CALS Discoveries Seminar. From Teosinte to Corn. John Doebley. 2018.02.22

hello and welcome to the next episode of the groundbreaking research at the College of Agriculture and life sciences at Wisconsin last Monday Road Sussman taught us told us about the work of brink which was with corn and identified jumping genes at about the same time in about the same way that Barbara McClintock did it today is our usual program the talk is current work drive from this earlier work and the speaker is John EE professor of genetics and medical genetics pleasure to have you thanks thanks Dave I'm glad they've made the distinction between the groundbreaking work of brink and my current work which I make no claim of being groundbreaking but I am going to sort of walk you through maybe 40 45 minutes of what we've been trying to do in my lab to understand the genetic basis of one of the most remarkable or probably the most remarkable case of a crop domestication like a domestication that involves really profound changes in morphology and yet we know that it just happened by genetic changes and our attempts to try to figure out what those genetic changes were so the talk is featured on the genetic architecture which just means the numbers of genes and how big the effects those genes had on traits that differ current modern maze from its wild ancestor and what were the molecular mechanisms by which those genes changed which we mean that they have an amino acid substitution or was there a change in the way they were regulated my laser sticks not any good good make this one all work and I have this subtitle low-hanging fruit and dark matter and the low-hanging fruit is the stuff we can grab and understand and yet we know there's a lot we don't understand they're not but I'll say something about it that's the dark matter so let me introduce you to the plans this you hopefully recognize that's modern corn usually that's just the single stock wheel modern corn has just one year on the side you probably all had some sweet corn or popcorn this is a side branch it's a very short side branch and it has a female structure here on the tip and this is the wild ancestor of corn and it looks reasonably similar as a plant but it's very branched has lots of side branches some from the base and some from all the way up along the stem if we just look at one of those side branches it'll have a tassel or a male structure at the tip and then it has a bunch of little ears along the side and so what is happening is this tassel in this ancestor teosinte is replaced by an ear in modern days and all these little leaders have kind of disappeared there's just one big ear at the tip and all of these branches are gone - you just have that single very short side branch a couple of things going on here this actually is what while plants do often when they are grown out in the lot what out in the open with lots of sunshine they branch profusely if you took it to a synth a plant and you shaded it by lots of other plants it would get unbranched too so plants respond to their environment by either branching a lot or not branching so much and if you think about it in another way this is for a wild plant that's got it's a tiny little ears that's fine but if you are a farmer and you're going through your field to pick your corn do you want to have to pick two or three hundred little tiny ears off the plant where right would you rather just get one giant beer that it's just as much grain but in a single easily harvested unit and so what ancient peoples did is they converted this with lots of little tiny ears difficult to harvest into a crop that has one giant you're very easy to harvest now as different as the plants are the real difference is the ear so that's an ear of modern maize sort of the very tiny little ear modern maize and this is an ear of teosinte and just to give you a little bit of more of an understanding of it I'm gonna pass around the cup it has these little triangular shaped what we call fruit cases but make up the teosinte ear you can see they're just about a half dozen of them there they're all hooked together here actually with Krazy Glue but they naturally break apart because each one has a single seed and that's how the plant sews the seed for the next generation each one of these has a single seed and that goes and flies off to a different location a lot of times birds eat them they'll pass through the bird and then get planted somewhere in a nice pile of manure and start the next generation here all the kernels are on the cob as you typically find with many systems you can actually touch some of these teosinte kernels or fruit cases in here I'm gonna put in a little ear of corn to for comparison if you like you can keep some of those teosinte fruit cases I've got bushel bags of them there aren't so many in there but you can stick one in your pocket they might even grow so if you want to try it in your garden you can do that now here's a little more about this two different structures and I'll explain that further as through you don't actually see the seeds here the seeds are hidden on the inside and these are some specialized casing that surrounds the seed here the seed is visible on the outside there's no casing and so what actually the transformation of teosinte year it's amazing involved it involved turning the teosinte ear inside out okay sounds rather dramatic you had to bring the seeds to the outside and all of the tissues that make up the casing surrounding the seed they form the cob on the inside so essentially you had to turn to the ear inside out you can see why this is very hard to believe in fact for a long time no one ever believed that teosinte could be the ancestor of maize because they look so different and so they didn't want to believe that these primitive farmers ten thousand years ago could by selective breeding convert that into this there's a little more about that teosinte fruit case it has two