 recording and then welcome everyone and welcome to lecture number two of the bioinformatics course. Today we will be talking about phenotypes and databases which contain a lot of phenotype information. All right so let me close some windows and I think we're all set to go. So for today we will be talking about phenotypes and I will be using the word traits or trait as well. Hello commando 471 you're an active viewer actually. So phenotypes or traits can come in two different ways. They can be qualitative and quantitative. In genetics we also have another classification so we either talk about phenotypes or traits being Mendelian or being complex. We will talk a little bit about statistical analysis. Statistical analysis will come back more and more and every lecture has a little bit of it but I just wanted to run through a little example that I made a couple of years ago. It's actually from a published paper that we published and I just wanted to show you some figures and explain how you can kind of look at those figures. And then we will talk about different phenotype databases so in case you're a researcher and you don't have a lot of money but you still want to do nice research then you can kind of borrow all the stuff which is out there because a lot of people capture a lot of phenotypes or a lot of traits and they put them in big databases so you can get a whole bunch of data for free which since I'm Dutch I like because Dutch people don't like paying for stuff and getting stuff for free is something that we really really enjoy. And then I have a little word about project planning or why it is important to contact a bioinformatician when you are starting up a new project so those will be the topics for today. I don't have any pen and paper let me get some paper as well so I can make some notes write down some questions that you guys have and other suggestions. All right so phenotypes. So phenotypes or traits kind of come into two major groups and one of the groups that people talk about when they talk about phenotypes is usually the classical phenotypes. So nowadays we also have things like endo phenotypes which means for example the expression level of a gene or the amount of mRNA that you are producing or an amount of metabolite that a certain cell has but normally when we talk about traits and since I want to start from the beginning we talk about classical phenotypes. So phenotypes or observable elements of an animal or plant which are interesting for economic reasons or other reasons like people just like like it. So very classical phenotypes are things like yield so how much yield do we get from a certain plant things like flowering time so how much time does a flower need from being a little plant to getting its first flower. So generally flowering time can be defined as two periods you have the periods until it from the sea to germination and then from germination to flowering. So that's kind of the flowering time of a plant but other classical phenotypes which have been well studied in genetics are things like human stature. So how high a person is what is its BMI and these kinds of things. And of course all of these classical phenotypes have been used for many many years as markers when you do plant and animal breeding right. When you think about things like potatoes had the quicker a potato flowers the quicker you can harvest the potato in the end. So had planting potatoes which have a very short flowering time will in the next generation give you potatoes quicker and the same thing holds for yield. If you have a cow which gives a lot of milk so high milk yield and then of course this cow you would preferentially breed compared to a cow which has a low milk yield. All right so the difference here or the thing that I want to make get across here is that many of these classical phenotypes are also markers. So they are something which you can observe but are not the thing that you are directly interested in. So we'll get back to that in a couple of seconds but why does a bioinformatician like myself concern myself with phenotypes. Well here you see a picture by Lemnatec and this is how they grow plants. So all of their plants are more or less on a conveyor belt system and that means that all of these plants are scanned two or three times a day automatically in a little room and all kinds of phenotypes are gathered from these plants like how big is the plant, what is the color, how much water does it have, how do the leaves look, how many leaves does it have and so there's a big amount of automation currently going on in bioinformat or in biology and of course this automation means that there's more data to process leading to a phenomenon which we call big data and big data is one of these kind of buzzwordy terms in bioinformatics is like what do you do? Well I deal with big data but big data can mean anything from a couple of hundred MBs to literally terabytes of data but of course when you're doing a system like this so you're having plants which are on rails which are photographed and scanned two or three times a day and then of course for each plant you get a lot of data like have you get two or three pictures you get some machine learning output like how many leaves does it have and all of these things have to be stored in a database and then in the end statistics has to be done on all of this data that you have gathered don't forget recording no I'm recording we're already like six minutes in so that's fine thank you commando for reminding me I think it's more important to remind me after the breaks after the breaks I generally tend to come back and