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.


 

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.

***

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.