rows of kernels there's a row that points out this side and then a row that points out that side here's a cross-section through an immature one you can see the young developing kernel in there if you crack one of these open there's the kernel inside it so they're just two rows of kernels corn has at least eight rows a grain modern corn can have sixteen rows a grain that has this protective fruit case surrounding the grain the ear itself shatters because does any like any wild plant that wants to shatter and disperse its seed and they're only about eight to twelve kernels where modern ear of corn will probably have 500 kernels on it so that's much different from most other crops this is wild wheat and that's cultivated wheat pretty easy to see this one is long and slender it just got a little more compact the grains are a little bit larger but they're pretty much the same here's a wild tomato and here's the cultivated tomato it's the same structure just change in size so it's very easy to think that this could be converted into that but it's very hard to think that teosinte could be converted into meas the same principles at hand though if you were picking tomatoes in your garden would you want to have to pick 200 little Tomatoes off this plant or we'd rather just grab one big giant one it's much faster if you just can get one big giant one so easier harvest ability so as teosinte the ancestor basis native to Mexico and Central America it comes in different flavors I think they're about five different species it may be six depending on who you want the species names you like most of the places it grows are in southwestern Mexico we did a evolutionary tree using DNA sequence data to understand the relationships among different types of maize that's a phylogenetic tree this would be like corn from the Andes Mountains corn from South America here's corn from Highland Mexico corn from eastern United States court from southwestern us these are all the different types of corn grown by the Native American peoples when Europeans first arrived in the new world so those types of corns were collected from the Native American tribes been preserved in germ plasm banks and we could get them and study their DNA and then using the DNA make it a genetic tree of all the different types of corn and we included a couple of teosinte s that are right here at the bottom they have some strange Latin names I don't need to worry about but what you'll see here's all of corn from all over Latin America or the New World and it all comes from one branch point which is right here and at that branch point is this green which is a type of teosinte so all of corn arose from one single evolutionary event from this green type of teosinte this is another type of teosinte and down at the bottom is a third type of teosinte you could also use our DNA sequence data to apply something called the molecular clock which is you can basically get a time in calendar years that two species diverged from one another by counting the number of DNA sequence differences there are between them and knowing the rate at which DNA sequences the sequence differences arise over time so our molecular clock data date was 92 hundred years ago which is about what the archaeological data say as well so if we go back here oops I for one second there are a few types of this teosinte here shown with stars that are the ones closest corn and if we look at where they are on the map this is a map of Mexico this would be Mexico City right here they're just southwest of Mexico City so the genetic data suggests that the Tia synthase that are most like modern corn come from this region southwest of Mexico City and that's why we think that's the area in which corn was domesticated about 9,000 years ago and as luck should have it as I'll show you a lot that's where the oldest archaeological court comes from - if you go down to that region in Mexico which I've done several times here's a small hill and all along over this hill you see these plants that's teosinte and we'd collected teosinte there you can see some in the foreground we hiked up to the top of the hill took us a doesn't that big that it took us a couple hours to get there and there are just millions and millions of teosinte plants on that hill when we get to the top if you look out over the landscape it's just hill after hill after hill covered with teosinte so this was a tremendous resource for people's ten thousand years ago each of those plants produces hundreds of seeds and if you could collect them and eat them you had a lot of grain to use in your diet so my thinking is that that's what was going on they were taking advantage of this very productive wild plant as a food gathering for a wild food and then over time they converted it into teosinte or converted it into Me's here's some cobs from the archaeological record if you go the oldest cobs from this particular site are six thousand years ago and that's a very small one and that's exactly about the same size it's the little yellow eared one that's in the cup I passed around and then through time at that site they get larger and larger and larger and this would be about the time when Europeans first arrived in a new world and basically at that point it's the same as modern corn all of the sort of real changes to corn to make it the crop it is today took place before modern breeders got their hands on it and again what they're doing again instead of harvesting hundreds of little ears now you could go to each plant and harvest one giant here so what the Native American peoples did with corn is just remarkable so teosinte comes from here at but this is corn culture in ancient America at the time that Europeans arrived in the new world it was grown everywhere from Canada down to Chile now that's a really remarkable plant breeding feat if you think about it taking this plan that comes from tropical Mexico and adapting it to grow in Canada adapting