Lec 1 production PDF

# Chapter (1) ## Genetic Structure or Constitution of Populations **Faculty of Veterinary Medicine** **Department of Animal Husbandry & Wealth Development** **General Program - Animal Production - 2nd Level Students** **What is the "Best" Animal?** - The purpose or aim of animal breeder: - Th...

# Chapter (1) ## Genetic Structure or Constitution of Populations **Faculty of Veterinary Medicine** **Department of Animal Husbandry & Wealth Development** **General Program - Animal Production - 2nd Level Students** **What is the "Best" Animal?** - The purpose or aim of animal breeder: - There are two fundamental questions faced by animal breeders. The first asks, what the "best animal is?" **For example, in dairy cattle** - Is the best dairy cow: - The one that gives the most milk; - The one with the best feet, legs and udder support or - The one combine performance in these traits in some optimal way? - **The answers that breeders decide upon determine the direction of genetic change for breeding operations, breeds, and even species.** **Genetics is a science that studies heredity and variation.** - **Heredity** is the transmission of traits from the parents to the offspring via genetic material. - **Variation** (refers to genetic variation) is the occurrence of differences among individuals of the same species. **Therefore, genetics in general concerns with:** - The genetic constitution of organisms, and - The laws governing the transmission of this hereditary information from one generation to the next. **The science of genetics can be broadly divided into four major sub disciplines:** 1. Transmission genetics (classical genetics). 2. Molecular genetics. 3. Population genetics. 4. Quantitative genetics. **Transmission genetics** is primarily concerned with genetics processes that occur within individuals, and how genes are passed from one individual to another. Thus, the *unit of study* for transmission genetics is the individual. **In molecular genetics**, we are largely interested in the molecular nature of heredity how genetic information is encoded within the DNA and how biochemical processes of the cell translate the genetic information into influencing the phenotype. Consequently, in molecular genetics we focus on the cell. **Population genetics**, the subject of this book, is the field of genetics that studies heredity in groups of individuals for traits that are determined by one, or only a few genes. **Quantitative genetics**, also the subject of this book, considers the heredity of traits in groups of individuals, but the traits of concern are determined by many genes simultaneously. **A Mendelian population:** - Is a group of sexually reproducing organisms with a relatively close degree of genetic relationship (such as species, subspecies, breed, strain, etc.) residing within defined geographical boundaries where inbreeding occurs. - In animal breeding, we deal with the genetics of populations of individuals (population genetics). ## Extension of Mendelian Genetics - Concerned with the distribution of genotypes resulting from a single progenies - Or The classification of individuals (kind) | | | | | :------------------------------------ | :-------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------- | | Introducing new concepts connected with the genetic properties of populations | Introducing new concepts connected with the inheritance of measurements (degree). | | | | ↓ | | | **Population genetics** | **Quantitative genetics Or Biometrical genetics علم الِوراثة البيومتري** | | **The second question asks, how are animal populations improved genetically?** - This question involves genetic principles and animal breeding technology. **The main purpose of animal breeder is not to genetically improve individual animals - once an individual is conceived, it is a bit late for that - but to improve animal populations, to improve future generations of animals.** ## Genetic structures of populations: An understanding of the genetic structure of a population is a key to out understanding of: a. The importance of genetic resources, and b. The importance of genes for the conservation of species and biodiversity. **The genetic structure of a population is determined by the total of all alleles (the gene pool).