Tag Archives: plant breeding

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8 billion . . . and counting

This is the latest estimate of the world’s population announced by the United Nations on 15 November 2022. Can you imagine? I was born 74 years ago when the population was just over a quarter of what it is today.

So many more mouths to feed, so many challenges to overcome. And population growth fastest in many of the world’s poorest countries.

The UN’s latest prediction is that another billion will be added by 2037, and that . . . half of the world’s population growth will be concentrated in just nine countries: India, Nigeria, the Democratic Republic of the Congo, Pakistan, Ethiopia, the United Republic of Tanzania, the United States of America, Uganda and Indonesia (ordered by their expected contribution to total growth).

In 2021, the Food and Agriculture Organization of the UN or FAO reported that 193 million people in 53 countries or territories were facing acute food insecurity. And while conflict and the effects of the Covid pandemic are contributors to this state of affairs, there is no doubt that weather extremes are also a major contributing factor, affecting many more people worldwide. More frequent storms. Too much water—or too little. Rising temperatures reducing the agricultural productivity in many regions.

Sustainable food and agricultural production were appropriately important themes at the latest climate change conference—COP27—in Egypt. The Consultative Group on International Agricultural Research or CGIAR, the Food and Agriculture Organization of the UN or FAO, and the Rockefeller Foundation together were prominent at COP27 with the aim of putting agrifood systems transformation at the heart of the conference.

So, whether you are a believer in climate change or a denier (I’ve never been a climate change denier—quite the opposite, in fact), surely you have to accept that something strange is happening to our climate.

More than 30 years ago, two University of Birmingham colleagues—Brian Ford-Lloyd and Martin Parry—and I organized a workshop to discuss the impact of climate change on agriculture and the conservation of plant genetic resources (and how they could, and should, be used to mitigate the effects of a warming climate). The proceedings were published in 1990. Twenty-five years later, in 2014, we followed up with a second volume reflecting how the science of climate change itself had progressed, and how better we were equipped to use genetic resources to enhance crop productivity.

So while agriculture has been—and continues to be—one of the contributors to climate change (livestock, methane from rice paddies, use of fertilizers and the like) it can and has to be part of the solution.

Since more than half of the world’s population are now urban dwellers, they do not produce their own food. Or at least not enough (even if they grow their own vegetables and such on small holdings or allotments) to support many others.

Subsistence farming is not a solution either, even though these farmers can increase productivity by adopting new agricultural practices and higher-yielding crop varieties, if appropriate and affordable. And those campaigners who advocate the abolition of livestock farming (and I have seen one young person state that all farming should be stopped!) have little notion of how that would affect the lives of farmers globally, or where the rest of us would source our food.

There has been much talk recently about diversification of farming systems and adoption of so-called ‘orphan crops’ as part of the solution. Of course these approaches can make a difference, but should not diminish the role and importance of staple crops like wheat, maize, rice, potatoes, sorghum, and many others.

So what are the options? Investment in plant breeding, among others, has to be central to achieving food security. We will need a pipeline of crop varieties that are better adapted to changing environmental conditions, that are one step ahead of novel pest and disease variants. Crop productivity will have to increase significantly over the next few decades.

My first encounter with plant breeding—or plant breeders for that matter—was during a visit, in July 1969, to the Plant Breeding Institute (PBI) in Cambridge during a field course at the end of my second year undergraduate degree course at the University of Southampton. We heard all about wheat breeding and cytogenetics from Dr Ralph Riley FRS (right) no less (later knighted and Director of the PBI from 1972 to 1978). Our paths crossed again several times during the 1990s when he was associated with the CGIAR.

During my third and final year at Southampton, 1969-1970, I enjoyed a plant breeding module taught by genetics lecturer Dr Joe Smartt whose original research background was in peanut cytogenetics. He had spent some years in Africa as a peanut breeder in Zambia (then known as Northern Rhodesia).

It was in that course that I was introduced to one of the classic texts on the topic, Principles of Plant Breeding by University of California-Davis geneticist, RW Allard (first published in 1960). Sadly I no longer have my copy that I purchased in 1969. It was devoured by termites before I left the Philippines in 2010.

I’ve never been actively involved in plant breeding per se. However, the focus of my research was the conservation of genetic resources (of potatoes and rice, and some other species) and pre-breeding studies to facilitate the use of wild species in plant breeding.

It’s been my privilege to know and work with some outstanding plant breeders. Not only did they need a knowledge of genetics, reproductive behavior, physiology and agronomy of a plant species, but this was coupled with creativity, intuition and the famous ‘breeder’s eye’ to develop new varieties.

Perhaps the most famous plant breeder I met in the early 1990s was 1970 Nobel Peace Laureate (and ‘Father of the Green Revolution’) Norman Borlaug, who spent a lifetime breeding wheat varieties, first with the Rockefeller Foundation and then with the International Center for the Improvement of Maize and Wheat (CIMMYT) in Mexico. I wrote about that encounter here.

