arte TV reports on pavlovsk

by Jeremy on January 4, 2011 · 1 comment

Perhaps because they didn’t see fit to name the Pavlovsk Experiment Station, I missed this very thorough and moving report from arte TV. My French isn’t what it ought to be, so I would welcome your views. It is also available in German, I believe. Thanks to the Global Crop Diversity Trust for sharing.

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Yuri Vavilov remembers his father

by Jeremy on December 3, 2010 · 0 comments

The BBC World Service’s Outlook programme yesterday broadcast an interview with Yuri Nikolaievich Vavilov. He spoke movingly about his father’s globetrotting ways, the importance of education, and of how he slowly came to to know the truth about his father’s fate. I’m not sure how long the programme remains available at the BBC website, but here’s a little snippet, in which presenter Lucy Ash first asks Yuri why the collections established by his father were so important, and then what he thinks will happen to the collection at Pavlovsk Experiment Station.

Listen to an extract from Outlook’s interview with Yuri Vavilov.

Photo from Gary Nabhan.

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Anarchists at the gate

by admin on November 25, 2010 · 0 comments

Thank heavens for human beings. How else would we have known that Google’s “Biofond importantly profit!” is better translated as “where money rules – nature perishes?” Thanks to Hannes Dempewolf and his friend Lisa Strecker, who responded to a request for a better version of this article: Пикет в защиту Вавиловской коллекции. And apologies for apparently ignoring their help; it got caught up in a change of spam filters at work.

Picket in support of Vavilov collection

31 August 2010
Today a Commission from the Accounts Chamber came to the Pavlovsk Experiment Station in order to decide in a “closed procedural hearing” if the unique plant collection of Vavilov will be preserved or if the land occupied by the collection will be sold for high-end homes. As a reaction to this, anarchists organized an unauthorized protest.

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The activists stood up in front of the station’s entrance and held banners and posters like: “There, where money rules – nature perishes?”, or “Let’s save the Vavilov collection”. Although there were members of the police in plainclothes present, who tried to calm the protesters, no one was arrested.

With the explanation, that this area is not used for its intended purpose, this piece of land with all its unique plants has already formally been taken away from the scientists. Moreover, the composition of the commission that judged the “inappropriate use” verdict was inappropriate: none of the members was a specialist with expertise in agriculture. This is a testament to the lack of an adequate analysis of the collection’s value. We argue that these decisions are wrong and that they should be annulled, and the territory together with the plant collection should be preserved as a scientific research centre.

Let us remind ourselves, the Vavilov collection is the biggest field genebank of fruit, fodder and berry crops in Europe. The famous collection was founded more than 80 years ago. Hundreds of scientists carried out thousands of expeditions in order to gather sample plants from all corners of the world and brought them back to the experimental station. Some species do not exist in nature anymore, they are only preserved here, in this suburb of Saint Petersburg. Today, scientists from all over the world (of the Pavlov type) are trying to recover lost plant diversity.

Other submissions would be most welcome, as we wait for more news.

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Pavlovsk’s cherries

by Jeremy on November 17, 2010 · 1 comment

The parties arguing about the future of Pavlovsk Experiment Station have disagreed over the state of the collection. Inspections claimed that parts of the collection were neglected and in disarray. The researchers at Pavlovsk are now beginning to respond with their own view of the collections in their care. First [1] to report are Dr A. A. Yushev, Curator of the sour cherry, sweet cherry, bird cherry and nut crops collections, with Dr S. Yu. Orlova, a senior researcher in the Department of Fruit Crops.

They say that cherries have been collected and studied at Pavlovsk since its founding in 1926, and that because sour cherries produce for only about 15 years in the conditions of Pavlovsk, the collection has been replanted several times. The most recent replanting took place from 2004 to 2010, to replace trees that were themselves planted in 1989-91. Crucially, Yushev and Orlova say that the expert group based its conclusion of neglect on seeing the old, 1989-91 trees only, and without the advice or assistance of any members of staff.

