The ‘tourism’ of genebanks

Even though I managed a large genebank for ten years, I still don’t fully understand why seeing lots and lots of packets of seeds in a cold store at -18C—essentially a very large refrigerator—holds such a fascination for so many people. There’s nothing particularly glamorous about that, but it just seems everyone wants to walk inside and see for themselves. In a tropical country like the Philippines this is a novel experience, of course. Not so at the Svalbard Global Seed Vault inside the Arctic Circle. I guess there are times of the year when it must be colder outside than in. There again, that genebank has a particular attraction and significance*.

Let’s hope that when visitors do visit a genebank they see more than just packets of seeds on cold shelves, and get to appreciate just what it entails to conserve these important varieties and wild species, and why that is important for society at large. And of course, they should finish their genebank visit with a little more understanding about genetic diversity, how it came about, and how plant breeders can tap into this gene pool to breed new crop varieties.

The International Rice Research Institute (IRRI) receives thousands of visitors each year. Most of them are parties of Filipino schoolchildren, however, who come to learn what rice and rice agriculture is all about. Not surprising really, given that many children raised in urban environments have little idea where their food comes from. But a visit to the genebank is no longer part of their visit.

Rice museum and children

That was not always the case. At the start of my tenure as head of the genebank in 1991, I had the impression that most of the visitors to the institute were given, or seemingly entitled to, a tour of the International Rice Genebank (IRG). Now, most visitors are shown the Riceworld Museum and Learning Center (developed with support from the German government) where there is a display of the genebank’s work.

But if you are one of the ‘chosen’, a tour of the genebank can still be part of your visitor program. In this gallery (courtesy of IRRI) my former colleague and successor as head of the Genetic Resources Center (GRC), Dr Ruaraidh Sackville Hamilton, describing what the genebank is all about to participants of the 6th Meeting of the APEC Policy Partnership on Science, Technology and Innovation, who visited IRRI on 12 August 2015.

So why was free access to the genebank restricted?

A few months after I joined IRRI, I needed to talk to one of my staff. Going downstairs to the ground floor, I saw a line of 50 or more high school/university students filing in through the front door of the building, a line that snaked its way around the corridors and into the genebank itself. My colleagues in the institute’s Visitors Service felt they had carte blanche permission to take any number of visitors into the genebank, at any time.

Not only was the front door of the building open, but also every door between there and the -18C long-term storage vault, notwithstanding that it must have been over 30C outside with humidity approaching 90% or more. Although the configuration of the various genebank rooms and laboratories has changed since 1991, they were (and remain) temperature and humidity controlled. It made no sense to me to have hordes of visitors passing through, leaving all the doors open to the outside in their wake. This had to stop. And it soon did, with visitors scheduled in a more coordinated way.

However, I soon realized that if I hosted all these visitors myself, that’s about all I would be attending to daily. So I roped in the other genebank international staff and senior Filipinos to take their share of handling the visitor load (burden on some occasions). As head of GRC, I would generally host only the VIPs.

So who were (and are) these VIPs? Well they ranged from royalty (HRH Princess Maha Chakri Sirindhorn of Thailand, Prince Albert of Monaco, and HRH The Duke of Gloucester from the UK); heads of state (from the Philippines, India, Lao People’s Democratic Republic, Myanmar to name just a few, even disgraced former President Fujimori of Peru); heads of government and other politicians (from Bangladesh, Vietnam for example, and the Philippines of course); ambassadors and other members of the diplomatic community in the Philippines; Nobel Laureates such as Norman Borlaug (Peace, 1970) and Joseph Stiglitz (Economics, 2001); heads and representatives of donor agencies to IRRI; eminent scientists; and germplasm specialists with a particular interest in seeing how IRRI tackled the challenge of managing such a large germplasm collection. Usually I had just 10-15 minutes at most to describe why conserving rice seeds was so important for the future of rice agriculture—after all, rice is the staple food of half the world’s population. Most visitors had never been inside in a genebank before, let alone seen the diversity of rice varieties, or in fact realized that such diversity even existed.

In 1994 or 1995,GRC held a one-day Open House for over 1000 IRRI staff and colleagues from the nearby University of the Philippines Los Baños. It was then we made the world map from rice grains of different shapes, sizes and colors that you can see in a couple of the photos above. A duplicate of that map is also on display in the Riceworld Museum and Learning Center. Some of the other cartoon display materials showing how seeds are dried and stored are still on display in the genebank, but have been updated periodically.

Here is a small selection of some of the people I met. I wish I had a better record of all those VIPs I met over a decade in GRC.

Heads of State

Politicians

Nobel Laureates

There’s no doubt however that explaining the role and work of the genebank to these visitors is not only necessary, but it is actually a rather important aspect of genebank management. These visitors are ‘genebank ambassadors’ and can spread the good word about the strategic importance of genetic conservation. Time (mostly) well spent!

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*I’m waiting for my invitation to visit.

Like a lady revealing her petticoats . . .

Standing proudly since the mid-16th century on the edge of the Cotswolds escarpment (map), with a magnificent vista southeast and west as far as the Marlborough Downs in Wiltshire and the Mendips in north Somerset, Newark Park began life as a Tudor hunting lodge. In the intervening centuries it has undergone many transformations, but it was not until the last years of the 20th century that this building began to yield up some of its hidden secrets. It has been in the hands of the National Trust since 1949.

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The south face of Newark Park, from the lower terrace [9 on the map below].

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The view from the south terrace, towards the Mendips and the Marlborough Downs.

Built by Sir John Poyntz, Newark Park (originally the ‘New Worke’) has changed ownership several times over the centuries, and each generation has left its mark. It was constructed over four floors: ground, first and second, and a basement. The original Tudor building was aligned north-south, with the main entrance on the east face.

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Newark Park as it might have looked in 1550. Note that there are no windows on the south wall (nearest). All the windows are on the east face.

In the seventeenth century another wing was added, parallel to the Tudor one, and connected centrally, so that the overall shape of the building was like the letter ‘H’. This is what I remembered from the explanation using a model by one of the volunteers. I wish I’d taken photos of that model, which could be taken apart to show how the various building projects came together in the building we see today. Here’s my plan (not to scale).