just ramble on it on the next slide but because of this automated phenotyping bioinformaticians get more and more interested or get more and more involved in the gathering of data on phenotypes it used to be that kind of sequence was the base level of bioinformatics or everything which had to do with DNA sequence or protein sequence you would go to a bioinformatician but nowadays a lot of the classical phenotypes which used to be measured by either PhD or master students on a field are now automatically gathered using a computer using optical sensors and other things so I have asked a friend of mine who is doing closed ecosystems to tell a little bit about his project so I will see when that lecture will be but I think somewhere in the beginning of January I will invite him to share like a little bit of his insight on how he does this automated phenotype capture for his closed ecosystems so I think that's going to be a very interesting lecture also for me I haven't seen a lot of his work but I know kind of what he's doing but it's interesting that we can have a discussion about how he is using bioinformatics in gathering his phenotypical data or his measurements so it didn't really use to be a field of bioinformatics but nowadays phenotypes and measuring phenotypes is more and more becoming an automated system meaning that bioinformatics is involved in in processing this all right so a question for you guys because we're talking about phenotypes and we're talking about markers and if we are I'm showing you two pictures here so on the one side we see a nice black and white cow like we see them all over Germany and on the other side you see more or less a different type of cow which you also see a lot but what is the difference between these two cows because there is a very clear difference between these two cows which you can just see from their appearance so if you have any idea what the difference is between these two cows then throw it in the chat and then we can discuss about that and I'm hoping that we will get some answers the coloration pattern and the expression of pigmentation yeah yeah yeah that's the most obvious difference between these two cows of course what you can see but there's a very there's a very economical phenotype on which you can kind of classify these two cows as well which is not directly obvious from the coloration pattern the coloration pattern here is a is a marker for something which is really important when you are breeding cows the genotype yeah the genotype will be completely different as well they're actually two completely different cow breed all right so the one on the right is not a milk cow maybe more for meat yes that's the right answer so the black and white frisian holstein is for milk and the other one is for meat and just by looking at the cows you can already see right so if you have a baby cow and you look at the coloration you can from the colors that the cow has and the color pattern that the cow has you can already see if the cow will be a milk cow or if it will be a meat cow so head here we have something which is clearly observable a phenotype which we are very which we are not really interested in right we don't care if our cow is black and white or if it's gray but the phenotype that we're interested in is highly linked to this coloration so when you see a cow which is black and white you know that it will be a milk cow and when you see a cow which which is more or less a single color cow and it's kind of brownish then you you know that this cow is going to be a good meat cow instead of a milk cow so here we have like what i'm trying to get across is that there is an observable phenotype the color pattern and there's an unobserved phenotype which we're really interested in and which is linked to the phenotype that we can observe so milk production in this case is highly linked to the coloration of the cow all right so very good so again another picture or another two pictures so what is the difference between these two types of tomato or potato plants so a slightly more difficult question and again here we have a very clear observable phenotype so there's a massive difference in the color but which color is doing what and why is that important so just throw it in the chat can't be crazy enough there are no wrong answers and the more answers we get the better it is i think i should have taken a picture of two fish because there's a lot of people from the fish department that are following the course so coming with potatoes might have not been the best when there's not a lot of people that are interested in agriculture but more people are interested in fish no guesses no guesses whatsoever about the different colorations of the of the potato plants auto bay size of the potato um no the size of the potatoes can be very different but it can be very similar all right jan hage says there are also two strains um one is more poisonous starch and sugar the difference in color attract different insects well insects don't really see color they see in a uv spectrum the one is a gmo and how they're definitely both like normal natural occurring flavors so the one that's closest is jan so jan you're more or less right so the one which has the white flowers is potatoes which are used for consumption and the other ones the ones with purple flowers they are the ones which are used for starch production so next time that you're on your bike and you're biking through brandenburg and you see a field of potatoes then based on the color of the flower you can actually see what these potatoes will be used for so the white ones are the ones