Gene Editing Technology & New Opportunities for Plant Breeding, USDA/ARS Jeremy Edwards, 11.16.17
In. Today's, webinar dr., Jeremy, Edwards research, plant, molecular. Geneticist. With, USDA's. Agricultural. Research Service. Headquartered. At the Dale bumpers, National. Rice Research Center. Stuck on Arkansas, will. Be discussing, gene editing, technology. And new, opportunities. For rice, and plant, breeding. It's. A pleasure for us to be with you I'm Bobby coats a professor in, the Department, of Agricultural, Economics and, agribusiness, in the University of, Arkansas system Division of, Agriculture, now. USDA's. Dr.. Jeremy, Edwards, on gene. Editing, technology. And new, opportunities. For rice, and plant breeding, Jeremy. We certainly look forward to your presentation. Thank. You good afternoon. Gina, editing is a powerful, new. Genetic, technique, that. Is transforming, biology. It. There. Are a lot of new stories recently. About gene editing just, yesterday, it, was announced that scientists, have, edited, the genome of a live human being for the first time. And. This was to cure a metabolic disorder. Many. Of the stories you hear are about, about. Medical. Applications. But gene editing also has applications. For. Accelerating. Plant breeding efforts. So. Today I'm going to talk, about our, current, technology, and the. Need for our new technology, such as gene editing. Current. Applications, of being editing. That. Are happening now how. Do you anything will be integrated, with conventional, breeding, some. Of the challenges, that are associated with using gene editing, and. The, long term potential. Oh. Before, I start I want to make, this disclaimer. And make. Sure it's very clear that everyone. Understands, we are not doing gene editing at the. USDA or ass Dale bumpers National, Rice Research Center, we are only working with conventional, plant, breeding techniques and. Marker-assisted selection. Only. The. Reason for that is that we are located in the middle of a large rice growing area, in Arkansas. And we, would not want to take, any chance of an, inadvertent, release, of. Something. That is Benji and edited until. Until. The the regulatory system, and the. Consumer, acceptance, is in place if. That ever happens. So. The need for a new technology. The. So it's estimated by 2050. These. To say nine there will be nine billion people now. There will be now they're estimating, nine and a half million people and. To. Feed that many people we're going to need a double, global, crop production, by the year 2050. So. Technologies, have helped. Us improve, our you, know than the past this is looking at corn and modern. Plant breeding, techniques, came, in and the, early 1900's looking. At double. Corn. Hybrids, and. Step. Up in the technology to single cross hybrids, we see in a. Steeper. Slope and. Continue. On to the modern, biotech. GMO. Technologies. And this trend continues. However. If we, project our. Current rate of increase for yield. In the shown, here in the solid, lines, and. Compare, that with what we would need to. To. Have to reach, the the, goals, for 2050. We're. Clearly falling short and so there's a need for something, new, to make up that gap and. It's not only about yield, we. Also have to consider the. Quality, of, the the. Of. The grain or or, whatever the product is to. One. Fit, the needs of the producers, Millers processors. And also, for. The nutrition, health and taste. For can see, we. Also consider, stress tolerance. We. And and pest, resistance. Destined. Pests with disease weed pressure. Response. To environmental, changes, and. Limited. Resources and, going, into the future. And. If. You ask any breeder trying. To breed in it for any one of these things alone is, difficult. Enough when you're trying to put all of these things together in the, same package, it's. Extremely, extremely difficult. So. How is gene editing compared, to. Earlier, technologies. So. We have conventional, plant breeding that takes many years to, develop, and, test a new variety. That. Truffles. Many. Genes at once in the genome. Completely. Rearranging, the deck every. Time you make a cross. It. Can be accelerated by marker-assisted, selection. And. Has. Provided and will provide consistent. Progress. Nothing. Is good probably going to replace conventional breeding, at. This point and, then. We have the biotechnology, approach, that has been used in the past and this, is where foreign, DNA is, added, to the genome typically. This is done one, gene at a time and. It's, relatively a fast process, compared, to the. Many. Years five six years minimum it might take to develop a new variety. And. So, this is done by introducing. Foreign. DNA into, a cell and, a. Plants, have a cell. Wall that, animals. Do not have it's. Made of cellulose, it's very tough to get through and so, to get these, you. Get that foreign DNA into, the cells, they. The first technology. That was used was biolistic, particle, delivery the gene gun the. Early models were done, from, an actual gun they. They, coat a gold.
