Plant Genetic Resources: Our challenges, our food, our future

phillips-jade

Jade Phillips

That was the title of a one day meeting on plant genetic resources organized by doctoral students, led by Jade Phillips, in the School of Biosciences at The University of Birmingham last Thursday, 2 June. And I was honoured to be invited to present a short talk at the meeting.

Now, as regular readers of my blog will know, I began my career in plant genetic resources conservation and use at Birmingham in September 1970, when I joined the one year MSc course on genetic conservation, under the direction of Professor Jack Hawkes. The course had been launched in 1969, and 47 years later there is still a significant genetic resources presence in the School, even though the taught course is no longer offered (and hasn’t accepted students for a few years). Staff have come and gone – me included, but that was 25 years ago less one month, and the only staff member offering research places in genetic resources conservation is Dr Nigel Maxted. He was appointed to a lectureship at Birmingham (from Southampton, where I had been an undergraduate) when I upped sticks and moved to the International Rice Research Institute (IRRI) in the Philippines in 1991.

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Click on this image for the full program and a short bio of each speaker.

Click on each title below; there is a link to each presentation.

Nigel Maxted (University of Birmingham)
Introduction to PGR conservation and use

Ruth Eastwood (Royal Botanic Gardens, Kew – Wakehurst Place)
‘Adapting agriculture to climate change’ project

Holly Vincent (PhD student, University of Birmingham)
Global in situ conservation analysis of CWR

Joana Magos Brehm (University of Birmingham)
Southern African CWR conservation

Mike Jackson
Valuing genebank collections

Åsmund Asdal (NordGen)
The Svalbard Global Seed Vault

Neil Munro (Garden Organic)
Heritage seed library

Maria Scholten
Natura 2000 and in situ conservation of landraces in Scotland: Machair Life (15 minute film)

Aremi Contreras Toledo, Maria João Almeida, and Sami Lama (PhD students, University of Birmingham)
Short presentations on their research on maize in Mexico, landraces in Portugal, and CWR in North Africa

Julian Hosking (Natural England)
Potential for genetic diversity conservation – the ‘Fifth Dimension’ – within wider biodiversity protection

I guess there were about 25-30 participants in the meeting, mainly young scientists just starting their careers in plant genetic resources, but with a few external visitors (apart from speakers) from the Millennium Seed Bank at Kew-Wakehurst Place, the James Hutton Institute near Dundee, and IBERS at Aberystwyth.

The meeting grew out of an invitation to Åsmund Asdal from the Nordic Genetic Resources Center (NordGen) to present a School of Biosciences Thursday seminar. So the audience for his talk was much bigger.

asmund

Åsmund is Coordinator of Operation and Management for the Svalbard Global Seed Vault, and he gave a fascinating talk about the origins and development of this important global conservation facility, way above the Arctic Circle. Today the Vault is home to duplicate samples of germplasm from more than 60 depositor genebanks or institutes (including the international collections held in the CGIAR genebank collections, like that at IRRI.

Nigel Maxted’s research group has focused on the in situ conservation and use of crop wild relatives (CWR), although they are also looking at landrace varieties as well. Several of the papers described research linked to the CWR Project, funded by the Government of Norway through the Crop Trust and Kew. Postdocs and doctoral students are looking at the distributions of crop wild relatives, and using GIS and other sophisticated approaches that were beyond my comprehension, to determine not only where there are gaps in distributions, lack of germplasm in genebank collections, but also where possible priority conservation sites could be established. And all this under the threat of climate change. The various PowerPoint presentations demonstrate these approaches—which all rely on vast data sets—much better than I can describe them. So I encourage you to dip into the slide shows and see what this talented group of scientists has been up to.

Neil Munro from Garden Organic described his organization’s approach to rescue and multiply old varieties of vegetables that can be shared among enthusiasts.

n_munro

Seeds cannot be sold because they are not on any official list of seed varieties. What is interesting is that one variety of scarlet runner bean has become so popular among gardeners that a commercial seed company (Thompson & Morgan if I remember what he said) has now taken  this variety and selling it commercially.

julian

Julian Hosking from Natural England gave some interesting insights into how his organization was looking to combine the conservation of genetic diversity—his ‘Fifth Dimension’—with conservation of natural habitats in the UK, and especially the conservation of crop wild relatives of which there is a surprisingly high number in the British flora (such as brassicas, carrot, and onions, for example).

So, what about myself? When I was asked to contribute a paper I had to think hard and long about a suitable topic. I’ve always been passionate about the use of plant genetic diversity to increase food security. I decided therefore to talk about the value of genebank collections, how that value might be measured, and I provided examples of how germplasm had been used to increase the productivity of both potatoes and rice.

m_jackson

Nicolay Vavilov is a hero of mine

Although all the speakers developed their own talks quite independently, a number of common themes emerged several times. At one point in my talk I had focused on the genepool concept of Harlan and de Wet to illustrate the biological value (easy to use versus difficult to use) of germplasm in crop breeding.

Jackson FINAL - Valuing Genebank Collections

In the CWR Project research several speakers showed how the genepool concept could be used to set priorities for conservation.

Finally, there was one interesting aspect to the meeting—from my perspective at least. I had seen the titles of all the other papers as I was preparing my talk, and I knew several speakers would be talking about future prospects, especially under a changing climate. I decided to spend a few minutes looking back to the beginning of the genetic conservation movement in which Jack Hawkes was one of the pioneers. What I correctly guessed was that most of my audience had not even been born when I started out on my genetic conservation career, and probably knew very little about how the genetic conservation movement had started, who was involved, and what an important role The University of Birmingham had played. From the feedback I received, it seems that quite a few of the participants were rather fascinated by this aspect of my talk.

Through hard work, great things are achieved

BirminghamUniversityCrestPer Ardua Ad Alta

That’s the motto of The University of Birmingham, and ‘these sentiments sum up the spirit of Birmingham and illustrate the attitude of the people who have shaped both the city and the University.’

Almost 50 years ago, I had no inkling that I would have more than half a lifetime’s association with this university. Receiving its royal charter in 1900 (although the university was a successor to several institutions founded in the 19th century as early as 1828), Birmingham is the archetypal ‘redbrick university‘, located on its own campus in Edgbaston, about 3 miles southwest of Birmingham city center.