which have a high sugar content low starch content so they're really nice to eat and the ones which are purple they have a high starch content so they are grown for like the chemical industry to make things like glue and and other things in which you use starch so again very clear observable phenotype and there's a difference in color and based on the difference in color you can directly say oh this is the potato plant that I want so if you're growing potatoes at home and the potato starts flowering make sure that the flowers are white because the purple ones they don't really taste very good so this is a very old observation this is something that people already knew in like 16 1700 when they were growing potatoes and they were breeding cows right they had no idea about genetics and DNA is something that has been invented in like the 1950s 1960s or perhaps a little bit earlier the idea of DNA and so it's completely unrelated to anything about sequence it's just that you have an observable phenotype and this observable phenotype is just by experience a good marker for an economically interesting trade so in this case white you can eat them purple you can make glue of them or something else all right so here we've been talking about phenotypes and how phenotypes can be markers I want to take one step back and first describe phenotypes as being as when we talk about phenotypes there are things which are qualitative properties which are properties that are observed but are generally not measured with a numerical result so for example a piece of meat tastes good or it has a really nice texture at these things you can generally not really quantify you can say well this piece of beef is this many kilograms per square meter or these kinds of things hey you can only put a qualitative measurement on it so you can say this is a good quality or this is a bad quality and on the other hand we have phenotypes which are which have a quantity property and that those are properties so quantitative traits which have a magnitude or multitude so something that you can measure like color which has like an RGB value or another type of definition of color I have the same thing holds for things like height hey you can say well I like people who are big or I don't like people who are small but something like height is per definition a quantitative phenotype because it has quantity properties meaning that you can measure height in either meters or centimeters and you can use this numerical value to compare two things so when I talk about quantitative and qualitative things there's always something that requires discussion so let's just go through the list and say if something is a qualitative or a quantitative trait so something like high fat milk yield just throw in chat is it quantitative or is it qualitative? Well if you would say that high is good then it is quality right but in this case it's really a quantitative thing you can you can quantify how much fat per kilogram milk is there no don't be sorry just it's good that you throw in some suggestions right that like like I said there's no real wrong answers but in this case I would say that high fat milk yield so it's something that you can express as a numerical value you can say I have this many units of fat over this many units of now don't be mean Ethel B if you say high or low then it's a quality yes yes so if you would if you would say that fat milk yield is is quantitative and high is good or bad then hey you might want to and normally when we talk about these things high fat milk yield is generally having good qualities for cheese making or bad qualities for cheese making so then hey you would put a quantitative trait has something that you can measure but then you would put a quality on there so meat structure let's go ahead and get some suggestions hey Sandra welcome to the stream didn't see you saying anything before quality yeah that's indeed quality so the structure of meat is something that is very hard to grasp in numbers so in that sense it's a it's a qualitative trait hey if you talk about meat structure then you can you have people who like a lot of fat on the meat and you have people who don't like fat at all so the amount of fat on meat or the amount of marbling as it's officially called there are nowadays some ways of measuring it and because again it's kind of a fat over protein ratio but which structure people prefer is very different between people so it's really a qualitative trait starch content just throw in your suggestion quantitative yes very good testosterone sores you're now really getting excited about getting the right answers all right wine quality come on people wine quality is wine quality qualitative of quantitative okay so in this case a olexandra is right it's actually both wine quality nowadays is a quantitative as well as a qualitative trait because in the old days it used to be a very qualitative trait so there would be some guy who has a degree in phenology and that would taste the wine and then would say this is good wine or this is bad wine however nowadays all of this wine tasting is more or less done by robots so the wine is just put into a machine and the machine then says i'm giving this wine a score of 7.3 and then the next wine that it puts in it gives a score of 6.8 so the the qualitative trait of wine quality has been changed into a quantitative trait by being able to measure all kinds of these properties from these from this wine so the robot it analyzes the wine and then based on its analysis it gives us a quantitative score so wine quality used to be qualitative now it's definitely a