 Also, if you're watching this later on Moodle, or if you're watching it like in five years on YouTube, welcome to lecture number two of the Bioinformatics course. Today we will be talking about phenotypes, also known as traits. So the whole lecture will be showing you guys, or kind of explaining to you guys what phenotypes are, what different distinctions we make between different types of phenotypes. So the gliderung for today or the overview is we will be talking about phenotypes or traits. I will try to instill on you the knowledge that there is a difference between qualitative and quantitative traits. We will be talking about Mendelian traits and complex traits. I wanted to say a little bit about statistical analysis and things like multiple testing. But last week we did a quick asking around and people said that people were aware or followed an SAS course or at least some basic statistical knowledge. I'm out of sync, lip sync. Okay, is there anything I can do about that? Am I in front or behind? Let me check some of the properties. Let me just read time stamp it. Audio is in front of the video. It is a little bit slow though, the video thing. Let me see if I can fix that for you guys. So let's go to properties, configure video and disable buffering. Is it better now? Is it better now? I hope so. Yes, okay, cool. So that's what the update changed then. So I updated the streaming software and it sneakily put on the buffer audio thingy. So it buffered the video and then it's behind. All right, good. So that's all fine. I said that you already had some statistical analysis. I won't be dwelling too much on it and I will just show you that it's important to do things like multiple testing. So when you're doing a lot of statistical tests, then you need to compensate for that. We'll be talking about phenotype databases. So where can you guys get free phenotype data? And in this case, I will be focusing mostly on phenotype databases that are related to animals and humans. Of course, these same databases exist for plants as well, but since I'm not working a lot with plants, I'm probably not the best guy to give an overview of that. But if you are working with plants and you think like, oh, I really want to know a lot of the databases that are out there, for example, for Arbidopsis or for Brasica Rappa, then just shoot me an email and I can put it on the list so we can add it to the next lecture. Phenotypes will come back as well. So let's just see how it goes and where I can fit it in then. And a word about project planning, because that fits in really nicely. It's one of the first lectures. So if you're planning a project, which for most master students, generally not the case, but if you're a PhD student, you might be planning your own project. So just a small word about that. All right, so when we talk about phenotypes or trade, generally we consider these things as classical phenotypes. So there's a distinction between what is called the classical phenotypes and things what we call nowadays endofenotypes. So classical phenotypes are things like the yield, so how much potatoes does a potato plant make, things like flowering time like from seed to first flower, how much time is taken by a plant, and things like human stature. So human stature is just how big you are, so height. And often, and that's one of the confusing things here, is that phenotypes are used as markers during breeding. So the word marker is generally reserved for genetics, right? A genetic marker means a position in the genome that we can track and we can follow or we can determine if someone is AA or GG or AG, for example. But phenotypes have been used for the last like 500, 600 years as markers for breeding. So I kind of want to go into that because phenotypes and genetic markers, they are used interchangeably as well. So first, why does a bioinformatician concern themselves with phenotypes and trades? Well, here we see a really nice example. This is an image by Lemnatec. So Lemnatec is a big company which does plant phenotyping. And this is the way that they do plant phenotyping, so all of the plants are in these little buckets. They're on a conveyor belt and they are moved in and out of kind of a scanning chamber where every plant is scanned every hour. So there's a lot of automation going on. There's a lot of data that's being collected. And this is one of these kind of classical big data problems where we have five, six hundred plants, which are videotaped and photographed and monitored continuously. So this will result in gigabytes of data. Of course, all of this data needs to go into a database and in the end you want to say something about statistics because you want to do some analysis and improve something about certain plants. And of course these automated phenotyping systems are not just there for plants, they are also there for animals. So we have mice cages where mice are tracked using RFID and they are videotaped continuously to see their behavior. And then head that all goes into a big statistical model and then people want to prove something like, well, if there's a cat smell in one of the cages, then mice tend to not go there or mice tend to go there. And then you can do all kinds of experiments. All right, so big data is the reason why bioinformaticians are here. And of course, big data in this case means gigabytes of data. If you're just a biologist measuring like plants on a field and you have a very limited amount of plants and you only measure one thing, then of course it's not really big data. So it's really about the automated phenotyping nowadays where bioinformatics comes into play. Good, so first question for chat, just to see how much you guys know about phenotypes and about phenotypes being used as markers. So here we see a picture of two different types of cows. And the question for you guys is what is the difference between these cows in relationship, of course, to their phenotypes. So I'll just wait a couple of minutes because there's not only a delay in me speaking to the camera, which we kind of solved. But there's also a delay, of course, in you guys having to think and type. All right, so