it to grow a 3,200 meters up in the Andes Mountains adapting it to grow in the deserts of southwestern the United States they bred it in just so many different ways it's it's a astounding in the Amazon basin Amazon forests they grow out there too so the native plant leaders of the new world I have another lecture I give they're probably the best plant breeders in the history of the human species so the new world people really knew how to make a crop these are the archaeological dates for those regions and the oldest archaeological date as luck should have it is right here where the teosinte grows and where our DNA data said maize was domesticated and you can see it gradually disperses so it's about 2,500 years ago that Eastern the United States a little later in the Andes Mountains give you a couple pictures of what they did so this is maize in the Guatemalan Highlands this is my PhD thesis advisor his name is Hugh eltis he died a few years ago he was a professor of botany he on our campus I was a graduate student here and I took biochemistry with that guy and uo+ is around six feet tall and he has his hand on the stalk this ear is about 15 feet above the ground and the plant is in my estimate is something like 22 feet tall or 24 feet tall so this is how corn looks like where they adapted it to grow in the wet forests that we dropped whatta Malin Islands it grows for about 11 months you know just grows and grows and grows because they've got a very long season there the post there the stalks of it are so strong they can use them for like a building material fence post or whatnot so they've got very strong stops this is out of a book this is corn in the Arizona desert on a Hopi Indian farm Hopi Indian Reservation had taken in about 1900 this is USDA scientist his name was Collins and he collected corn there you know but you you almost think that must be cactus or something but it's not it's very short compared to our the one in Guatemala it's a different adaptation by plant breeders one of the remarkable things about it is they there's not much moisture in the desert but where the moisture is is very deep in the soil so they've bred the corn that they can plant the seed 12 inches into the soil and it'll grow up after germinates through the 12 inches of soil and get the seedling will come out above if you took modern corn like we grow in the Midwest and you put it 12 inches ground down it would germinate but we get about three or four inches and then it would die I'd never make it all the way up so they've bred that to adapt to the desert and then just to give you one more sort of slide on corn diversity and how variable it is this is corn from the single farmers ear in Mexico down there collecting we be out talking to the farmers they have bins fruit full of corn and we just that's this guy he let us take bunch arrange them in a nice circle and take a picture you can just see all the color diversity that's there and when you heard about brink you might have heard something about these color variance on corn kernels well these are the people these ancient farmers and modern native farmers of Latin America who selected all of those there's one other story in that regard they you heard about trans poseable elements and there's a story from the anthropological literature in the new world and they had corn that had transpose ax Bulow moments so the kernels were striped because one form of transpose of element calls cost as striping in the kernels an anthropologist having know nothing about knowing nothing about corn interviewed the people who wrote this in her book she said well what's the one with the stripes and the people she was interviewing said oh those are the most special of all the corn we put one seed with stripes in every field so they would have been in a way promoting more mutation because they were spreading around the transposon elements they really missed nothing you know if you think about you spend all your time like this right these people have just had nature and they knew it in great depth in a way that we can hardly appreciate let alone ever equal so back to teosinte how could you make teosinte in the corn well this is the guy who figured it out if your biology major you may have heard about the one gene one enzyme theory I commit make a Wisconsin connection George beetle shared the Nobel Prize with someone that Miller talked about a I guess a few weeks ago Joshua Lederberg so they shared the Nobel Prize beetle got it for one gene one enzyme along I needed Tatum and beetle also is interested in corn evolution and he proposed that teosinte could be converted into corn by a relatively small number of chain changes mutations and beetle did a little work to support his idea he said well you can cross corn and teosinte and that's the f1 hybrid that's what it looks like and the fact that they're crossing is a sign that they're not so different and he studied the hybrids and he saw that the hybrids are fully fertile which is what you would expect if they were closely related species right and you can cross a lion and a tiger and get a hybrid but the hybrids not fertile right but here the the hybrid is fully fertile and he did some experiments to conclude that there may be about five genes and here's the beetles experiment they used basic Mendelian logic so if I take corn and cross it with teosinte I get the f1 hybrid and then I self pollinate the f1 hybrid to get an f2 generation what you're going to find is a quarter of the offspring are four if there's one gene difference 1/4 of the offspring will look like maize and 1/4 of the offspring looked like teosinte and half will be somewhat intermediate this is a 1 to 2 to 1 ratio which is basic Mendel ISM so he said if there's one gene that's responsible for making amazing Co since they different I should see 1/4 look like of the f2 plants should look like maize and 1/4 look like you sent those two genes 16th and 1/16 and he