Lecture – 25
Preliminaries & Introduction to genetics
[FL] Today we will start our next module, which is conservation genetics. In this module, we will have 5 lectures.
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The first one is preliminaries and introduction to genetics followed by population genetics, chromosomal and genetic disorders and inbreeding population viability analysis, reintroductions and out breeding.
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So, let us begin with the first lecture, preliminaries and introduction to genetics. (Refer Slide Time: 00:45)

So, let us begin with what is conservation genetics? Now, we know what conservation is, we have dealt with in the first module. Now, conservation biology the biology of conservation plus genetics gives us conservation genetics. Now, we can define conservation genetics as conservation genetics is the branch of science that aims to understand the dynamics of genes in populations, principally to avoid extinction. We need to look at this definition in more details. It is a branch of science that, aims to understand the dynamics of genes in population. So, essentially we are concerned with population of animals the populations is the group of animal that are living together of the same species. Now they will be having genes inside them, we will come to genes in a the short while and these genes function in dynamic ways.
So, essentially we are talking about population genetics or how genes are changing from one generation to the next in the same population? And once we understand their dynamics, we can use that knowledge to avoid extinction.
So, conservation genetics is the branch of science that aims to understand the dynamics of genes in populations principally to avoid extinction. So, our aim is to avoid the extinction of the population of species.
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Then we come to the definition of genetics. Genetics is the study of heredity and the variation of inherited characteristics the study of heredity. Now heredity is how different traits move across different generations. So basically, when a child is born then you would often here, statement such as this child has the eye of his mother or this child has the hairs of it is father or the things like that. So, essentially the traits that were there in the parental generation also express themselves in the child.
So, this movement of straight across the generation goes by the name of heredity. So, genetics is the study of heredity, how this thing is happening and the variation of inherited characteristics. So basically, everybody of us has inherited certain characteristics but all of us are different. So all of us have different heights, in different colors of skin, different colors of eyes, different colors of hair, whether the hair are straight or whether they are rounded and so on, whether they are curled or whether they are straight and when we look at the cross sections whether they have a flat cross section or rounded cross section or an oval cross section.
So, all of these a different inherited characteristics that vary between different organisms or different individuals in the same population. So, genetics is the study of heredity and the variation of inherited characteristics. Gene on the other hand, is a unit of heredity which is transferred from a parent to offspring and is held to determine some characteristic of the offspring. So, when we talk about all of these different characteristics the height. So, we will say that, there could be a genes for a height, because of which this character of height becomes an inherited character, whether a child has curly hair or whether he or she has straight hair. So, we would say that there must be a gene that is determining, whether the hair is curly or whether this hairs is straight, because of which this is being transferred as an inherited characteristic.
So, gene is the unit of heredity. Now in strict biological terms, you could even say that gene is a distinct sequence of nucleotides forming part of a chromosome, the order of which codes for a molecule that has a function. So essentially, when we say that there is a gene for height. So, how is this gene impacting the height of the organism? So, this gene would be a sequence of nucleotides. So, this gene would be have a some sequence of nucleotides and this gene where is it located; it is located in chromosome and the order of these nucleotides or the information that is there in the gene is used by the organism to code for something especially for a molecule that has some function.
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So basically, this gene could be for instance, coding for a molecule that impacts height. So in that case we would call it that gene is the distinct sequence of nucleotides, forming part of a chromosome, the order of which codes for a molecule that has a function. (Refer Slide Time: 05:30)

Then when we say chromosome, so then what is a chromosome? Now, before we go to a chromosome, let us understand, how our cells are made? So, in the case of all of our cells, they will be an animal cell. So, they would be a nucleus inside. So, this is a cell membrane, this is a nucleus and then we will be having a number of other things like cytoplasm, which is the sap that is filling the cell, we might be having a few mitochondria, which are organelles, where energy is produced.

this is mitochondria, we might be having an endoplasmic reticulum. So, which is a distinct structure that is used by different organelles to move things from one part to another, we could be having Golgi bodies and so on. But for the case of genetics the only thing, that you are interested in right now is the nucleus. So, we can forget everything else.
So, there is cell and there is nucleus inside.
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Now, this nucleus will be having a number of fibers inside that remain entangled for most of the part. But when the cell is dividing, so when the cell is moving from 1 cell to 2 cells, then all of these fibers condense together to form things that go by the new chromosomes.