The old trees are being kept only to verify the identity of the new young plantings, the researchers say, which is good practice.

The collection has also almost doubled in size in recent years, as the breeders have brought in new cultivars bred recently in Russia and some East Asian wild relatives that are potential sources of resistance to Coccomyces fungal diseases. [2] On current reckoning, the collection includes 187 accessions of sour cherry and steppe cherry, 52 of sweet cherry, 14 varieties of Microcerasus and 49 of bird cherry, 302 in total. Then there are 140 seedlings of Microcerasus tomentosa seedlings, and some of the accessions are being brought into tissue culture. “The total plants at the new replanted site is 852,” Yuchev and Orlova write, which must mean that there are some duplicates. They add that “accessions at the site are in good condition” and include 18 sour and sweet cherry cultivars that are of historic interest because they formed the basis of the collection before 1939.

Maintaining collections of genetic resources in good condition is hard, time-consuming and often both thankless and neglected. It must be tempting, under those circumstances, to let documentation slide. Documentation, however, is really the life-blood of any collection, for unless people know what is there, how can they possibly give it any value?

Notes:
  1. At least, I hope that there will be more reports. [↩]
  2. VIR lists these all as Cerasus species: C. kurilensis, C. maximowiczii, C. sachalinnensis (sic) and C. maackii. USDA GRIN prefers Prunus maximowiczii and P. sargentii for 2 and 3, and does not have entires for 1 and 4. Wikipedia does list P. maackii, but not P. kurilensis. Ah, taxonomy. [↩]

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Pavlovsk awaits change of law

by admin on November 15, 2010 · 1 comment

There has been very little information recently about the fate of the Pavlovsk Experiment Station. The Vavilov Research Institute (VIR) reported that on 26 October Igor Igoshin, a deputy head of the parliament’s Committee on Science and Scientific Technologies, introduced a draft law that treats the status of genetic resources collections. The draft modifies a section of the Land Code of Russia, which refers to valuable land that belongs to the State.

According to VIR, article 100, paragraph 4, item 1 of the Code reads, in part.

“…the most valuable lands are lands within which there are natural sites as well as cultural heritage sites of special scientific, historical and cultural value (typical or rare landscapes, cultural landscapes, communities of plant and animal organisms, rare geological formations, lands to be used for activities of research organizations”

A change in wording to ensure that field genebanks are also covered may help to resolve the disputes over the ownership and future of the land. The collection may also gain the status of National Heritage, which could in theory help to protect it.

Not much to go on …

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A glimmer of hope?

by admin on October 27, 2010 · 0 comments

Hard to know what to make of this story from RIA Novosti, reprinted below in its entirety.

The Russian Pubic Chamber believes the unique collection of fruits and berries at the Pavlovsk Experimental Station near St. Petersburg are a national heritage, a member said on Tuesday.

The Vavilov Institute of Plant Industry and its Pavlovsk station are trying to retain two plots of land of 71 and 19 hectares. The land has been sold to a private developer who plans to build private homes on the site.

Pavlovsk contains a collection of rare specimens of fruit and berries that cannot be seen in the wild. More than 90% only exist at Pavlovsk.

“The most important thing we need to do is ensure control over this collection,” Nadezhda Shkolkina said.

A second set of responses from the VIR to the Expert Commission has been published, further question how the experts arrived at their various recommendations. We reported Part 1 here.

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Banana domestication revisited

by admin on October 19, 2010 · 1 comment

Edible bananas have very few seeds. Wild bananas are packed with seeds; there’s almost nothing there to eat. So how did edible bananas come to be cultivated? The standard story is that some smart proto-farmer saw a spontaneous mutation and then propagated it vegetatively. Once the plant was growing, additional mutants would also be seen and conserved. In fact this “single-step domestication” is considered the standard story for many vegetatively-propagated plants, such as potato, cassava, sweet potato, taro and yam. And while it may be true for those other crops, evidence is accumulating that it may not be the whole story for bananas.