Particle. With the DNA that they want to put into the plant and they. Fire. It at the. Cells of the plant some. Of it gets into the into the cells some of it integrates. With the plant. And. In. The small percentage of cases they're able to recover a. Transformed. Line. Another. Way that this happens is with the use of agrobacterium. So. Agar bacterium, we is well you've all probably, seen gulls walking, through the forest, or, in our yards some, of these gulls are made from insects and others are made from bacteria, like. Edgar bacteria, and what they do is they they, insert, genes into, the plant genome that. Create. Make, the plant produce. That big mass of cells that you see is a gall and that makes a happy home for the bacteria living. So. What what these do is is a bacteria, finds, its way to the plant cell and they, have a natural mechanism, for penetrating, the, plant cell and. Integrating. Whatever, DNA that they carry into. The, plant. And scientists. Have packed. Co-opted, the system. So, that they could insert whatever gene that, they want into, a plant cell what. Is gene editing do you know anything you can think of it as a genetic, microsurgery, using. Molecular scissors as the ability to insert, delete, replace, DNA, at, particular, locations, and that's key at particular, locations, in the genome and. CRISPR. Casts 9 which you may have heard about is a system, that is, programmable. And being. Programmable. Makes it cheaper faster and, more accurate, than previous. Methods of gene editing this. CRISPR, casts is. Another, natural system, that we've co-opted, it. In nature it it, exists, in bacteria, as a defense, against. Invading viruses. So. What happens is that in. These bacteria, they have an enzyme, that. Searches. For a. Particular. Virus. DNA, sequence, and when it finds it it chopped up so, it can't function. So. The, the. The. Key to this though is this enzyme has to chop. Up the virus DNA but, not chop up the DNA of the of the, bacteria. Itself and so. It needs to wait at needs a way to recognize. Its. The DNA. Sequence, so, here's how that system, works there's the CRISPR part. Of it and that's the programmable. Guide it's. An RNA sequence, so there's DNA and there's RNA. They're, both nucleic acids, the.
Particular. Sequence that, is encoded. Along. This CRISPR. Finds. Its match in. The. In the genome of a. Cell and, wherever. There's. A sequence, in the genome that matches, what's. In this RNA, it'll. Bind together and. The. Caste 9 is a. Molecular scissors, so. This is an enzyme that will cut a DNA, strand. There's. A little piece of. There's. An additional piece on this RNA strand, that. That. Is, used to bind. Attract. This molecular. Molecular, scissors so. That all of this forms of one complex. That. Complex, finds its way to the place of the genome where this RNA sequence matches and the. Molecular scissors will cut, that. DNA sequence. And. You get a double strand break they. Call it once. You have a double strand break, there. Are two things that can happen one. The cells machinery, will try to repair the double strand break using. Enzymes and just. Put it back together. This. Is called non-homologous end joining, and, in. This process, it's not it's, not always a, perfect. Enjoining. There are often small. Deletions, small changes, that, are made as these. As these, DNA strands are stuck, back together and so. You can kind of think of this like the old mutation, breeding, it. Would give similar, types of changes, except. Here, you, instead, of mutations, happening randomly in the genome they. Are happening at a gene, of your choice. There's. Also homology, directed repair and, that's. Where. You. Include an additional DNA. Sequence. And the, sequence is designed so that the ends, match. The. Other side of where the, the. Genome, DNA, sequence, is cut and so, these will find their way here and, when. This is repaired, whatever. Was in the middle gets integrated into that place where the DNA was cut and so, that would that way you can add a, sequence. At a particular, location. These. The. Non-homologous end joining, happens. At a very high frequency this, is a much lower frequency, event. And there's, ongoing. Research, to. To. Implement these kind of methods in plants, the, this, kind of method the non-homologous end joining, is.