quantitative trait because the measurement is not really done by people anymore but it's really done by robots all right so last two i think we can do that in one go so flowering time and racing time quantitative or qualitative just throw it into the chat and then we can we can see all right so i see quant quantitative quantitative yeah so it's something that you can measure in seconds or hours or these kinds of things so it's it's definitely a quantitative trait flowering time is usually measured in days while racing times for horses and stuff are in the order of a couple of minutes but here there's a very definite time component so the time component is something that you can measure and very definitely a quantitative trait all right so if i would kind of describe the world and all of the phenotypes fall into this big circle so all of the traits are qualitative traits because any trait that there is you can say if it's good or if it's bad however a small part of the qualitative traits can also be measured and given a unit so then they become quantitative traits and like we saw with the wine this quantitative circle is growing and growing and growing so it becomes bigger and bigger the more we are able to catch things like quality measures into a quantitative way and so developing a new wine tasting robot takes away a phenotype from the qualitative circle and makes the quantitative circle a little bit bigger so the definition is is that something is a quantitative trait when you can measure it using the international system of units a qualitative trait is something which is very subjective so different people will give different grades to the same thing and of course if you're measuring a mouse then of course not everyone measures exactly the same but in the end people measure a certain amount of centimeters and that's it there's no real discussion about it while a qualitative trait there's always discussion what's good what's bad what do we want and this is very difficult for breeders because for breeders qualitative traits are very difficult to deal with so I've once been part of a research on brussel sprouts and this was an interesting research because here we were looking at like what is the amount of sugar into brussel sprouts and how bitter are and we did this together with Wageningen University and Wageningen University they have this tasting panel of people and then we found out that we could that there was like a genetic switch so at a certain locus in the genome you could determine how much sugar versus how much bitter there was so just by by having a certain genotype at this locus then the plants would become more bitter having the other genotype means that there would be more sugar so for a geneticist this is a very nice thing right we have a genetic locus on the genome which controls the phenotype of interest but then when it came to the taste panel we actually ran into a massive issue because the taste panel consisted of people who liked bitter and people who liked sweet so in the end the breeder that wanted to have like what should we do should we make our brussel sprouts more bitter or should we make them more sweet we couldn't give them an answer because the the tasting panel could not agree and in that sense the only reason that we had um yeah I have a moderator for that Anna can you uh just mute the the the tall 506 with the spammy things um so like the moral of this story is sometimes you can have a really nice qualitative trade yeah so uh or you can have a really nice quantitative trade you can measure how much how much sugar there is you can measure on how much how bitter it is um but in the end if the the experience of the user is qualitative so if they are wanting sugary brussel sprouts or if they're wanting brussel sprouts which are very bitter then in the end you cannot decide the only thing that we could have advised the breeder is that they should sell two types of brussel sprouts one which is more sweet than the current ones or they should sell another type which is more bitter than the other ones and then they could have like a genetic difference between the two species um but then the breeder said no we we can't do that we can't have a double investment and and buy twice the amount of space in the supermarket um so a very interesting research um have we found a really nice genetic effect but in the end this did not lead to any new product being put on the market um because the people in the tasting panel could not agree on which direction um we should go on all right so another kind of definition which is in quantitative and qualitative trades is that you can have a Mendelian trade some Mendelian means that there's one gene or genetic locus involved in uh in in controlling your phenotype um so something like dwarfism is a Mendelian trade right there's a single gene and if that is broken uh then you become uh you you have like a limited growth um so but not all types of dwarfism actually are Mendelian trades um and there are complex traits so complex traits just means that there are two or more genetic loci involved in making the phenotype or expressing the phenotypes so most phenotypes that we have um that we are investigating nowadays are complex phenotypes because almost all Mendelian phenotypes um have been found or have been defined um so there's there's there's not a lot of work anymore for people who do Mendelian genetics um has so most phenotypes currently are things like intelligence um however there's hundreds of genes involved and we call these things complex all right so when we talked about um or when I talked about the