ResearchBlogging.org Edmond de Langhe and his colleagues pose a question: Did backcrossing contribute to the origin of hybrid edible bananas? And their answer is, “yes, we’re pretty sure it did”. [1] Truth be told you could probably count the number of people who are really interested in (and able to fully understand) the details of how they got there on one hand. For the rest of us, here’s my take on it.

The hybrid bananas they refer to, our edible bananas, are almost all the results of a cross, either between two wild species, Musa acuminata (A for short) and M. balbisiana (B), or within just one of the species that nevertheless gave rise to a plant that doesn’t need pollen to trigger the growth of a fruit (it is parthenocarpic) and doesn’t itself usually make seeds, although it may produce pollen. Some cultivated bananas are diploid, with two A chromosomes, just two are AB, and none, of more than a thousand, is BB. The rest are all triploid, with three sets of chromosomes: AAA, AAB and ABB with, again, no BBB. Stay with me.

On that basis, Simmonds and Shepherd [2] put the characteristics of the two wild relatives at the opposite ends of a 15 point scoring system to characterise all bananas. Unfortunately, the bananas themselves don’t fall neatly into the categories one might expect them to.

De Langhe and his colleagues looked at the chromosomes and DNA in more detail, using important observations that were not available to Simmonds and Shepherd. Most importantly, for bananas where the parentage is known with certainty, the mitochondria are inherited from the father, or pollen parent, while the chloroplasts come from the mother, or ovule parent. There is also good evidence for exchange among the A and B chromosomes in banana varieties, which would also explain the failure of many varieties to sort neatly under the Simmonds and Shepherd scheme. This kind of evidence allows De Langhe and colleagues to propose alternative, more complex routes to the seedless bananas of today.

Most of these involve a more-or-less fertile AB hybrid being fertilized by A pollen, and then a little nuclear DNA jiggery-pokery (meiotic restitution) and perhaps some rearrangement of the DNA. And that could happen — and more importantly could be noted — if those proto-farmers were growing their newly found edible bananas in close proximity to their wild relatives, as they would have been in southeast Asia. Something very like that is going on today among cassava farmers, for example; they allow volunteer seedlings, the product of sexual reproduction between already favoured clones and wild relatives, to flourish in their fields and then select among them. [3] Banana farmers could easily have done the same.

The details really are not for the faint-hearted; they do, however, make sense of most of the observations on bananas today, including the rarity of certain chromosome combinations and the anomalies in the banana scoring system. And the paper goes out of its way to suggests methods that might verify the backcross hypothesis, including various approaches to direct examination of the DNA.

The big question, of course, is “what does any of this matter?”. And the surprise is that it really does. Banana breeding is difficult at the best of times; no seeds, no pollen, you can imagine. But if the backcross hypothesis is true, then the current approach to banana breeding, which De Langhe et al. describe as “substituting an A genome allele by an alternative derived from a AA diploid source of resistance or tolerance to biotic and abiotic stress”, might be misguided. If the chromosomes are not “pure” A or B, and if backcrosses were involved in the origin of banana varieties, maybe breeders should look again at some of the diploid offspring from their crosses and see whether they could be further backcrossed to come up with types that are more use to farmers.

Notes:
  1. De Langhe, E., Hribova, E., Carpentier, S., Dolezel, J., & Swennen, R. (2010). Did backcrossing contribute to the origin of hybrid edible bananas? Annals of Botany DOI: 10.1093/aob/mcq187 [↩]
  2. Simmonds, N., & Shepherd, K. (1955). The taxonomy and origins of the cultivated bananas. Botanical Journal of the Linnean Society, 55 (359), 302-312 DOI: 10.1111/j.1095-8339.1955.tb00015.x [↩]
  3. Pujol, B., Mühlen, G., Garwood, N., Horoszowski, Y., Douzery, E., & McKey, D. (2005). Evolution under domestication: contrasting functional morphology of seedlings in domesticated cassava and its closest wild relatives New Phytologist, 166 (1), 305-318 DOI: 10.1111/j.1469-8137.2004.01295.x [↩]