Newark plan

Further changes were made in the 18th century, and the building was squared to the shape we see today. But in doing so, and to retain the symmetry there are several false windows on the west face, or windows placed over internal chimneys on the south side of the Tudor wing. Other windows, on what would have been the west face of the original Tudor wing, were bricked in during the 18th century and became internal walls. A side wing was added in the late 19th century, and an entrance porch added after 1971.

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Coat of Arms of the Clutterbuck family, part of a large stained glass window on the first floor over the main door leading to the walled garden on the east side of Newark Park.

In the 1700s, Newark Park became the property of the Clutterbuck family and remained so until given to the National Trust, although they had not lived there since the late 1800s. A number of tenants took over Newark Park, but by 1970 it was in a considerable state of disrepair, the gardens were overgrown, and no-one remembered the buildings illustrious Tudor past. In fact, at one stage, the National Trust had contemplated letting the building become completely derelict.

But the savior of Newark Park came along in 1971, and under the terms of a ‘repairing lease’ began to discover much of Newark’s past, uncovering many of its Tudor features that visitors can now see for themselves. Access to the Tudor basement is permitted only with a tour guide, but it’s worth it. The rest of the house is open almost everywhere.

And what a delight it is. Not only is there eclectic collection of ornaments, paintings, furniture, glassware and the like, but the renovations made after 1971 opened much of the top floor.

Click to enlarge

Click to enlarge

So who was this ‘Newark savior’? American architect Robert ‘Bob’ Parsons was born in Texas in 1920, and served as a soldier in the Second World War getting to know the Cotswolds at that time. After the war he settled in London, and apparently was looking for a ‘country house project’ to take on. He resided at Newark Park with his partner Michael Claydon until his death in 2000. And it was due to all the repair work that Parsons undertook—far in excess of the lease commitment he had agreed with the National Trust—that Newark Park is what we see today. And that’s also why it now has Grade 1 listed building status.

The gardens were completely overgrown, and when Parsons cleared those he uncovered several interesting features like the summer house [14] and a folly (11] in the process. Today the walled garden [7] on the east side of the hall looks like it has been there forever. But it was one of Parsons’ additions, and is completely in tune with the rest of the property. The whole estate extends to some 750 acres. Just click on any of the galleries below to view larger images.

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So many features of the gardens were uncovered by Bob Parsons. Strange that their existence had been completely forgotten.

The oldest Tudor part of the house, from 1550, can be seen in the basement, accessed by 18th century stairs in the company of one of the NT volunteers. Health & Safety regulations don’t permit free access downstairs!

On the ground floor, there is a plain but elegant entrance hall through curved, wooden double doors. There is a wonderful view south over the terrace through yet another door. There are two rooms in the west (17th century wing): a dining room, and a sitting room with the most wonderful collection of Staffordshire pottery figurines, perhaps too many in the glass-fronted cabinet to do them justice. Wonderful nevertheless!

Up the stairs to the first floor, you get a wonderful view of a 17th century glass window (the bow window on the east face), and a green bedroom off to the left. It apparently still displays the bed that was brought in during filming of the BBC1 2008 adaptation of Thomas Hardy’s Tess of the D’Urbervilles; two other scenes were filmed in the Tudor cellars.

Then up another floor, you emerge on to the most wonderful long gallery, with bedrooms, a study and other rooms leading off on both sides. The south end of the gallery has a large window offering, once again, incredible views over the Cotswolds escarpment and south. On one side there’s a cabinet with a collection of Bristol blue glass (and ruby and turquoise; envy once again!). In one of the bedrooms at least Parsons uncovered a Tudor fireplace during his renovations. The rooms certainly had that ‘lived-in’ feel about them. At the north end of the gallery a rope hangs down from the small bell tower on the roof, which is itself surmounted by a 16th century dragon weather vane in the form of a golden dragon.

Reflecting on our visit to Newark Park during the drive home, Steph and I agreed that it had definitely been one of our best National Trust days out. Not only was the property itself interesting, and its location stunning, but from the moment we passed through the ticket office and shop, the catering pavilion (for a welcome cup of coffee), and around the house itself, all the NT staff and volunteers were exceptional in their friendliness. It was almost as if they were welcoming visitors into their own home.

Well done, Newark Park staff and volunteers! We’ll be back in the Spring to see the display snowdrops and other flowering bulbs.

 

When is white not white? When it’s green, of course.

Or maybe another color altogether. Then again, I could ask when tall is actually short, or a whole host of apparently contradictory questions.

What a conundrum.

No, this isn’t some fiction. It was the reality I faced when I took up the reins as head of IRRI’s Genetic Resources Center (GRC) in July 1991 and asked for a demonstration of the ‘genebank data management system’.

free-images-for-websites-computer_clipart1A large germplasm collection, or was it?
The International Rice Genebank (IRG) at IRRI holds the world’s largest and (almost certainly) the most genetically diverse collection of rice varieties of Asian rice (Oryza sativa), African rice (O. glaberrima) and wild species of rice (not only Oryza species, but representatives from related genera).

Besides providing the very best conditions to ensure the long-term survival of these precious seed samples (as I blogged about recently), it’s also essential to document, curate, and easily retrieve information about the germplasm stored in the genebank. That’s quite a daunting prospect, especially for a collection as large as the International Rice Genebank Collection (IRGC), with over 126,600 samples or accessions at the last count¹. (During my tenure as head of GRC, the collection actually grew by about 25% or so, with funding for germplasm collecting from the Swiss government.)

I discovered that the three rice types—Asian, African and wild species—were being managed essentially as three separate germplasm collections, each with its own data management system. What a nightmare! It was almost impossible to get a quick answer to any simple question, such as ‘How many accessions are there in the genebank from Sri Lanka?’ It took three staff to query the databases, formulating their queries in slightly different ways because of the different database structures.

But why was it necessary to ask such questions, and require a rapid response? In 1993 the Convention on Biological Diversity (CBD) came into force. I had anticipated that IRRI would receive an increasing number of requests from different countries about the status and disposition of rice germplasm from each that was conserved in the IRG. Until we had an effective data management system we would have to continue trawling through decades of paperwork to find answers. And indeed there was an increase in such requests as countries became concerned that their germplasm might be misappropriated in some way or other. I should say that the changes we subsequently implemented put IRRI in good stead when the International Treaty on Plant Genetic Resources for Food and Agriculture came into force, with its requirements to track all germplasm flows and use. But I’m getting ahead of myself.