Explaining how rice seeds are stored in the International Rice Genebank at IRRI to Nobel Peace Laureate Norman Borlaug

In the potato world I met Stan Peloquin from the University of Wisconsin, George Mackay in Scotland, and John Hermsen from Wageningen University. I worked alongside Peruvian potato breeder and taxonomist Carlos Ochoa (below) for several years.

When I joined IRRI in the Philippines in 1991 as head of the Genetic Resources Center, one of my close colleagues was 1996 World Food Prize Laureate Gurdev Khush (below left) who led the institute’s breeding program. He and his team bred more than 300 varieties of rice, some of which—like IR36 and IR72—have been grown over millions of hectares and saved countless millions from starvation.

And another rice breeder (and 2004 World Food Prize Laureate) famous for NERICA rice was Monty Jones (above right) at the Africa Rice Center in West Africa. Monty was a graduate at Birmingham and I was the internal examiner for his PhD thesis in 1983.

Plant breeding has come a long way since I first became interested 50 years ago. Breeders now have access to a whole new toolbox to accelerate the development of new varieties, some of which were not available just a few years ago.

A decade ago I asked my friend and former colleague at IRRI, Ken McNally to contribute a review of genomics and other ‘omics’ technologies to discover and analyse useful traits in germplasm collections to the 2014 genetic resources book that I referred to earlier [1]. I’m sure there have been many useful developments in the intervening years.

One of these is gene editing, and Nicholas Karavolias (a graduate student at Berkeley University) has written an interesting review (from which the diagram above was sourced) of how the CRISPR gene editing tool is being used to improve crops and animals.

Among the climate change challenges that I mentioned earlier is the likelihood of increased flooding in many parts of the world. Just last year there were devastating floods along the Indus River in Pakistan where rice is an important crop, as it is in many Asian countries. Although grown in standing water in paddy fields, rice varieties will die if totally submerged for more than a few days when floods hit.

Rice paddies near Vientiane, Laos.

There are rice varieties that can grow rapidly as flood waters rise. Known as deepwater rice varieties, they can grow several centimeters a day. But they are never submerged as such for long.

The harvest of deepwater rice varieties in Thailand.

Over several decades, submergence tolerant rice varieties were developed in a collaborative project between US-based scientists and those at IRRI using marker-assisted selection (not genetic engineering) to identify a gene, named Sub1 (derived from an Indian rice variety) and incorporate it into breeding lines. My former IRRI colleagues, plant physiologist Abdelbagi Ismail and breeder David Mackill have written about response to flooding. In the video below you can see the impact of the Sub1 gene [2]. And the impact of that gene is readily seen in the video below which shows two forms of the rice variety IR64 with and without the Sub1 gene.

To date, the impact of genetic engineering in crop improvement has not been as significant as the technology promised, primarily because of opposition (environmental, social, and political) to the deployment of genetically-modified varieties. I wrote about that issue some years back, and focused on the situation of beta-carotene rich rice known as ‘Golden Rice’. After many years of development, it’s gratifying to see that Golden Rice (as the variety Malusog) has now been grown commercially in the Philippines for the first time, and can now deliver real health and nutritional benefits to Vitamin A impoverished communities in the Philippines and hopefully elsewhere before too long.

In recent weeks there have been interesting news releases about the development of perennial rice and its potential to mitigate some climate change effects, and reduce labor usage. Researchers at the John Innes Centre in the UK have identified a gene that they hope will make wheat varieties more heat-resistant. The need for trait identification has never been greater or the importance of the hundreds of thousands of crop varieties and wild species that are safely conserved in genebanks around the world. Fortunately, as mentioned earlier, there are now better and more efficient tools available to screen germplasm for disease and pest resistance, or for genes like the wheat gene just discussed.

In terms of adaptation to a changing climate through plant breeding, I guess much of the focus has been on developing varieties that are better adapted to changing environment, be that the physical or biotic environment.

But here’s another challenge that was first raised some years back by one of my former colleagues at IRRI, Melissa Fitzgerald (right) who was head of the Grain Quality, Nutrition, and Postharvest Center, and is now Professor and Interim Head of the School of Agriculture and Food Sciences at the University of Queensland, Australia.

And it’s to do with the potential global savings of carbon. Melissa and her colleagues were looking at the cooking time of different rice varieties. This is what she (and her co-authors wrote in an interesting 2009 paper):

The cooking time of rice is determined by the temperature at which the crystalline structures of the starch begin to melt. This is called gelatinization temperature (GT). Lowering the GT of the rice grain could decrease average cooking times by up to 4 min. Although this might initially seem entirely insignificant, by computing the number of times rice is cooked in any one day by millions of households around the world, a decrease of just 4 min for each cooking event could save >10,000 years of cooking time each day. This represents massive potential for global savings of carbon and is of particular relevance to poor, rural households that depend on scarce local supplies of fuel.