** Thus the genetic structure (i.e. gene pool) is **described** in terms of calculating allelic frequencies and genotypic frequencies, within the population. ## **Population and gene pool:** - A population may be defined as: - Set of individuals or a group of individuals of the same species in a defined location. - A population, in the genetic sense, is not just a group of individuals, but a breeding group. - Populations are dynamic; ## **Traits, phenotypes and genotype:** **A trait: is any observable or measurable characteristic of an individual.** a. **Observable traits**: Traits we would normally mention in describing the appearance of an animal. - **Example**: Coat colour, size, muscling, leg set, head shape and so on. b. **Measurable traits**: traits we would likely refer to in describing how an animal has performed. - **Example**: weaning wt., lactation yield, time to run a mile, etc. - Many of them are specific to a species or breed. - **For example**: staple length which is a measure of the length of wool fiber. It is useful trait for wool sheep but *not for animals that do not produce wool*. - Note that, any animal may be red coat colour and weight 100 kg at weaning, but red coat colour and 100 kg weaning weight are not traits – the traits are simply coat colour and weaning weight. - **Red and 100 kg are observed categories or measured levels of performance for the traits of coat colour and weaning weight. They are phenotypes for these traits.** ## 2. The phenotype: **The phenotype** is the *value taken by a trait*, in other words, *it is what can be observed or measured*. - Phenotype is defined as observed category or measured levels of performance for a trait in an individual. - **For example**: - Individual cow’s milk production, - The percentage of fat in milk, - Red or black colour, - Growth rate, and - Backfat thickness. | Trait | Possible phenotypes | | ------------------ | ------------------------------- | | Presence of horns | Horned, polled, dehorned | | Yearling weight | 400, 550 kg | | Shell colour | White, brown | | Calving ease | Assisted, unassisted | | Litter size | 5, 11, 14 | ## Phenotype - Appearance - Performance - Phenotype can describe much more than appearance. - We often use the word performance instead of phenotype for trait that are *measured rather than observed* with the eye. - Phenotype and performance are used interchangeably. ## 3. Genotype: **The genotype of an animal** represents the gene or the set of genes responsible for a particular trait. - i.e. the **genetic makeup of an individual.** - **Animals with similar genotypes** are said to be of the same biological type. This does not mean that they are genetically identical – they are **just more alike** than the animals of a different biological type. - **Biological type**: a classification for animals with similar genotypes for traits of interest. - **Examples include**: - Heavy draft types (horses). - Prolific wool types (sheep). - Large dual purposes types (cattle). - And tropically adapted types (many species). **There is an important difference between genotype and phenotype:** **A. Genotype:** - Genotype is essentially a fixed characteristic of the organism; - It remains constant throughout life and is unchanged by environmental factors. **B. Phenotype:** - When **only one** or few genes are responsible for a trait (qualitative traits): 1. The phenotype usually remains unchanged throughout life (e.g. hair colour). In this case, the phenotype gives a good indication of the genetic composition of an individual. 2. **Since qualitative traits are usually not affected by the environment**, the phenotype of a qualitative trait is a **good indicator of the genotype.** - **When many genes are responsible for a trait:** 1. The phenotype changes continually throughout the life of the individual in response to environmental factors. In this case, the phenotype is not a reliable indicator of the genotype. 2. **Environmental effects do influence the phenotypic expression of a quantitative trait.** - Example is **milk yield of cow** which is often expressed as follows: - **Phenotypic milk yield** = G + E, where: - **G** is the **genetic merit** of the cow for milk yield (the effect of the genes). - **E** refers to the **effect of the cow’s management and environment.** **As animal breeders, we are mainly concerned with changing animal populations genetically** **From a breeding standpoint, therefore, we want to know not only the most describe phenotypes, but also the most describe genotypes as well. That is because an animal’s genotypes provide the genetic background for its phenotypes.