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Pavlovsk’s potato problems

by Jeremy on October 10, 2010 · 0 comments

ResearchBlogging.org A paper published earlier this year used the historic potato collections assembled at the Pavlvosk Experiment Station to shed light on the confused and confusing taxonomy of potatoes. [1] The good news is that the conclusions of the paper “are very similar to other recent studies of cultivated species, and show the need to reclassify the collection of cultivated potatoes by modern taxonomic criteria”. That’s good, and may help to reduce the vast numbers of taxa of the Russians down to a more manageable, and more scientifically justifiable, smaller set. But it isn’t the main reason I’m interested in the paper, which is that it offers a unique glimpse into the state of the Pavlovsk potato collection.

To do their study, Tatjana Gavrilenko and her colleagues selected a subset of the 8680 accessions in the Russian National potato collection, many of which go back to before Vavilov himself. They wanted representatives of the main categories of the collection: 2640 examples of wild species, 600 of primitive cultivated species, 2650 Andean cultivated varieties, 120 Chilean lowland cultivated varieties, 2100 breeding cultivars and 570 interspecific hybrids. [2] Many of the accessions are stored as tubers. Others, especially the wild species and primitive cultivated types, as true potato seed.

A first task was to establish the viability of the true potato seed. The researchers went back to the earliest seed reproductions they could, many 20 or 30 years old. Seed had been stored at room temperature — not optimal — and two different methods of enhancing germination produced viable seeds from only 35 out of 99 accessions in one case and 89 out of 166 and 63 out of 146 in the other.

Of 411 accessions of potato seed, only 187 were viable. The sample now consisted of 187 seed accessions and 172 tuber accessions.

Passport data, which provide information about the accession, were also not in the best condition. The researchers scoured each of the three independent sets of records, where the same accession had a different identifying number in each, to collate the information. As they laconically observe, “our checking of all these three sets of records uncovered mistakes and increased the accuracy of our database.”

That wasn’t the end of it. Starting again with the 412 known, viable accessions, 35 had to be discarded “because of missing or ambiguous data”. Another 27 were eliminated after the first grow-out “due to gross taxonomic misidentifications”. And 16 wild species did not produce tubers under the Pavlvosk’s conditions, not their fault. In the end, the experimental subset of 359 Russian accessions had been whittled down to 239 for a variety of reasons, almost all the result of the way the collection had been managed.

It would be easy at this point to throw up one’s hands in despair and moan about the sorry state of the Russian potato collection. Remembering what the collections had been through, however, the miracle is that the collections are in as good a state as they are. Subject to active hostility and then, at best, neglect, the collections and their curators have done miracles. And they have had some help.

In 2000 a Cornell University project brought equipment and training to the Pavlovsk scientists, with efforts to improve storage conditions and the condition of the collection. I tried to find out what happened as a result. The two principal investigators redirected me to the curator of the wild Solanum collection at VIR, and a week later she has yet to respond.

That is understandable. The people at Pavlovsk have a lot on their minds at the moment. That may also be why the lead author of the GRACE paper seemed a tad defensive when I asked about the state of the collection. She pointed out that samples from other genebanks came with errors too. Fair point. And that, as they wrote in the paper, “[t]he low levels of seed viability from these early reproductions is not representative of the entire collection, but reflects our choice of older seed reproduction to be close as possible to original material”. One reason they chose to go to the earliest seed reproductions possible, however, was precisely because they weren’t sure that later reproductions had been carried out under the best possible conditions to maintain the genetic integrity of the accessions.