Now there’s a huge breeding challenge.

Anyway, in this post I’ve really only scratched the surface of the topic, but hopefully for those readers not familiar with plant breeding, what it entails, and what it can promise, I hope that I’ve explored a few interesting aspects.

[1] McNally, KL. 2014. Exploring ‘omics’ of genetic resources to mitigate the effects of climate change. In: M Jackson, B Ford-Lloyd & M Parry (eds), Plant Genetic Resources and Climate Change. CABI, Wallingford, UK. pp. 166-189

[2] Ismail, AM & Mackill, DJ. 2014. Response to flooding: submergence tolerance in rice. In: M Jackson, B Ford-Lloyd & M Parry (eds), Plant Genetic Resources and Climate Change. CABI, Wallingford, UK. pp. 251-269.

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Almost as rare as hen’s teeth . . .

For about a two week period each Spring, around the end of April, The Alnwick Garden comes alive with an abundance of Japanese cherry blossoms, just as the rest of the garden is beginning to emerge from its winter slumber. We made a return visit there last Thursday only a week after we had been there, which I wrote about at the time. We noted then that the orchard was about to bloom, and didn’t want to miss the opportunity to see this wonder of Nature.

In 2008, this orchard of more than 320 great white cherry trees (Prunus ‘Taihaku’) was planted in the east-southeast section of the garden. Now 20 feet tall or more, words are insufficient to describe the wonder of this cherry orchard in full bloom.

The orchard is touted as the largest in the world of ‘Taihaku’ cherries. And this particular variety has an interesting history linking Japan, an Englishman, and a Sussex garden.

Cherry trees are central to Japanese culture, but tastes in different varieties have changed over the centuries. ‘Taihaku’ cherries apparently went extinct in Japan in the late 19th century. Move on a few decades, and up steps a very interesting Englishman, Captain Collingwood Ingram (1880-1981) who, after an early career interest in ornithology, became one of the world’s authorities on cherries. Indeed he was often referred to as ‘Cherry’ Ingram, a colossus, introducing many different Prunus species and varieties to the UK.

And it was through his passion for cherries that, in the 1920s, he came across a single, rather decrepit tree of Prunus ‘Taihaku’ in a Sussex garden. He successfully took cuttings, returning some to Japan. The trees at Alnwick (and indeed all ‘Taihaku’ trees worldwide) derive from that single Sussex tree.

In 2016, Japanese author Naoko Abe published an account about Ingram’s contribution to the survival of Japanese cherries. Here is a 2019 review of that book published by the Irish Garden Plant Society.

Abe herself also wrote an article for the Literary Hub, which is well worth the time to delve into. It gives some interesting background about Japanese cherry culture, why varieties became extinct, and of course, how Ingram turned this situation around.

Since all ‘Taihaku’ trees are derived from a single individual following vegetative propagation, there is zero genetic diversity worldwide for this variety. It’s an extreme example of genetic vulnerability, but that’s not a situation unique to Prunus ‘Taihaku’. The danger is that a pest or disease may emerge to which the trees have limited or no resistance, and there are no opportunities for selection of genetically-different individuals that might withstand such challenges.

Another example is the potato in Ireland. During the Irish Potato Famine of the 1840s which decimated the Irish population, potato crops (predominantly of the variety ‘Irish Lumper’ or ‘Lumper’) were wiped out by the late bight pathogen Phytophthora infestans, all plants equally susceptible to the disease. Unfortunately there are too many examples of crops with a narrow genetic base that are under threat.

Let’s look at the situation in rice, a crop I am familiar with. It’s the world’s most important staple crop, providing sustenance daily (and indeed often several times a day) to half the world’s population. Since time immemorial farmers have cultivated tens of thousands of varieties. But over the past half century, new varieties such as IR36 and IR72 (from the breeding program at the International Rice Research Institute, IRRI, in the Philippines where I worked from 1991-2010) have been adopted across across millions of hectares in Asia, replacing many of those farmer varieties, and effectively becoming genetic monocultures.

In the world of genetic resources conservation, which was the focus of much of my professional life over many decades, scientists are continually concerned about losing different varieties, and genetic diversity overall. However, this loss of diversity, or genetic erosion as it’s known, has been occurring forever, as farmers swap varieties and adopt new ones, the sorts of choices that farmers make all the time. There’s nothing strange or concerning about that as such.