First encounter in 1967

My first visit to the university was in May or June 1967—to sit an exam. Biology was one of the four subjects (with Geography, English Literature, and General Studies) I was studying for my Joint Matriculation Board Advanced Level high school certificate (essentially the university entrance requirement) here in the UK. We were only four or five biology students at my high school, St Joseph’s College in Trent Vale, Stoke-on-Trent (motto: Fideliter et Fortiter).

Now, I don’t remember (maybe I never knew) whether we were too few in number to sit our biology practical exam at the school, or all students everywhere had to attend an examination venue, but we set off by train from Stoke to Birmingham, and ended up at the School of Biological Sciences building. It was a new building then, and the (federal) School had only recently been formed from the four departments of Botany, Zoology & Comparative Physiology, Genetics, and Microbiology.

Just before 2 pm, the five of us—and about 100 other students—trooped into the main laboratory (that I subsequently came to know as the First Year Lab) on the second floor. Little did I know that just over three years later I’d be joining the Department of Botany as a graduate student, nor that 14 years later in 1981 I would join the faculty as Lecturer in Plant Biology. Nothing could have been further from my mind as I settled down to tackle a dissection of the vascular system of a rat, and the morphology of a gorse flower, among other tasks to attempt.

Birmingham was not on the list of universities to which I had applied in December 1966. I’d chosen King’s College, London (geography), Aberystwyth (zoology and geography), Southampton (botany and geography), York (biology), Queen Mary College, London (general biological sciences), and Newcastle (botany and geography). In the end, I chose Southampton, and spent three very happy if not entirely fruitful years there.

Entering the postgraduate world

Jack Hawkes

Jack Hawkes

The next time I visited Birmingham was in February 1970. I had applied to join the recently-founded postgraduate MSc Course on Conservation and Utilization of Plant Genetic Resources. I was interviewed by Course Director and Head of the Department of Botany, Professor JG Hawkes and Senior Lecturer and plant ecologist, Dr Denis Wilkins.

Despite the grilling from both of  them, I must have made an impression because I was offered a place for the following September. The only problem: no support grant. Although Hawkes had applied for recognition by one of the research councils to provide postgraduate studentships, nothing had materialized when I applied (although he was successful the following year, and for many years afterwards providing studentships to British students). So, after graduation from Southampton in July 1970 I was on tenterhooks all summer as I tried to sort out a financial solution to attend the course. Finally, around mid-August, I had a phone call from Hawkes telling me that the university would provide a small support grant. It was only £380 for the whole year, to cover all my living expenses including rent. That’s the equivalent of about £5600 today. The university would pay my fees.

All set then. I found very comfortable bed-sit accommodation a couple of miles from the university, and turned up at the department in early September to begin my course, joining four other students (from Nigeria, Pakistan, Turkey and Venezuela). It was during this one year course that I really learned how to study, and apart from my weekly Morris dancing night, I had few other distractions. It was study, study, study: and it paid off. The rest is history. I graduated in September 1971, by which time I’d been offered a one-year position at the newly-founded International Potato CenterCIP logo (CIP) in Lima, Peru, and I was all set for a career (I hoped) in the world of genetic resources and conservation. As it turned out, my travel to South America was delayed by more than a year during which time I registered for and commenced a PhD study on potatoes, finally landing in Lima in January 1973 and beginning a career in international agricultural research that lasted, on and off, until my retirement in 2010. I carried out most of my PhD research in Peru, and submitted my thesis in October 1975.

Jack Hawkes and me discussing landrace varieties of potatoes in the CIP potato germplasm collection, Huancayo, central Peru in early 1974.

Graduation December 1975. L to R: Jack Hawkes (who co-supervised my PhD), me, and Trevor Williams (who became the first Director General of the International Board for Plant Genetic Resources). Trevor supervised my MSc dissertation.

Then I returned to Lima, spending another five years with CIP in Costa Rica carrying out research on bacterial diseases of potatoes among other things.

I should add that during the academic year 1971-72, a young woman, Stephanie Tribble, joined the MSc course. A few months later we became an ‘item’.

Steph’s MSc graduation at the University of Birmingham in December 1972, just weeks before I flew to South America and join the International Potato Center in Lima, Peru.

After graduation, she joined the Scottish Plant Breeding Station just south of Edinburgh, but joined me in Lima in July 1973. We married there in October, and she also had a position with CIP for the years we remained in Lima.

A faculty position
On 1 April 1981 I joined the University of Birmingham as a lecturer in the Department of Plant Biology.

Richard Sawyer

By mid-1980, after almost five years in Costa Rica, I felt that I had achieved as much as I could there, and asked my Director General in Lima, Dr Richard Sawyer, for a transfer to a new position. In November, we moved back to Lima, and I was expecting to be posted either to Brazil or possibly to the Philippines. In the meantime, I had been alerted to a recently-established lectureship in the Department of Plant Biology (formerly Botany) at Birmingham, and had been encouraged to apply¹. With encouragement from Richard Sawyer², and having been invited for interview, I made the trek back to the UK from Lima towards the end of January 1981. The interview process then was very different from what might be expected nowadays. No departmental seminar. Just a grilling from a panel chaired by the late Professor John Jinks, FRS, Dean of the Faculty of Science and head of the Department of Genetics. There were three staff from Plant Biology (Hawkes, Dennis Wilkins, and Brian Ford-Lloyd), and the head of the Department of Biochemistry and Deputy Dean, Professor Derek Walker.

We were three candidates. Each interview lasted about 45 minutes, and we all had to wait outside the interview room to learn who would be selected. I was interviewed last. Joining the other two candidates afterwards, we sat side-by-side, hardly exchanging a word between us, nervously waiting for one of us to be called back in to meet the panel. I was the lucky one. I was offered the position, accepted immediately, and a couple of days later flew back to Lima to break the news and make plans to start a new life with Steph and our daughter Hannah (then almost three) in Birmingham.

Over the 10 years I spent at Birmingham I never had the worry (or challenge) of teaching any First Year Course – thank goodness. But I did contribute a small module on agricultural systems to the Second Year common course (and became the Second Year Chair in the School of Biological Sciences), as well as sharing teaching of flowering plant taxonomy to plant biology stream students mtj-and-bfl-book-launchin the Second Year. With my colleague Brian Ford-Lloyd (with whom I’ve published three books on genetic resources) I developed a Third Year module on genetic resources that seems to have been well-received (from some subsequent feedback I’ve received). I also contributed to a plant pathology module for Third Year students. But the bulk of my teaching was to MSc students on the graduate course on Conservation and Utilization of Plant Genetic Resources – the very course I’d attended a decade earlier. My main focus was crop evolution, germplasm collecting, and agricultural systems, among others. And of course there was supervision of PhD and MSc student research projects.