Xanaxin, coloration of the hair and patterns. Yes, no, that's one of these obvious phenotypes that you can see, right? So the one is black and white and has this kind of, well, Holstein-ish pattern. And the other one has a completely different color. Sam, what's color and pattern? Muscles, that is a answer. So very basically, right? If we think about cows, there's a phenotype of economic interest. All right, so the answer from my moderator is one is for milk and one is for meat. And here we see this really interesting thing, right? And this interesting thing is that traits, phenotypes of things that we can observe are used to kind of represent economical traits, right? We don't keep the one cow because it's black and white. And the other one, because it's nice and kind of one single color, we keep one cow because it is black and white. And we keep that because the black and white pattern actually is linked to high milk yield. All cows which are black and white and have this kind of Holstein-type pattern are high-yielding milk cows, while cows which are more or less uniformly colored generally are cows that are held for meat production. So here we see this phenotype, this clearly observable phenotype, right? The difference in the colors, the difference in the patterns, and that is very tightly connected, correlated with the phenotype that we are interested in. In one case, milk production, and in the other case, it is meat production. So if we would breed two of these cows together, we would get offspring. And then just based on the color pattern of the offspring, we can already say if the next generation of cow will be suitable for milk production or if it would be suitable for meat production. And that, of course, is the phenotype of interest, right? We don't keep cows because they look beautiful. Well, in a way, some people do, but the phenotype here is that, yes, they look very different, and this difference is, of course, connected to the phenotype that we are interested in. All right, another one, what is the difference between these two types of potato plants? And again, I know that the color is different, right? I'm not colorblind. Yeah, I'm not colorblind. I can see that the color is different. But what is the difference? Why would I as a farmer look at the color of the potato flowers and then say, oh, now I know something about my potatoes, which is of economic interest. We're interested in economics. So that's generally, you're not breeding potato flowers just because they're nice and white. Well, you could, but that's not really of a... Festkochen versus Meelig, that is kind of the idea here. So when you see potatoes, right, and you see a potato field, and that potato field is flowering and the field is white, then you know that these are potatoes that are used for human consumption. If you see a potato field and all of the potatoes are purple, you know that these are going to be used for producing starch because the color of the flower, so the purple color, indicates a very high amount of starch in the potato. So here, the color of the flower is not really of interest to the farmer, but of course the farmer has an interest in either making potatoes, which are suitable for human consumption. The right one seems to have more flowers in gluten. I think the one is just a little bit zoomed in and the other one is more zoomed out. But the basic thing here is, again, as a farmer, if I look at my field and I see that the field is white, I need to call the supermarket to kind of sell my potatoes to the supermarket. While if I look at my potato field and all of my potatoes are purple, then I cannot call the supermarket because they won't take my potatoes and they're just horrible, and I have to call a starch company, which things like the Avebe or big companies that extract the starch and then make all kinds of other products from it. So again, this is called, in genetics terms, it is called linkage. So one phenotype, the color of the flower, is very tightly linked to the starch content of the eventual potato. So when we talk about phenotypes, we have to distinguish between two types of properties. So we have qualitative properties. So those are properties which are observed, but cannot generally be measured with a numerical result. So qualitative properties are things like taste. Taste is very subjective to the one or the person who tastes it and you can't really put a number on it. You can't say this potato plant tastes like five meters per second and the other one tastes like seven kilometers per second, right? That there's no unit to taste. So qualitative property are things like does it look good? Does it smell good? Does it make me feel good? So these are qualitative properties. You can put kind of a scale on there, right? You can say this one tastes better than the other one, but you can't put a real numerical multitude or magnitude on there. So if we can do that, right? If we can measure something in a quantitative property, then it is a property that exists and that has a magnitude or a multitude. So it is something that we can express, right? Like the height of a cow. You can say this cow has a height at the shoulder bone of like 1.5 meters and the other one is 1.6 meters, right? So we can exactly define the quantitative property of height, but we cannot do this for qualitative properties. All right, so a little bit of discussion. Normally we do this in the lecture, so it's easier so anyone can just shout, but so let's just start at the top. So high fat milk yield. Is this something which is qualitative or quantitative? And just as a hint, there will be a question like this on the exam and the exam is not so much about getting it right, but it's about your reasoning. So if something is qualitative or quantitative. So for high fat milk yield, just throw in chat, what do you think is high fat milk yield quantitative or a qualitative property? Can we measure it in a numerical sense or is it just something that is more like, we don't know exactly, but quantitative, quantitative. Yes, Sam Watts, 21, perfectly right. Xanaxin, yes, quantitative. Quantitative property, definitely, because you can just