quantitative traits um I was talking about uh the system of units so the international committee on system of units and um there are actually seven fundamental SI units and a question to you guys is um and that's why I needed a pen is um what are the seven fundamental SI units so just throw something in I already mentioned a couple of them um so um I'm just curious to see how how much people remember from um high school um I think this is something that they should teach in high school um because it's kind of fundamental right like how do you describe the universe well if you're measuring things inside our universe um then you're always measuring one of seven of the SI units or you're measuring like a combination of these SI units so all right so we have mole Kelvin meter and kilogram and then we have time in seconds um mole and mole kilograms yes length length that that fits in with something in meters so there's two things right there's there's the there's the unit and then there's the um um the the thing that you're wanting wanting to measure kandel kandel all right we just put it on the list so now we have mole Kelvin meter kilogram time um length and kandel so that's one two three four five six seven so we should have all seven mass yeah so mass is is something that you would express in in in kilogram light yes yes all right so the seven fundamental SI units as they are defined are length and length is officially measured in maitre not meters but maitre we have mass mass is measured in kilogram we have time which is measured in seconds we have electric current also measure or measured in ampere we have thermodynamic temperature which is measured in Kelvin we have amount of substance which is measured in mole and we have luminosity intensity which is measured in candela or cd and these are the only seven fundamental SI units that are there and we owe these to the French except for one and do you know which one is not a French unit Kelvin yeah that's correct Lord Kelvin was a nobleman from the UK um and um all the other ones are French and the reason why the French came up with this standardization system is actually quite an interesting story and it has to do with the fact that France traded with countries like Spain and Germany and the UK and Holland and the problem there was that everyone was using their own units so something in an old measurement would be a hand or a foot um and of course an English foot used used to be different from a Dutch foot um so head that would be a massive issue if you would do trades because you would expect like a certain amount of stuff and you would only get like two-thirds of it just because the guy that you bought it from had a certain different understanding of fundamental units um so the French were um the official kilogram is located in France yes the kilogram is defined as a block of platinum I say it's kind of a block of metal somewhere um and there are actually six kilograms scattered around the world um one of them is still located in French somewhere near the Eiffel Tower um and they recently or like couple of years ago they brought all the six official kilograms back together and then they figured out that all of them had a slightly different weight so if you would weigh them then they would not be the same weight anymore well originally when they were made they were made very accurately and um so um there is a problem in this this having something define a unit but the kilogram um is is a physical object which is located in in France um there's five more or less backup kilograms scattered across the world um but these all weigh a little bit different um so the current idea is to redefine the kilogram as not being a kilogram anymore but to define it as a cube of seletium atoms or not a cube but a sphere of seletium atoms and since seletium has a known molecular weight and if you have a sphere which is a perfect sphere you also know how many mole of substance is in there then you can define that as being the kilogram um so there are some um some ways of kind of redefining these units but the kilogram was the last unit to go from a physical object definition to a molecular definition and things like seconds are based on the amount of vibrations of a quartz atom um and these kinds of things and luminous intensity is uh is as well but all of these units are thanks to the French because the French were sick and tired of being scammed over during trade because hey if they would trade with a Dutch guy they would get like less than they would expect it and if they would trade with a with a Spanish guy then the prices would be too high because the Spanish guy would have a different definition of what is a a kilogram in a way so after the French got screwed over enough they actually decided we don't want that anymore and we're just going to standardize everything and force everyone to kind of um use our system which kind of worked out for them. All right so enough about the fundamental units so um let's go into some more genetic aspects so let's talk more about Mendelian where there's one genetic locus and talk more about complex traits where there are um more two or more genetic loads I involve and of course you can kind of mix and match this you can have a qualitative trade which is Mendelian but you can also have a complex qualitative trait and the same thing holds for quantitative traits you can have quantitative traits which are complex and there are quantitative traits which are Mendelian of course so all right so and when we go back and we talk about phenotypes or we talk about traits then of course the first guy that you have to