One of the responsibilities I enjoyed was tutoring undergraduate students, and always had an open door if they needed to see me. It quite shocked me in the late 1990s when my elder daughter, then a student at Swansea University, told me that her tutors had very limited and defined access hours for students. Of course you can’t be on call all day, every day, but you have to be there if a student really need to see you. And my tutees knew that if my office door was open (as it mostly was) they were free to come in and see me.

Once the four departments of the School of Biological Sciences merged into a single department in 1988, I aligned myself with and joined the Plant Genetics Group, and found a better role for myself. I also joined and became Deputy Chair of a cross-disciplinary group called Environmental Research Management (ERM) whose aim was to promote the strength of environment-related research across the university. Through ERM I became acquainted with Professor Martin Parry, and together with Brian Ford-Lloyd we published a book on genetic resources and climate change in 1990, and another in 2014 after we had retired.

Moving on
Even though the prospect of promotion to Senior Lecturer was quite good (by 1989 I’d actually moved on to the Senior Lecturer pay scale), I was becoming somewhat disillusioned with university life by that time. Margaret Thatcher and her government had consistently assaulted the higher education sector, and in any case I couldn’t see things getting any better for some years to come. In this I was unfortunately proved correct. In September 1990 a circular dropped into my post, advertising a new position at the International Rice Research Institute (IRRI) in the Philippines. This was for a germplasm specialist and first head of the Genetic Resources Center. So I applied, was interviewed in January 1991, and accepted the position with a view to joining the institute from 1 July. They actually wanted me to start on 1 April. But as I explained—and IRRI Management accepted—I had teaching and examination commitments to fulfill at the university. In February I began to teach my third year module on genetic resources for the last time, and set the exams for all students to take in May and June. Once the marking and assessments had been completed, I was free to leave.

Friday 28 June was my last day, ending with a small farewell party in the School. I flew out to the Philippines on Sunday 30 June. And, as they say, the rest is history. I never looked back. But now, retirement is sweet, as are my memories.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
¹ Jack Hawkes was due to retire in September 1982 and, recognizing that his departure would leave a big hole in the MSc teaching, the university approved the recruitment of a lecturer in plant genetic resources (with a focus on crop evolution, flowering plant taxonomy, and the like) essentially covering those areas where Jack had contributed.
² Dick Sawyer told me that applying for the Birmingham position was the right thing to do at that stage of my career. However, the day before I traveled to the UK he called me to his office to wish me well, and to let me know whichever way the interview went, he would have a new five-year contract waiting on his desk for me on my return. From my point of view (and I hope CIP’s) it was a win-win situation. Thus I left for the interview at Birmingham full of confidence.

 

It’s publish or perish, Jim – but not as we know it

perishOr to put it another way: The scientist’s dilemma . . . Where to publish?

Let me explain.

It’s autumn 1982. And just over a year since I joined the faculty of The University of Birmingham. Our department had a new Mason Professor of Botany, someone with a very different academic background and interests from myself.

At one departmental coffee break several of us were sitting around discussing various issues when the topic of academic publishing came up.

“In which journals do you publish, Mike?” the new head of department asked me. 1355408371_883_00_800I told him that I’d published several papers in the journal Euphytica, an international journal covering the theoretical and applied aspects of plant breeding. It’s now part of the Springer stable, but I’m not sure who the publisher then.

His next question surprised me. It’s not an exaggeration to say that I was gob-smacked. “Is that a refereed journal?” he asked, and went on to explain that he’d never even heard of Euphytica. In my field, Euphytica was considered then as an excellent choice for papers on genetic resources. In a sense he was valuing my academic output based on his ‘blinkered’ view of our shared discipline, botany, which is after all a broad church.

10722Springer now has its own in-house genetic resources journal, Genetic Resources and Crop Evolution (I’m a member of the editorial board), but there are others such as Plant Genetic Resources – Characterization and Utilization (published by Cambridge University Press). Nowadays there are more journals to choose from dealing with disciplines like seed physiology, molecular systematics and ecology, among others, in which papers on genetic resources can find a home.

But in the 1970s and 80s and beyond, I’d always thought about the visibility of my research to others working in the same or allied fields. My research would be of little or no interest to researchers beyond genetic resources or plant breeding for example. So choice of journal in which to publish was predicated very much on this basis. Today, with online searches, the world’s voluminous scientific publishing is accessible at the click of a mouse, it’s perhaps less important exactly where you publish.

Back in the day we had to seek out a hard copy of a journal that interested us, or use something like Current Contents (I’m surprised that’s still going, even in hard copy) to check, on a regular basis, what was being published in various journals. And then contact the author for a reprint (before the days of email).

I can remember way back in the mid-1980s when I had to write a review of true potato seed, when you had to pay for a special literature search through the university library. Now everyone can do it themselves—from their own desk. Nowadays you just search for a journal online, or tap in a few key words, and Hey Presto! there’s a list of relevant papers, complete journal contents lists, abstracts, and even full papers if your institute has a subscription to the journal or the article itself is Open Access.

So the dynamics of scientific publishing have changed from the days when I first began. In some respects then scientific publishing has never been easier but then again never more challenging. Not only are scientists publishing more but they are expected to publish more. Sink or swim!

About a year ago, I was ‘invited’ to join ResearchGatea social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. Since then I receive almost daily (if not more frequent) stats about my science publications and who is citing them. It’s obviously quite gratifying to know that many of the papers I published over the decades are still having scientific traction, so-to-speak. And ResearchGate gives me a score indicating how much my papers are being cited (currently 32.10—is this good? I have no idea). There’s obviously no metric that determines the quality of these papers, nor whether they are being cited for good or bad.

In the 1980s there was some discussion of the value of citation indices. I remember reading an interesting article in an internal University of Birmingham newsletter, Teaching News I think it was called, that was distributed to all staff. In this article the author had warned against the indiscriminate use of citation indices, pointing out that an excellent piece of scholarship on depopulation in rural Wales would receive a much lower citation than say a lower quality paper on the rise of fascism, simply because the former represented a much narrower field of academic pursuit.