came up with a number that was somewhere between 4 and 5 and so he suggested about 4 or 5 gene changes could make teosinte in the corn basically when he looked at his f2 s he saw that somewhere around 1 in 500 looked like maize and 1 in 500 look like to you someday and these are just some f2 hybrids they you the but the range you can get you get some back f2s that's an f2 plant so it looks just like teosinte pretty much a little odd there but it's pretty much a teosinte here's an f2 that looks pretty much like corn here's an f2 that looks pretty much like maize a very short stalk and here's an f2 that looks pretty much like teosinte a very long stalk with a tassel and so that was beetles experiment mm-hmm I shouldn't mention one other link oh I want to go back for a second is this has another Wisconsin connection this is from a book written by a guy named Paul Mangelsdorf and how many of you know the name Sara Mangelsdorf she's our Provost Sara Mangelsdorf is Paul Mangelsdorf granddaughter and he also worked on corn evolution but okay no I'm not being recorded am i anyway her grandfather was wrong and Beatle was right so and and she actually fully accepts that so okay so that's where Beatle left it a few genes might make corn into your something and that was about 1972 was winning he's sort of pub last published on that now what my lab has done is tried to say well what are the genes can we find the genes that differ between corn and teosinte and see how they've changed and the way we did that so we use a fancy word or phrase for corn we are for a gene we call it a quantitative trait locus QTL for short it's really just a gene and if you think about a trait like say help tall people are its quantitative it goes from very you people can be short all the way up to extraordinarily tall all right 4 foot 11 up to 7 foot 6 or something and so there are many many genes that make those difference so the trait is quantitative and a trait a gene that affects a trait this quantitative is a quantitative trait locus or gene and most of the traits that make maize and teosinte different or quantitative so we took this approach of trying hunt for quantitative trait low side that make Mason's he isn't they different and this is a little cartoon that shows you what we found corn has ten chromosomes that's the numbers one through ten and this just shows you the kind of map along the chromosome so it's got like map positions from zero to two hundred and something and these gray Peaks show you where we found evidence that that part of the chromosome makes the plant look different corn from teosinte so right here this is chromosome one on the long arm of chromosome one that peak tells us that somewhere on that region of chromosome one is a gene or maybe many several genes that make corn and see is simply different so we did a genetic mapping experiment mapping QTL for the differences between corn and Co synthase studying an f2 population basically we did Beatles experiment but we use DNA from the chromosomes to track where the genes are located I'm gonna tell you about a few of these Peaks and what genes are under them and what we learned about them and I'm gonna start here with this peak on this end of chromosome one and this is work done here by a graduate student in my lab her name's Laura Shannon she's now a professor at the University of Minnesota and Laura did QTL mapping she was sort of our lead person on a big QTL mapping project and one of the traits that she studied is whether you have lots of little years like teosinte or just one ear like mains and here are some plants from her population which is the population is a mix of corn and teosinte and here's one that looks more like maize just one ear and here's one that's it's mostly maize but it looked past the tio since they trained it's got lots of little ears along the branch but it has a ear rather than a tassel at the tip so when she asked where is the gene that makes this they are the genes that make this different on the chromosomes here's chromosomes one through five she didn't find any genes on chromosome six through ten but she found some genes on chromosomes 1 through 5 but there was one gene with a really really big effect and this y axis measures the size of the effect no is it something that really makes a difference and so what you can see she it looks like there's one gene that's really really important here on chromosome 1 and then some other genes that are having an effect but very little effect so then this is David wills he was a postdoc in my lab and he said let's see if we can figure out what the gene is there on that long arm of chromosome 1 and so he created a bunch of genetic stocks and each row represents a genetic stock and that differ from one another in how much maize and teosinte they had so this is a genetic stock and in that region two chromosome 1 it has maize all the way up to here and then there was a recombination or crossover event and then it has two teosinte chromosome there here's another one that has teosinte chromosome here but then switches becoming maize chromosome and so forth and so on so he created all these genetic stocks and then he looked at their plants and for them and here's what he found these stocks produced lots of years these stocks only produced two ears these thoughts that produced only two ears their maize in this region the chromosome we're the ones that produced many ears are teosinte in that region of the chromosome so the part of the chromosome that gives you many years versus just a few ears is right there it's just upstream of a ORF as an open reading frame for a type of gene that is called a transcription factor that's a gene that controls other genes it's a regulatory gene and the open reading frame is the part that makes the protein and this is the part that tells you when and where to make the protein and so he found that what's happening is that maize and teosinte differ from a