talk about is Gregor Mendel so Gregor Mendel was a German monk slash scientist who was really interested in how phenotypes are transferred from parents to offspring so he did a whole bunch of experiments very famous experiments using peas so the little things that you that you eat and he looked at the shape and there will be a slide about some of his work but he was the first one to to come up with a theory which is called the gamete slash gene theory which is kind of a beads on a string theory so his theory was that there is something like a a rope um and there are different phenotype beads on this rope and so you have a rope and then there's a bead and this bead says color then there's another bead which says shape and then there's another bead which has length um and his idea was that if you have parents then both parents come with a string of these beads and then have when when they create offspring parts of these beads are transferred from the parents to the offspring so and this was a relatively new theory um especially because in this time um the the leading theory on how people got pregnant was still the homoculus theory um which was the idea that in the sperm cells of men there were like little people um which would then grow inside of a woman so hey he was the first one to kind of ignore all of that and say no we have phenotypes and phenotypes are more or less attached to each other on a string and when parents mate then these these beads they get mixed and then passed on to the children and with that he could explain for example when you have two people um so a pair of parents of one which is small and another one which is really big why the children tend to be kind of the average between the two parents hey because he would say well no then you have a small bead and you have a big bead the child gets both beads so that is why the child is kind of half of what the parent is um and that was his that was his theory and he had some data to back it up um although most of this data we know today is probably a little bit polished so it's not it's not perfect um so but he had some good data to at least back up his his theory of of of genes and gametes um so he called these beads on a string the beads the individual beads were called genes and a whole string of these things is called a gamete so a gamete is a combination of different phenotypes um more or less what we today would call a chromosome but in his theory there was only one chromosome um so yep the parent had both parents had one chromosome and the child got a combination of both chromosomes from from the parents so that is why we still call a Mendelian trait a Mendelian trait hey because there is a difference in a single gene so a single bead uh which is causing the difference in the phenotypes which we can observe between um individuals um so a couple of um interesting or interesting uh phenotypes which are Mendelian is for example if you have wet or dry earwax so if you just like go around in your ear and you look at your finger then you can more or less see um which kind of the gene you inherited if you have wet earwax um you are generally more of asian descent while if you have dry earwax that means that you are more from european uh descent and that is a very clear kind of separation um on average like 99 out of 100 europeans will have dry earwax and 99 out of 100 asians will have wet earwax and that just has to do with uh a single gene and if you have a mutation in this gene you go from having dry to having wet earwax another very clear Mendelian trait is of course albinism um so if there's a there's a single gene which causes melatonin to be reproduced which gives you your skin color and also gives you the color of your eyes and if this gene is broken and you can't make uh the um the melatonin uh then you become an albino so hey you have white hair white skin red eyes um and that's just because there's one gene which is normally active that is broken another one which is pretty Mendelian not always is brachydactyde so brachydactyde means having six fingers or having four fingers on a hand um and the number of fingers is um Mendelian inherited so if both of your parents have um six fingers then you will have six fingers as well because there's no no head there's both parents have broken genes so had the chances of you getting a a functioning gene is is almost zero and then one of the um um most interesting one is the ability to taste phenyl theocarbonite um which is one of the main component in brussel sprouts it gives that it gives it the um the very specific taste of brussel sprouts um some people are not able to taste it and they like brussel sprouts some people are able to taste phenyl theocarbonite and they are not able to eat brussel sprouts just because the taste of it is very chemical it's the same as with asparagus asparagus also have this um substance in there so when you eat asparagus then um you don't notice any difference but when you then go to the toilet and you pee then you can either smell the asparagus in your pee or you can't smell them um and this is kind of a one to one and this is again a single gene on the genome which gives you the ability to to smell or taste this this chemical um and um if this gene is broken then you can't and there's there's just a single gene so and of course there are literally thousands and thousands of phenotypes like this uh which are Mendelian phenotypes and there's a big database which we'll discuss later in the lecture where you can look up all of these known Mendelian phenotypes so if we look then at a cross diagram right um so hey I told you that