measure the percentage of fat or the total amount of fat in the milk and you can do this using real numbers, right? So you can just say, well, there are 500 parts per million fat in every milliliter of milk. All right. So next one, meat structure is meat structure, something that you can measure quantitatively or qualitatively. Should actually put a little music while we wait. Or we should just put the qualitative, very good genie 88. That is indeed a very qualitative trait. Although people are trying to make it quantitative because meat structure, yeah, like Sam Watts says, quantitative if you count the number of fibers. So meat structure is a little bit weird, right? Because in a way you can say this meat is good or this meat is bad. But nowadays there are machines which measure the marbling of meat and the marbling of meat gives you a kind of an idea, you put it in an MRI machine and then you get the amount of fat versus the amount of lean mass and then you get more of a quantitative measurement. So that's really a discussion point here. But if you say it is a qualitative, then you can argue, yes, because meat structure is something that for every person has a different meaning. Some people like meat with high amounts of fat and some people like very lean meat. If you argue like this, then it would be a qualitative measurement and you could say, well, this is good meat because it has good structure. But of course, what is good structure depends really on the person that's saying it. All right, so let's just go through the other one. Starch content, of course, is a very quantitative trait. It is very easy to measure the amount of starch. Again, you can express it in parts per million. Wine quality is more or less the same as meat structure. It used to be a qualitative trait. Is it a good quality or bad quality? But since like five to seven years, the quality of wine is determined by robots. So robots just kind of sniff the bouquet and see how many flavonoids there are in the bouquet of the wine and then they give a score for the wine. So it is nowadays a quantitative trait. Well, it used to be a qualitative trait. Like you used to have people who were vinoleges, right? And they would drink wine and they would give it a score and then there would be a panel or a jury and they would decide on how the quality of the wine was. Flowering time is of course quantitative, very quantitative because you can just measure it in the amount of days and then of course, race times are again discussable. Race times are of course measurable in a quantitative way however, the fastest horse is not always the best horse, right? So depending on what you want, if you want to have like a horse which is good at stamina, then of course stamina and like highest top speed are not correlated. A horse which runs at like 50 meters per second is not per definition the best horse for the type of race. So depending on what type of race you're participating in, I would argue that across the whole spectrum of races for some races which are based on speed, then yes, if a race is based on endurance, then it is not really that quantitative. Although you could express it in a way, but here a lot of things come into play and it's not as easy to make it a real quantitative trait. So generally you would analyze race times especially in like multi-day races where you look at stamina of Arabian horses, then this would be defined as being a trait which is qualitative. So a horse is good or a horse is bad. So if I think about quantitative and qualitative traits, then of course all of the traits in the world that there are, the big circle, so everything can be given a quality score because you can have an opinion on anything even if you can't measure it. So the qualitative traits are much bigger than the quantitative traits. There are more qualitative traits than quantitative traits because every quantitative trait, everything that you can measure with SI units, you could also define this in a qualitative way. So the quantitative traits are a subset of all qualitative traits which are out there. So quantitative traits generally are defined by the international system of units. So if you can measure a trait by using the international system of units, then it is a quantitative trait. And a qualitative trait is a very subjective measurement which depends on the observer. And of course in the recent years with more measuring techniques, the quantitative trait bubble became bigger and bigger and bigger. So wine quality used to be here in the qualitative traits but nowadays wine quality is in the quantitative traits. It happens with more and more traits. So the more technology we get, the better we are in expressing certain properties of an animal or a plant in terms of the SI units. So besides having a qualitative and a quantitative trait definition, we also have something which is Mendelian and complex. So we say a phenotype or a trait is Mendelian when there is a single genetic locus and a single gene in the genome controlling this phenotype. However we can also have more complex traits and a complex trait is defined by having two or more genetic loci in the genome which control the amount or the score that you give this phenotype. So we will get back to Mendelian and complex traits. I just wanted to ask you a question, right? Because you're all scientists. Everyone is doing a master or a PhD or a bachelor and what are the seven fundamental SI units? And normally I would write it on the board and just write down what you guys answer to have an overview but I will just take a pen today and just a piece of paper and then I will just have you figure out the seven SI units. So just to kind of see how well-versed you guys are in more or less basic science, right? So this is something that you should have learned in high school in either physics or in chemistry or some other like very beta field but just as a question to you guys, so just throw in chat what you think is a fundamental SI unit because only when you know what the seven fundamental SI units are can you define what a quantitative trait is, of course. So I'm just going to give you guys some time to