As I write this on the eve of the 40th anniversary of Earth Day, I’m reflecting on how the world has changed since April 22nd, 1970. While some might say we haven’t come very far, I think the awareness of conservation, the 4R’s, consumption and efficiency has indeed grown. People have started, particularly in the last decade, to take action that is helping to change our attitudes and lifestyles in tremendously exciting ways. Many of these actions are, at their core, connected to research and the new information that researchers are finding out about the flora and fauna that we share our world with. The potential of plants to become food, produce powerful medicines and even create new sources of fuel is an exciting area of scientific research that I look forward to hearing more about in the future.

Genome Canada has supported a wide variety of innovative research projects in the areas of agriculture, environment, fisheries, forestry, health and new technology development over the past ten years. One such research project is the genome sequencing of the sunflower. This particular project, started in 2008, will take place over four years and cost over 17 million dollars.

There are a number of really good reasons that Genome Canada and other donors have invested such large amounts towards this research. At a length of about 3.5 million ‘bases’ or nucleotides, the DNA strands of sunflowers are actually longer than those of humans. Sunflowers are a part of the largest plant family (Compositae) on earth, which includes economically important crops like sunflowers, artichoke and lettuce. Within this family there are also wildflowers like daisies; common allergens like ragweed and goldenrod; valuable medicinal and costly invasive plants and weeds such as thistles and dandelions. Understanding how the sunflower grows, produces seeds and protects itself from pests will allow researchers to apply that information to all plants in that family. The sunflower is an economically significant crop currently producing $14 billion dollars yearly from seed production alone. The University of British Columbia, who is leading the international team of researchers on this project, intends for the research to be the basis for a future breeding program.

As agricultural land becomes more valuable, we need to make use of our crops more efficiently and turn what is now considered waste into a priceless resource. The creation of a hybrid sunflower species is hopefully one of the outcomes of this genome research project.  One wild species of sunflower, the Silverleaf, is known for its tall woody stalk that grows between 10 to 15 feet tall with a diameter of around 4 inches. This stalk would ideally be used as a wood product or converted into an ethanol product that could replace current ethanol sources such as sugar cane, corn and barley. This plant could be crossbred with a commercially viable sunflower species that produces high-quality seeds and will allow producers to capitalize on two incomes from the same plant. And, because the plant is using the same amount of hectares but producing both food and ethanol, there is no reason to debate whether harvesting environmentally-friendly fuel sources should take precedence over growing food for our increasing populations. Another attractive quality of the Silverleaf variety is that it is also highly drought tolerant so it would allow farmers, even those in sub-Saharan Africa, to sow them in environments where other crops would refuse to grow.

Understanding derived from the genome sequencing work of the researchers will increase the speed and precision of crossbreeding that would have traditionally been done using the old style trial and error process of selective breeding. Their research has already discovered some traits in the sunflower that decreases yield and reduces seed quality. This particular variety, the Silverleaf sunflower, has a resistance to downy mildew, which destroys plant tissue as well as a trait that shows a potential resistance to harmful plant rust.

It’s innovative ideas and actions such as this research project that inspire me to look for other ways to reuse the products that I purchase; to buy things that not only last a long time but also have multiple uses with minimal waste. To me, that’s what Earth Day stands for. Living more lightly, while increasing our awareness and striving everyday to make changes in our lives to become less wasteful and to use our resources to reconnect with our amazing planet.

» Genome Canada

On February 11, 2010 Nature, a British scientific journal, published the genome sequence of Brachypodium distachyon, commonly called Purple False Brome.  The process of fully mapping the grass species’s genome was undertaken by The International Brachypodium initiative, and was part of a European Union funded project aimed at uncovering the genome sequences of some strategically chosen plants.  Before we start talking about the benefits of uncovering the genome sequence of a plant like Purple False Brome, let’s step back and look a little closer at what makes the genome such an important gem of knowledge.

Chances are you’ve heard of the Human Genome Project.  It was a massive scientific initiative that began in 1990 to map the 3 billion nucleotides within the roughly 24,000 genes of the human genome.  In 2000 a working draft of the genome was published, followed by a complete map in 2003.  In 2006 an even more detailed version was released, filling in gaps and clarifying anomalies, and further analysis continues to be published today.  By understanding the human genome scientists are able to understand what makes individuals the way they are; why some people are more susceptible to certain diseases, and why others grow to be seven feet tall.

Researchers have been working tirelessly for years to map the genomes of a variety of other organisms ranging from rice to ring worms. With every fully sequenced genome the scientific community’s understanding of how life on our planet works is increased.  The results of these discoveries have been advantageous in a number of ways. Because many genes are shared between species, mapping one organism’s genome can often provide information that is useful in our understanding of a host of other species.

(For more information on the structure of DNA, and how it is sequenced, read this helpful guide provided by the University of Michigan.)

We know genome sequencing holds a great amount of information towards our understanding of how life works on our planet, but it’s also important we take a moment to understand just what the genome actually tells us.  