um if both of your parents have six fingers then you are very likely to end up with six fingers as well um and then we are usually referring to these things as cross diagrams so here you see a cross diagram when we are talking about a single gene so in this case we have a gene which comes in two forms so we have the a form the big a and we have the small a so you can for example imagine that uh big a is the ability to um to smell or to taste uh let me look that up phenyl theocarbonite and the small a is the is the is you are not able to yeah so you have a phenotype or you don't have that so when you look at your mother and you look at your father of course nowadays we know that your mother has two chromosomes and your father has two chromosomes so your mother has two copies of the gene your father has two copies of the gene and this is more or less the default crossing screen so here we have a mother which has two copies so it she has the ability to taste and she has another gene which does not work your father has a gene which works and another copy that doesn't work um and then here we see the resulting possibilities so you see that there are three possibilities in the children so either the children have two broken genes they have two functional genes or they end up being similar to the to the parents meaning that they have one functional gene and one broken gene um have which is the same as the parents because here the mother has one broken gene and one functional gene and the same as as the father so i'm hope that i'm explaining this because it will be more complex and i have a question for you guys about about kind of these cross diagrams as well because i think it's a very useful tool of understanding genetics the thing which was before on the board was a big cross diagram from four different parents just so that i could work on a project where we had four different parents which we mixed so four different mice and so if we're talking for example about mixing flowers so again we see the cross diagram here and here we see the parental genotype so here we see that the mother has a white gene and a red gene here the father has a white gene and a red gene as well and then there's two things that can happen because in genetics either phenotypes function in an additive way so that means that when you have a red gene and a white gene then the flower will be pink of course when you get two white genes you will be white when you get two red genes you will be red however this is called additive inheritance so it means that there's just a mixture of the two genes so the phenotype will be in between the phenotype of the of the of the parent then we also have dominance and dominance means that one of the genes is is kind of overcompensating for the other one right so for example if you have a dominant red phenotype in this example and then of course the heterozygous they will have inherited one white allele and they will have inherited one red allele but in this case of course since the red phenotype is dominant if you have a single gene working you will get the red phenotype and this is a very basic phenomena where sometimes you have to have two broken genes before a certain phenotype shows so and that is also the reason why sometimes children can be affected even though both parents are not affected so all right so additive so in additiveness we see of course the standard Mendelian inheritance pattern of 25 percent red 50 percent pink and 25 percent white offspring well if we have dominant phenotypes then we have 75 percent of the offspring being red and 25 percent of the offspring being white and this is this is all still Mendelian theory and this was all invented long before 1900 so this this was well known that if you had phenotypes that some phenotypes inherited in an additive way and other phenotypes Mendelian phenotypes would be inherited in a dominant way so the question that I always ask the people here how do the parents look and if we first focus on this crossing scheme what are the colors of the parents so what is the the color of the mother and what is the color of the father so that's a question to you guys just throw it in the chat will it be red will it be white or will it be pink what is the color of the parent all right alexandria pink yes so very good so in this case the parent will be pink and that is of course because when you mix a red allele with a white allele you get a pink color so here the parent will be pink and in this case the other crossing scheme scheme how will the parent look very good because the red is dominant so if you have only one red allele you will be red so they look like this this is a pretty hard question already like many people are kind of tricked by this because like they always think about two of the gametes but they never think about the phenotype of the parent and of course this is very surprising that if you take two red flowers and you cross them together that all of a sudden 25 of the offspring will be white that's something that a lot of people don't realize can happen but this is all very explainable very basic Mendelian genetics it's just a single gene causing it so you have a broken gene and the broken gene doesn't function so the red gene takes over while in here you have kind of a mixture between the two all right very good very good a plus for yourself pat yourself on the back very good all right so it's now almost 250 so let's do like two more slides and then we'll take a little break so Mendelian inheritance was kind of the de facto how do you call it the de facto theory for inheritance but then in 1917 this