throw something in chat. It doesn't matter what you think. There are no right or wrong answers. Meters per second. So meters per second are, I would say two, right? Because you have meters which is kind of a distance measurement and you have seconds which is a time measurement. So the SI unit itself would then be distance and on the other time it would be time. And Ksanakzin says seconds, meters and kilograms. So kilograms would be weight, right? So you would say that the unit is weight. Matter for length. Yes, so meters are a measurement of distance, so a length measurement, but then we still have three, right? So we have seconds which is time. We have meter or the distance measurements and then we have kilogram which is the weight. So those are three out of seven. So there's four more fundamental SI units that you can guess. So what else do we use for measurement and can we use to define? Temperature in Kelvin. Yes, very good. Ksanakzin, temperature is definitely as fundamental as a unit and it is actually a property of an object, right? So an object has a certain temperature and this temperature is something that you can determine. Ampera, very good bacon, very good. Ampera is indeed the speed at which electrons flow through a wire or because it's connected to like resistance. But yes, electrons flowing through either metals or other objects is indeed a fundamental SI unit which you can determine. All right, so then we're at five out of seven. I'm just going to show you the rest. So we have length which is measured in meter, not meter, like the English one. We have mass which is measured in kilograms. We have time which is measured in seconds. We have electric current measured in ampera. We have thermodynamic temperature. So it's not really, it's thermodynamic temperature which is of course measured in Kelvin because that's always based on the absolute zero where atoms do not move. Then we have the amount of substance which is measured in mole and we have luminosis intensity which is measured in candela. All of these units except for one are invented by the French around the time of Napoleon. That's why I show Napoleon here. So the only one which is not invented by the French is the thermodynamic temperature which was done by Lord Kelvin or posed by Lord Kelvin. And of course Lord Kelvin came from the UK which you can argue based on like history that the UK and France they are kind of the same thing in a way but still very different. You can see France as the European part of the UK but Kelvin is the only one which is not French. So we can talk more about units and also these units get redefined once in a while because mass of course is defined in kilograms and it used to be defined as just a piece of metal which was stored at one of the SI offices because the system international just has offices around the world and they had like an example kilogram there. Nowadays the kilogram is defined as the weight of a sphere which has a certain diameter which is made out of certain atoms so these things get redefined but everything that you can measure in the whole world is a combination of these seven fundamental units and if you cannot express it in one of these units then your phenotype or your trade is not quantitative. It is a qualitative trade. Good, so Mendelian, I already said, one locus, complex, two or more loads. And of course you can mix and match these. So you can have a Mendelian qualitative trade or you can have a complex quantitative trade and you can also have complex qualitative trades. So it's two parts. So the one part describes if you can measure it or if you just kind of give a subjective score to a phenotype and the Mendelian and complex is of course talking about how a trade is encoded by an individual so if it is encoded by a single locus or if it's encoded by multi-load size. So if we talk a little bit about the history of phenotypes and of trades then of course we always start with Gregor Mendel. Everyone I think working in biology should know Gregor Mendel. And I just took a nice image of him from Wikipedia. But he is kind of the godfather of modern genetics, right? Because everything which we know about genetics began with Gregor Mendel. So Gregor Mendel has posed his theory and his theory is that trades or phenotypes are inherited from the parents. He also posed that there is something which he called gametes. We nowadays call these genes. So gametes are things that are produced by, so men produce sperm cells, women produce egg cells and these things contain something called genes. And he imagined genes to be like beads on a string, right? So you have a little string of wire and the phenotypes are encoded on this string of the wire by individual beads and these beads you get, half of the beads you get from your father, half of the beads you get from your mother. So his theory is kind of fundamental because even before we knew that DNA existed he already had this theory that there should be genes and he actually wrote down also all kinds of mathematical formulas which allows us to reason about the phenotypes of the offspring based on the observations of the phenotypes of the parents. So if one of the parents is very tall, the other one is very small, then the child will be somewhere in the middle. So kind of a mixture of the two and also this whole mixture was posed by him. So Gregor Mendel is more or less the godfather and he posed that there is beads that are on a string which are in the gametes, so in the sperm cells or in the egg cells. And this is a very big step in, or it's not the biggest step in genetics but it is a very big step because before this time the leading theory was the homiculus theory. So that meant that people thought that there was a very, very tiny person inside of a sperm cell. So the women was nothing more than a vessel to incubate these little humans which came out of men, right? So very man-centric. The woman had no influence, everything comes from the man. So the homiculus theory where you can even see these old pictures online if you search for a theory and then you see like this little sperm and then within the sperm you see kind of a little human