Today there are so many more metrics, journal impact factors and the like that are taken into account to assess the quality of science. And for many young researchers these metrics play an important role—for good or bad—for the progression of their careers. Frankly, I don’t understand all of these, and I’m glad I didn’t have to worry about them when I was a young researcher.

David_Colquhoun

Prof. David Colquhoun, FRS

And there are many pitfalls. I came across this interesting article on the blog of Professor David Colquhoun, FRS (formerly professor of pharmacology at University College London) about the use (and misuse) of metrics to assess research performance. There was one very interesting comment that I think sums up many of the concerns about the indiscriminate use of publication metrics:

. . . in six of the ten years leading up to the 1991 Nobel prize, Bert Sakmann failed to meet the metrics-based publication target set by Imperial College London, and these failures included the years in which the original single channel paper was published and also the year, 1985, when he published a paper that was subsequently named as a classic in the field. In two of these ten years he had no publications whatsoever.

Application of metrics in the way that it’s been done at Imperial and also at Queen Mary College London, would result in firing of the most original minds.

We seem obsessed by metrics. And whenever there is a request for publication metrics for whatever purpose, there are always perverse incentives and opportunities to game the system, as I discovered to IRRI’s cost during the CGIAR annual performance exercise in the late ‘Noughties’. And when the submitted data are scrutinized by someone who really does not understand the nature of scientific publishing, then you’re on a slippery slope to accepting scientific mediocrity.

Transitions . . .

The community of the Consultative Group on International Agricultural Agriculture (CGIAR) has mourned the loss of three giants of agricultural research for development, two of whom I have blogged about earlier in the year. For a number of years they were contemporaries, leading three of the research centers that are supported through the CGIAR.

Sawyer3

Richard Sawyer

In March, Dr Richard Sawyer, first Director General of the International Potato Center (CIP) in Lima, Peru passed away at the age of 93. Richard was my first boss in the CGIAR when I joined CIP in January 1973. He remained Director General until 1991. Not one to suffer fools gladly, Richard set CIP on a course that seemed – to some at least – at odds with the way they thought international agricultural research centers should operate. He was eventually proved correct, and CIP expanded its mandate to include sweet potatoes and other Andean crops. His legacy in potato research lives on.

Trevor Williams

Trevor Williams

In April, Professor Trevor Williams, the first Director General of the International Board for Plant Genetic Resources (that became the International Plant Genetic Resources Institute, and now Bioversity International) passed away after a long respiratory illness, aged 76. Trevor had supervised my MSc thesis when I first joined the Department of Botany at the University of Birmingham in September 1970. We did some interesting work together on lentils. Here is my blog post. I also published an obituary in the scientific journal Genetic Resources and Crop Evolution.

Nyle Brady

Nyle Brady

Now we have just heard that Dr Nyle C Brady, third Director General of the International Rice Research Institute (IRRI), based in Los Baños, Philippines, passed away at the end of November. He was 95. I never worked for Brady, although I met him on several occasions during the 1990s and early 2000s. However, for a decade I worked at IRRI in the building that was named after him when he retired from IRRI in 1981. There is a long-standing tradition of such naming honours at IRRI for former Directors General (and two other dignitaries who were instrumental in setting up IRRI in 1959/60).

This is what IRRI just published recently on its website (where you will find other links and videos):

Dr. Nyle C. Brady, the third director general of the International Rice Research Institute (IRRI) and long-time professor and leader in soil science at Cornell University in the United States, passed away on 24 November in Colorado at age 95.

After 26 years at Cornell, Brady became IRRI’s director general in 1973. During 8 years at the helm, he pioneered new cooperative relationships between the Institute and the national agricultural research systems in Asia.

In October 1976, Dr. Brady led an IRRI group of scientists on a historic 3-week trip to China where they visited most of the institutions conducting rice research, as well as rice-growing communes where they interacted with farmers (a rare circumstance in 1976). Brady had previously provided China with seeds of IRRI-developed varieties, which jump-started the Institute’s formal scientific collaboration that facilitated the development of the country’s rice economy. The October 1976 trip marked the beginning of dramatic changes in China and of a close relationship between China and IRRI that has resulted in major achievements in rice research.

In a 2006 interview, Dr. Brady said, “My IRRI experience ranks very high. I had three careers: one at Cornell as a professor and a teacher, one at IRRI, and then one in Washington, D.C. with the U.S. Agency for International Development (USAID; as senior assistant administrator for science and technology, 1981-89), the United Nation Development Programme (UNDP), and The World Bank. I won’t say which one was the more critical. I will say that my experience at IRRI, not only for me but for my wife and family, was a highlight because we were involved in something that would help humanity. I felt I was working with a group of individuals, men and women, who wanted to improve the lot of people. They were not there just to do research and write papers; they were there to solve problems.”

“Nyle Brady led IRRI into a tremendous period of growth in the 1970s, through which some of its greatest achievements came to fruition,” said Robert Zeigler, IRRI’s current director general. “Even after he left IRRI to join USAID, and through his retirement, he was always looking out for IRRI’s best interest. He understood the power of what IRRI had to offer some of the world’s least advantaged people and did what he could to help us realize our full potential. IRRI and the world are better places for having had Nyle at the helm for so many productive years.”

Born in Colorado in the U.S., he earned his B.S. in chemistry from Brigham Young University in 1941 and his PhD in soil science from North Carolina State University in 1947. An emeritus professor at Cornell, he was the co-author (with Ray R. Weil) of the classic textbook, The nature and properties of soils, now in its 14th edition. “He was a giant in soil science and agriculture, and left an important legacy in many ways,” said Weil, professor of environmental science and technology at the University of Maryland.

“Brady was one of the giants of our field, and yet known for his personable approach to students and colleagues,” said Pedro Sanchez, director of the Agriculture and Food Security Center and senior research scholar at Columbia University’s Earth Institute, whom Brady mentored.

Completing a PhD – was it worth the effort?

A topical story in the Lima press
Overnight, there was an interesting and topical post (as far as I’m concerned) on the Facebook page of one of my ‘friends’—the son of one of my graduate students when I was a faculty member at The University of Birmingham in the 1980s. He hails from Peru. Carlos Arbizu Jr. is studying for his PhD at the University of Wisconsin-Madison and, as far as I can determine, he’s working on carrot genetics under the supervision of my friend and former potato scientist David Spooner.