regulatory region in a gene that controls other genes feel free to interrupt those questions too so I didn't invite you to do that in I apologize okay this is a collaborator like Clint Whipple he's at Brigham Young University and he did another experiment for us which is to say if we can figure out how that change in gene regulation took place telling you that where the difference is is in in controlling when and where the protein is made and he clicked it something called a tissue asset to hybridization this is actually a side branch of a genetic stock that has the teosinte version of that gene and this is a genetic stock that has the maize version of that gene and so this is the side branch so there would be an ear right at the tip here or an ear formed right up there and what you can see are supposed to see there's a little band of gene expression here I won't go into the technical details of how we measure gene expression but here again the maize allele you see a band of gene expression right across the nodes and until synth a with the TSN sailu you don't see that band of gene expression what the gene is doing is it's the node is where a Sidr a little ear would be made and when the gene comes on here it blocks the little ear from being made the node so what we got was a gain of expression in a particular tissue there's nodes and when the gene is expressed in those nodes it stops the plant from making the little side years so it just makes one big giant top year so we've identified the gene a transcription factor and we've identified that what has changed in how that's regulated so now the gene is turned on in maze in a place where it's not turned on into your synth a okay let me give you another example this is on chromosome four this is our QTL mapping n we found QTL on chromosomes one five six and four but we found one big giant QTL something was a big effect on for this trait here is making a fruit case so we measured making a furred case like teosinte or no fruit case like maize these are the people in my lab here who did this work by Wang he now is a bio technologist with Monsanto Tina is a high school teacher she was a technician in my lab and Kirsten bumbie's is a research scientist group leader at in England that the John Innes Institute so she's also a MacArthur Genius award winner so she's quite a remarkable young woman so they as a team cloned this team that makes the fruit case and it's another regulatory gene it's another gene that controls other genes and here's what it does so here's a normal T of sin that year here's one in which by just back crossbreeding we substituted in the maize version of this gene and I didn't mention its name but I'll mention it now is called TGA is the name of the gene and when you substitute here's a normal teosinte fruit case when you substitute in the main version of the gene the fruit case doesn't fully develop so the kernel becomes partially exposed now if you're an ancient person and you want to eat the grain wouldn't you much rather have it out there easy to get rather than locked up in there and so this was probably a very important step in making teosinte a more edible crop I'm gonna point out one more thing I'd like to point out think about teosinte wild plant it's got its seed locked up in this fruit case how can it grow right it's got to germinate and grow it has a system for doing that this is a little poor that the root comes out so that this will imbibe water the seed will germinate the root will come out that little hole and then the chute will come out on this crack up here so it's adapted to protect the seed but then leave a kind of an escape hatch when it when it germinates so that I point that out because I'm going to show you another slide where you're gonna see that little hole again and here it is so this is the opposites form of bat crossbreeding we took the teosinte allele for that TGA gene and we put it into modern maze by back crossbreeding and now it makes little fruit cases all within the corncob and it does it so perfectly even remakes the little hole where the root will come out so that single gene has a huge effect on development and this is Jerry chemical he was a genetics professor in this department and he in parallel to me discovered of this TGA gene and we published a paper together describing it so we studied the DNA of the gene the how it differs from maize and teosinte and that's Jean Zhao she was a graduate student here in my lab she's now a statistical it's her fourth title she's a statistician with a pharmaceutical company in New Jersey so and Joan did the DNA or that what we called molecular evolution and she sequenced the maize and teosinte copies of this TGA gene and compared them and found that the only place they differ is for one amino acid so his maze has an asparagine and teosinte has a lie gene lysine so one amino acid change is what makes maize and teosinte different and this is a fancy-pants complicated experiment which I know that is probably too much to try to go through so I'm not going to do it I'll just say it in words it's these are really great experiments if you like science you like this kind of stuff but what it told us is that that single amino acid change from a lysine to an asparagine converted the protein from an activator into a repressor of its targets this is a regulatory gene it's a gene that you know what regulates other genes and that single amino acid change switched it from being a gene that kind of up regulates other genes to a gene that suppresses its targets reduces their expression a little bit and that's the fancy-pants experiment that did that and this is another fancy-pants experiment I again I don't know this is a gel shift assay I'm not going to go into this but basically when you have a polypeptide they Kinnick sometimes exist as a monomer one copy but other times they will bind with tentacle copy like themselves and form a dimer and so what that amino