So, what is chromosome? Chromo means color and soma means body.
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So, it is a body that has some color. So, basically if we take a cell that is dividing and we break that cell will get to the nucleus, we break the nucleus again and in that case, we will be able to see the chromosomes. Now in certain cells in certain animal cells, whenever we are undergoing a cell division then there are stages in which this nuclear membrane so this membrane dissolves by itself so that all of these chromosomes come out into the cell body, into the cytoplasm. So, if you look at these structures out there in a microscope, we see there are some bodies and they are having some color, because of which we call them is chromosomes.
So now, technically we would say that chromosome is a thread like structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes. So now coming back to the drawing board, here we saw that all of these threads, they are in an entangled form. So, if you take any of this thread outside, it would be an extremely long thread and when this thread is condensed, it forms a small, completely condensed body, which we call is chromosome. So, this chromosome will be having. So, this is a thread like structure of nucleic acids and proteins, now proteins bind this thread into the tightened structure or other coiled structure.
So, a thread like structure of nucleic acids and proteins found in the nucleus of most living cells, why that most living cells? Because certain cells, such as RBCs, the red blood cells will not have a nucleus. So, they are enucleated. But in most of our living cells, we will be having a nucleus that will be having chromosomes inside, that is found in the nucleus of most living cells and the function is that it carries genetic information in the form of genes. coming back to the drawing board, so, if this is a long thread that becomes called as
chromosome, if we take any small portion, so, say this portion or say this portion.
So all of these, small portion or some of these small portions, may be coding for certain genetic information. So, not all parts of the chromosome will be coding for some genetic information, but such portions of the chromosome that a coding for genetic information, in the form of genes will also be there. So, chromosome is a thread like structure of nucleic acids and proteins found in the nucleus of most living cells carrying genetic information in the form of genes.
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Next we have Alleles. So, in this class will be discussing a number of definitions that we will be making use of in the next classes. So, an alleles is each of 2 or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.
For example, capital P and small p represent flower color alleles for a pea plant.
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So, what are we saying here is that, alleles- each of 2 or more alternative forms of a gene. So, when we considering say, the gene for height of a human being. So, let us say height. So, this height gene may come in a number of varieties. So, there could be a gene that codes for a very tall individual, there could be a gene that codes for a very short individual, there could be a gene that code for somewhere in between and also somewhere in between. So, all of these are different forms of the gene and why do they have different forms? Because they have different sequences, so these alternative forms that arise by mutation. So, how do we get changes in the sequences? So here, we saw that this is a sequence of the gene. So, this is the green portion, now suppose some part of it was replaced by say, a red dot. So, these sequences are made out of A,T,G, or C, which is adenosine, thymine, guanine and cytosine. So, these are 4 different nucleotides that code this whole chromosome.
So, for instance in the case of English language, we say that, we have 26 different letters, a, b, c up till z. In the case of the genetic information, we have 4 different letters A, T, G and C. In the case of computers, we have only 2 letters 0 and 1. So, with just 0 and 1, you can form everything, you can make a drawing, you can make words, you can make music and so on. Similarly in the case of the chromosome, just by using these 4 alphabets, we can make anything. Now when we are having these 4 alphabets, then if there is a change at any location in which, one alphabet gets replaced by some other alphabet, then it is known as a mutation.
this is a simplified understanding of mutation, we also different other kinds of mutations, that will come to in one of the next lectures. But each of 2 or more alternative forms of a gene, that arise by mutation and are found at the same place on the on a chromosome, why the same place on a chromosome? Because coming back to the drawing board, even when this portion was changed, even when this letter was changed, but the whole of those gene remains at the same place. So, when we consider 2 different chromosomes.
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So, let us say that this is 1 chromosome. This is the second chromosome and both of these were having a gene at this location and 1 gene suffered a mutation. So, even then we are having these genes that are coding for the height of the individual at the same location. So, here it says that, an allele is each of 2 or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome. Now we represent alleles with alphabets of groups of alphabets.