being which is inside of there. And that was the idea. The idea was that the sperm of the male went into the female and the female was nothing more than a kind of incubator for the sperm cell. A very interesting theory and this is a theory which kind of throughout the Middle Ages was the leading theory of how humans were produced and how animals were produced. So of course Mendelian traits come from Gregor Mendel so a difference in a single gene causes the difference in the observed phenotypes between different individuals and some examples of Mendelian traits are for example wet or dry earwax. So if you would do your finger in your ear which I can't and then you can roam around and then you look at it then either what you pull out is either wet or it is dry. And depending on that you actually know the state of a single position in your genome. So without having to use all kinds of machines and had sequencing technology like we can already know something about your genetic make up by just looking at the ear wax that comes out of your ear and based on that you can say well you are definitely having a GG at this position or you're having an AG. And the nice thing is that this ear wax thingy is actually distributed across the world because most people in Europe or from European descent have dry earwax while most people from Asian descent have wet earwax. So there's also a correlation between this Mendelian trait and how it is distributed on the world. Another very common example is albinism. So of course there are many different genes that cause albinism but generally the albinism is caused by a single mutation in a melatonin gene. So you have either a working gene or you have a broken gene and when the gene is broken you can't produce melatonin so your hair becomes white and also your skin becomes white or whiter than normal and you also have red eyes because you can't make the pigment into your eyes. So albinism, although there are several genes which can cause albinism, generally the phenotype itself is determined by a single mutation in a single gene shutting the whole gene off and then of course the other genes in the pathway cannot fix this because this is a single Mendelian trait. Another interesting phenotype which is also very Mendelian is brachydactyly. So brachydactyly is the fact that you would have six fingers instead of five or four fingers instead of five. So you have polydactyly and brachydactyly so polydactyly means that you have more and brachy means that you have one less. So again single gene, if it's broken you just are born like someone from the Simpsons who has four fingers instead of having five. And since it is Mendelian if you have two people with brachydactyly if they get children, then their children will also have brachydactyly because it's a dominant phenotype. And then there's the one that is my favorite which is the ability to taste finial theocarbonite which is found in high amounts in Brussels sprouts and this is also a Mendelian phenotype. So some people when they eat Brussels sprouts taste if they are bitter. So finial theocarbonite is a very bitter substance if you have the genes to taste it. If the gene to taste this substance is broken then you don't notice finial theocarbonite at all. So the reason why some children just hate Brussels sprouts and will never ever eat them is because of a single gene being well active in them so not broken meaning that they can taste a very bitter taste of Brussels sprouts. Of course there's also some environmental influence based on if you're a smoker or if you're a non-smoker or if you drink a lot of alcohol you can modify the ability to taste this substance but on a very basic level there's a single gene which controls your ability to taste it yes or no and if this gene is broken you cannot taste it and you don't have any qualms with Brussels sprouts because you don't think that they are bitter. Alright, so when we talk about Mendelian traits we always show these kinds of cross diagrams and I just wanted to kind of explain to you guys how this works I bet that many people saw them before so if you know what a cross diagram is then just say in chat I've seen this before I know how this works but we'll just go through it because you can make them as complex as you want so I just want people to understand kind of the basics of this so what we are seeing here is we are having a maternal individual so the mother and we have the paternal individual which is the father so in this case our mother is a heterozygous individual so the genome of the mother because everyone since we are diploid organisms we have two copies of each chromosome so our mother in this case has a big A chromosome and has a small A chromosome so one of the chromosomes inherited from her mother one of the chromosomes inherited from her father on the paternal side we have the same so we have a father who is also big A small A and then of course we can do the cross diagram and the cross diagram means that we are just going to say well what type of offspring can these two people produce together right so if the maternal side is heterozygous AA and the paternal side is heterozygous AA then of course there is a 25% chance that the children will be big A big A there is a 25% chance that the children will get the small A from their mother and the big A from their father there is of course a 25% chance that the opposite happens so hey you get from your mother the big A from your mother the small A and of course there is also a 25% chance that you get two small As so a small A from your mother and a small A from your father so as I already said the state in which you have two different chromosomes is called heterozygous so just a definition thing so we call a small A big A heterozygous but we also call the opposite heterozygous so we call AA as well as small A big A and there is many different ways that people encode these things so generally we use big letters small letters but you can also use a single letter with a little plus so you can have like J plus J minus and we mean the same thing by that that just means that on one chromosome the gene is plus meaning that it works