Let me elaborate with an example from the Philippines. In the mid-1990s, a major typhoon swept across the north of the main island of Luzon, destroying in its path much of the local rice agriculture. Since we had been carrying out fieldwork in that region prior to the typhoon and, with permission from the farmers, taken small samples of their varieties for genetic analysis, we were able (after seed increase at IRRI) to return to farmers the varieties they had been growing before the catastrophe. Some willingly took them back. Others decided that this was an opportunity to make changes to their farming systems and adopt new varieties. But that was their choice, not ours (Pham et al., 2002).

Varieties may be lost, but is the actual genetic diversity itself totally lost? We have some evidence from rice (Ford-Lloyd et al., 2008) that’s not the case:

. . . where germplasm and genetic data have been collected throughout South and Southeast Asia over many decades, contrary to popular opinion, we have been unable to detect a significant reduction of available genetic diversity in our study material. This absence of a decline may be viewed positively; over the 33-year timescale of our study, genetic diversity amongst landraces grown in traditional agricultural systems was still sufficiently abundant to be collected for ex situ conservation.

However, the authors go on to raise concerns about future threats to diversity caused by climate changes or different agricultural practices. While landrace varieties are grown they can continue to adapt to environmental changes.

Overall, however, with thousands of different varieties of rice (and a multitude of other crops and their wild relatives) safely conserved in genebanks around the world, genetic diversity has not been lost. It’s available to dip into by breeders who incorporate traits from the landraces into new varieties (just look at the example of IR72 below that has 22 landrace varieties and one wild species in its pedigree), or as we showed in the Philippines example above, returned to farmers so they can continue to benefit in different ways from these old varieties.

Just recently I’ve been involved in an online discussion among old friends and colleagues about the loss of genetic diversity over the decades, and how much has actually been lost. As Brian Ford-Lloyd and I wrote in our 1986 introduction to genetic conservation:

Hard facts relating to genetic erosion are not easy to come by; what has been lost already can no longer be accounted. One therefore has to resort mainly to personal impressions and subjective accounts.

What is important is that over the past half century, efforts have been stepped up to safely conserve old varieties and wild species in a network of genebanks across the globe. And, in recent years, that effort has been backstopped financially and technically by the Crop Trust with grants in perpetuity to major world genebanks (such as those managed by eleven CGIAR centers) and the opening of the Svalbard Global Seed Vault in the permafrost high above the Arctic Circle.

However, even as these initiatives gain traction and deliver on their promises, we cannot remain complacent. Situations such as the ‘Taihaku’ cherry will continue to emerge (although perhaps not so extreme), and crops, wild species—and rare breed animals—will remain under threat. With habitat loss, and the threat of climate change that is gaining pace, never has genetic conservation (and use) been so important. ‘Taihaku’ can teach us a lesson if we take our eye off the ball.

 

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Exploring the mysteries of sex . . . and taking control!

I’ve been fascinated with sex (especially controlled sex) since my undergraduate days at the University of Southampton between 1967 and 1970. We were the socially permissive flower power generation.

But before you get too excited about this post’s content, I need to point out that, as a former botany student, I’m referring to sex among plants! And plant breeding. The real flower power!

Joe Smartt and Edgar Anderson

I guess it all started with two final year honours course on plant speciation (how different species evolve) and plant breeding, taught by geneticist Dr Joe Smartt. It was through the first that I discovered the beauty of introgressive hybridization (a mechanism that blends the gene pools of separate species; see a diagrammatic explanation in this post), a concept first expounded by another of my botanical heroes, Dr Edgar Anderson. And, there was this transformative book to dip into: Variation and Evolution in Plants (published 1950) by another great American botanist, G Ledyard Stebbins. In Joe’s introduction to plant breeding, we followed yet another classic text: Principles of Plant Breeding by American plant breeder and geneticist, Robert W Allard.

Trevor Williams

And when I moved to the University of Birmingham as a graduate student in September 1970, to study for a Master’s degree in plant genetic resources, Trevor Williams taught a fascinating course on plant variation, emphasising their breeding systems, and how understanding of these was important for the conservation and use of genetic resources. Much of my career subsequently was then spent studying variation and breeding systems in two important crop species, potatoes and rice, and a minor legume species, the grasspea.

Plants reproduce in the most weird and wonderful ways. If they didn’t, humanity’s days would be numbered. Where would we be if wheat and rice plants failed to produce their grains, the potato its underground treasure of tubers, or the banana those abundant hands of green fruits? No wonder in times past folks celebrated a Harvest Festival each autumn to give thanks for a successful harvest.

Beautiful acorns on the pedunculate oak, Quercus robur

You only have to look about you in late summer, as I did each day on my walks last year, to see Nature’s bounty all around—the consequence of plant sex. The trees and bushes were dripping with fruit—2020 was a mast year (as I have written about before). I don’t think I’ve seen such a year for acorns on the oak trees. And the chestnuts, hazels, and so many others. Such exuberant fecundity!