So, for example, capital P and small p represent flower color alleles for a pea plant. So, we would say that the color of the flower in a pea plant, could be purple or it could be white. So, we would say that purple, we will represent as capital P and when another form of this alleles found will represented by small p, if you had even more number of form, when we could be using things like P 1, P 2, P 3 and so on. So, all of these will be referred to as different alleles of the same gene, the gene that is coding for the flower color of a pea plant. Now next is trait, a trait is a genetically determined characteristic caused due to the presence of some allele. So, these are 2 different ways of representing the same thing. So, trait is the flower color of a pea plant and this trait is caused by genes and these genes come in different varieties, which we call as alleles.
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So, when we say that they are found in the same location, we can locate it using McFish, McFish stand for multi colored fluorescence in situ hybridization.
So, here we are looking at chromosome number 3 and in the case of chromosome number 3 the areas that are having the same or very similar sequences of nucleotides in them are represented by different colors. So, all of these chromosomes come in 2 pairs, why a pair? Because one of these chromosomes will be coming from the father, one of these chromosomes should be coming from the mother.
Now in the case of the father chromosome and the mother chromosome and both of these, we are saying that these colors pink, red, yellow, dark yellow, pink, red, yellow, dark yellow, this white on the on the top all of these come in the same sequence, why? Because this region suppose, this is coding for height gene. So, the height gene in the chromosome number 3 coming from the father will be having, will have a position here. In the case of the height gene coming from the mother in chromosome number 3, it will also be having the same position. We would not be having a height gene here and height gene here. So, these come in pairs.

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Next we have a genotype. A genotype is the genetic constitution of an individual organism. So, what sorts of alleles are present in that organism, is represented by the genotype for example, capital P capital P. Now in this case, what we are saying when we say capital P capital P is that this individual or got the allele for purple color from the mother and also for the purple color from the father. In case, this individual had suppose a capital P from one parent and small p from another parent. So, we would say that, this is a purple allele and here, we have a white allele, white allele both of which are coding for the same trait that is the color of the flower.
Now in case we have capital P capital P or small p small p, we call these individuals as homozygotes. Homozygotes for the gene that is coding for the flower color, homo means same and this is a homozygote, because both of these alleles are the same, but if one of these was capital, one of this was small will call it a heterozygote. So, genotype is the genetic, constitution of an individual organism such as capital P capital P. Now, phenotype will be the set of observable characteristics of an individual resulting from the interaction of it is genotype with the environment.
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So, for instance, this capital P capital P, in the presence of a suitable environment will give purple color flowers. Now why is environment important here? Because suppose there is an individual and the mother is very tall, the father is also very tall and this individual is homozygous for the tall gene. So, essentially this individual is having all the capabilities that it should grow up into a very tall individual, but then suppose this individual did not get proteins during its childhood. So, essentially this individual was suffering from starvation. So, during those starvation period protein is required for building up the muscles of the body and basically, if this individual lacked protein so it was not able to grow very well, or suppose this individual was lacking calcium or maybe this individual was infested with some parasites which did not allow it to absorb all of those nutrients that were there in the food.
So, this individual even though he or she is having the genetic constitution that would code for tall individual, but in the presence of an environment in which he or she is not getting sufficient nutrients, he or she may turn out to be a dwarf individual. So, which is why, we say that phenotype is the observable characteristics of the individual resulting from the interaction of it is genotype with the environment. Now on the other hand, if this individual was having short mother and a short father and it is genetic constitution was also coding for a short individual.
So, even if you provide this individual with lots and lots of nutrients, this individual would not grow up to be a tall individual. So, which is why we say that, in the case of a phenotype, both the genetic constitution and the environment both are important and it is an interplay between both of these that tells us what sort of a phenotype would come out? (Refer Slide Time: 19:30)

Now, from here we move on to the Mendel’s laws of genetics. Now, Gregor Mendel was a monk, an Australian monk, who first figured out the different laws of genetics. So, the first law is the law of dominance. So, recessive alleles will always be masked by dominant alleles for example, purple capital P flower trait is dominant over the white or the small p flower trait.
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What it says? Is that if you have an individual that is capital P capital P so, the first allele is coding for purple, the second allele is also coding for purple.
So, in this case you get purple flowers. If you have a small p small p so, let us write it like this. So, the first one code for codes for white, the second one also codes for white. So, in this case, we get white flowers. But what do we have when we have a capital P with a small p? So, here this one is coding for purple and this one is coding for white. So, in this case, do we get individuals that have color, that is somewhere in between purple and white? Or do we have situations in which, sometimes it will show purple, sometimes it will show white? So, the law of dominance tells us the answer to this question, it says that whenever we have 2 alleles and one allele is dominant; in we generally, represent dominant with a capital letter; so anything that is dominant will mask over the phenotype of recessive one.
