Lecture 6 Quantitative Genetics PDF

Quantitative Genetics (T 211) Lecture 6 Breeding Values & Population mean at inbreeding  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbre...

Quantitative Genetics (T 211) Lecture 6 Breeding Values & Population mean at inbreeding  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Some Definitions Phenotype (P) ▪ What we observed and measured. ▪ Is determined by the genetic make up, environment and genotype- environment interaction. P = G + E + GE Genotype (G) ▪ Sum of all genetic effects of genes.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Some Definitions  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Some Definitions Genetic value ▪ Breeding value + dominance deviation ▪ A (additive genetic effect) is also referred to as breeding value. G=A+D ▪ It is the value of an individual’s genes to itself. ▪ Genetic value is not transmitted to a progeny because only one of the genes is given to a progeny. Average Effect: ▪ Average effect of the gene substitution, i.e., the mean change due to changing A2 genes chosen at random into A1 genes.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Genotypic effects-one locus model  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Genotypic effects-one locus model  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Breeding value (BV) ▪ Breeding value refers to the value of an animal in a breeding program for a particular trait. ▪ A value associated with the genes carried by the individual and transmitted to its offspring. ▪ Breeding value is sum of average effects of genes. ▪ Breeding value is the value of an individual as a genetic parent. ▪ Breeding value is the part of an individual’s genotypic value that is due to additive gene effects that can be transmitted from parent to offspring.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Breeding value (BV) ▪ Because parents transfer a random sample of their genes to their offspring, it is impossible to control or predict whether a particular offspring will inherit a superior, average or below average sample of genes from each parent. ▪ Thus, an offspring’s breeding value for a trait will be, on average, the average of its parents’ breeding values for the trait.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Breeding value (BV) ▪ It is important to understand that the average of the parental breeding values does not determine the breeding value or performance of every offspring from a mating – just the average offspring. ▪ Estimated breeding values give an estimate of the average transmitting ability of the parent. ▪ Breeding value = the value of genes to progeny. ▪ Genetic value =It includes non-additive effects (such as dominance) which cannot be passed on to progeny.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Expected Breeding value ▪ Expected progeny differences are useful in comparing or ranking individuals within a breed for traits of interest. ▪ They also are a prediction of future progeny performance for a specific trait of one individual compared to another individual. ▪ Thus, the differences in EPDs are informative. The animal with the highest or lowest EPD is not necessarily the most desirable animal. ▪ The most desirable animal often represents a balance of EPDs for various traits. ▪ The EPD values can only be used to compare animals within a breed.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Breeding value ▪ The difference between genetic and breeding value is largely dominance deviation. ▪ An individual can express dominance deviation. e.g. an A1A2 heterozygote, e.g. an A1A2 heterozygote. ▪ However an individual cannot pass on dominance deviation to its progeny as it only transmits one allele. e.g. an A1A2 heterozygote produces an A1 gamete and an A2 gamete. ▪ Non-additive genetic effects and environmental effects cannot be inherited by offspring  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Genotypic and Breeding Values ▪ Populations can be characterized by the amount and type of genetic variability contained within them. ▪ Genetic improvement of a quantitative character is based on effective selection among individuals that differ in what is known as the genotypic value. ▪ Variation among the genotypic values represents the genotypic variance of a population.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Genotypic and Breeding Values ▪ The genotypic value is the phenotype exhibited by a given genotype averaged across environments. ▪ A related concept is the breeding value, which is the portion of the genotypic value that determines the performance of the offspring. Genotypic value breeding value Is property of the genotype and Describes the value of genes to therefore is a concept that describes progeny and therefore helps us the value of genes to the individual understand how a trait is inherited and transmitted from parents to offspring ▪ Remember that only additive genetic effects can be passed on to progeny.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Breeding value Genotype Breeding Value 𝐴1 𝐴1 2 q α = 2 α1 𝐴1 𝐴2 (q – p) α = α1 + α2 𝐴 2 𝐴2 - 2 p α = 2 α2  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Breeding Value ▪ An animal's breeding value is estimated to be twice the expected performance of its progeny. ▪ The reason for doubling the expected progeny performance is that only half of the genes from the individual are transmitted to any offspring (with the remaining half coming from the other parent)  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Transmitting ability ▪ The expected progeny performance is called transmitting ability and is, therefore, half of the breeding value. ▪ In other words, transmitting ability: ✓ Is the genetic advantage an individual transmits to its offspring. ▪ When mating is random the breeding value of a genotype is denned as the sum of the average effects of the two alleles in the genotype, which is the additive value as noted above.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Transmitting ability ▪ The usefulness of the concept is that the expected phenotypic value of the progeny is the mean of the breeding values of the two parents. ▪ This leads to the practical definition, which allows the breeding value of an individual to be measured: ✓ Breeding value of an individual is twice the deviation of its progeny from the population mean when the individual's mates are chosen at random.