Basically, understanding an organism’s genome means understanding the entirety of that organism’s hereditary information.  That means knowing what genetic information is going to be passed on from one generation to the next.  The genome is encoded in the DNA and is the road map for an organism’s development.  It holds the information for what color your hair is going to be, the longevity of a fruit fly, or the diseases that a prairie grass will be most susceptible to.  Some of the information we can gather from the genome isn’t going to help humanity drastically, but other bits could save lives.

Let’s step back and re-evaluate that friendly grass species, Brachypodium distachyon.

Since the agricultural revolution some 10,000 years ago humans have come to rely on many grass species to meet nutritional needs.  But, with populations increasing and arable land becoming difficult to come by, hungry mouths now surpass the food supply.  There’s less food than there ought to be, there’s less places to grow it, and the need for workable solutions is becoming more important by the day.  This is where the field of genetics can step in to help.  

Genetics is capable of offering solutions to problems where many other fields of study are incapable.  Through genetic sequencing of certain plants scientists can gain understanding of the obstacles that are preventing grains from higher yields and resiliency to disease.  By understanding our food, scientists are able to understand the problems and come up with adequate solutions.

Purple false brome presented itself as an ideal candidate for sequencing because of its relatively small genome and short lifecycle. This inconspicuous grass species is related to a number of the major cereal grain species such as wheat, barely, oats, maize, rice, and rye.  Even though Purple false brome isn’t especially useful as a food source, the information contained within its genome offers researchers a wealth of information about its relatives.

In an article on the Cordis website Professor Michael Bevan, a researcher who worked on the Brachypodium genome project, states that their “analysis of the Brachypodium genome is a key resource for securing sustainable supplies of food, feed and fuel from established crops such as wheat, barley and forage grasses and for the development of crops for bioenergy and renewable resource production”.  The information retrieved by sequencing a single plant’s genome is a testament to the far-reaching effects of the field of biotechnology.  

As a species sharing the planet with a myriad of other organisms it is vital that we increase our understanding of our environment as much as possible.  By being proactive in the understanding of our sources of food, the ways it grows, and how it competes with the wealth of other plants in its environments, we can ensure increased productivity in ways that will reduce human suffering and increase quality of life for much of earth’s population.

» Wiki

While writing my first foray into the blogo-sphere for Ecollo, I had the opportunity to explore the world of genome mapping and the significant impact it could have on the agricultural community and food production. See How Genome Sequencing Helps Food Production. Truthfully, genetic sequencing was an area I didn’t know that much about and was skeptical about its benefits prior to that first assignment. But the more I read about it, the more I began to realize that this type of research also has tremendous potential for applications beyond higher yields in our fields.

Like all of the contributors to this site, I am passionate about the environment and am always looking for ways to do my part. I realize that my impact is just one small piece of the giant planet puzzle and that we will need to use all available tools if we are going to solve the problems we have created. If leveraging biotechnology and similar research into supporting our efforts for a cleaner and greener planet is possible, then I am all for it. Using genetic sequencing, we have the opportunity to make changes that will contribute to our effort by changing the impact we have on our environment.

Before I get into some examples of how this research could benefit the environment, you might be wondering what I am talking about when I refer to genome or genetic sequencing. Far from an expert on the subject, I turned to my favourite search engine for a definition and an idea of the scientific process behind mapping an organism’s genome.

As we know, all living matter is made up of millions of cells that are directed to perform various tasks by their genetic makeup or DNA. Each strand of DNA strand is made up of millions of its four component parts, called nucleotides. The order of these nucleotides determines the genetic sequence of the organism’s DNA. Identifying the order of an organism’s genome sequence can tell us details about how the animal or plant grows, defends itself from disease and produces identifying characteristics and behaviors of that plant or animal. Understanding these details can allow scientists to help species express more desirable traits while limiting ones that are not as beneficial to development of the plant or animal. As I have discovered through a bit of exploration into the matter, there is a lot of work being done in Canada and around the world to catalogue the genomes of species so that we can use this knowledge to benefit both the agricultural sector and our environment.

One of the largest challenges we face when dealing with our current climate crisis is the development of new clean and safe energy sources. Microbial genomic research will increase the efficiency with which plant matter from sugar cane, sunflowers, wheat and corn can be fermented into ethanol for a more planet friendly fuel. Current processes result in a lot of waste with comparatively little product. This investigation will allow us to use plants more efficiently and increase their economic value. The waste products from the biofuel and plastic production process can be used as adhesives and resins. Very little needs to be wasted. By increasing productivity and minimizing waste, we can ensure that we have enough of these plant products for food production as well as developing energy resources, which is the central argument in the food versus fuel debate.