and on the other chromosome you have J minus meaning that the gene doesn't work so these cross diagrams will come back because they are very very fundamental so I just wanted to explain to you how it works do remember that in genetics females go before males so if you write AA it means mother father so the big A comes from the mother the small A comes from the father so that is a definition that we agreed upon in genetics so adhere to that because otherwise you are just in the opposite way and there can be phenotypic differences between individuals getting an A small A from their mother versus individuals getting a small A from the father and we call this parent of origin effects so parent of origin effects is when the phenotype of the individual carrying the maternal A maternal small A is different from when the individual is carrying the paternal small A phenotype alright so I think everyone knows this right so I'm just wanting to show so here we have again the cross diagram and now I actually colored the gametes differently so I just made little flowers here and there are several situations so we can have the when we take two flowers so we take a flower that has a white allele and a red allele and we take another flower which also has a white allele and now we start mixing them right so we cross these two flowers together then if this is the resulting situation so if we take like a hundred offspring and we see that 25% of the offspring are white 25% of the offspring are red and we see that 50% of the offspring are kind of a mixture right between the two colors like pinkish then we call this an additive phenotype so this phenotype is called additive why because both parental genomes kind of contribute right and they mix together so it's a mixture besides the mixture we also have a dominant recessive phenotype right so here is an example where the red phenotype so the red coloring is dominant over the white coloring and so when we then do the cross between these parents then what do we see well we see that 75% of the offspring will be white well 75% of the offspring will be red right so if you have an allele which is coding for white and you have an allele which is coding for red then your phenotype will be red alright is this clear just say yes or no or something like that because this is very fundamental and I will start asking questions about it because it is important and we will start expanding it we won't be just talking about a single locus but also two loci and then three loci because that's very fundamental in genetics so just give me a little bit of feedback just say yeah I understand I know now what an additive phenotype is or I know now and I understand what dominance is just do the cricket sound until someone answers nah I won't do the cricket sound I won't annoy you guys with crickets all the time no answer means yes that's always the case so if you have no questions then I assume so if no one says something what is the difference between allele and gene that is very fundamental that is different but it's a very very good question somewhat because an allele is generally the state of a piece of DNA while a gene is something that you get inherited from your parents but in so in genetics a gene is a unit of inheritance so something which is inherited and this gene can come in different states you can have the white gene and the red gene and we call this alleles of the gene so a gene can have a white allele and a red allele so it's the same gene but it comes in two different forms and indeed I kind of use it sometimes interchangeably and of course when you talk about gene in a molecular biology sense gene against means something relatively different because then a gene is something which has introns and exons and codes for a protein which is on the DNA but in genetics a gene very basically is defined as a unit of inheritance and that can have different alleles so it can be in the white state or it can be in the red state or it can be in the purple state so you can have all kinds of different alleles of the same gene is that clear? I hope it is clear good then we move on to my first question about Mendelian traits and a lot of people know these diagrams but I never saw someone that asks you how the parents look so how does the mother look here? right so we have a phenotype which is additive how does the mother look when the mother has the white and the red allele at least in my head so I'm not going to bother you with it right and this is one of these trick questions that you probably will get on the exam well not this exact question but it is like you know now what additive phenotypes are it's very clear from the crossing scheme that it is additive so the very basic question would be how does the parent look so what color does the mother have don't be scared there are no wrong answers well there are but I don't care about wrong answers and the answer is better than no answer yeah this does work better in the classroom where I can just point at someone and say beacon what do you think right that that's always the difficulty about like online lectures is that you can't just drag someone in front of the board and say well you do the assignment which is one of my favorite things I know students hate it when I was a student I also hated it a lot so no one no no guesses on how do the parents look for the first crossing scheme not even a guess like is it going to be a green plant like mice how do you mean like mice like dragging mice in front of a classroom or like pink at least my moderator answers and she's not even studying biology so yeah of course like you can you can see it in the diagram right if you have a white allele and you get a red allele then you are pink so you have two different alleles the alleles are working together right so they mix together and in this situation will be pink so for this situation it is of course different so in this situation both parents will be red right because the red is the dominant phenotype so if a plant is red but it has so if you as a mother have a white allele of the gene and you have a red allele of the gene then of course a white allele combined