It made no sense to me that the rice types should be managed as separate collections, since once in the same genebank vaults seeds were stored under identical conditions.  So, as I indicated elsewhere on this blog, I appointed Flora de Guzman as genebank manager with overall responsibility for the entire rice collection, and started to study various aspects of germplasm regeneration and seed conservation. Since the wild rices had a special nursery screenhouse for multiplication of seed stocks (a requirement of the Philippines Quarantine Service), another member of staff became curator of the wild species on a day-to-day basis.

The data management challenge
In 1991 the IRG had three very competent data management staff: Adel Alcantara, Vanji Guevarra, and Myrna Oliva, soon to be joined by a technical assistant, Nelia Resurreccion.

Due to the lack of oversight for data management, I realized the trio were each doing their own thing for the sativas, the glaberrimas, and the wild species, so to speak, with limited reference to what the others were doing. To make any significant improvements to data management, it would be necessary to build a single data system for all germplasm in the genebank. I thought this would be quite a straightforward undertaking, taking maybe a couple of months or so. How wrong I was! It was much more complex than I had, in my naivety, envisaged.

Back in 1991, PC technology was still in its infancy; well maybe approaching juvenility. The databases were managed using ORACLE on a VAX mainframe. More nightmares! Fortunately, with some investment in office design and furniture, providing each staff with a proper workstation, and the ability to work better as a team, and more powerful PCs, we were able to migrate the new data management systems to local servers. We left the VAX behind, but unfortunately still had an ORACLE legacy that was far more difficult to ditch. I also wanted to develop an online data management system that would permit researchers at IRRI, and eventually around the world, to access germplasm data for themselves rather than always having to request information from genebank staff. This was the less than ideal situation when I joined IRRI. In fact, in order to access genebank data then it was necessary to make a request in writing that was approved by the head of the genebank, then Dr TT Chang. I put a stop to that right away. Because data had been accumulated using public funds they should be made freely available henceforth to anyone.  Direct and unhindered access to genebank data was my goal.

The underlying problem
However, the three databases could not ‘talk’ to one another, because their structures and data were different for the three ‘collections’. Let me explain.

There are basically two types of germplasm data, what we call passport data, and characterization and evaluation data. The passport data include such pieces of information as the identity of germplasm (often referred to as the accession number), the donor number and the collector’s number, for example. These data are, or should be, unique to a piece of germplasm or an accession. But passport data also include information about the date of acquisition, when it was first stored in the genebank, who has requested a seed sample, and when. Of course there’s a great deal more, but these examples suffice to explain something of the nature of these data.

Characterization (qualitative) and evaluation (mainly quantitative) data describe various aspects (or traits as they are known) of rice plants such as leaf and grain color, or plant height, days to flowering, and resistance or tolerance to pests and diseases, using agreed sets of descriptors and scoring codes or actual measurements. The International Board for Plant Genetic Resources (IBPGR, which became the International Plant Genetic Resources Institute, then Bioversity International) had developed these crop descriptors, and the first—for rice—was published jointly with IRRI in 1980 (and revised and updated in 2007).

An essential condition for a successful data management system therefore is that information is recorded and stored consistently. In order for the three databases to talk to each other, we had to correct any differences in database structure, such as the naming and structure of database fields, as well as consistent use of codes, units, etc. for the actual information. This is what we discovered.

Take the most basic (and one of the most important) database field for accession number, for example. In one database, this field was named ‘ACC_NO’, in another ‘ACCNO’. And the structure was different as well. For the sativas it was a five digit numeric field; for the glaberrimas, a six digit numeric field; and for the wild species, a seven digit alphanumeric field. No wonder the databases couldn’t talk to each other at the most basic level.

But why were there three structures? The field name was easily resolved, incidentally. Well, when the collection was first established, the accession numbers from ‘00001’ to ‘99999’ were reserved for the O. sativa accessions. Then the the numbers from ‘100000’ and above were assigned to O. glaberrima and the wild species. However, thirteen wild species samples were found to be mixtures of two species. So they were divided and each given a suffix ‘A’ or ‘B’, such as ‘100569A’ and ‘100569B’ (not actual numbers, just illustrative). That meant that the wild species now had a seven digit alphanumeric field. Why one of the mixture wasn’t just assigned a new six digit number—as we did—I’ll never understand. Then we had to convert the O. sativa accession number into a six digit numeric field (‘000001’ etc.) and, with a consistent field name across databases (‘ACCNO’ perhaps), we could then link databases for the first time. In 1991, there was a gap between the sativa numbers (perhaps between ‘80000’ and ‘99999’) before the other accessions started at ‘100000’. Irrespective of rice type, we just inserted consecutive numbers as we received new samples, until there were no gaps at all in the sequence.

White is white, yeah?
Now imagine achieving consistency right across the databases for all fields. We found that a character was often recorded/coded in different ways between rice types. So in one, the color ‘white’ might have been coded as a ‘1’, but as a ‘5’ in another. Or ‘1’ was ‘green’ in another database. And so it went on. We had to convert all codes to a meaningful and consistent description, each independent of the other. So ‘1’ was converted in one database to ‘white’ and ‘5’ to ‘white’ as well, etc. Having made all these conversions, with very careful cross checking along the way, and regular data back-ups, we finally had consistent field names and structures, and recording/coding of data for the entire germplasm collection. I don’t remember exactly how long this took, but it must have been between 18 months and two years.

The next step
IRGCISBut once completed, we could move on to the next phase of developing an online system to access genebank data, the International Rice Genebank Collection Information System (IRGCIS), with inputs from the former System-wide Genetic Resources Program (SGRP), an initiative of all the CGIAR centers with genebanks and genetic resources activities.

IRGCIS is a comprehensive system that manages the data of all rice germplasm conserved at IRRI.  It is designed to manage the genebank operations more efficiently. It links all operations associated with germplasm conservation and management from acquisition of samples through seed multiplication, conservation, characterization, rejuvenation and distribution to end-users.