Relatively. More. Easy to do. And. Here are just a little bit of history on CRISPR Kass, it. Was the the CRISPR, itself was discovered. Back. In in. 1993. In. Spain and this. Was this. Was discovered by scientists, that had no funding and he. Was a new lab and so, he did to buy from addicts search, of, bacteria. In. Which just, using. A computer, to look through DNA sequence it found an unusual repeat. Pattern and. And. Investigated. That further. And. Then. You can see laboratories, around the world spent. Many more years trying to figure out what all the parts of this, thing do, what. It's even used for in the. In the bacteria, and then. Finally, in 2012. Researchers. At, MIT. Were. Able. To edit the, genome of a, mammalian. Cell for, the first time with, this and that's when it took off so. This was just the Google Trends for the terms of United, and CRISPR cast nine and you can see flat. And then the sudden. Suddenly. There's activity. Increasing. Until. The day the. Gene editing is changing biology, in general at, an unprecedented pace, a. Lot. Of this is drew by innovation, for medical, applications, we're. Lucky in plants that the. Medical people have big budgets we don't but, we get to benefit from a lot of these technologies, that they develop, and we can apply them in plants and, I. Just have a selection of a few news stories that have been out recently that, are mostly, about medical, things. They've. Done as, yesterday, in editing inside the human body. Being. Adding to to. Treat. Many. Different diseases cancer. HIV. Major. Investments, into gene. Editing and so. When we can edit suddenly. Information, becomes really important, we can use information from the entire Tree. Of Life and. And. Put. That into a plant with editing, and. To, do this we need databases. And we're going to need new. Computational. Tools. To. Use all of this information so. A big data problem. So. Do. Everything is is first, of all a very useful tool for discovery. It. Allows us to quickly test the hypothesis. A genetic, hypothesis, about a gene so. If we think we've discovered. A gene we need to validate the. Function of that gene we. Need to prove that. What we think is. The gene is really the gene and. Gene. Editing is a very convenient way to do that you could go in and edit that gene and look, for an effect, in the trait, that. You're, expecting. To be affected. So. That allows, us to discover genes connect. Genes with traits, much. Faster, and. It allows, us to better use our natural variation. We. Have large, collections of. Plant. Varieties, that. That, are maintained, and and. Contain. A tremendous. Amount of natural variation DNA. Sequencing, allows us to go in and see. That variation, and. With, gene editing we can now take.
Those Those, rare variants, and test them to see if they do anything. Impact. Traits in any way that is of use to us so. In general some gene editing, applications, in plants that that. Are. Happening or will be happening soon herbicide. Resistance, is an easy target. For that, there. Are many genes that can be knocked out that will provide. Resistance. To particular, herbicides, and then that is useful in weed management. It's. Being used in starch modification. Change. Also in changing fatty acid composition, enhancing. The nutrition, and, and. In. Post harvest. Of. The plants. Some. Specific, examples. Hi, emili´s rice has been created by, editing starch frenching enzymes. There. There has been the enhanced. Blast resistance, shown and rice. But blast, disease, resistance, and that's, from a ERF, transcription, factor gene that was edited, they've. Shown it in maize improved, yield under drought conditions by, editing the agro, green, tomato. Fruit ripening genes, have been modified the brin gene and, and. This, and. Improved. Fatty acid has been. Done. By gene editing in, oilseed. Crops, so. Here, are some examples, of. Specific. Examples, of gene editing research. Projects, and i start. With a few that are happening. Here. At the university of arkansas, and. This. Is work by, kim. Korth provided. These slides. For me and. What. They're doing is using gene editing to. Improve. Grain quality for. One-four. For changing the way the, type of fat that is stored in the, and the brand layer so, that in brown. Rice it, doesn't go rancid as fast and has. A much longer shelf life and also, for growing quality. Cooking. They're. Altering starch, enzymes. Start. Synthesis, enzymes to, change the. The, starch deposition. And and, cooking. Temperatures, also. Here. Biba, this group works, on some basic, technology. Development, using, CRISPR. Cask. So, there they're working on methods, one. To make large deletions, in genes to. Knock, out their