the white allele means that you look red so it's just an understanding question right so it's just like can you guys reason about what's going on in the phenotype and I never saw anyone ask this question and I would have loved to get this question when I was starting out with genetics because everyone knows the crossing scheme everyone knows the AAAB and 25, 50, 25 right that's the Mendel thing but you have to really think about what is the implication of the state of certain alleles together for the phenotype of an individual so depending if something is additive or something is dominant the parents will look different right because the white and the red allele combined in a dominant system where red is dominant will mean that the parents are red while here with an additive inheritance system it will mean that the parents are pink good is this clear any remarks any like that's so surprising that's so boring I knew this good alright so that's Mendel that was Mendel's big theory and that's why everyone nowadays still remembers Gregor Mendel because he did this with different types of seed peas and his peas had different colors and shapes and he would cross them together and then he figured out indeed that there are additive phenotypes and there are dominant phenotypes so in 1917 we made or someone made an observation and Mendelian inheritance breaks down so we discovered a phenotype which did not adhere to the rules that Gregor Mendel posed because Gregor Mendel posed every time that you take two parents you mix them together you will get these ratios but Thomas Hunt Morgan image here he figured out or he had the observation when he was working on drosophila that some phenotypes are only observed in one of the sexes so for example some phenotypes occur in male drosophila while in female drosophila they do and that is completely against Mendel's rules because Mendel just said everyone has two alleles you get one from your father, one from your mother they mix together and of course we now know that this is of course not true because we know that you have autosomes and you have sex chromosomes so there are chromosomes which determine which sex you have and of course on these chromosomes there's also genes located and of course these genes they determine because if you're a female you get the X chromosome from your mother and the X chromosome from your father but if you are so there's three possibilities you can get the X chromosome number one from your mother, X chromosome number two from your mother so that's your first one and then the second one will always be the X chromosome from your father who your father got from his mother but for the Y chromosome that doesn't work that way for the Y chromosome you always that gets passed from father to son to son of the son and these kinds of things so not only did he observe that some phenotypes seem to be only in one of the sexes he also observed that some phenotypes seem to be connected together right because if you if you take not just one phenotype like the color of the plant but you take like four or five of them then you start noticing that some phenotypes tend to occur more together right being red and having a wrinkly eye or having red eyes and weird wings on Drosophila then other phenotypes and this is a massive advancement in genetics because we had no idea about chromosomes right DNA we didn't know anything about DNA in 1917 the discovery of DNA is like 50 years later we didn't even know that there was something like nucleic acid which was the carrier of genetic information but he already said no there has to be something which he called a chromosome on which these things are located so instead of having like one string with beads on there like Mendel thought it actually he probed and said no there's a discreet number of these strings each with the beads on there but you have multiple of these strings and you get two strings so one from your father and one from your mother and like not just for chromosome one but also for chromosome two and for chromosome three so this is a massive massive advancement and using his theory of the chromosomes and of linkage so that two phenotypes occur together like I showed you also in the cows right because in the cows we know that if it's white and black and it has like then it's probably a milk cow and that is because the color of the cow so the black and white coloring is on the same chromosome as the milk production trade so high milk production is very close on the chromosomes so the genes causing higher milk production are very close to the genes controlling the color of the cow so using this theory of chromosomes and linkage so the chromosome Morgan started mapping Mendelian phenotypes back to their genome right so he posed the idea there are chromosomes and you have a discrete number of chromosomes and this he called the genome right and how did he do this well he did this by measuring trades in parents and offsprings and then calculating the co-occurrence between different phenotypes in the offspring generation and now we say that if the phenotypes are linked together like the color of the cow and the milk yield then we call these two phenotypes linked and the unit of how strongly they are linked is called Morgan and we generally don't use Morgan's but generally we use centimorgan so one hundredth of a Morgan because a Morgan is generally a whole chromosome alright so one of the experiments that he did was this experiment so in Drosophila when we think about these little fruit flies right then in Drosophila there is a gene which is controlling your white eye right so that is called the W gene and there is a gene for miniature wings so small wings on the Drosophila so M and both of these genes are located on the X chromosome so they are located on the X sex chromosome so what did he do so he crossed white miniature females so females with miniature wings so that is so it's white miniature white miniature right so these individuals have and then he crossed them with a wild type male so the wild type male of course has a normal eye black eye in Drosophila called W plus and he has normal wings which is M plus and