The system aims to:

  • Assist the genebank staff in day-to-day activities.
  • Facilitate recording, storage and maintenance of germplasm data.
  • Allow the request of desired seeds and provide direct access to information about accessions in the genebank.

The data that are accessible are:

  • Passport data.
  • Morpho-agronomic descriptions.
  • Evaluation data on the International Rice Genebank Collection.
  • Germplasm availability.

A couple of years after IRGCIS, work began to develop the International Rice Information System (IRIS) as part of the International Crop Information System (ICIS) for the management of improved germplasm, breeding lines and the like, with full genealogy data. INGER also developed the INGERIS, but to tell the truth I’m not sure exactly where IRRI is these days with regard to cross system integration and the like.

But as I mentioned earlier, of one thing I am certain. Had we not taken the fundamental steps to clean up our data management act almost 25 years ago, we would not have had an effective platform to respond to global germplasm initiatives like the International Treaty or CBD, nor take advantage relatively easily of new data management software and hardware. It did require that broad perspective in the first instance. That I could bring to the party even though I didn’t have the technical know-how to undertake the detailed work myself.

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¹ Source: the International Rice Genebank Collection Information System (IRGCIS), 8 June 2015.

I used to be uncertain, but now I’m not so sure (updated 5 December 2015)

Regular visitors to my blog will, by now, know that for many years from July 1991 I worked at the International Rice Research Institute (IRRI) in Los Baños in the Philippines, south of Manila. For the first 10 years, I was head of the Genetic Resources Center (GRC), having particular responsibility for the International Rice Genebank (now supported financially by the Global Crop Diversity Trust). Elsewhere on this blog I have written about the genebank and what it takes to ensure the long-term safety of all the germplasm samples (or accessions as they are known) of cultivated rices and related wild species of Oryza.

Well, consider my surprise, not to say a little perplexed, when I recently read a scientific paper¹ that had just been published in the journal Annals of Botany by my former colleagues Fiona Hay (IRRI) and Richard Ellis (University of Reading), with their PhD student Katherine Whitehouse, about the beneficial effect of high-temperature drying on the longevity of rice seeds in storage. Now this really is a big issue for curators of rice germplasm collections, let alone other crop species perhaps.

So why all the fuss, and why am I perplexed about this latest research? Building on a paper published in 2011 by Crisistomo et al. in Seed Science & Technology², this most recent research¹ provides significant evidence, for rice at least, that seed drying at a relatively low temperature and relative humidity, 15C and 15RH—the genebank standard for at least three decades—may not be the best option for some rice accessions, depending on the moisture content of seeds at the time of harvest. It’s counter-intuitive.

But also because germplasm regeneration and production of high quality seeds is one aspect of germplasm conservation most likely to be impacted by climate change, as Brian Ford-Lloyd, Jan Engels and I emphasized in our chapter in Genetic Resources and Climate Change.

To explain further, it’s necessary to take you back 24 years to when I first joined IRRI.

20150202-klaus-lampe

Dr Klaus Lampe, IRRI Director General 1988-1995

The first six months or so
The Director General in 1991, Dr Klaus Lampe, encouraged me to take a broad view of seed management services at IRRI, specifically the operations and efficiency of the International Rice Genebank (IRG). It was also agreed that I should develop research on the germplasm collection and its conservation, something that had not been considered when the GRC Head position was advertised in September 1990. I should add that in negotiating and accepting the GRC position, I had insisted that GRC should have a research arm, so to speak. I guess I was in a fairly strong negotiating position.

Dr TT Chang, first head of the International Rice Germplasm Center at IRRI

Dr TT Chang

Once at IRRI, I didn’t rush into things. After all, I had never run a genebank before let alone work on rice, although much of my career to that date had been involved in various aspects of germplasm conservation and use. But after about six months, I reckon I’d asked enough questions, looked at how the genebank was running on a day-to-day basis. I had developed a number of ideas that I thought should vastly enhance the long-term conservation of rice germplasm, but at the same time allow all the various operations of the genebank run smoothly and hopefully more efficiently. In one sense, managing the individual aspects or operations of a genebank are quite straight-forward. It’s bringing them all together that’s the tricky part.

There was another ‘delicate’ situation to address, however. All the Filipino staff had worked for only one person for many years, my predecessor as head of the genebank (then known as the International Rice Germplasm Center, or IRGC), Dr TT Chang. It’s not an understatement to say that many of these staff were fiercely loyal to Dr Chang (loyalty being one of their greatest virtues), firmly fixed in their ways, and didn’t feel—or maybe understand—that changes were desirable or even necessary. It was a classic change management situation that I was faced with. I needed to help them evaluate for themselves the current genebank management focus, and propose (with more than a little encouragement and suggestions from me) how we might do things differently, and better.

Some radical changes
But I don’t think anyone foresaw the radical changes to the management of the genebank that actually emerged. The genebank was ‘the jewel in IRRI’s crown’, the facility that every visitor to the institute just had to see. It seemed to run like clockwork—and it did, in its own way.

Staffing and responsibilities
Apart from several staffing issues, I was particularly concerned about how rice germplasm was being regenerated in the field, and how it was handled prior to medium-and long-term storage in the genebank. There were also some serious germplasm data issues that needed tackling—but that’s for another blog post, perhaps.

In terms of genebank operations, it was clear that none of the national staff had responsibility (or accountability) for their various activities. In fact, responsibilities for even the same set of tasks, such as germplasm regeneration or characterization, to name just two, were often divided between two or more staff. No-one had the final say. So very quickly I appointed two staff, Flora ‘Pola’ de Guzman and Renato ‘Ato’ Reaño to take charge of the day-today management of the seed collection (and genebank facilities per se) and germplasm regeneration, respectively. Another staff, Tom Clemeno, was given responsibility for all germplasm characterization.

Working in the field
But what seemed rather strange to me was the regeneration of rice germplasm at a site, in rented fields, some 10km east of the IRRI Experiment Station, at Dayap. This meant that everything—staff, field supplies, etc.—had to be transported there daily, or even several times a day. It made no sense to me especially as the institute sat in the middle of a 300 ha experiment station, right on the genebank’s doorstep. In fact, the screenhouse for the wild rice collection had been constructed on one part of the station known as the Upland Farm. To this day I still don’t understand the reasons why Dr Chang insisted on using the site at Dayap. What was the technical justification?

