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All our food is ‘genetically modified’ in some way – where do you draw the line?

The Conversation

James Borrell, Queen Mary University of London

In the past week you’ve probably eaten crops that wouldn’t exist in nature, or that have evolved extra genes to reach freakish sizes. You’ve probably eaten “cloned” food and you may have even eaten plants whose ancestors were once deliberately blasted with radiation. And you could have bought all this without leaving the “organic” section of your local supermarket.

Anti-GM dogma is obscuring the real debate over what level of genetic manipulation society deems acceptable. Genetically-modified food is often regarded as something you’re either for or against, with no real middle ground.

Yet it is misleading to consider GM technology a binary decision, and blanket bans like those in many European countries are only likely to further stifle debate. After all, very little of our food is truly “natural” and even the most basic crops are the result of some form of human manipulation.

Between organic foods and tobacco engineered to glow in the dark lie a broad spectrum of “modifications” worthy of consideration. All of these different technologies are sometimes lumped together under “GM”. But where would you draw the line?

1. (Un)natural selection

Think of carrots, corn or watermelons – all foods you might eat without much consideration. Yet when compared to their wild ancestors, even the “organic” varieties are almost unrecognisable.

Domestication generally involves selecting for beneficial traits, such as high yield. Over time, many generations of selection can substantially alter a plant’s genetic makeup. Man-made selection is capable of generating forms that are extremely unlikely to occur in nature.

Modern watermelons (right) look very different to their 17th-century ancestors (left). Christies/Prathyush Thomas, CC BY

2. Genome duplications

Unknowing selection by our ancestors also involved a genetic process we only discovered relatively recently. Whereas humans have half a set of chromosomes (structures that package and organise your genetic information) from each parent, some organisms can have two or more complete duplicate sets of chromosomes. This “polyploidy” is widespread in plants and often results in exaggerated traits such as fruit size, thought to be the result of multiple gene copies.

Without realising, many crops have been unintentionally bred to a higher level of ploidy (entirely naturally) as things like large fruit or vigorous growth are often desirable. Ginger and apples are triploid for example, while potatoes and cabbage are tetraploid. Some strawberry varieties are even octoploid, meaning they have eight sets of chromosomes compared to just two in humans.

3. Plant cloning

It’s a word that tends to conjure up some discomfort – no one really wants to eat “cloned” food. Yet asexual reproduction is the core strategy for many plants in nature, and farmers have utilised it for centuries to perfect their crops.

Once a plant with desirable characteristics is found – a particularly tasty and durable banana, for instance – cloning allows us to grow identical replicates. This could be entirely natural with a cutting or runner, or artificially-induced with plant hormones. Domestic bananas have long since lost the seeds that allowed their wild ancestors to reproduce – if you eat a banana today, you’re eating a clone.

Each banana plant is a genetic clone of a previous generation.
Ian Ransley, CC BY

4. Induced mutations

Selection – both human and natural – operates on genetic variation within a species. If a trait or characteristic never occurs, then it cannot be selected for. In order to generate greater variation for conventional breeding, scientists in the 1920s began to expose seeds to chemicals or radiation.

Unlike more modern GM technologies, this “mutational breeding” is largely untargeted and generates mutations at random. Most will be useless, but some will be desirable. More than 1,800 cultivars of crop and ornamental plants including varieties of wheat, rice, cotton and peanuts have been developed and released in more than 50 countries. Mutational breeding is credited for spurring the “green revolution” in the 20th century.

Many common foods such as red grapefruits and varieties of pasta wheat are a result of this approach and, surprisingly, these can still be sold as certified “organic”.

‘Golden Promise’, a mutant barley made with radiation, is used in
some premium whiskeys. 
Chetty Thomas/shutterstock

5. GM screening

GM technology doesn’t have to involve any direct manipulation of plants or species. It can be instead used to screen for traits such as disease susceptibility or to identify which “natural” cross is likely to produce the greatest yield or best outcome.

Genetic technology has allowed researchers to identify in advance which ash trees are likely to be susceptible to ash dieback disease, for instance. Future forests could be grown from these resistant trees. We might call this “genomics-informed” human selection.

6. Cisgenic and transgenic

This is what most people mean when they refer to genetically modified organisms (GMOs) – genes being artificially inserted into a different plant to improve yield, tolerance to heat or drought, to produce better drugs or even to add a vitamin. Under conventional breeding, such changes might take decades. Added genes provide a shortcut.