** **Mathematically, P=G + E** - Environmental effects - Its Genotype An individual’s phenotype ## **E. Why makes the genotype of cows unique** - **One chromosome pair** - When ova are formed, they receive one of the two members of a chromosome pair. - Thus a particular chromosome in an ovum can be like either the first member or the second member of the parental chromosome pair. - There are only two different kinds of ova for that particular chromosome. - **Two chromosome pair** - What does the total number of different ova become? - In other words, what is the total number of possible chromosome combinations? - Like flipping two coins at the same time. - 1st coin 2nd coin = 22 = 4 different possibilities - 2 2 - The number of different genotypes for an ovum is FOUR - The probability of any particular combination of chromosomes is 1/4 - **When the 30 chromosome pairs of a dairy cow are separated during the formation of the reproductive cells and then reunited at fertilization** - The total number of possible chromosome combinations is 230 x 230 - = 1,152,900, 000, 000, 000, each being unique. - **With this number of possibilities for each mating, it is easy to understand why no two individuals are alike in a population, even when they have same parents.** ## **F. Gene and genotypic frequencies:** - **How do you genetically describe a population?** - In describing an individual for a simply inherited trait, you might refer to: the specific genes that individual possesses, or you might describe its one – locus or two – locus genotype. - **The answer is to use gene and genotypic frequencies.** - A gene frequency or allelic frequency or *gametic array*: - **The concept of gene frequency is basic to all models attempting to describe the genetic structure of natural populations.** - **The gene frequency of A, is the proportion or percentage of all genes at this locus that are the A allele.** - **Naturally**, The frequencies of all the alleles at *any one locus* must add up to unity, or 100 percent. - **Genotype frequency:** - To describe the genetic constitution of **a group of individuals we should have to specify their genotypes** and say how many of each genotype there were, so what is the genotype frequency? - The genotype frequency is the proportion or percentage of a particular genotype in the population. - **Naturally**, the frequencies of all the genotypes together **must** add up to unity, or 100 percent. - **What are the agencies through the genetic properties of a population may be changed?** 1. **Population size:** - The genes passed from one generation to the next are a sample of the genes in the parent generation. - Therefore, the gene frequencies are subject to sampling variation between successive generation and the small the number of parents the greater is the sampling process. - For practical purposes a “large population” is one in which the number of adults is hundreds rather than in tens. 2. **Fertility and viability (Fitness traits):** - Their differences influence the genetic constitution of the succeeding generation, so we can not ignore the phenotypic effects of the genes affecting them. - The different genotypes among the parents may have different fertility's and contribute unequally in the next generation, in this way the gene frequency may be changed in the transmission. - Further, the genotypes among the newly formed zygotes may have different survival rates (selection). 3. **Migration and mutation:** - The gene frequencies in the population may also be changed by immigration of individuals from another population and by gene mutation. 4. **Mating system:** - The genotypes of the progeny are determined by the union of the gametes in pairs to form zygotes and - The union of the gametes is influenced by the mating of the parents. - So the genotype frequencies in the offspring generation are influenced by the genotypes of the pairs that mate in the parent generation. - Random mating or panmixia means that any individual has an equal chance of mating with any other individual in the population. - **Random mating or panmixia means that any individual has an equal chance of mating with any other individual in the population.