Also the staff were attempting to regenerate the germplasm accessions all year round, in both ‘Dry Season’ (approximately December to May) and the ‘Wet Season’ (June to November). Given that the IRRI experiment station has full irrigation backup, it seemed to me that we should aim to regenerate the rice accessions in the Dry Season when, under average conditions, the days are bright and sunny, and nights cooler, just right for a healthy rice crop, and when the best yields are seen. The Wet Season is characterized obviously by day after day of continuous rainfall, often heavy, with overcast skies, and poor light quality. Not to mention that Wet Season in the Philippines is also ‘typhoon season’. So we separated the regeneration (Dry Season) from the characterization (Wet Season) functions.

But could we do more, particularly with regard to ensuring that only seeds of the highest quality are conserved in the genebank?  That is, to increase the longevity of seeds in storage—the primary objective of the genebank, after all, to preserve these rice varieties and wild species for future generations? And in the light of the latest research by Katherine Whitehouse, Fiona and Richard, did we make the right decisions and were we successful?

Seed environment and seed longevity
That’s where I should explain about the research collaboration with Richard Ellis at that time (Ellis et al. 1993; Ellis & Jackson 1995), and helpful advice we received from Roger Smith and Simon Linington, then at Kew’s Wakehurst Place (and associated with the founding of the Millennium Seed Bank).

Dr N Kameswara Rao

Dr N Kameswara Rao, now head of the genebank at the International Center for Biosaline Agriculture (ICBA) in the UAE-Dubai.

I hired a post-doctoral fellow, Dr N Kameswara Rao, on a two-year assignment from sister center ICRISAT (based in Hyderabad).  Kameswara Rao had completed his PhD at Reading under seed physiologist Professor Eric Roberts.

We set about studying the relationship between the seed production environment and seed longevity in storage, and the effect of sowing date and harvest time on seed longevity in different rice types, particularly hard-to-conserve temperate (or japonica) rice varieties (Kameswara Rao & Jackson 1996a; 1996b; 1996c; 1997). And these results supported the changes we had proposed (and some even implemented) to germplasm regeneration and seed drying.

In 1991, the IRG did not have specific protocols for germplasm generation such as the appropriate harvest dates, and seed drying appeared to me to be rather haphazard, hazardous even. Let me explain. Immediately after harvest, rice plants in bundles (stems, leave and grains) were dried on flat bed dryers before threshing, heated by kerosene flames, for several days. Following threshing, and before final cleaning and storage, seeds were dried in small laboratory ovens at ~50C. It seemed to me that rice seeds were being cooked. So much for the 15C/15RH genebank standard for seed drying!

During the renovation of institute infrastructure in the early 1990s we installed a dedicated drying room³, with a capacity for 9000 kg, in which seeds could be dried to an equilibrium 6% moisture content (MC) or thereabouts, after a week or so, under the 15/15 regime.

A rethink
Now this approach has been apparently turned on its head. Or has it?

To read the headlines in some reports of the Whitehouse et al. paper, you would think that the 15/15 protocol had been abandoned altogether. This is not my reading of what they have to report. In fact, what they report is most encouraging, and serves as a pointer to others who are engaged in the important business of germplasm conservation.

In her experiments, Katherine compared seeds with different initial MC harvested at different dates that were then dried either under the 15/15 conditions, or put through up to six cycles of drying on a batch drier, each lasting eight hours, before placing them in the 15/15 seed drying room to complete the drying process, before different seed treatments to artificially age them and thereby be able to predict their longevity in storage before potential germination would drop to a dangerous level.

This is what Katherine and her co-authors conclude: Seeds harvested at a moisture content where . . . they could still be metabolically active (>16.2%) may be in the first stage of the post-mass maturity, desiccation phase of seed development and thus able to increase longevity in response to hot-air drying. The genebank standards regarding seed drying for rice and, perhaps, for other tropical species should therefore be reconsidered.

Clearly seeds that might have a higher moisture content at the time of harvest do benefit from a period of high temperature drying. Because of the comprehensive weather data compiled at IRRI over decades, Katherine was also able to infer some of the field conditions and seed status of the Kameswara Rao experiments. And although the latest results do seem to contradict our 1996 and 1997 papers, they provide very strong support for the need to investigate this phenomenon further. After all, Katherine studied only a small sample of rice accessions (compared to the 117,000+ accessions in the genebank).

The challenge will be, if these results are confirmed in independent rice studies—and even in other species, to translate them into a set of practical genebank standards for germplasm regeneration and drying and storage for rice. And it must be possible for genebank managers to apply these new standards easily and effectively. After all many are not so fortunate as GRC to enjoy the same range of facilities and staff support.

I’m really pleased to see the publication of this research. It’s just goes to demonstrate the importance and value of research on genebank collections, whatever the crop or species. Unfortunately, not many genebank are in this league, so it behoves the CGIAR centers to lead from the front; something I’m afraid that not all do, or are even able to do. Quite rightly they keep a focus on managing the collections. But I would argue that germplasm research is also a fundamental component of that management responsibility. Brownie points for IRRI for supporting this role for almost a quarter of a century. And for Fiona as well for ensuring that this important work got off the ground. Good luck to Katherine when she comes to defend her thesis shortly.

A recent seminar
On 12 November, Fiona gave a seminar at IRRI in the institute’s weekly series, titled How long can rice seeds stay alive for? In this seminar she explores changes that have been made to genebank operations over the years and the extent to which these did or did not affect the potential longevity of rice seeds in the genebank. She talks in some detail about the benefits of initial ‘high temperature’ drying that appears to increase potential longevity of seeds. As I queried with her in a series of emails afterwards, it’s important to stress that this high temperature drying does not replace drying in the 15/15 drying room. Furthermore, it will be necessary at some stage to translate these research findings into a protocol appropriate for the long term conservation of rice seeds at -18C.

Fiona has graciously permitted me to post her PowerPoint presentation in this blog, and the audio file that goes with it. You’ll have to open the PPT file and make the slide changes as you listen to Fiona speaking. I’ve done this and it’s actually quite straightforward to follow along and advances the slides and animations in her PPT. Click on the image below to download the PPT file. Just open it then set the audio file running.

Fiona Hay seminar title

Here’s the audio file.