Carlos had posted a link to an article published on the website of the Lima-based Newspaper Perú21: ¿Por qué estudiar un doctorado?  (Why study for a PhD?). To which Carlos had added the byline: PhD = Permanent Head Damage.

Maybe he’s going through a difficult patch right now. I’ve seen from several of his posts that he’s immersed in some pretty ‘heavy’ molecular genetic analysis. It’s beyond my comprehension.

But all PhD students go through peaks and troughs. I know I did. Some days nothing can go wrong, progress is swift. The world is your oyster, and there really is a light at the end of the tunnel. On other days, you just wish the earth would open up and swallow you.

And for many PhD students, the most trying time often comes when they begin to draft their thesis and eventually prepare to defend it. Unfortunately many science graduates have received very little formal training in how to write clear and concise prose. Writing just doesn’t come naturally. So what should be one of the most important aspects of completing a PhD can become a long and tedious chore. And before submission regulations were tightened up at UK universities, some students could take a couple of years or more to write up and submit their thesis for examination.

40 years ago today
Well, this Perú21 article was published yesterday. And today, 23 October (if memory serves me right) is exactly 40 years since I defended my PhD thesis: The Evolutionary Significance of the Triploid Cultivated Potato, Solanum x chaucha Juz. et Buk. I was almost 27 (old by UK standards, average or maybe young compared to many US graduate students), and had been working on my degree for four years. I’d completed a one-year MSc degree in genetic resources at Birmingham in September 1971 (having graduated from the University of Southampton with a BSc in botany and geography in July 1970), and then been offered the opportunity to work in Peru for a year at the newly-established International Potato Center (CIP). Well, for various reasons, and to cut a long story short, That opportunity didn’t materialize in September 1971 so my head of department, Professor Jack Hawkes (who went on to supervise my PhD) persuaded the Overseas Development Administration (now Department for International Development, DfID) to cough up some support until the funding for my position at CIP was guaranteed. Thus I began my study in Birmingham, and finally moved to Lima in January 1973, working as an Associate Taxonomist and conducting research that went towards my PhD thesis. And since I was employed and having a regular income, I took another three years to complete all the experimental work I had planned. In any case, when I joined CIP in 1973 the institute was still establishing and developing its own infrastructure. That was also one of the exciting aspects to my work. It was a real opportunity to build up and curate a large collection of Andean potato varieties and wild species, and study them in their native environment.

CIP collection

The CIP field collection of potato varieties planted in the Mantaro Valley near Huancayo in central Peru.

spuds

The diversity of Andean potato varieties.

The next couple of photos show some of the field work I carried out in various parts of Peru.

Mike Jackson and Jack Hawkes in the CIP potato germplasm collection, Huancayo, central Peru in early 1974

Learning from my supervisor, Professor Jack Hawkes, during one of his visits to Peru while I was carrying out my study.

MTJ in CIP

With CIP taxonomist, Professor Carlos Ochoa, a renowned Peruvian expert on potatoes and their wild relatives.

I was looking at the relationship between potato varieties with different chromosome numbers, so-called diploids and tetraploids, with 24 and 48 chromosomes respectively. If you can cross these two types you expect to produce some with an intermediate chromosome number. So, 48 x 24 = 36, the triploids. For the first years at CIP we didn’t have any glasshouses where we could work. Instead we had rather rustic polytunnels right in the field next to the germplasm collection, where I would make all those pollinations using the so-called cut-stem technique.

Experimental data from other parts of the world had shown that triploids were formed only rarely in such crosses. Yet triploid varieties were quite common and highly prized by potato farmers in the Andes. I was trying to determine if the crossability relationships of these native potatoes might be different in their indigenous environment. So I went on to make hundreds of crosses (and thousands of pollinations), as well as study indigenous farming systems in the south of Peru. This next gallery show some of the triploids potatoes grown by farmers. One of the most prized was the variety Huayro, and there were two forms, one round and the other elongated (and quite large). Both had red skins and yellow flesh.

Back to Birmingham
In May 1975, Steph and I headed back to the UK. But not directly. On the assumption that I would successfully defend my PhD thesis, CIP’s Director General had offered me a new position in the Outreach Department, and with the possibility of moving to Central America. So we headed for Costa Rica (where I’d eventually move to in April 1976) to see the lie of the land, so to speak. And from there we went on to Mexico for a few days to visit our old friends, and former CIP colleagues, John and Marion Vessey who had moved to maize and wheat center, CIMMYT, near Mexico City. From Mexico we headed to New York (first flight on a wide-bodied jet, an Eastern Airlines L-1011 Tristar) for a connection with British Airways to Manchester where my parents met us. We spent a further week looking for somewhere to live in Birmingham, and were fortunate to find an apartment very convenient to the university and only a few minutes walk from the Department of Botany (as it was then) Winterbourne Gardens where I had been assigned some lab space and a desk.

A nightmare waiting to happen
Now remember, there were no PCs or laptops, cloud computing, USB sticks or floppy disks in 1975. All my thesis data was available in hard copy only, and I carried a briefcase with four years of work with me from Lima to the UK on that journey I just related. The briefcase was hardly ever out of my sight! In those days it was not unknown for a graduate student to have lost a briefcase on a journey containing a complete draft of a thesis. No backup!

Getting into a routine
Once settled in Birmingham, I planned out my work for the coming months, with a deadline of 1 October. That was the final day of submission if I wanted to have my thesis examines and (if approved) have the degree awarded at the next congregation or commencement in early December that same year. But by the beginning of June I had not even begun to write, never mind complete the last minute field experiment I had planned (checking the ploidy of a set of hybrids produced earlier in the year) or create the figures I would include. Again, there was no digital technology available. I had to hand draw all my maps and other figures (my geography training in cartography at Southampton finally came in useful). While the department’s chief technician actually photographed all of these, I had to print all my own photographs (again, the experience I’d gained from my father, a professional photographer all his life, came in handy).

Working to a regular schedule every day, from around 7:30 am until 5 pm with a break for lunch, and spending another couple of hours after dinner, I soon began to make progress, although I didn’t actually start putting pen to paper until the beginning of July. It took me only six weeks to draft my thesis. Once I’d completed a chapter I’d hand it over to Jack Hawkes for review and revision. And to give him credit, he usually handed me back my draft with his comments within a couple of days only (and this was an approach I adopted with all my graduate students during the 1980s).