So in this case, because capital P is dominant will be having purple flowers only, law of dominance see is that this alleles will always been masked by the dominant alleles. So, if you have capital P and small p will have in the expression of the capital P. Next we have the law of segregation, the 2 alleles of a gene separate or segregate during gamete formation. So, that a sperm or an egg carries only 1 allele of each pair. (Refer Slide Time: 21:34)

So what it says is that, suppose you have a parent i.e. capital P capital P and this parent is giving out sperms. So, each of these sperms would be having a capital P, but if everything goes well, if there is no abnormality, we will not be having a sperm that has 2 copies of this capital P or a sperm that does not have any copy of this allele. So, this is the law of segregation and secondly, both of these alleles, let us represent it as by a red color and by a purple color
So, both of these alleles are one and the same, but then we are representing them by different colors, just to see how they will segregate out? So, when you have the sperms, there would be some sperms that carry this allele that is coming from one chromosome and there will be some that will be having the second allele that is coming from the second chromosome. So, the 2 alleles of a gene, in this case capital P capital P, separate or segregate during gamete formation. So, both of these will become separate and a sperm or an egg carries only 1 allele of each pair. So, it does not carry both the alleles, it does not carry 0 alleles and this explains the 3:1 F 2 ratio.
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Now what is this F 2 ratio? F 2 is stands for or F stands for a filial generation. So, will come to this here. So, the example case, if you have done across between 2 individuals; one was having capital P capital P and the second one was having small p small p.
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So, what do we mean by this? When you had an individual with capital P capital P, then this individual was having purple flowers and when you had an individual that had a small p small p, you were having and individual that was having white flowers and we are beginning with this example case in which were assuming that both of these individuals are homozygous, which means that in the case of this capital P capital P, it is homozygous so both of these are capital P, it is not a case in which, there is one capital and one is small. So, we are starting with 2 homozygous individuals. Now when we do a cross between both of these so let us say, that this one is a male plant and this one is a female plant. Now in the case of P plant it is having both the main organs and the female organs together, but for the case of this example, let us say that we have different plants, one is a male plant and one is the female plant.
So in the case of the male plant, the sperms will be having capital P, capital P, capital P, and capital P, because two of the sperms would be having this capital P and two of the sperms would be having this capital P. Now in the case of this, female plant will have the 4 eggs, that are small p, small p, small p, and small p; these come from one chromosome and these two come from the other chromosome.
Now when there is across so, this is how we represent across, this is known as a Punnett square. So, we represent the gametes from one parent on the left side, we represent the gamete from the second parent on the top. So, in this case one parent give us capital P and capital P and the second parent give us small p and small p. So, when both of these gametes come together so we have an individual which will be getting a capital P from the father and a small p from the mother.
So, in this case this individual becomes capital P small p. Similarly, this individual also gets a capital P from the father and a small p from the mother. So, it is capital P small p. So similarly, all other individuals are also capital P small p. So, in this case, we will say that in the first generation. So, in the first filial generation that is the result of this cross all of these individuals are having a genotype of capital P and small p all of these and the phenotype will be purple flowered, because capital P will dominate over the small p. Now why do we called a filial generation? Filial means brotherhood, brotherhood or sisterhood or individuals that are siblings. So, this is the first sibling generations. So, all of these are together.
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Now if we perform across between the individual in the first case. So in the first case, we had all the individual, that is capital P and small p. Now, we are doing an inbreeding experiment here in which we are breeding between both of these.
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Now the law of segregation will say that, suppose this is the male plant so the male plant will gave out sperms in this fashion. So, we have a capital P and a small p. So, when it gives out sperms will have two that will be having capital P and two that will be having small p, which we are representing here by putting it on the left side.
So, one is having capital P, one is having small p. So, there are only two different kinds of sperms that have been produced. Similarly in the case of ova, we also have only two different kinds of ova, capital P and small p. So, what happens when both of these come together? So, this is capital P from father, capital P from mother, this is small p from father, capital P from mother, this one is capital P from father small p from mother and this is small p from the father and small p from mother.