I am also pleased to see that the CGIAR genebanks have also established a seed longevity initiative under the auspices of the Global Crop Diversity Trust. You can read more about it here.

Seed storage – an interesting anecdote
In 1992 we implemented the concept of Active (+3-4C) and Base (-18C) Collections in the IRG. Before then all rice seeds were stored in small (20g if I remember correctly) aluminium cans. We retained the cans for the Base Collection: once sealed we could expect that they would remain so for the next 50 years or more. But in the Active Collection there was no point having cans, if they had to be opened periodically to remove samples for distribution, and could not be re-sealed.

So we changed to laminated aluminium foil packs. Through my contacts at Kew – Wakehurst Place (home of the Millennium Seed Bank), Roger Smith and Simon Linington, we identified a manufacturer in the UK (from near Manchester I believe) who could make packs of different sizes, using a very high quality and tough laminate of Swedish manufacture (originally developed to mothball armaments). It had an extremely low, if not zero, permeability, and was ideal for seed storage. Unfortunately by the time we made contact, the company had gone into liquidation, but the former managing director was trying to establish an independent business. On the strength of a written commitment from IRRI to purchase at least 250,000 packs, and probably more in the future, this gentleman was able to secure a bank loan, and go into business once again. And IRRI received the seed storage packages that it ordered, and still uses as far as I know. The images below show genebank staff handling both aluminium cans in the Base Collection and the foil packs in the Active Collection. You can see the Active Collection in the video below at minute 1:09.

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¹ KJ Whitehouse, FR Hay & RH Ellis, 2015. Increases in the longevity of desiccation-phase developing rice seeds: response to high-temperature drying depends on harvest moisture content. Annals of Botany doi:10.1093/aob/mcv091.

² S Crisostomo, FR Hay, R Reaño and T Borromeo, 2011. Are the standard conditions for genebank drying optimal for rice seed quality? Seed Science & Technology 39: 666-672.

³ If you would like to see what the seed drying room looks like, just go to minute 9:40 in the video below:

 

‘More glass than wall’ – a palace or prison?

It’s unusual to find properties managed or owned by English Heritage and the National Trust side-by-side. But that’s precisely the situation at Hardwick Old Hall and Hardwick ‘New’ Hall in Derbyshire.

With the weather set fair last Wednesday, we made the 177 mile round trip from our north Worcestershire home to visit ‘Hardwick Hall’, which we regularly pass on the M1 motorway when traveling to visit our younger daughter and her family in Newcastle upon Tyne. I had visited Hardwick once before, at least 50 years ago when my father organized an outing for the Leek Camera Club.

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Hardwick Hall from the ruins of Hardwick Old Hall.

Standing on a ridge looking west over the Derbyshire countryside, Hardwick Hall was the later home of one of the most influential persons in Tudor times. Friend and confidante of Queen Elizabeth, Bess, Countess of Shrewsbury was originally from quite lowly stock, but through four and prestigious marriages (at least two of them in any case), she gained status and accumulated incredible wealth.

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Hardwick Hall proclaims the status of the owner to all and sundry. Not for nothing is her monogram ‘ES’ displayed proudly on at least three sides of each of the six ‘towers’ of the hall.

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The descendants of her second marriage, to Sir William Cavendish (d. 1557) are the Dukes of Devonshire, and Bess spent much of her married life to twice-widowed Sir William, at Chatsworth, still the ancestral seat of the Devonshires since 1549. She had eight children, two of whom died in infancy.

In 1568, Bess married George Talbot, 6th Earl of Shrewsbury (d. 1590), her fourth marriage, and one that brought her close to the royal court. For a number of years The Earl and Countess were given custody of Mary, Queen of Scots until she was removed from their care (essentially house arrest) and ultimately executed.

Hardwick Old Hall is now essentially a shell. After Bess moved to the ‘new hall’, and for centuries after, the house fell into disrepair, and during the 18th centuries, the building was reduced on purpose by the Dukes of Devonshire. One whole quarter of the hall, which housed the great hall I believe has disappeared altogether. But there is still a great deal to see, and English Heritage have made the greatest efforts to allow visitors to see the ruin in its entirety. The original stone staircase leads up to the top floor where there is now a wooden platform that enables everyone to view the wonderful plaster friezes on the walls, and the fireplaces at all levels. Of course the plaster friezes were never intended to be exposed to the elements. It’s a conservation conundrum—put an expensive new roof on the building or leave them possibly to deteriorate further. The views from the top of the building are stunning—these aristocrats knew where to build.

One can only imagine what sumptuous furnishings must have adorned Hardwick Old Hall. But just cross the lawn to the new hall, and you these in all their glory. What a feast for the eyes.

Climbing a broad stone staircase to the second floor ( ground, first and second), you enter the High Great Chamber with its ‘throne’, and unbelievable painted frieze high up on the wall.

Passing through an adjoining door, you are in the Long Gallery, one of the longest (but the highest) in any stately home in this country. Everywhere the walls are adorned with original tapestries, although I did overhear one of the guides saying that in Bess’ time the walls would have been plain. But in one corner of the Long Gallery are the Gideon Tapestries, hung by Bess 400 years ago and still hanging there today!

There is some fine furniture in the Withdrawing Chamber.

Several bedrooms on this floor house spectacular four-poster beds. The hall was still occupied by a Dowager Duchess of Devonshire until the 1960s.

Tall glass windows—in fact, glass everywhere—proclaim Bess’ status as a very wealthy lady. The hall has a very pleasing symmetry to it, and as I mentioned earlier, there’s no doubt whose house this was. Formal gardens lie to the south (since the house was built on a north-south axis) with the expanses of glass windows on the west and east sides.

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Arbella Stuart, granddaughter of Bess of Hardwick.