So, by mid-August or so I had a completed text, I’d checked the chromosome numbers of the hundred or so plants in the field, and set about the figures. I found someone who would type my thesis, but at the last moment he had to use a manual typewriter since the electric one he’d wanted to rent was no longer available. In 1975 The University of Birmingham changed the thesis submission regulations and it was no longer necessary to submit a thesis fully bound in a hard cover. I was able to submit in temporary binding, and this in fact saved perhaps three weeks from my tight schedule. I hit the 1 October deadline with about twenty minutes to spare just before 5 pm.

Thesis defence
I was quite surprised when my external examiner planned the defence of my thesis just three weeks later. All went to plan. In those days, the exam consisted of the graduate student, the external examiner and an internal examiner (usually the thesis supervisor). Today things might have changed, and even when I worked at Birmingham in the 80s the supervisor was no longer permitted to act as the internal examiner. I believe there may now also be a third panel member, to see fair play.

From the outset it was apparent that my thesis would pass muster, since the external examiner told me that he’d enjoyed reading the thesis. But we then went on to have a thorough discussion over the next three hours about many of the details, and the implications for potato genetic conservation and breeding. Phew!

And in early December, the 12th actually, I was able to celebrate with others from the department as we were awarded our degrees at the mid-year congregation.

19 Ed & Mike

L to R: Pam Haigh, Brenig Garrett,  me, Prof Trevor Williams, Prof Jack Hawkes, Dr Jean Hanson, Margaret Yarwood, Jane Toll, Stephen Smith

20 Ed & Mike

With my PhD supervisor, Prof. Jack Hawkes on my right, and MSc supervisor, Prof. Trevor Williams on my left; 12 December 1975.

PhD congregation, 12 December 1975 - with Mum and Dad

With my Mum and Dad.

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Was it worth it?
So let me come back to the question I posed in the title of this post. Was it worth it? Unequivocally Yes! Would I want to do it again? No!

Actually completing a PhD is probably the most selfish piece of research that a scientist will ever get to do. There’s one aim: complete a thesis and have the doctorate awarded. PhD research does not have to be ground-breaking at all. In fact much of it is pretty mundane, and that’s one of the down sides when things are not going so well. For Birmingham at least, the PhD regulations stated that the thesis had to represent a piece of original research, completed under supervision. And it’s the ‘under supervision’ that is critical. A PhD student is still maturing, so to speak. The work is guided by a mentor. Of course there can be breakthroughs that lead to the most prestigious prizes. I believe that Sir Paul Nurse’s PhD research set him off on the path that eventually led to his Nobel prize.

I have encouraged others to research for a PhD, and I hope I was able to give them the support and advice that my supervisors gave me. In that respect my PhD was a positive experience. It’s not always the case, and when student-supervisor relationships break down, every one suffers. It does not necessarily have to take many, many months (or years even) to write a thesis. It takes self-discipline but also support from the supervisor.

Without a PhD I would not have enjoyed the career in international agricultural research and academia that I did. My PhD was like a ‘union card’. It enabled me to seek opportunities that would probably have been closed without a PhD. But I also acknowledge that I was lucky. I moved into a field—genetic resources—that was just expanding, as were the international centers of the CGIAR. And I had mentors who were prepared to back me.

Forty years on I can look back to those days in 1975 with a fair degree of nostalgia. And then reflect on the benefits that accrued from that intense but disciplined period in the summer of 1975 (when there was a heat wave, and Arthur Ashe won the men’s title at Wimbledon), and which allow me now to enjoy the retirement I started five years ago.

Both of our daughters, Hannah and Philippa, went on to complete a PhD (in 2006 and 2010, respectively) in their chosen field: psychology! So I can’t have passed on so many negative vibes about graduate study, although their choice of psychology does make a profound statement, perhaps.

Peer-reviewed papers
Incidentally, I finally got around to publishing three papers from my thesis. When I returned to CIP just before New Year 1976, I moved into a new role and responsibilities. And even though I eventually found time to draft manuscripts, these took some time to appear in print after peer review, revision and acceptance. One of the papers—on the field work at Cuyo Cuyo—was originally submitted to the journal Economic Botany. And there it languished for over two years. I received an invitation from the editor of Euphytica to submit a paper on the same topic, so I withdrew my manuscript from Economic Botany. About that same time I received a letter from that journal’s interim editor in chief that manuscripts had been discovered unpublished up to 20 years after they had been submitted, and what did I want to happen to mine. It was published in Euphytica in 1980.

Jackson, M.T., J.G. Hawkes & P.R. Rowe, 1977. The nature of Solanumchaucha Juz. et Buk., a triploid cultivated potato of the South American Andes. Euphytica 26, 775-783. PDF

Jackson, M.T., J.G. Hawkes & P.R. Rowe, 1980. An ethnobotanical field study of primitive potato varieties in Peru. Euphytica 29, 107-113. PDF

Jackson, M.T., P.R. Rowe & J.G. Hawkes, 1978. Crossability relationships of Andean potato varieties of three ploidy levels. Euphytica 27, 541-551.PDF

“Education isn’t what you learn, it’s what you do with what you learn.” Anon.

degreeThere’s been quite a bit in the news again recently about the value of a university education, after George Osbourne, the UK’s Chancellor of the Exchequer, announced the scrapping of maintenance grants from the 2016/17 academic year. From that date, grants will be replaced by loans, adding yet further to the financial loan burden that university students are already facing to pay their tuition fees through loans. These financial challenges are making some (or is it many?) prospective students question whether they really do want or need a university education. Add to that the pressure on prospective students to study a subject that ‘should contribute’ more effectively to society and the economy, it’s no wonder that students are beginning to have second thoughts about going to university.

Also, with the publication of this year’s university exam results, the issue of grade creep is once again on the political agenda, since more than 50% of all students have graduated with a so-called ‘good’ degree. In the UK, this is a First or Upper Second (2:1) Class degree.

So why have these issues now attracted my attention?

Life on the south coast
Early July 1970. Forty-five years! It’s hard to believe. Yes, it’s forty-five years since I graduated from the University of Southampton with a BSc degree (not a very good one, I’m afraid) in Environmental Botany and Geography. There again, no-one in my year gained a First in botany, only a couple in geography. They didn’t hand out many top degrees in those days. More than 70% of students today are awarded a First or Upper Second. What is interesting from my point of view is during my high school years, going to university was not a foregone conclusion, or even an expectation for that matter. However, a university education was something that my post-war generation did begin aspire to. I was only the second person in my family to attend university.