acid does at this level here is maze and here's teosinte in teosinte most of the protein is as a monomer but when you switch it to maze most of its as a dimer and so we think that single amino acid change is affecting the monomer versus dimer balance of the protein and that's affecting whether it activates or oppresses its target genes you have to be a science nerd to love this kind of stuff I mean I just really like it so this is why Wang again and why did some other experiments this is our gene that controls the fruit case and he said well what are the target genes that it controls or activates and so he identified a series of deep down stream genes that it controls or activates and this is just several of them and as luck should have it they're all so regulatory genes so this gene sits atop of a kind of a regulatory cascade it's like a regulatory gene that regulates other regulatory genes and somewhere down the line our genes that actually carry out the work of cells but and this is this I don't again want to go into too much but here you can see when you have the mais allele the amount of expression the product of the target gene is lower than when you have the teosinte allele so if you have the teosinte Lily you make a lot of this zag one target when you substitute in the maze allele that single amino acid change you repress the target and one more let's see I'm about yeah okay one more peek I'll go through this one pretty quick this is the peek for being a very branchy plant or just having a single stalk it's on chromosome one this is my technician from Minnesota I did this work when I was in Minnesota where I was a professor before I came here and we cloned this we did it actually using what Miller talked about transposons we did this by an ancient technique called transposon tagging and so here's teosinte very branched here's modern maze and this is a mutant of modern maze called teosinte branched tb1 so it's a gene that when you knock out this gene a corn plant looks just like teosinte so this right here is a hundred percent modern corn it's just that one of its genes knocked out and it makes it look like teosinte again teosinte has a tassel at the tip of its branch a mail structure when you knock out this one gene you get the same thing it converts the ear into a tassel so it's a pretty remarkable one gene change so we cloned it oh and it turned out to be another regulatory gene another transcription factor so this kind of a developing theme here that transcription factors are the genes that control what the plant looks like so what this gene does it blocks the outgrowth of branches it's a repressor of organic growth so this is another tissue Institue hybridization this is a young seedling this is B the growing tip of the plant so this would just be a little seedling like this big and it's a cross-section through it and it's been stained so we can see where this tb1 gene is expressed and it's expressed in the bud so that's the bug that would grow out and make a branch but when it's expressed in that bud it represses the outgrowth of the and so what happened in evolution then is this gene was not on in that bud and so the bear had to go out and he assumed a in maze the gene got turned on in the bud and stopped the branch from growing out and this is just the experiment to shape show you that we measure how much is this tb1 gene expressed and when you have maize in that bud it's expressed a lot but in if you have a teosinte allele at the gene then the bud is the expression is much lower and without going into the details here the way this gene works is it turns off the cell cycle so the it doesn't the bug can't grow out because the gene is the TV one gene represses genes involved in cell division I'm gonna skip so we well this is a Tony Studer he was a grad student in my lab he's now professor at the University of Illinois well assistant professor and this is Richard Clark was a postdoc and he's now an associate professor at the University of Utah and they said well you know that tb1 gene was important but what part of it what part of that gene changed and they were able to map the part that makes maize and teosinte different to sixty thousand base pairs away from the part that makes the protein so here's the part that makes the protein sixty thousand base pairs upstream is the part that makes maize and teosinte different and it's another regulatory region so it controls when TV one is turned on and how much it's turned on so up here is something that's telling the gene they have turned on a lot higher in maize that in teosinte and they could measure how much of an effect it had when you get rid of all the other genes in the genome and you say how much effect does this one little change in this region have on the plant well it would take if you took a plant that was pure maize and you substitute it in this control region from teosinte you would get a plant with two little branches like that so I've been mentioned trance possible elements again so it turns out what was the key change in that gene is a transpose xi it's a transpose well element has a clever little name called hopscotch and in maze hopscotch jumped into the control region in teosinte the hopscotch is not there and then this is another fancy-pants experiment and basically what it tells you is when hopscotch jumps in the target gene gets expressed at a much higher level so the hopscotch element is an enhancer it's enhancing the expression of the open reading frame for the TB one when you get more of this TB one protein you're repressing more repression so you get less reaction health growth all right so that's the low-hanging fruit we can get the fruit case gene and get the mini ears gene we can get the branching gene we've done five genes like this all five are these regulatory genes called transcription factors in four cases it was changes in the regulation of the transcription factor and in one case of us an