of course he has a Y chromosome so there is no second side to the genome right so here we see WM which means that on the first X chromosome you are white eyed small wings on the second X chromosome you are white eyed small wings well the males that he crossed them with actually had normal eyes normal normal wings and a Y chromosome so he did an F1 cross which means that you take two of these individuals and you cross them together and then he observed that the males were white eyed with miniature wings and females were wild type for both eye color and wing size so they were showing this inheritance better right so now my question to you guys is is this a dominant phenotype or is this an additive phenotype based on what we just discussed with the inheritance diagrams so there are two possible answers and so just throw one in chat you don't even have to type the whole word just say D for dominance or A for additive and I like that because my name is Danny Aldrin so you can just say D A but yeah so question here is there dominance or is there additivity going on here so you see that it's not as easy as just looking at the diagrams and thinking oh I understand how this diagram works and it's a little bit sneaky because I haven't shown you a second or a two phenotype inheritance diagram so is eye color and wing size is that dominant or additive I'm just gonna do a I am going to use the cricket sound then while we wait normally I would point to someone like genie88 dominant or additive go or am I not getting the chat at all at the moment A Sam West says additive B Khan says additive very good then we stop the cricket sound it's dominant so how do you know it's dominant right because here it says that females were wild type for both eye color and wing size but their genotype is having W plus M plus W and M so they didn't have like gray eyes because the mixture between white and black would be gray eyes and between miniature wings and normal wings would be kind of half sized wings right but because the females have normal eyes and normal wings we know that the W plus allele so the wing allele right so the W allele so the allele for standard eyes is dominating the white eye allele because if it would be a combination then the W plus W would create gray eyes the M right so the wings if you would have a normal wing combined with a small wing then the additive model would say that you have like half a wing not small not big but in the middle so this is a clear phenotype dominance thing right and of course the males here don't provide us any information because they only have one copy of each of the genes so they only have one copy while females have two copies so here we can determine based on the females because it's a sex length sex length phenotype we can determine that in the females we can see they are normal so because they are normal they have to have gotten half of their genome from the mother half of the genome from the father so you would expect a mixture if it was additive but there's no mixture let's make it a little bit more difficult right so here we are doing an F1 interbreeding with X length genes so all of these genes the genes for the eyes the genes for the wings are located on the X chromosome and we call males hemizygous recessive right and what does hemizygous mean hemizygous means that we only have one copy of a gene or DNA sequence in a diploid cell so normally for every gene you have two copies one from your father one from your mother but if you are male then on the X chromosome or on your sex chromosome because you only get one X chromosome from your mother and this X chromosome or the genes on the X chromosome from your mother are not comparable to the Y chromosome that you get from your father because the Y chromosome is more or less a stub it has almost no genes on there so on the X chromosome the X chromosome is one of the biggest chromosomes generally so it's almost the biggest chromosome one so it literally has thousands of genes on there but the Y chromosome only has like four or five real genes on there so and these are not homologous to the genes that are on the X chromosome so for ok just ignore the phone so we call this hemizagus so hemizagus means that you are a diploid organism so you have two copies of of normal genes but as a male in this case you have only one copy right so hemizagus recessive means that you always pass on the recessive and no X length alleles to your son right and this is in this is very important when we talk about phenotype causing diseases that are linked to the X chromosome because as a male you only have one X chromosome so if you get a copy of a gene which is broken then of course you will always transfer this broken copy to your daughter but you won't to your to your son right because your son gets the Y chromosome and your daughter always gets your X chromosome let me just answer this very quickly I'm very sorry about that I tell people that I have a lecture but then they still start calling me so I will be right back I am very sorry I'm back the problem is about the phone thing is we got voiceover IP phones new ones here in the office and they changed all of our numbers and now everyone who wants to call the laboratory is actually calling me which is just a pain it's just a pain I get so many phone calls but they're not for me and I like getting phone calls that are for me is this clear that males are hemizygous recessive meaning that if you are a male and you get a daughter then the daughter automatically gets your X chromosome and if you are a if you are a son then of course the son gets the X chromosome time for a break yeah yeah why not why not we're at slide 23 of 75 so I was actually planning to do two more but I can I can use a break as well so yeah let's go to the break I changed the small animated gift things I think we are going to do copy badass in the first break but don't don't pin that on me if it's not copy badass so if you guys want any like sound or music as well otherwise it will just be silent which is perfectly fine for me but um you friend shaped yes friend shaped animals this time alright at least I will stop the recording