Through her marriage to the Earl of Shrewsbury, Bess became linked to royalty. In 1574, her sixth child, Elizabeth Cavendish married Henry Stuart, 1st Earl of Lennox, younger brother of Lord Darnley, husband of Mary, Queen of Scots. Their daughter, Arbella, was thus of royal blood (since Lennox was also descended from Margaret Tudor, sister of Henry VIII, through her second marriage). Arbella was a cousin to Elizabeth I and James VI of Scotland (who would become James I of England in 1603 on Elizabeth’s death). Arbella, Bess’ granddaughter, was effectively kept under house arrest at Hardwick for years and not permitted to marry. Neither Elizabeth (and subsequently James) need or want any more possible aspirants to the English throne. Arbella had an unhappy life. I doubt Arbella appreciated the grandeur of Hardwick. For her it was a prison. She eventually did secretly marry the Earl of Somerset, but was captured before she could escape to Holland. She spent her final years imprisoned in the Tower of London, and died there aged 40, supposedly having starved herself to death. 2015 is the 400th anniversary of her death and Hardwick is housing a special exhibition now to commemorate her death.

Without doubt, Hardwick is one of the most impressive National Trust properties I visited since we became members in 2011. And it’s popular, if the full car park was anything to go by. Now, as we speed along the motorway and see ‘ES’ peeping over the trees we will remember our interesting and enjoyable visit and a glimpse into Tudor life 400 years ago.

Iron and stone . . . heritage in Shropshire’s landscape

We’ve had a mixed summer, weather-wise, here in the UK. For the past month we’ve endured lower than average temperatures even though it’s supposed to be mid-summer. Some mornings it feels as though autumn has arrived six weeks early. The mixed weather we ‘enjoyed’ during our road trip around Scotland at the end of May and early June seems, in retrospect, quite good in comparison.

Fair weather days may be few and far between as autumn begins to encroach, so Steph and I are taking advantage of every good weather opportunity to get out and about. Last week, we traveled to Hardwick Hall in Derbyshire, a round trip of about 177 miles. So I wasn’t particularly inclined to take on a long journey for our outing yesterday.

We are fortunate that there are many interesting places to visit that are not too far from our home in northeast Worcestershire. With that in mind we headed northwest yesterday to visit two heritage sites in Shropshire’s beautiful landscape (map). And one of them really is part of a UNESCO World Heritage Site. One of them reaches back more than a thousand years, the other a mere 236 years. One is a ruin (almost) deliberately destroyed during the reign of Henry VIII in 1540. The other is a celebration of engineering ingenuity in the ‘home of the Industrial Revolution’.

Of course I’m referring to Wenlock Priory (in the small town of Much Wenlock, and incidentally the birthplace of the modern Olympic Games), and the world’s first bridge constructed of cast iron in the aptly named village of Ironbridge on the banks of England’s longest river, the River Severn. And both, in their different ways, are superb examples of architecture and construction.

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Remains of the church and monks’ residence at Wenlock Priory. The building on the left is now a private residence, and was not destroyed during the Dissolution of the Monasteries in the sixteenth centruy under Henry VIII.

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The iron bridge at Ironbridge, constructed in 1779, and now a UNESCO World Heritage Site.

Wenlock Priory—or its predecessor—was founded in the seventh century long before the Normans arrived on these shores in 1066 (and all that!). But thereafter it was refounded and expanded as a Cluniac (reformed Benedictine) priory.

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From the dimensions of the various building (or parts of) that are still standing, Wenlock Priory must have once been a very impressive complex of buildings. The length of the church and the girth of the bases of the columns that would have held up the roof give testament that Wenlock Priory was once an important ecclesiastical community. Having visited Fountains Abbey, Hailes Abbey_DSC0069, and viewed Rievaulx Abbey from above, I’m convinced that Wenlock was equally important. These were owned by the Cistercian order. Just a few miles down the road from Wenlock Priory lie the ruins of Cistercian Buildwas Abbey on the banks of the River Severn.

And I never to wonder as I wander around these ruins what they must have been like in their heyday. Busy of course, but also a haven of peace and tranquility I hope, notwithstanding the wealth that these ecclesiastical communities manifested and the power they exerted.

Wenlock Priory is privately owned, and part of the originally priory is still occupied as a residence. Obviously these buildings did not suffer at the time of the Dissolution of the Monasteries in 1540. Much of the stone from the priory was taken away and used in the construction of homes and farms in the surrounding countryside. Today, Wenlock Priory is managed by English Heritage.

The iron bridge at Ironbridge is, in my opinion, one of the most elegant ever constructed. And because of its association with the beginnings of the Industrial Revolution in Coalbrookdale, and Abraham Darby and his descendants, it’s even more special. I first visited Ironbridge in 1966 when, as a high school student, I attended a weekend course at nearby Attingham Park about the origins and reclamation of industrial landscapes.

What also makes the iron bridge special, and surely contributing to the World Heritage Site status of the Ironbridge Gorge, is its construction in the manner of a wooden bridge. The span of the bridge high over the River Severn is impressive indeed, and the various struts lock together and are fastened with nuts and bolts. All the iron for the bridge was cast in the nearby furnaces of Coalbrookdale where the art of smelting and production of steel was developed on an industrial scale.

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There’s a lot more to explore slightly further afield in Shropshire. Plenty to keep us busy and active members of English Heritage (and the National Trust) for many years to come.

Opportunities delayed: INGER @ 40

I don’t expect that the International Network for the Genetic Evaluation of Rice (INGER) will be familiar to many readers of this blog. Nor will the International Rice Testing Program (IRTP), the forerunner of INGER from 1975 to 1989.

INGER demonstration plots - the variation between varieties is striking

INGER demonstration plots – the diversity among these rice varieties is striking.

INGER is undoubtedly a rice germplasm exchange and testing network success story. You only have to look at the statistics on varieties tested, the number of testing sites, the collaboration between scientists, etc. to see the scope of what IRTP-INGER has achieved over its lifetime. More importantly, however, is the significant number of rice varieties that have been selected from INGER trials and released in one country even though they were bred in another. It’s also interesting to note how many varieties from Sri Lanka have been adopted in other countries through INGER.

rt-logoMany examples are highlighted in a recent article, INGER@40—and the crossroads, that just appeared in IRRI’s flagship magazine riceTODAY. Not only can the value of rice germplasm exchange be quantified in terms of millions (probably billions) of dollars of increased productivity of rice agriculture, but also think about how new varieties have benefited rice farmers and those who eat rice every day (or several times a day).

When IRTP-INGER was founded in 1975, it was fortunate to receive substantial funding each year from the United Nations Development Program (UNDP). That funding lasted for 20 years, but was both IRTP-INGER’s boon and its bane.