So, we have a genotypic ratio of capital P capital P as 1, capital P small p as 2, and small p small p as 1. So, we have genotypic ratio of 1:2:1. Now if you look at the phenotypic ratio, what will these individuals look like when they grow up? Will be having purple color flowers, this capital P capital P will give us a purple color flower and so will a capital P and small p, we have 2 plus 1, 3 individuals that are having purple color flower and only 1 individual that is having white flower. Now in the case of genetics, when we talk about these ratio these are an averaged out ratios.
So, it is not necessary that if you are having just, 2 individuals will be having these 4 different phenotypes, but then if you are doing these crosses in a large numbers and then you take averaged out ratios usually get this ratio of 3:1.
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The next law is the law of independent assortment which says that, each pair of alleles segregates into gametes independently of the other pairs and this explains the 9:3:3:1, F 2 ratio.
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Now what do you mean by this is, each pair of allele’s segregates independently of the others. So, in this case, we are considering individuals that are having two different traits. So, we have this flower color, which is given by P and small p and we have pod color. So, in the case of a pea plant we get pods.
So, there is a pod inside which we have the seeds. So, what is the color of the pod? Now in this case, we have colors as green and yellow. Now green here is dominant. So, it is written as capital G and yellow is recessive so it is written as small g. (Refer Slide Time: 28:48)

Now in this case, when you have this individual capital P, capital P, capital G, capital G, when it is gives us sperms, what is different kinds of sperms will be found? So, the first is capital P capital G, the second is capital P capital G, the third was capital P capital G and fourth one is again capital P capital G. So, we are getting only one kind of sperm that is having capital P and capital G together.
Similarly, when we considered the second case and which we have small p, small p, small p, small g, we are getting one kind of ova that is small p and small g. Now when we say that both of these alleles are separating independently of each other, i.e. independent assortment, we mean that when considered this case of capital P, capital P, capital G, capital G, then if you are considering this capital P, then whether this sperms gets this G, whether this sperm gets this G is immaterial.
So, most of ours situations will consider that, this P can come with this G or this P can come with this G; the second G. So, this is independent assortment, because these alleles are separating independently of each other; they are not coming as the combination. So, they are not coming as the combination like this P will always come with this G and this G is also come with this G, there is no such combination, they are coming out independently of each other.
So, now, when we look at the Punnet square, we have only one kind of ova and only one kind of sperm and so we have only one kind of individual that is heterozygous for both these alleles. So, capital P and small p and capital G small g. The genotype is the same for all the individuals and the phenotype is also same for all the individuals. (Refer Slide Time: 30:54)

So, capital P dominates over small p so we get purple flowers and capital G dominates the small g we get green pod for all of them. Now in the F 2 generation, we are crossing this individuals with each other.
So, we have capital P and small p, capital G and small g crossed with the capital P small p capital G small g. Now in the case of this individual, what kinds of sperms of will get? Because these alleles are assorting independent of each other so we can have capital P with capital G or capital P with small g or small p with capital G and small p with small g. So, we have written all these 4 combinations here. So, these are the 4 different kinds of sperms that will be formed. So, we have capital P capital G, capital P small g, small p with capital G and small p with small g. Now if these alleles were not assorting independently of each other.
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So, in that situation we would have a case in which in the first generation, now suppose these two come together always. So, we would be having capital P and capital G and these would give us small p and small g. Now when we have a cross, we get an individual that is capital P small p capital G with a small g, but in the next generation, this would not give us 4 different kinds of sperms, but would only 2 different kinds of sperms because, capital P and capital G always come out together. So, it will give us capital P capital G and small p small g and similarly in the case of the mother plant as well.
So, if that were the situation, we would be getting capital P capital G, small p small g, capital P capital G, small p and small g. So, making out the Punnett square will have, these individuals that are completely homozygous and these are the 2 individuals that are heterozygous and in this case, we would be getting genotypic ratio of 1:2:1. So, you have one of this, one of this and these two are the same as the genotypic ratio and the phenotypic ratio will be given by 3:1. But if these alleles are separating independently of each other, we will get these 4 different combinations; so, these four are for the father, these four are for the mother.
Now you can make all of this combination back again. So, this individual is getting capital P from here and capital from P from here, capital G from here and capital G from here.