Cisgenic simply means the gene inserted (or moved, or duplicated) comes from the same or a very closely related species. Inserting genes from unrelated species (transgenic) is substantially more challenging – this is the only technique in our spectrum of GM technology that can produce an organism that could not occur naturally. Yet the case for it might still be compelling.

Campaigns like these are aimed at cis- and transgenic crops. But what about the other forms of GM food? Alexis Baden-Mayer, CC BY

Since the 1990s several crops have been engineered with a gene from the soil bacteria Bacillus thuringiensis. This bacteria gives “Bt corn” and other engineered crops resistance to certain pests, and acts as an appealing alternative to pesticide use.

This technology remains the most controversial as there are concerns that resistance genes could “escape” and jump to other species, or be unfit for human consumption. While unlikely – many fail safe approaches are designed to prevent this – it is of course possible.

Where do you stand?

All of these methods continue to be used. Even transgenic crops are now widely cultivated around the world, and have been for more than a decade. They are closely scrutinised and rightly so, but the promise of this technology means that it surely deserves improved scientific literacy among the public if it is to reach it’s full potential.

And let’s be clear, with global population set to hit nine billion by 2050 and the increasingly greater strain on the environment, GMOs have the potential to improve health, increase yields and reduce our impact. However uncomfortable they might make us, they deserve a sensible and informed debate.

The ConversationJames Borrell, PhD student in Conservation Genetics, Queen Mary University of London

This article was originally published on The Conversation. (Reblogged by permission). Read the original article.

 

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The genetic blueprint of an octopus reveals much about this amazing creature

The Conversation

Jan Strugnell, La Trobe University and Alvaro Roura, La Trobe University

Octopuses are among the most impressive of the invertebrates thanks to their ability to solve puzzles, camouflage perfectly with their surroundings, mimic other species, use tools and potentially predict world cup victories.

Now that scientists this month have published the first octopus genome we are a step closer to understanding how these feats are achieved in a lineage so divergent from our own.

The octopus genome was of the California two-spot (Octopus bimaculoides) and it may provide us with some leads on how the highly unusual octopod body plan evolved.

Interesting body plan

Octopods are contained within the group Cephalopoda, which literally means “head-footed”, as the foot (i.e. the octopus arms) are connected directly to the head.

One family of genes that is known to influence body plan in animals is called Hox. These genes usually occur together, clustered in groups, and the order of the genes directly corresponds to the order in which they are activated along the body during development.

In the octopus genome the scientists found the Hox genes are completely scattered, with no two of them occurring together. This scattered nature of the Hox genes across the genome may provide insights into octopod body plan development and why octopus have a much more unusual body plan than their cousins, such as snails and oysters.

Another big finding of this octopus genome project is actually something the authors did not find: whole genome duplication. That is, evidence that the entire genome was duplicated throughout history so that two copies of the genome were present.

It was previously believed that a whole genome duplication event in the octopus lineage may have driven the evolution of some of the remarkable characteristics present within octopus, such as complicated behaviours including the use of tools or vertebrate-like eyes.

The idea was that a whole genome duplication event frees up a set of genes, allowing these copies to take on new functions. But the lack of evidence for this suggests other mechanisms are at play.

Blended genome

One of these mechanisms appears to be the huge expansion in some gene families previously thought to be expanded only in vertebrates and not in other invertebrate lineages. One of these families is the protocadherins, which are cell adhesion molecules required to establish and maintain nervous system organisation.

The octopus genome boasts 168 protocadherin genes, which presumably play a crucial role in the highly modified octopus nervous system and complex brain. In contrast, these protocadherins are found in relatively small numbers (17 to 25) in organisms such as limpets and oysters, and are completely absent in several invertebrate model organisms including the fruit fly and nematodes.

The fact that protocadherin genes occur in large numbers in vertebrates and octopus but not in other animals, and that they are expressed in octopus neural and sensitive tissues (suckers and skin), suggests that they might play an important role in the evolution of cephalopod neural complexity.

Protocadherin diversity provides a mechanism to establish the synaptic connections needed to interpret the vast amount of stimuli, including touch and smell perceived through the suckers, and organise complex behavioural responses like camouflaging through the change in skin colour and texture/sculpture. It is interesting that the diversity in these genes has been generated by different mechanisms in octopus and vertebrates.