guy Thomas Hunt Morgan actually not he but one of his students observed a failure of Mendelian inheritance so they were doing experiments where they were working on Drosophila and they were crossing the Drosophila and what they noticed is that some phenotypes did not seem to mix the way that Mendel had predicted they they seem to be only occurring in one of the sexes and what they also observed is that some phenotype seem to be connected right so if you would be have a red color of of eyes as a Drosophila then you were also more likely to have for example large wings so had they these two things did not seem to be independent of each other and they they had a really hard time explaining this because no one had the idea of a chromosome yet so had that since DNA wasn't known yet people did not know how stuff got inheritance from parent to children but they did see that there was something which was sex specific so it only occurred in females but never occurred in males and they seemed and they had this observation where they saw that seemed some phenotypes like hey when you think about this beads on a string thing it seemed that this string some beads were closer to each other than than other beads on this string so their observation was a very observation that they did based on thousands and thousands of Drosophila that they had and Thomas Hunt Morgan is generally credited for launching the idea of a chromosome so that there are that there is not one string with beads on there but that there are multiple strings with beads on there and that one of these strings is determining your sex so had this was a revolutionary idea long before DNA was invented they know that DNA more or less existed as a chemical substance but they had no idea that it was the the fundamental carrier of genetic information and so Thomas Hunt Morgan actually developed his theories of chromosomes and linkage and used that to start making a genetic map using Mendelian phenotypes so what they did is they they measured the traits in the parents then they measured the same traits in the offspring has so they measured for example five different phenotypes like the size of the eyes the color of the eyes the length of the wings the size of the feet the size of the abdomen and then using these measurements from parents and children they started calculating how often they co-occurred and how often they did not co-occur so that would that led to this and that led to the first genetic map of Drosophila and this is also why the unit of inheritance or the unit of linkage between two phenotypes on a chromosome is called a centi Morgan or a Morgan because of his invention that the phenotypes are linked to each other and that some phenotypes occur only in one of the sexes so at this this invention is at the first observation that they had was published in 1917 and had they started doing experiments and then had they did for example they have the white eye gene which causes white eyes in Drosophila and then they have a gene which causes miniature wings are located on the Drosophila X chromosome right so they figured out that only females had a not only females but had they so this was their hypothesis and then they crossed a female white miniature right which has a wm slash wmgeal with a wild type male so the male had w plus which is just big w meaning normal eyes normal wings and it had a y chromosome and then what they observed is when they crossed this genotype with this genotype so the the genotype of the female with the genotype of the male then they saw that males were white eyed with miniature wings so wm y well females from this cross were wild type for both eye colors and wing size um so they they had um they had their inheritance so males of course when you cross a female it always when you when you get a male out of it it always has the y chromosome from the male so it cannot be anything else than getting the wm allele from the from the mother right so white eyes miniature wings on the males however females were white uh wild type for both eye color and wing size so um had wm uh w plus m plus um w and m so the question here is this a dominant or an additive inheritance so so john hager said dominant and why do you think it's dominant john all right now more people are chiming in saying that it's dominant good so can can anyone explain to me why they say it's it's dominant it's like on an exam and then just answering dominant is good enough depending on how i phrase the question all right john hager says because the heterozygote females have it yes so in this case if you have a single functional wild type allele like w plus right then you get the dominant so the w plus is dominant over w and the m plus so had the the the miniature wings the the standard wings are dominant over um the um over the miniature wings so indeed having one functional allele gives you the wild type um and there's no in between so it's not that one of the eyes is white and the other one is black and it's not that one of the wings is small and the other wing is is big um so this is a very clear um indication of it of a dominant gene effect where having a functional gene um makes it so that the the phenotype of the non-functional gene is completely gone all right so let me do one more slide um yeah so they did more um more more breeding experiments but i i think we should take a break first and then um we'll come back and um we can talk more about dominant and hemizagas and recessive genes all right so let's take a 10 minute break i will be back at three o five um and someone remind me to start the recording when i get back all right so