While scientists strive to make changes in the way we develop new energy sources, they are also looking at how we will be able to deal with the waste that is being created from our current energy sources. Understanding which genomes control carbon dioxide absorption in various plant species could help us deal with the enormous challenges we face in meeting the carbon emissions reduction targets. Since we are dependent on current energy sources for the time being, other genome research is investigating how the current processes can be made more efficient and environmentally sensitive. By understanding the bioprocesses and bacteria in the oil sands and coal beds, scientists will improve their knowledge of how methane is produced in these processes and their ability to identify the enzymes that control the natural cracking of hydrocarbons into methane and carbon dioxide, two of the major contributors responsible for our changing climate.

Microbial genomic research is also investigating an increase in the efficiency of environmental remediation and the development of environmental monitoring techniques that will detect pollutants. Organisms in bioreactor waste processing are also being sequenced so that scientists can increase the organism’s ability to deal with our waste.

Beyond plants and microorganisms, the genomes of insects and animals are being sequenced. Understanding the genomes of pests can allow farmers to place directed insecticides that target pest species and don’t harm the useful insects. While I couldn’t find any direct evidence to suggest that there is research currently being with endangered species, I feel that this is where genetic research could have one of the most significant benefits. Many endangered species are facing new and evolving diseases that are threatening the efforts of individuals trying to re-establish populations around the world. An example of this is the Elephant endotheliotropic herpes virus that is killing elephants in both zoos and their natural habitats. There is currently no cure for this disease although animals can be carriers of it and not show any symptoms. By isolating the genomes that influence this resistance to the disease, scientists may be able to access knowledge that will help save one of the world’s most recognizable and charismatic species.

I recognize that with any research in the field of genetics there is always going to be an element of controversy. I am also not saying that genome sequencing is going to be the best fix for the problems that we have created in our environment. I do believe however, that with careful use of the technologies and knowledge available to us, that they can become part of a large toolkit of resources that can help our environment for the better.

» SciBlogs

Scientists have recently announced the completion of two projects that sequenced both pig and cucumber genomes. According to the reports, this scientific achievement stands to have a tremendous impact on future research, particularly in the areas of human medicine and agriculture. As I read through the article my first question was, and probably that of most people, what the heck is genome sequencing anyway?

After a quick trip to my favourite search engine and a visit back to my days in high school biology (who knew I would use this stuff again?!), here is what I learned:
All living matter is made up of millions of cells that are directed to perform various functions by their genetic makeup or DNA. The DNA strand is made up of millions of its four component parts, called nucleotides, which determine the genetic sequence of the organism’s DNA.

Identifying the study subject’s particular genome sequence can tell us details about how the animal or plant grows, defends itself from disease and produces the characteristics and behaviours that we identify the plant or animal with.

While I think I will leave this type of work to the professionals, I was most intrigued about the part of the announcement that describes the possible impacts this research will have on human medicine and the agricultural sector. What will this understanding do to our Sunday pork loin roasts or my grandmother’s cucumber sandwiches?

A link to agriculture

As scientists now have an understanding of how plants and animals express certain characteristics, they can genetically modify organisms to express more of the desired characteristics and less of those that are not so desirable. Being able to help organisms express their most desired characteristics will reduce waste, increase productivity of an organization, save producers time and money and produce higher yielding, higher quality food products necessary to feed a growing and starving world.

As the latest organisms to contribute to the ongoing research in genetic sequencing, the genomes of pigs and cucumbers hold the secret to more than a great tasting roast and a refreshing crunch. For example, in a swine breed that commonly develops leg problems, scientists will be able to isolate the sequence that controls leg conformation and be able to modify that gene to lower or even eliminate the occurrence of that type of problem. Pig producers, particularly those in dry areas, will be able to raise livestock who use water more efficiently and have a resistance to parasites and zoonotic diseases, such as H1N1, which also happens to affect humans. As pork represents about 40% of the world meat production, overcoming these common challenges should have a pretty huge effect on the global economy. Being pretty health conscious, I get pretty excited at the prospect of increased food quality and the promises of lower fat pork products. And since pig organs are commonly used for transplantation into humans, the more information we have about them, the better chance of transplant success.

Similarly, in cucumbers, understanding how the plants defend themselves from something like the mosaic virus, scientists can help develop a plant that expresses those characteristics and thus reduce the amount of crop lost to this common cucumber disease or any other type of pest. They will also be able to develop varieties that germinate faster, have a greater cold tolerance, have larger yields and have the potential to grow in a wider variety of climates. As the cucumber is a representative of the cucurbit family, which includes pumpkins, melon, squash and watermelon, this research will extend to a large variety of crops that have economic consequences worldwide.

A continuing challenge

While this story is encouraging, it can’t be finished without mentioning that there are many concerns about using biotechnology to change the way we raise or grow our food supply. Even as the genome sequencing of these organisms leads to a greater understanding of how they work, pigs and cucumbers are just a small part of a larger natural system. Genome sequencing research and biotechnology have the amazing potential to change our economy, human health and agricultural systems in many positive ways, we just have to be prepared to address the challenges that this new technology will bring along the way.

» Science Fair