55 Ed & Mike

Graduation Day, July 1970 at the University of Southampton, with my Mum and Dad, Lilian and Fred Jackson. Was I ever that young looking?

Now, although I didn’t exactly excel academically at Southampton, I wouldn’t have traded those three undergraduate years for anything. Some of the best years I have ever spent. Ah, the enthusiasm of youth. Did I ever have second thoughts? Never. I was extremely fortunate that my parents were very supportive, even though it must have been hard financially for them at times. My elder brother Ed had (in 1967) just graduated from the London School of Economics (with a First in geography) when I started at Southampton. So my parents were faced with another three years of support, even though my tuition fees were paid by the state, and I did receive a maintenance grant which Mum and Dad had to top up.

I guess I was lucky that Southampton took me in the first place, and didn’t throw me out after my first year. I never was very good at taking exams, well not in those school and undergraduate years. I only found my métier once I’d moved on to graduate school in 1971.

I went for an admissions interview at Southampton in early 1967 and immediately knew that this was where I wanted to study at, if they offered me a place. So once I received the results from my high school A-level exams (in biology, geography, and English literature, but not quite what I’d hoped for, grades-wise) I was on tenterhooks for a couple of weeks waiting for a response from the university. I was earning some cash, working as a lorry (truck) driver’s mate for a company based in Leek called Adams Butter. We delivered processed butter to retail outlets all over the UK, often being away from home for several nights at a stretch. Then once we delivered our load of about 25 tons of butter, we would head to the nearest port to pick up another 25 tons of Australian or New Zealand ‘raw’ butter, in large 56 lb frozen packs. I soon got fit throwing those boxes around.

Anyway, to cut a long story short, I arrived back at the depot after a long day on the road, and my father had kindly left a brief message with the dispatcher on duty: “Southampton wants you!” Obviously elated, I began to make plans to start my university life in October. The rest is history.

Back to the Midlands
Having graduated, I still didn’t know what the next stage of my life held. I’d applied to The University of Birmingham for a place on its newly-established MSc course Conservation and Utilization of Plant Genetic Resources in the Department of Botany. In February 1970 I’d been interviewed by course director Professor Jack Hawkes, and was offered a place, but with no guarantee of any financial support. It wasn’t until mid-August that I received a phone call confirming that he had been able to secure a small maintenance grant (just over £6 a week for the whole year, equivalent to about £80 a week today) and payment of my tuition fees. Undaunted at the prospect, I quickly accepted. And what a joy studying at Birmingham was. I certainly found an area of plant sciences that I could really immerse myself in, the staff were (on the whole) inspiring (particularly Trevor Williams with whom I completed my thesis), and I knew that I’d made the right choice.

But still there was no guarantee of gainful employment in my chosen field. That is until Jack Hawkes invited me to consider a one-year position in Peru. As things turned out, I did make it to Peru, registered for a PhD (which I completed in 1975), and made a career for myself in international agricultural research and academia. I received my degree from the Chancellor of the University, Sir Peter Scott, renowned ornithologist and conservationist, and son of ill-fated Antarctic explorer, Captain Scott at a graduation ceremony at the University of Birmingham on 12 December 1975.

20 Ed & Mike

Graduation on 12 December 1975, with Professor Jack Hawkes on my right, and Dr Trevor Williams on my left. I’m with my Mum and Dad in the two photos above.

Was it worth it?
When I decided to study botany at university I had no idea whether this would lead to a worthwhile career. Actually, it was not something I considered when applying. I just knew I wanted to study plants and geography, and then I’d see what life had in store for me afterwards, assuming I did actually graduate.

Steph studied botany at Swansea University (BSc 2:1), and we met at Birmingham when she studied for her MSc (also in genetic resources conservation) in 1971-72.

1972 002 Steph MSc

Steph’s MSc graduation in December 1972. This was about three weeks before I headed off to Peru. Steph joined me there in July 1973, and we were married in Lima in October that same year. We both had considerably longer hair then – and darker!

I think there was more expectation that our daughters, Hannah and Philippa, would go on to university, from our point of view and theirs. Indeed, having had the advantage of attending an international (and quite competitive) school in Manila, and studying for the International Baccalaureate diploma, university was the logical next step. And they both chose psychology (with an anthropology minor)—it wasn’t planned that way, that’s how it turned out.

Hannah originally started her university years at Swansea University in 1996, but after two years she transferred to one of the top liberal arts colleges in the USA: Macalester College in St Paul, and graduated BA summa cum laude in 2000 (left below, with the gold tassel). She then went on to the University of Minnesota to complete her PhD in industrial and organizational psychology in September 2006 (right below).

Philippa joined Durham University in 2000, and graduated in 2003 with her BSc (2:1) Honours degree (left below). After spending a year in Canada, she returned to the UK in 2004 and spent six months of more searching for a job. Eventually she secured a Research Assistantship in the Brain, Performance and Nutrition Research Centre at Northumbria University in Newcastle upon Tyne. After a couple of years she decided to register for a PhD and she was awarded her doctorate in December 2010 (right below).

So we’ve all benefited from having attended university, and have gone on to have successful careers. But I still believe it was the overall experience of university life as much as the academics that contributed those benefits. Unlike students today, we were fortunate not to have racked up significant debts while studying, and already Hannah and Philippa and their spouses are making plans for college education for their children—should they opt to follow that option.

I think the words of Cardinal John Henry Newman (1801-1890) are appropriate and as good today as when he wrote them in his essay ‘The Idea of a University’ in 1852: If then a practical end must be assigned to a University course, I say it is that of training good members of society… It is the education which gives a man a clear, conscious view of their own opinions and judgements, a truth in developing them, an eloquence in expressing them, and a force in urging them. It teaches him to see things as they are, to go right to the point, to disentangle a skein of thought to detect what is sophistical and to discard what is irrelevant.