** - If we given the relative frequencies of A and a gametes in the gene pool, we can calculate (on the basis of the chance union of gametes) the expected frequencies of progeny genotypes and phenotypes. If p = percentage of A alleles in the gene pool and q = percentage of a alleles, then we can use the checkerboard method to produce all the possible chance combinations of these gametes. - Thus: - P2 is the fraction of the next generation expected to be homozygous dominant (AA). - 2pq is the fraction expected to be heterozygous (Aa), and - q² is the fraction expected to be homozygous recessive (aa). - **All of these genotypic fractions must add to unity to account for all genotypes in the progeny population.** - This formula, expressing the genotypic expectations of progeny in terms of the gametic (allelic) frequencies of the parental gene pool, is called the **Hardy-Weinberg law.** ## Hardy-Weinberg law: **Goodfrey Hardy, English mathematician, and Wilhelm Weinberg, a German physician developed in 1908 mathematical models and equations to describe what happens to gene pool of a population under various conditions.** - **An example is the set of equations that describe the influence of random mating on the allele and genotypic frequencies of an infinitely large population, a model called the Hardy–Weinberg law.** ## State the Hardy Weinberg law: **The Hardy–Weinberg law states that:** - In a large random-mating population with no selection, mutation, migration or chance, the gene frequencies and the genotype frequencies are constant from generation to generation and furthermore, there is a simple relationship between the gene frequencies and the genotype frequencies. **The importance of the Hardy-Weinberg law is two fold:** - **1. The Hardy-Weinberg law establishes a set of ideal conditions that allows us to estimate allele frequencies and genotype frequencies in populations in which initial assumptions hold true.** - **2. Moreover, it provides a mathematical relationship between genotype frequencies and gene frequencies that allows the prediction** of the frequency of offspring genotypes based on parental allele frequencies. - Obviously, it is difficult to find natural populations in which all these conditions are met. - In nature, **populations are dynamic and changes in size and structure are part of their life cycles.** ## Assumptions of the Hardy-Weinberg law - (Equilibrium conditions): 1. **The population is sufficiently large--- sampling errors and random effects are negligible.** 2. **Mating within the population occurs at random.** 3. **There is no selective advantage for any genotype i.e. no differential mortality and no differential reproduction.** 4. **The population is closed i.e. no immigration nor emigration** 5. **There is no mutation from one allelic state to another.** 6. **Meiosis is normal so that chance is the only factor operative in gametogensis.** ## Properties and prediction of the Hardy-Weinberg law: - If the conditions of the Hardy-Weinberg law are met, the population will be in genetic equilibrium and two results are expected: - **First**: If population is at equilibrium, the **allelic frequencies do not change from one generation to the next.** Moreover, allelic frequencies predict genotypic frequencies. **The Hardy – Weinberg law for two alleles:** | | Male gametic frequencies | Female gametic frequencies | | ---- | :----------------------- | :-------------------------- | | P(A) | p (A) | p (A) | | q (a) | q (a) | q (a) | | | | | | | | p² (AA) | | | | pq (Aa) | | | | pq (Aa) | | | | q² (aa) | - Moreover, the genotypic frequencies will be in the proportions p², pq and q² after one generation of random mating. | Genotype | Frequencies | | :-------- | :---------- | | AA | p² | | Aa | 2pq | | aa | q² | - The frequency of the A allele among the offspring in above table - = Freq. of AA + 1/2 Freq. of Aa - = p² + pq - = p (p + q) - =p - **Second,** the equilibrium genotypic frequencies are attained in one single generation, of random mating. - Whatever, the genotypic frequencies among the parents, if the allelic frequencies are p and q in males as well as in females, the genotypic frequencies among the offspring will be p², 2pq and q². ## Verification or proofing of the Hardy-Weinberg Law: - To proof the Hardy-Weinberg law considering a hypothetical, randomly mating population as the following: - Consider **a locus with two alleles** and let the frequency of genes and genotypes in the parents be as the following: | Genotypes | Alleles | Frequency | | :---------- | :------ | :-------- | | aa | a | q² | | AA | A | p² | | Aa | | 2pq | | | q | | | | p | | * **With random mating, there are nine types of mating with their frequencies as the