function, and. To. Make edits in the regulatory, parts, of genes their outside of the coding regions but, affect the gene expression, around. Around the country there, there a number of other efforts in, D, editing, there's. A large, effort going on at Ohio State University. These. Are typically. Connected. With plant, transformation. Facilities. Because there is a tissue culture step, that. Is required, after. The gene editing and then, over at Texas A&M Mike, Thompson and, has established a, gene. Editing core, facility, on, campus and. And. And so. That will. Start. With rice but, and. In, wheat but they will expand other crops in the future. So. Some of the challenges you have to be able to tissue culture, and so that does limit what. Material, you can work with it has to be plants, that are, able. To go through tissue, culture, and, again. This is from Mike Thompson, talking. About how he wants to use this technology. One. Of the directivity knockouts. One. Is again. To validate. Is. About. A, sequence. Variations, and replace. Alleles, so. That we can rapidly test, different. Genetic, variants in the same genetic background, holding everything else constant and. If. This were to be accepted for commercial, purposes, use as a replacement for marker system back crossing, so, instead, of going. Through many generations of that crossing, just. Edit in the change that. You want from, the donor so. Here one of the challenges, in breeding is that. We. Off want to work with with, multiple, genes and. And. If you're even if you know the, genes that, you want and you can select for them with marker-assisted, selection. It. As you, increase the number of genes you're working with the harder and harder it gets so. If you have one. Gene and you make. A cross between two parents that. Differ in that gene then half. Of your half of what you get is going to have what you want the other half is, not but. As you add genes each. Time it drops by half so, working with with. With. Two genes. You. Only have 25% that, have both that you want if, you go to 3 goes down to 12 and 1/2 on. And on to 6 down here when you get to six genes it's, about one and a half percent of all the plants you grow that's. All you're gonna be able to work with and, six. Genes is a small number a lot of the traits we use are very complex, and would. Require, a. Lot, more genes than that for one trait and there, are many many traits that we want to work with and so those numbers get incredibly.
Small And. On, top of that every. Time you make a new cross and breeding all of this gets. Reshuffled, and you have to play the same game all. Over again and. That's. Where gene editing comes in if. If. You. Edit instead, of, select. Then, you. Can take you can breed from, the. Variety or you can take an existing variety. And you can just directly edit in as many. Genes as you want in one. Step so this is kind of how we do our, how we. Envision. The, breeding, process and, plan approve that process right now. Using. Information. Using. Marker-assisted selection and, everything, at our disposal so. The. Ideal plan type the idea type we would come up with based. On our knowledge of, look, at a biology, physiology biochemistry. In, the, environment, and, we. Would assemble that. Using. Using. Our very, our existing, variation. That comes from characterized, diverse, Durham, plasm, and. And. We, use we use that germplasm for, discovery. To. To, find genes linked, to those traits that we want and. Introduce. Those traits to elite varieties so they're that. Cross them in and. And. Eventually come back and test, and, see. Whether that worked and refine, our, ideal. Plant type, now. With gene editing. This. Discovery, phase is, is. Faster, so if we can only use gene editing as a research tool it'll, improve our game discovery, we'll be able to do that faster, more efficiently, work. With more traits. And. That helps. Us better characterize, our diversity. Our plasm, in. Our collections. And. As. This. Technology revolutionize. Has biology, where we're just going to know a lot more about all of these. Types. Of information, that go into, putting. Together our ideal plant types now. If. We're, able to use. Gene. Editing to, create a commercial variety, then. Suddenly, information. From. Not just rice but anywhere, can. Be used and. Introduced. Directly, edited, in to. Elite varieties, and. Now, instead. Of this back crossing, and permitting. Step which takes many many generations many, years of work. We. Can edit in those, edit. In that information and make those changes immediately, and. Come. Back to a ideal. Plant type and, so, are our, fuel for all of this is still natural diversity we, still learn from, what exists in nature, we.