By the mid-1990s when UNDP support came to an end, it was always going to be difficult to find a donor to step in and provide long-term funding at the same level. And believe me, it was a struggle to persuade donors to emulate UNDP. Because the INGER model presented to donors was the one that UNDP has decided to discontinue funding, it was analogous to trying to sell a second-hand car rather than a brand new model with all the extras. We needed some bridging funds, and I was heavily involved in persuading a couple of IRRI’s donors, from Germany and Switzerland, to stump up USD1.5 million following review of a project proposal and a presentation to donors in Washington, DC in October 1994. However, the long-term funding situation was not resolved. Earlier that year I had made a review of INGER in Africa for the Directors General of IRRI and Africa Rice (WARDA as it then was), Drs Klaus Lampe and Eugene Terry, and made my first visit to Africa Rice headquarters in Bouaké, Ivory Coast. In the phot below, I planted a tree at the Bouaké site. I wonder if it’s still there. The other person in the photo is economist Dr Peter Matlon, who was DDG-Research in 1994, and later became Chair of the Board of Trustees.

In my opinion, INGER could—and should—have been more. According to the riceTODAY article, INGER is today, 40 years after it was founded, at ‘the crossroads’. But it was already at a crossroads almost 25 years ago when it became clear that UNDP support would end. Opportunities were not seized then, I contend, to bring about radical and efficient changes to the management and operations of this important rice germplasm network, but without losing any of the benefits of the previous 20 years. I also believed it should be possible to add even more scientific value.

Did we miss an opportunity?
But first, a little background, as it’s relevant to what subsequently took place—or rather didn’t.

In 1990 IRRI Management made the decision to reorganize the institute’s rice germplasm conservation and exchange activities. The Genetic Resources Center (GRC) was established bringing together INGER, the International Rice Germplasm Center (IRGC, the genebank), and the Seed Health Unit (SHU) into a single organizational unit, but with these three retaining their identities and functions. Recruitment for a founding head of GRC began in September 1990, and I was appointed from 1 July 1991. By then a decision had already been made (wisely in my opinion) to keep the SHU as an separate unit, given its important role of ‘policing’ the health of incoming rice germplasm and that being exported to other rice programs around the globe, under the auspices of the Plant Quarantine Service of the Philippines. We quickly lost the name International Rice Germplasm Center (how was it possible to have a center within a center?), and on my appointment GRC comprised the International Rice Genebank and INGER. While I was given overall responsibility for all GRC facilities and staff, the head of INGER (then Dr DV Seshu) ran the network on a daily basis, as I did the International Rice Genebank.

And it was through my role in GRC that I became involved in discussions about the future of INGER. I had joined IRRI from The University of Birmingham, where I had been a member of the Plant Genetics Group. Birmingham had a fine reputation for quantitative genetics, and my colleagues there had a lot of experience in running germplasm evaluation trials. Actually they had been trialing populations of tobacco for decades to understand the nature of quantitative variation in their experimental lines. With my colleagues Brian Ford-Lloyd and Martin Parry I’d also spearheaded discussions (controversial at the time) about climate change and how genetic resources could contribute towards adaptation. I had proposed a system of germplasm testing in Europe.

So with this dual focus, I felt that with a re-jigging of the INGER trials it would be possible to increase the data value of a smaller number of precision trials without losing the valuable germplasm testing and selection opportunities for breeders. There’s considerable evidence to demonstrate that it’s not necessary to run hundreds of trials to achieve a thorough evaluation and analysis of genotypes and their performance in different environments. Two trials are better than one, of course, four better than two. And twenty better than ten. More than twenty and the ‘Law of Diminishing Returns’ apparently kicks in, so my Birmingham quantitative genetics colleagues advised me.

A new approach to germplasm testing
In a nutshell, my proposal was to identify key sites across a range of rice-growing environments, characterize them thoroughly, keep careful weather data at each site, and trial germplasm there using different experimental designs as appropriate in order to develop a critical analysis of germplasm performance across environments, or genotype x environment interaction. With quality data being collated for analysis by IRRI—and rapidly—it would then be possible to predict and propose a smaller set of varieties to be tested more widely by breeders round the globe at their own sites. They would no longer be ‘required’ to test a large number of germplasm lines, most of which would not be suitable for their conditions in any case. Nor would INGER be ‘burdened’ with the costly distribution of a large amount of seeds in multiple trials annually.

During my travels many breeders had told me, off the record so-to-speak, that they found the large trials a burden. And as early as 1992 I’d had discussions with a post-doctoral fellow at IRRI (I can’t remember his name) how we might use geographical information systems (GIS), or perhaps I should say proto-GIS, to enhance and rationalize germplasm testing across multiple sites.

Just imagine what we could achieve today in terms of germplasm testing. There are now sophisticated GIS applications, satellite imagery, as well as all the molecular approaches to characterize germplasm lines even before they’ve been tested in the field. As early as 1995 we had shown that molecular markers could be used to predict the performance of germplasm. Think what might be possible today with the application of various ‘omics’ technologies*.

Let’s not delay
I don’t think that I’ve done particular justice to the ideas I raised almost a quarter of a century ago. Nor am I suggesting that they are necessarily the only or appropriate ones. But different ideas did—and still do—need to be put on the table. Unfortunately, at that time institutional politics, vested interests and, I have to say, some unimaginative leadership of the network for at least a decade or so after Dr Seshu retired, did not permit consideration in any meaningful way, let alone introduction, of a new strategy and approach for INGER.

In that sense I feel it was an opportunity (or opportunities) delayed. By now we could have had almost 25 years of solid and reliable data for G x E analyses that would stand up to critical scientific scrutiny. I just hope that when the time comes for further discussions about the future of INGER, as indicated in the riceTODAY article, that the new opportunities are not squandered. The network and its benefits are too important.

But the network has to be fit for purpose. It has to demonstrate its relevance and adopt new approaches. Only then can it contribute more effectively to the ‘Big Data’ approach highlighted in a recent Thomson Reuters web publication.

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* My former IRRI colleague Ken McNally wrote an excellent chapter for our Genetic Resources and Climate Change book in 2014. My friend Rodomiro Ortiz has just published a book on plant breeding and ‘omics’.