Have you ever looked closely at a ‘typical’ flower? Well, for the most part you can see the female pistil(s) comprising the style, stigma, and ovary, and the male stamens that carry the pollen.

However, there are many variations on this basic theme, different arrangements of the sex organs, even separate male and female flowers on the same plant (known as monoecy; maize is a good example) or separate plants (dioecy; holly). Differences in plant reproductive morphology promote self fertilization or cross fertilization. In addition, there is a host of physical and genetic mechanisms to promote or prevent self fertilization, as well as limiting sex between different species. All of this is aimed at ensuring a next generation of plants, and the one after that, and so on.

Plants attract a host of pollinators: visiting insects such as bees and moths, even some nectar-feeding marsupials and bats. I watched a remarkable sequence on David Attenborough’s latest blockbuster series, A Perfect Planet a few nights ago, about the fascinating pollination role of fig wasps.

Then I came across this tweet. Cockroaches of all creatures!

Wind pollination is a common feature of many grasses. However, several wheat and rice species, for example, promiscuously dangle their stamens apparently seeking cross fertilization. But they have often self fertilized before their flowers open. That’s not to deny that some cross pollination does occur in these species, but it’s generally the exception.

Some plants appear to reproduce sexually, but they have got around actual sex through a mechanism known as apomixis. These plants produce seeds but not following the normal fertilization process, so each seedling is a genetic copy of the ‘mother’ plant.

Berries on a diploid potato species, Solanum berthaultii

Other species have given up sex (almost) altogether, instead reproducing vegetatively with the ‘offspring’ being genetically identical (or essentially identical) to the mother plant. In others, like the potato, propagation is primarily through tubers. Yet, in the Andes especially where potatoes were first domesticated, many varieties are extremely sexually fertile, and produce berries rather like small tomatoes, although they are inedible. They contain lots of small seeds that we often refer to as true potato seed or TPS. In fact, in one experiment I observed at the International Potato Center (CIP) in Peru where I worked during the 1970s, a colleague of mine recorded a particular variety known as Renacimiento producing more than 20 t/ha of berries, in addition to about 20 t of tubers.

Anyway, I digress somewhat. During the years I was active scientifically (before I joined the ranks of senior management at the International Rice Research Institute in the Philippines, IRRI in the Philippines), I looked into various aspects of reproductive biology of several species.

In my doctoral research, carried out in the Andes of Peru, I investigated the breeding relationships between potato varieties with different numbers of chromosomes. The potato we consume almost on a daily basis (at least in my home) is known scientifically as Solanum tuberosum, and has four sets (48 in total) of chromosomes. It is what we call a tetraploid. Many other potato species have only two sets or 24 chromosomes, and are known as diploids. The tetraploid forms are mostly self fertile; diploids, on the other hand, have a genetic system of self incompatibility, and will only produce seeds if pollinated with pollen from a different genetic type.

This or similar system of self incompatibility is known from other species, like poppies for example. Anyway, the outcome is that ‘self’ pollen will not germinate on the stigma. The two images below (of various pollinations among wild potatoes), show a typical compatible pollination and fertilization event. Lots of pollen grains have stuck to the stigma, have germinated and grown the length of the style to reach the numerous ovules in the ovary.

In these next images, showing incompatible pollinations, few pollen grains remain on the stigma, not all germinated, and those that did, grew erratically. A few pollen tubes may reach the ovules but compared to the compatible pollinations, they are many fewer.

In the 1970s, one of my colleagues at CIP, Chilean breeder/agronomist Primo Accatino, championed the use of TPS as an alternative to propagation from seed tubers. One of the weak links, as it were, in any potato production cycle is the availability and cost of disease-free seed tubers. So TPS was seen as potentially fulfilling a gap in many developing countries that had neither the infrastructure nor staff to support seed potato production.

As I mentioned earlier, the common potato is a tetraploid with four sets of chromosomes, and this complicates the genetics and breeding. Breeding at the diploid level could be more straightforward. At least that was the hope and the challenge when I embarked on a project to produce TPS lines through inbreeding diploid potatoes and single seed descent. Funded by the British government, it involved scientists at the University of Birmingham (where I had joined the staff in 1981), the former Plant Breeding Institute in Cambridge, and CIP in Peru.

Was this just a pipe dream? Perhaps. Before developing the project concept, I’d had extensive discussions with my colleague at Birmingham, geneticist Dr Mike Lawrence who worked on self incompatibility in poppies (that has a similar genetic system to that in potatoes). His experience with poppies showed that if one tried long and hard enough, it was possible to break the self incompatibility.