The point is not to criticise past efforts, which as I said are nothing short of miraculous, but to ensure that the painstaking work to establish the viability and collate the records, including a whole new set of characteristization and molecular data that underwrite the taxonomic study, is of lasting value. Gavrilenko and her colleagues have said that they “are currently ensuring that our now well-documented and diverse subset will be maintained in an in vitro collection to make it useful for future studies”. In response to my email Gavlrilenko replied that about 160 accessions were already conserved in vitro, and that she was looking for finding funds for their cryopreservation.

And that is the point. Genebanks, not all of them, but many, need secure, ongoing funding.

Notes:
  1. Gavrilenko, T., Antonova, O., Ovchinnikova, A., Novikova, L., Krylova, E., Mironenko, N., Pendinen, G., Islamshina, A., Shvachko, N., Kiru, S., Kostina, L., Afanasenko, O., & Spooner, D. (2010). A microsatellite and morphological assessment of the Russian National cultivated potato collection Genetic Resources and Crop Evolution DOI: 10.1007/s10722-010-9554-8 [↩]
  2. A separate curator is responsible for each of the six categories, which complicates matters. [↩]

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The Vavilov Institute responds to the Expert Commission

by Jeremy on October 6, 2010 · 0 comments

The NI Vavilov Research Institute of Plant Industry (VIR) has responded in some detail to the report of the Russian Academy of Sciences’ Expert Commission appointed by the Russian Ministry of Economic Development to look into the state of Pavlovsk Experiment Station. The response makes many points and asks many questions, in between heaping fulsome praise on the commission and its members. Among the most salient:

  • Why did the experts visit incognito and not engage the curators at the Station? VIR considers this a breach of scientific ethics. The VIR points out that it would be very difficult to find their way about and to locate the various collections. Fortunately the group ran into M. Lebedev, “a head of the research nursery and private entrepreneur,” who was able to guide them round at least part of the Station’s 500 hectares.
  • Why did the expert group include V.A. Dragavtsev the former head of the VIR? The VIR ays that Dragavtsev “is now widely known in Russian scientific circles … for his obsession to change the VIR directorate”.
  • Why did the group not include a horticulturalist? Although it included biochemists, lecturers and the director of a botanical garden, the group “contained no expertise specifically related to the crops at the Station”.
  • Why did the Expert Commission release its “report” in a press conference? No staff were involved in the broadcast, which was one-sided.
  • VIR says that the Expert Commission gave the impression that the real threat to the collections was not the proposed housing development but the existing management of Pavlovsk “which is protesting the destruction”.

There’s more (of course) and the latter part of VIR’s response focuses on the Expert Commission’s proposed solution: change VIR’s management and then move the whole Institute (including Pavlovsk and 7 other stations) from the Russian Academy of Agricultural Sciences into the Russian Academy of Sciences. On the face of it this does rather seem like the Russian Academy of Sciences is taking to heart sage advice about never letting a good crisis go to waste. At this point VIR’s response becomes a bit muddled, and who can blame them? They point out that the RAS has no idea of the costs or difficulties of managing the collections, and allude to the RAS’s own financial problems and institute scientists striking and demonstrating for budget increases. The VIR has its own set of funny numbers too.

[D]o the highly respected experts know that an average cost of collection, maintenance and preservation of one accession in a field genebank makes around 700 Euros (Smith & Livingston, 1997), while an average monthly salary of a curator does not reach 10 thousand Rubles (239 Euros).

In the end the entire story is beginning to resemble a giant turf war with too many players, shifting alliances and no clear outcome in sight yet. VIR points out that another expert group, this one under the Ministry of Agriculture, was at Pavlovsk on 23-24 September.

We do hope, results of this audit will be more objective and professional, [and] will provide a real picture about [the] importance and value of the fruit and berry crop collection.

But in case it doesn’t …

VIR reserves all rights to assemble a foreign commission consisting of experts in the sphere of plant genetic resources, who understand what preservation of a great amount of collection accessions in the field genebank means, considering the fact the collection is being preserved not only at Pavlovsk experiment station, but also at other 7 stations, and what are the true causes of “improper care” of these accessions.

Whose experts will prevail?

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