following:** | Male parent | | | | | :------------ | :-- | :-- | :-- | | AA p² | | | | | Aa 2pq | | | | | aa q² | | | | | **Female Parent** | **AA p²** | **Aa 2pq** | **aa q²** | | AA p² | p⁴ | 2p³q | p²q² | | Aa 2pq | 2p³q | 4p²q² | 2pq³ | | aa q² | p²q² | 2pq³ | q⁴ | * Similar reasoning generates the frequencies of genotypes among the progeny shown in the following table. | Type of mating | Mating frequency | AA | Aa | aa | Totals: | | :-------------- | :---------------- | :---- | :---- | :---- | :---------------------------------------------------------------------------------------------------------- | | AA x AA | (p²) (p²) | p⁴ | - | - | AA = p4 + 2p3q +p2q2 = p2 (p2+ 2pq + q2) = P2 | | AA x Aa | (p²) (2pq) | 2p³q | 2p³q | - | Aa = 2p3q + 4p2q2 + 2 pq3 = 2pq (p2 + 2pq + q2) = 2pq | | Aa x AA | (2pq) (p²) | 2p³q | 2p³q | - | | | AA x aa | (p²) (q²) | 2p2q² | 2p2q² | - | aa = p2q2 + 2pq3 + q4 = q2 (p2 + 2pq + q2) = q2 | | Aa x Aa | (2pq) (2pq) | p²q² | p²q² | p²q² | As we can see, after random mating the genotypic frequencies are still p2, 2pq and q2 and the allelic | | Aa x aa | (2pq) (q²) | 2pq³ | 2pq³ | 2pq³ | frequencies remain at pand q. | | aa x Aa | (q²) (2pq) | 2pq³ | 2pq³ | 2pq³ | | | aa x aa | (q²) (q²) | - | - | q⁴ | | - **Fig.( ), Frequencies of genotypes AA, Aa, and aa relative to the frequencies of alleles A and a in populations at Hardy-Weinberg equilibrium.** <start_of_image> graphically show the frequency of alleles and genotypes depending on the frequency of p or q depending on the Hardy-Weinberg equilibrium. - **Several aspects of this relationship should be noted:** - **1. The maximum frequency of the heterozygote is 0.5**, and *this maximum value occurs only when the frequencies of A and a are both 0.5*; - **2. If allelic frequencies are between 0.33 and 0.66; the heterozygote is the most numerous genotype;** - **3. When the frequency of one allele is low, the homozygote** for that allele *is the rarest of the genotypes*. This point is also illustrated by the distribution of genetic diseases in humans such as albinism, for example, is a rare recessive condition in humans. - It is important to note how fast heterozygous increase in a population as the value of p and q move away from zero. ## **Applications and uses of the Hardy-Weinberg law:** 1. **To determine the frequencies of alleles of a particular gene in a given population.** 2. **To track and predict how gene frequencies will be transmitted from generation to generation given a specific set of assumptions.** 3. **It represents an idealized situation (which may never happen). Real situation can be compared to the ideal.** - **The divergence from the equilibrium tells you how the population is changing (note that it doesn’t say why).** 4. **The Hardy-Weinberg principle can be also used to estimate allele frequencies of recessive genetic disorders (diseases).** - A practical use of the Hardy-Weinberg equation can be seen in analysis of genetic diseases example: cystic fiberosis, phenylketonurea (PKU) and albinism. - **Many genetic diseases are recessive so their expression is only exhibited by individuals who are homozygous.** | Genotype | Phenotype | | :-------- | :----------- | | AA | Normal | | Aa | Normal | | aa | Disease expressed | - Note that *in the case of a recessive allele, the heterzyote is indistinguishable from the domoninant homozygote.* ## 5. Estimation of frequency of heterozygotes or carriers of recessive - One of the practical applications of the Hardy-Weinberg law is the estimation of heterozygote frequency in a population. - The frequency *of a recessive phenotype usually can be determined by counting such individual in a sample of the population*. Their frequency in a population is represented by q², provided that mating has been at random and all Hardy-Weinberg conditions have been met in the previous generation. - If Hardy-Weinberg equilibrium can be assumed, the frequency of heterozygote among all individuals, including homozygotes is given by 2pq. - **The frequency of heterozygote among normal individuals**, denoted by H, is the ratio of genotype frequencies Aa (where, a is the recessive allele). AA + Aa - So that, when q is the frequency of a, <start_of_image> - **In general, the frequencies of all three genotypes can be estimated once the frequency of either is known and Hardy-Weinberg conditions are assumed.** - **H = 2pq/p²+2pq** - **H = 2pq/p(p+2q)** - **H = 2q/p+2q** - **H = 2q/p+q+q** - **H = 2q/1+q**