Flowers of Solanum chacoense

We tried—and ultimately failed—closing the project after five years. We decided it would take just too much investment to make progress. If only we’d had available then what are now helping to transform potato breeding: self compatible diploid lines. At the end of the 1990s, scientists working at the USDA potato collection in Sturgeon Bay, Wisconsin identified self compatible lines in the widespread wild species Solanum chacoense. The Sli gene that confers self compatibility is apparently more widespread than previously thought, and has now been bred into diploid lines. Had we had those self compatible lines back in the 1980s, our work would have perhaps have reached a better conclusion.

When I moved to the Philippines in 1991 to head IRRI’s Genetic Resources Center (GRC), I had a collection of around 100,000 different lines of rice, cultivated and wild, to conserve in the institute’s International Rice Genebank.

With my colleagues in GRC, Dr Lu Bao-Rong, Amita ‘Amy’ Juliano and Dr Ma Elizabeth ‘Yvette’ Naredo, I spent several years investigating the breeding relationships between the cultivated forms of rice, Oryza sativa from Asia, and O. glaberrima from West Africa, and the closest wild Oryza species with a similar AA genome. We made thousands of crosses with the aim of understanding not only the breeding relationships, which is important to be able to better use wild species in rice breeding, but also to understand the taxonomy of wild and cultivated rices.

Pollinations (L) in the genebank screenhouse among AA genome species from Asia, Australia, and the New World, and (R) a crossing polygon from those pollinations expressed in terms of spikelet fertility.

This work led to several scientific publications, which you can access here: just look for publications with our names.

Another aspect of plant sex, important for genebank managers, is how the environment can affect plant fertility. While the seeds of many species (including rice and potatoes) can be stored at a low temperature (typically -18ºC) and for decades if not longer, it is essential that only the best seeds are placed in a genebank for long term conservation. That means ensuring that the growing conditions are the best possible to produce seeds of high quality—and in abundance—during an initial multiplication or later on for rejuvenation after some years of storage, if seed stocks are running low, or there are signs that seed viability may be declining.

At IRRI, in Los Baños south of Manila, we were faced with managing a large germplasm collection of rice lines from all over Asia, from Africa, and South America as well. And these had been collected over a very broad latitudinal range, while Los Baños sits at around 14ºN. We were attempting to grow in a single location many different rice lines, some of which had evolved under more temperate conditions, under different temperature regimes and daylengths.

Kameswara Rao

With my colleague Dr Kameswara Rao (and Professor Richard Ellis from the University of Reading, UK) we spent three years carefully analyzing the effects of different growing environments on seed quality for conservation. Just look for publications here under our names to check out what we achieved. The important changes we made to how we grew rice lines for optimum seed quality have endured until today, although (as I have reported elsewhere) changes to post-harvest handling of seeds have been improved through the work of former IRRI seed physiologist, Dr Fiona Hay.

So, as you can see, there are many different, and interesting, facets to plant sex. And as plant breeders and gene conservationists, we aim to exploit the idiosyncrasies of each species to produce more productive crop varieties or ensure the long term survival of varieties that no longer find favor with farmers, or wild species whose habitats are threatened through agricultural expansion, increasing urbanization, or climate change.

 

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Would I eat genetically-modified foods? Damn right I would! (Updated 2020-02-18 & 2021-01-08)

MC900436915Eat genetically-modified foods? I’ve been eating them all my life and I haven’t noticed any negative effects yet.

There’s hardly a food plant that we grow today that hasn’t undergone some sort of genetic modification. Let’s take the potato as a good example. I can’t think of any modern potato variety that does not have one or more wild species in its pedigree somewhere. These have been used for their disease resistance, among other reasons, such as Solanum demissum from Mexico to control the late blight pathogen Phytophthora infestans (the culprit in the Irish Potato Famine of the 1840s). That’s just one species – plenty more have also been crossed with modern potato varieties. There are also good examples from rice for submergence tolerance or salt tolerance using distantly-related wild species.

That’s genetic modification. Plain and simple. I guess most people don’t even realize. It’s what plant breeding is all about: taking different varieties or species (and their genes), crossing them (where possible) to make a hybrid, and selecting the best from the ‘DNA soup’. To increase the precision of conventional plant breeding, molecular markers are often now used to follow the transfer of useful characteristics or traits in conventional plant breeding populations.

GMO – genetically modified organism. An emotive term for some. For others, like me, genetic engineering is one of the tools in the arsenal for feeding a world population of 7+ billion – that’s growing rapidly – especially under a changing climate. Genetic engineering is even more precise than conventional plant breeding for moving genes (DNA) between species. However, there has been a lot of scare-mongering – and more – when it comes to GMOs. 