The genome also shows a lot of evidence for transposon activity. Transposons are DNA sequences that move locations around the genome (sometimes called “jumping genes”) and they can drive evolution.

In comparison to other genomes, the scientists note that the octopus genome looks like it has been “put into a blender and mixed”. They show that these transposons play an important role in driving this mixing of the genome.

They also found that transposons are highly expressed in neural tissues. They suggest that these may play an important role in memory and learning as shown in mammals and flies.

The ability of octopuses to learn and solve puzzles is something that is fascinating to us and so this will be a fruitful area for further research.

Why did it take so long?

It is more than 14 years since the human genome was published in Nature and Science, and numerous genomes have been published since then such as pandas, bees and recently 48 species of bird.

But this latest publication represents the first genome of any cephalopod and one of only a handful of molluscs, (the group containing cephalopods). Other molluscan genomes include the limpet (Lottia gigantea), oyster (Crassostrea gigas) and the sea hare (Aplysia californica).

This first octopus genome gives us great insight into the evolution and function of this fascinating group and will serve as a great catalyst for further research on cephalopod genetics.

Jan Strugnell is Associate professor at La Trobe University and Alvaro Roura is Postdoctoral fellow at La Trobe University

This article was originally published on The Conversation. (Reblogged by permission). Read the original article.

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Pretty kitties: feline ‘friendly’ genes mapped in study

The Conversation

By Bryonie Scott, The Conversation
House cats are a great source of companionship for many people – 3 million cats are kept as pets in Australia. Now thanks to research published in the Proceedings of the National Academy of Science today, we understand the genetics behind some of the traits that make them such good pets, such as docility and affection.

While it seems cats have been in close contact with humans for around 9,000 years, it is only in the past 200 years or so that we have produced the domesticated breed we know today.

The research team behind today’s study, who were from various organisations including The Genome Institute, created the first complete domestic cat genome reference. To do this, they not only compared genomes of different mammals, such as cats, humans, cows and dogs, but they also compared the genomes of wild and domestic cats, and found the genes that make our household pets so friendly.

Domestication: it’s in their genes

Don Newgreen, head of the embryology laboratory at the Murdoch Childrens Research Institute, explained that when an animal is bred to affect its behaviour, other physical attributes also change. This is known as domestication syndrome.

“Even though you are choosing for pleasant-natured animals, you get other traits as well,” Dr Newgreen said. “These include a lot of changes in pigmentation, set up of the face and head, length of the nose or teeth as well as behavioural changes like becoming placid and unaggressive.”

The wildcat is more aggressive than its docile, domestic relatives.
Brian Scott/Flickr, CC BY-NC-ND

The study found the main factor in changing the feline genome was originally food rewards. By supplying cats with food, the cats became more docile, and due to domestication syndrome, these changes in their behaviour affected other traits, such as hair colour, texture and pattern.

Bianca Haase, research fellow at The University of Sydney, said one of the main signs of cat domestication is the presence of fur patterns not found on wild cats.

“From other species, we know that white-spotting is a disadvantage [for wild cats],” Dr Haase explained. “There is no need for the [pet] animal to be camouflaged because they are protected, so an increase of white-spotting is a sign of domestication.”

White markings are a sign of domestication.
Netzanette/Flickr, CC BY-NC

When comparing the feline genome sequence to other mammals, the team found traits specific to carnivores. These included heightened sensory development, such as excellent night vision and a keen sense of smell.

Cats are different from other carnivores in that they are hyper-carnivorous. While humans would be in danger of heart disease from a rich diet of fatty foods, wild and domestic cats have evolved to be able to process saturated and polyunsaturated fatty acids.

Breeding cats for domestication is a relatively new practice, and there’s not been much time for new traits to evolve.

On top of this, humans don’t entirely control most cats’ eating or breeding habits, meaning pet cats are really only semi-domesticated. In Dr Newgreen’s opinion: “cats are not really domesticated, just tame.”

So while cat domestication is modest compared to domestic dogs, today’s study showed that genetic changes in feline behaviour and appearance will be retained as long as cats are kept as pets.

The ConversationThis article was originally published on The Conversation. (Reblogged with permission). Read the original article.

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