amino acid change I'm gonna skip because I'm running out a little time we did some other experiments I'm not gonna give you the details of them and I told you this already that the TB one branch gene regulates the cell cycle teens I told you that the fruit case gene regulates a bunch of target genes but we also figured out that the this gene the branch gene controls also the fruit case gene and then the branch gene also controls the many years gene and there's from the literature several other genes we know about that are all part of this pathway there is something called a micro RNA that regulates that gene and then we know all of this is downstream of the shade avoidance pathway from plants so when you are getting lots of shade then this gene is turned on turned off and that makes TB one go off and so in this condition you can get lots of no branching and in this condition when you've got not shading then you do get lots of branching so this pre-existing sort of developmental pathway in a sense was hijacked by these ancient peoples to convert the highly branched teosinte into the unbranched phase and of course I don't want you to sue I don't expect you to remember remember any of that except to say that the without all the names just remember that evolution targets pathways and networks of genes all simultaneously why we can tease it apart and study one gene at a time what's really going on is you're you're targeting the entire genetic network controlling the traits all at once now that's the low-hanging fruit just to make sure you understand we don't we don't know all the stories I told you earlier on teosinte has two rows of kernels maize has eight to sixteen or so rows of kernels if you study that tree you don't see one big giant QTL you see a total of 24 cutie of all different sizes and the fact is the 24 is the statistical estimate that's going to be an under estimate the real number could be 300 okay and so well there are all these other Peaks like that that's the dark matter so we can find a few big genes of large effect but finding all these little genes will be essential possible with current methodologies but they're they're out there there is a lot of if you will dark matter controlling the trait differences between corn and teosinte and this is Zack lemon who was a grad student to my lab he now works for a company in Massachusetts in biotechnology and Zack did a different type of dark matter study he looked in the genome for genes that are differentially expressed between mason teosinte let's find genes that are say expressed high and teosinte but low in maize or low in teosinte and high in maize and when he did that he found over a thousand genes that are different between corn and teosinte in the extent to which they are either expressed higher expressed low and the most of them that were in the ear and the ear of course is where the action is that's what changed the most so that's more dark matter thousand genes that we don't really know what they do but we know their difference between corn and C or something so I am ready to close shut up shop here so we can get these genes of large effect and get a picture of evolution that way they're all transcription factors and sometimes they change by regulatory changes to be either upregulated or downregulated so once we add an amino acid change importantly it's a whole network of genes that are really being affected not single genes in isolation and we really can only see the tip of the iceberg there's just the vast amount of change in the genome when you convert one species into another so that's my cart as opposed to groundbreaking research done here at Madison so thank you milord yeah so when that's when the modern breeders you know change hybrid corn what are they actually fixing in that I don't specifically know the answer to that my expectation is that largely they're changing gene regulation you know that gene regulation is what's most important and controlling differences in as opposed to protein functional differences we show the picture with you notice yes yeah I didn't say anything about that he was a taxonomic botanist and evolutionist and he got interested in that because his father was a biologist and studied corn and so that where his interest started and then he was just reading the literature and he read the crazy theory of the grandfather of a certain academic administrator at this university whose last name I won't mention but and not upset him to see this crazy theory being promulgated in the literature and from his perspective as a taxonomist the answer was clear teosinte was the ancestor of maize and so he wrote a paper making that claim from a taxonomic perspective you know just from the way a taxonomic botanist would look at this say it's clear to some taste the ancestor of maize he wrote a NSF grant to study it and I was actually here on campus in the Anthropology to plant and he recruited me to join his lab and study corn instead of staying anthropology and study human genetics which was my lifelong desire which never really happened so and so so that was his sort of contribution was the taxonomic one you know to saying that if you beetle looked at it as a geneticist he looked at it as a taxonomist and said tear synthase got to be the ancestor yeah based on taxonomic approach and it was this is back in the 1970s and it was there are a number of sort of spirited conferences at which hue eltis George beetle and Paul Mangelsdorf were all present and apparently they had some powerful debates but beetle triumph in the end and so his view of things that it's fully accepted by anybody who's competent to you know study the data and come to conclusions okay well thank you

Channel: Wednesday Nite @ The Lab

Views: 1,923

Keywords: Biotechnology, UW-Madison, Science, WN@tL, Wednesday Nite @ the Lab, Science Outreach, Wisconsin Idea

Id: wewf31R_9dw

Length: 50min 59sec (3059 seconds)

Published: Sat Feb 24 2018