Now you might ask why I’ve focused on this topic all of a sudden. Well, on 8 August 2013, a field trial of Golden Rice (that contains beta carotene, a source of Vitamin A) in the south of Luzon, Philippines was vandalized by anti-GM activists (and maybe a few farmers), and destroyed.* This field trial was part of the important humanitarian research undertaken by the International Rice Research Institute (IRRI) and its partners in the Philippines, the Department of Agriculture and PhilRice (the Philippines Rice Research Institute) to develop biofortified rice varieties that can deliver Vitamin A and other micronutrients sustainably without having resort to supplementation or commercial fortification, which are expensive and only effective as long as such initiatives are funded.

In the video below, IRRI Deputy Director General, Dr Bruce Tolentino explains what happened on 8 August and why Golden Rice is so important for people who suffer from Vitamin A deficiency.

While GM crops are widely grown in the USA and some other countries, there has been significant public resistance in Europe, and particularly in the UK. I can understand, however, why the general public in the UK was – and is – wary. In the 1980s there were a couple of important food scares: a major foot and mouth outbreak in farm livestock; and BSE or ‘mad cow disease’. Furthermore, one or two commercial companies were attempting to commercialize some GM crops – without taking the time to explain why, how, and what for. The public lost faith in the ‘trust us’ line put out by the government of the day.

Environmental groups conducted major campaigns against even the testing of genetically-modified crops, let alone their commercialization. Very soon the activists had seized the initiative; the label of ‘Frankenstein foods’ stuck. An opportunity was lost, since scientists didn’t adequately step up to the plate and explain, in language that the average man in the street could understand, what GM technology was all about, and its importance. In the early days of GM research there were some inherent risks (such as the use of antibiotic markers to identify plants carrying the gene of interest); and some issues such as the ‘escape’ of genes from GMOs into wild plant populations. GM techniques have moved on, new approaches for identification of transgenic plants developed. But field research – based on the soundest of scientific principles, methods and ethics, generating good empirical data – is still needed to answer many of the environmental questions.

The vandalized Golden Rice field trial in Bicol, southern Luzon, Philippines

I do question the motives of some activists. Are they really concerned about real or perceived negative health and environmental impacts of GMOs? Or is the real issue that GM technology (as they see it) is in the hands of big agrochemical companies like Monsanto, Du Pont, Syngenta and others – an anti-capitalist campaign. In many countries much of the GM research is actually carried out by universities and publicly-funded research organizations such as the John Innes Centre in the UK.

I’ve had my own run-ins with these activists. In the early 1990s, then IRRI Director General Klaus Lampe opened a dialogue with a number of groups in the Philippines. He invited many anti-GM activists to IRRI for a two-day dialogue. I remember ‘challenging’ one prominent activist and future presidential candidate Nicanor Perlas about his anti-biotechnology campaign. As we analysed his perspectives, it became clear that his major concern was ‘genetic engineering’ – not biotechnology as a whole. I suggested to him that we could agree to disagree about genetic engineering (I appreciated there were risks, but as a scientist I wanted to study and evaluate those risks), but we should and could agree about the value of many of other biotechnology tools such as tissue culture, somaclones, or embryo rescue, among others. He concurred. Yet a few days after the meeting, he published a two page diatribe against ‘biotechnology’ (not just genetic engineering) in one of the Manila broadsheets. I find such actions (and positions) disingenuous, and typical of the lack of understanding that many of these people really have about GM. Just listen to the points of view presented by the activists in this Penn and Teller video (Eat This! Season 1. Episode 11. April 4, 2003). I already posted this before in my story about the late Nobel Laureate Norman Borlaug – but it’s worth repeating here. Just be careful – there is some strong language.

Here are a couple of classic quotes from Borlaug from that video:
Producing food for 6.2 billion people, adding a population of 80 million more a year, is not simple. We better develop an ever improved science and technology, including the new biotechnology, to produce the food that’s needed for the world today. And in response to the fraction of the world population that could be fed if current farmland was converted to organic-only crops: We are 6.6 billion people now. We can only feed 4 billion. I don’t see 2 billion volunteers to disappear.

Nevertheless, it is good to see the condemnation by the scientific community and media worldwide of the destruction of the Golden Rice field trial two weeks ago. In particular, it’s gratifying to hear that Mark Lynas, a well-respected British writer, journalist and environmental activist has turned his back on the anti-GMO lobby. He recently traveled to the Philippines to find out more for himself about Golden Rice research and the damage to the field trial.

Here are some of the media reports from around the world: in the New York Times; Slate; the Philippine Star; AGProfessional; Science 2.0; the BBC; and change.org. Even Fox News got in on the act in its characteristic over-the-top way! Here is an interesting piece about GM in general, published a couple of days ago in Forbes.

* Read this report by Mark Lynas after his visit to the Philippines recently.

Golden Rice has now been approved in the Philippines. Read this news story from the IRRI website, dated 18 December 2019:

After rigorous biosafety assessment, Golden Rice “has been found to be as safe as conventional rice” by the Philippine Department of Agriculture-Bureau of Plant Industry. The biosafety permit, addressed to the Department of Agriculture – Philippine Rice Research Institute (DA-PhilRice) and International Rice Research Institute (IRRI), details the approval of GR2E Golden Rice for direct use as food and feed, or for processing (FFP).