And That's why we have these. Gene. Bank resources, with many different. Varieties. Stored, and. Gene. Editing is going to help us better. Understand. What. We have and these in these gene banks and what it does what it can do for us so. Benefits for plant breeding if we have research we'll get faster less expensive dean, discovery, this will lead to molecular, markers that. We use for breeding. It. Improves our basic understanding of biology and environment. Interactions, so. We have smarter, breeding objectives, we know what's hanging for better and. That. Allows us to discover and test novel. Genetic variation. That we find in gene banks. If. It can be commercialized, then. It. Used in a variety that that. Is. Goes. To the field will. Have faster. Less expensive variety. Development, you. Can make upgrades to existing elite, varieties, without, reshuffling. The back and losing all that breeding progress, and. We can introduce some new useful, traits that maybe. Didn't even exist within the diversity, of that crop some. Of the technical challenges I, mentioned before. Gene. Editing needs, to go through a tissue culture step, and that's, because you're editing, individual. Cells. That. Then, need to be multiplied. And eventually, regenerate, to form a complete plant. There. Can. Be some off-target changes, sometimes that, that, RNA, doesn't, bind to, the exact right place and you. Can change other genes. And. And. So that needs to be perfected. And. Monitored. And, we've. Run into problems in research. If we want to measure traits that are relevant. Traits. For a field environment the relevant environments, so. Right. Now we could, we. Could edit. The gene in. A laboratory somewhere. If it was Bryce we would do it in, a laboratory in, a region where they don't grow rice and, if. If, a trait was something that we could measure in the lab we would be all set, but. If it's a trait something, like yield that. You can't. Adequately. Measure in a lab or even in the greenhouse, then. The only way to do it would be to take it to the field and. Preferably. To feel in a relevant part, of the country and we. Can't do that. And, unless. The. Regulations, and the consumer acceptance, were to be in place. So. Until that time we have limited, traits that we can work with. And. Then the question is consumer, acceptance, will this be perceived, as a just, like the GMOs or will it be seen as something different that's, basically, equivalent to natural. Mutations. Or natural, genetic variation. One. Of the big differences with gene editing compared, to, the. GMOs the GM crops is the genomes can be detected the, editing can't, be detected it's. Like the, GMOs, are like pasting pages in a book and, then. It sort of like changing, a few letters in the book, and. And. So, if they, can't be detected, then. If they get out we. Won't know so here's, an, example recently. There. Was a petunia. That. Was created, in 1987. Using. A GMO technology and. At a maze gene, corn. Gene that gave it a salmon. Color and. Somehow. Nobody, knows it made its way into the floral industry and, was. Being grown all over the world and. Recently. Someone saw. That it. Remembered that 1987. Experiment, tested, it and discovered, in fact it is GMO and these have been growing all over the world for. Many many years and they, all had to be destroyed. The. Regulation, situation. It's things. Are rapidly changing, there. There have been some rulings, but I think that. I'm. Not really I'm, not really up. To speed on it or qualified to comment on what's happening with regulations, other than I. Think. And I would hope that that. Stakeholder. Feedback is, being considered in this and. I. Hope. Today. Learning, a little bit more about gene editing will. Help. You provide a better feedback, and. Some licensing, situation, is. Also uncertain there. Has been an agreement. For. Research, purposes, so we're pretty, much in the clear. The. Crisper. Cast 9 technology, for research when. It comes to commercialization. And variety of development. That's. That's a lot more complicated and I, think every institutions gonna have to figure.
That Out and there are still legal battles going on to. Even decide who owns the intellectual property, rights so that's another of latency long. Term the transformative, change I see with gene editing is. That now we'll be able to transfer, knowledge directly. Without. Even, having access, to the DNA, sample, or the specimen. And. That. May change some of our strategies for how we preserve, diversity. Or. Understand. Diversity. And. We'll have a greater use of cross species information, and. What we learned in one crop we might be able to apply in another crop. It. Won't replace the conventional breeding but, it will make it faster cheaper and more, efficient. It. Provides a much more direct route. For gene discovery. That. Can be used to make better plants, and. You. Have to think long term this will be accepted, by consumers. At. Some, point though there will come a day that. Summary the. Situation, is rapidly changing technologies. New it will change. It. Will get better, scientists. Are just beginning to think of all the uses for it and. Right, now the extent, of commercial, potential, for commercialization. Is a. Bit uncertain it. Probably depends on the crop. And. It will be a valuable research, tool, no matter what happens with. With. The commercialization. Part of it and some. Things say the same conventional, breeding is still needed. Two-dimensional. Breeding can do things. Shuffle. Shuffle the genome, and. In ways that we. Still, can't do with gene editing and. So it'll it'll stick around and be just as important. And. I'll put it put this at the end just in case somebody jumped. In at the middle I just. Want to reiterate we're not doing anything at that that's, the USB autoscope on, first National Research Center we're. Only doing Convention, blam breeding and, marker-assisted selection but, if you think about these things and we work with. Work. With collaborators because, we need to be ready. For. The day if. And when we, can use this you'd. Like to thank the scientists. And staff to do bumpers. For. Their, discussions, of how we put this talk. Together today, and Mike. Thompson for some, of his ideas on this and. Getting. Easy slides and, Ken quartz. Katherine, Peyton Siva. For. Providing, the, slides of what's going on here at the University of Arkansas and. Thank. You to robert coats and Mary for having, me here today.