I’m not sure that we do achieve those lofty ideals today as perhaps they aspired to in Newman’s day. There are just so many students moving through the system, the pressures to achieve are greater. While I was teaching at The University of Birmingham (for a decade in the 1980s) I became even more convinced that a university education is, in itself, worthwhile. This is often the first time that a young person leaves home, and has the opportunity to grow up away from the ever-watchful eyes of parents. Not everyone takes to university it must be said. But I think the majority who do make it to university would agree that, just like me, the three years they spend studying—and playing—are not three years wasted. It also makes it especially worrying that politicians are increasingly threatening the very existence and roles of universities, as is happening, for example, in a high profile way at the University of Wisconsin.

What’s in a name? I’m on a germplasm ID crusade!

What’s in a name? Well, not a lot it seems when it comes to crop germplasm. It’s a particular ‘bee in the bonnet’ I’ve had for many years.

We use names for everything. In the right context, a name is a ‘shorthand’ as it were for anything we can describe. In the natural world, we use a strict system of nomenclature (in Latin of all languages) – seemingly, to the non-specialist, continually and bewilderingly revised. Most plants and animals also have common names, in the vernacular, for everyday use. But while scientific nomenclature follows strict rules, the same can’t be said for common names.

Stretching an analogy
However, let me start by presenting you with an analogy. Take these two illustrious individuals for example.

We share the same name, though I doubt anyone would confuse us. Certainly not based on our phenotypes – what we look like. In any case, I’m WYSIWYG. Our ‘in common’ name implies no relationship whatsoever.

Marian_and_Vivian_BrownWhat about identical monozygotic twins, such as Marian and Val Brown? Dressing alike, they became celebrities in their adopted city of San Francisco from the 1970s until their deaths. Same genetics, but different names.

Maybe I’m stretching the analogy too much. I just want to hammer home the idea that sharing the same name should not imply common genetics. And different names might mask common genetics.

Naming crop varieties
So let’s turn to the situation in crop germplasm resources.

I had found in my doctoral research that apparently identical Andean potato varieties – based on morphology and tuber protein profiles – might have the same name or, if sourced from different parts of the country, completely different names given by local communities. And it also was not uncommon to find potatoes that looked very different having the same name – often based on some particular morphological characteristic. When we collected rice varieties in Laos during the 1990s, we described how Laotian farmers name their varieties [1].

During the 1980s my University of Birmingham colleague Brian Ford-Lloyd and I, with Susan Juned, studied somaclonal variation in the potato cv. Record. We received a sample of 50 or so tubers of Record, and fortunately decided to give each individual tuber its own ID number. The number of somaclones generated from each tuber was very different, and we attributed this to the fact that seed potatoes in the UK are ultimately produced from different tissue culture stocks. This suggested that there had been selection during culture for types that responded better to tissue culture per se [2]. The implication of course is that potato cv. Record (and many others) is actually an amalgam of many minor variants. I recently read a paper about farmer selection of somaclonal variants of taro (Colocasia esculenta) and cassava (Manihot esculenta) in Vanuatu.

Dropping the ID
But there is a trend – and a growing trend at that – to rely too much on names when it comes to crop germplasm. What I’ve found is that users of rice germplasm (and especially if they are rice breeders) rely too heavily on the variety name alone. And I’d be very interested to know if curators of other germplasm collections experience the same issue.

Why does this matter, and how to resolve this dilemma?

During the 1990s when we were updating the inventory of samples (i.e. accessions) in the International Rice Genebank Collection at IRRI, we discovered there were multiple accessions of several IRRI varieties, like IR36, IR64 or IR72. I’m not sure why they had been put into the collection, but they had been sourced from a number of countries around Asia.

13572539893_3f4b43dfd2_k

We decided to carefully check whether the accessions with the same name (but different accession numbers) were indeed the same. So we planted a field trial to carefully measure a whole range of traits, not just morphological, but also some growth ones such as days to flowering. I should hasten to add that included among the accessions of each ‘variety’ was one accession added to the genebank collection at the time the variety had been released – the original sample of each.

We were surprised to discover that there were significant differences between accessions of a variety. I raised this issue with then head of IRRI’s plant breeding department, the eminent Indian rice breeder Dr Gurdev Khush. Rather patronizingly, I thought, he dismissed my concerns as irrelevant. As a rice breeder with several decades of experience and the breeder responsible for their release, he assured me that he ‘knew’ what the varieties should look like and how they ought to perform. I think he regarded me as a ‘rice parvenu’.

It seemed to me that farmers had made selections from within these varieties that had been grown in different environments, but then had kept the same name. So it was not a question of ‘IR36 is IR36 is IR36‘. Maybe there was still some measure of segregation at the time of original release in an otherwise genetically uniform variety.

I have a hunch that some of the equivocal results from different labs during the early rice genome research using the variety Nipponbare can be put down to the use of different seed sources of Nipponbare.

Germplasm requests for seeds from the International Rice Genebank Collection often came by variety name, like Nipponbare or Azucena for example. But which Nipponbare or Azucena, since the there are multiple samples of these and many others in the collection?

What I also discovered is that when it comes to publication of their research, many rice scientists frequently omit to include the germplasm accession numbers – the unique IDs. Would ‘discard’ be too strong an indictment?

I was reviewing a manuscript just a few days ago, of a study that included rice germplasm from IRRI and another genebank. There was a list of the germplasm, by accession/variety name but not the accession number. Now how irresponsible is that? If someone else wanted to repeat or extend that study (and there are so many other instances of the same practice) how would they know which actual samples to choose? There is just this belief – and it beggars belief – that germplasm samples with the same name are genetically the same. However, we know that is not the case. It takes no effort to provide the comprehensive list of germplasm accession numbers alongside variety names.

Accession numbers should be required
I’m on the editorial board of Genetic Resources and Crop Evolution. I have proposed to the Editor-in-Chief that any manuscript that does not include the germplasm accession numbers (or provenance of the germplasm used) should be automatically sent back to the authors for revision, and even rejected if this information cannot be provided, whatever the quality of the science! Listing the germplasm accession numbers should become a requirement for publication.

Draconian response? Pedantic even? I don’t think so, since it’s a fundamental germplasm management and use issue.

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[1] Appa Rao, S., C. Bounphanousay, J.M. Schiller & M.T. Jackson, 2002. Naming of traditional rice varieties by farmers in the Lao PDR. Genetic Resources and Crop Evolution 49, 83-88.
[2] Juned, S.A., M.T. Jackson & B.V. Ford-Lloyd, 1991. Genetic variation in potato cv. Record: evidence from in vitro “regeneration ability”. Annals of Botany 67, 199-203.