PhilRice Executive Director Dr. John de Leon welcomed the positive regulatory decision. “With this FFP approval, we bring forward a very accessible solution to our country’s problem on Vitamin A deficiency that’s affecting many of our pre-school children and pregnant women.”

Despite the success of public health interventions like oral supplementation, complementary feeding, and nutrition education, Vitamin A deficiency (VAD) among children aged 6 months to 5 years increased from 15.2 percent in 2008 to 20.4 percent in 2013 in the Philippines. The beta-carotene content of Golden Rice aims to provide 30 to 50 percent of the estimated average requirement (EAR) of vitamin A for pregnant women and young children.

“IRRI is pleased to partner with PhilRice to develop this nutrition-sensitive agricultural solution to address hidden hunger. This is the core of IRRI’s purpose: to tailor global solutions to local needs,” notes IRRI Director General Matthew Morrell. “The Philippines has long recognized the potential to harness biotechnology to help address food and nutrition security, environmental safety, as well as improve the livelihoods of farmers.”

The FFP approval is the latest regulatory milestone in the journey to develop and deploy Golden Rice in the Philippines. With this approval, DA-PhilRice and IRRI will now proceed with sensory evaluations and finally answer the question that many Filipinos have been asking: What does Golden Rice taste like?

To complete the Philippine biosafety regulatory process, Golden Rice will require approval for commercial propagation before it can be made available to the public. This follows from the field trials harvested in Muñoz, Nueva Ecija and San Mateo, Isabela in September and October 2019.

The Philippines now joins a select group of countries that have affirmed the safety of Golden Rice. In 2018, Food Standards Australia New Zealand, Health Canada, and the United States Food and Drug Administration published positive food safety assessments for Golden Rice. A biosafety application was lodged in November 2017 and is currently undergoing review by the Biosafety Core Committee in Bangladesh.

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About the Healthier Rice Program
Together with its national partners, the Healthier Rice Program at IRRI is working to improve the nutritional status in countries across Asia and Africa, where rice is widely grown and eaten. Delivering essential micronutrients through staple foods like rice offers a sustainable and complementary approach to public health interventions for micronutrient deficiency, which affects 2 billion people worldwide. In addition to Golden Rice, research is being conducted on high iron and zinc rice (HIZR) to help address iron-deficiency anemia and stunting.

8 January 2021: gene editing
There was an important news item in The Guardian yesterday, reporting that the UK’s head of DEFRA (Department for  Environment, Food & Rural Affairs) George Eustice MP had indicated that gene editing of crops and livestock might be permitted in the UK before long, and that he was launching a consultation into this, and was quickly welcomed by many in the UK scientific community like Professor Sophien Kamoun, a plant pathologist at the John Innes Centre in Norwich who tweeted his support.

Under strict EU rules, gene editing had been classified as genetic modification and therefore banned. Now that the UK has left the EU, it can decide for itself how to harness the power of these biotechnology tools.

Don’t get me wrong. I was—and remain—a strong supporter of EU membership, but on the issue of GMOs and other biotechnology tools, I believe the European Commission and the courts got it very wrong. We need these powerful tools so we can harness the genetic resources to improve crops and livestock in a fraction of the time that would be needed using more conventional methods. Doubt remains, however, whether foods produced using any of these techniques could, for the foreseeable future, be exported to any EU countries.

Immediately after announcing the consultation, the usual opponents of any biotechnology, such as GeneWatch UK condemned this development. I’m sure it won’t be long before the likes of Friends of the Earth and Greenpeace add their voices in opposition.

The technique of gene editing (more correctly the CRISPR/Cas9 technique) was discovered and developed by Emmanuelle Charpentier and Jennifer A. Doudna who were awarded the Nobel Prize in Chemistry 2020 last October. That’s how important the scientific community believes this technology is.

Emmanuelle Charpentier and Jennifer Doudna

In a press release that announced the award of this prize, the Royal Swedish Academy of Sciences stated that Charpentier and Doudna had . . . discovered one of gene technology’s sharpest tools: the CRISPR/Cas9 genetic scissors. Using these, researchers can change the DNA of animals, plants and microorganisms with extremely high precision. This technology has had a revolutionary impact on the life sciences, is contributing to new cancer therapies and may make the dream of curing inherited diseases come true.

My hope is that the proposed DEFRA consultation can be conducted in a calm and collected way. Although I fear that emotions will once again take the debate off in unwelcome directions. Even on Channel 4’s new program last night, presented Jon Snow referred to genetically-modified foods as ‘Frankenfoods’ Use of this terminology does not help one iota.