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Inbreeding ❑ Outbreeding ✓ Mating of individuals with a degree of relationship lower than the average degree of relationship in the herd. ❑ Inbreeding ✓ Is the mating of individuals with a degree of relationship greater than the average degree of relationship in the herd (Mating with close relatives). ✓ The highest degree of inbreeding is obtained by self-pollinated. Inbreeding ▪ Increases Homozygosity. ▪ Decreases Heterozygosity. ▪ Greater chance of inheriting a recessive disease.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Inbreeding  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Inbreeding Depression ▪ A phenomenon known as inbreeding depression is the reduced survival and fertility of offspring of related individuals. ▪ Occurs in both plants and animals. ▪ The occurrence of inbreeding depression varies across species. ▪ Inbreeding depression: is the average reduction in fitness, or of a character, due to inbreeding. AA X AA aa X aa Aa XAa AA aa 1A 2Aa 1aa  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Symptoms of inbreeding depression may include ✓ Reduced plant vigor. ✓ Smaller plant size. ✓ Decline in fertility. ✓ Suppressed seed production. ✓ Decreased pollen production. ✓ Inferior seed quality. ✓ Greater susceptibility to insect or pathogen damage or poorer standability.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Inbreeding vs Heterosis in effects ▪ Heterosis and (also known as Hybrid Vigor) have an opposite effects: The heterosis improves performance, while The inbreeding decreases performance, particularly in reproductive traits. ✓ Where Heterosis increases the number of different allele pairs and increases heterozygosity, resulting in the suppression of undesirable recessive alleles in one parent by dominant alleles from the other parent. ✓ Inbreeding results in homozygosity, which increases the chances of offspring being affected by recessive harmful alleles.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Heterosis (Hybrid Vigor) ▪ Heterosis is defined as the superiority of F1 hybrid over both the parents in terms of yield or some other characters.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Benefits of heterosis ▪ Increased yield. ▪ Increased reproductive ability. ▪ Increased size. ▪ Better quality. ▪ Greater adaptability.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Estimate of heterosis 𝑭𝟏−𝑴𝑷 ▪ 𝒉𝒆𝒕𝒆𝒓𝒐𝒔𝒊𝒔 = 𝑿𝟏𝟎𝟎 𝑴𝑷  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Important points about Inbreeding ▪ Inbreeding, a type of mating of individuals that is often of particular significance to plant breeders. ▪ Inbreeding is defined as the mating of individuals that are related by ancestry. ▪ Self-pollination (mating of an individual to itself) represents the most extreme form of inbreeding. ▪ Inbreeding leads to an increase in homozygosity at the expense of heterozygosity. ▪ A key feature of inbreeding is that as homozygosity increases in a population undergoing inbreeding in the absence of selection, the genotype frequency changes while the allele frequency stays unchanged.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Important points about Inbreeding Inbreeding may occur unintentionally as a result of selection or maintenance of small populations. Inbreeding is also deliberately practiced as: ▪ A method to create genetic uniformity in populations of interest for genetic. ▪ Breeding research, for retaining genotypes of inbred cultivars of self- pollinated species through many years of production. ▪ Reliable production of inbred lines to be used in the development of commercial hybrid cultivars.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Measurement of Inbreeding ▪ F= Inbreeding coefficient ▪ The probability that two genes are identical by descent is called the coefficient of inbreeding (denoted as F) and will be the measure of relationship between mating pairs. ▪ The coefficient of inbreeding (F) is defined as ▪ The probability that two alleles at the same locus are identical by descent.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Measurement of Inbreeding ❑ At the population level, F describes the average level of homozygosity. ❑ The coefficient of inbreeding is always expressed relative to a specified base population. ❑ The base population is defined to be non-inbred (F=0). ❑ The range of F is 0 to 1, with 0 indicating random mating and no inbreeding, while 1 means prolonged selfing.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Increasing Inbreeding ▪ Through increasing homozygosity, inbreeding brings together identical alleles at a locus. ▪ Homozygosity permits the expression of recessive alleles that may have been previously masked by heterozygosity (by more favorable dominant alleles) in the parent generation or it can be caused by overdominance in which homozygotes are less fit, resulting in poorer performance. ▪ If recessive alleles are less favorable than dominant ones, the overall fitness of the individual decreases. ▪ Inbreeding is often detrimental because it increases the appearance of lethal and deleterious recessive traits. ▪ The term inbreeding depression describes the decrease in fitness or performance that often accompanies inbreeding.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Increasing Inbreeding ▪ Fitness: is the relative ability of an individual to survive and reproduce to contribute its genes to the next generation. ▪ Plant stature, vigor, yield and other traits decline with increasing inbreeding, ▪ Although significant differences exist among species for the amount of inbreeding depression, expressed ranging from minimal among self- pollinated crops such as oat and wheat to severe in cross-pollinated polyploid species such as alfalfa, whereby homozygous genotypes do not survive.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Increasing Inbreeding  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Outbreeding Inbreeding Has crossing mechanism, approaches Closed flowering, approaches regular random mating selfing Individuals heterozygous at many loci Individuals approach homozygosity Variability distributed over the Variability mostly between component population lines Carries deleterious recessives Deleterious recessives tend to be eliminated Intolerant of inbreeding Tolerant of inbreeding Much heterozygote advantage Less heterozygote advantage (epistasis, overdominance)  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Overdominance Hypothesis ▪ Over-dominance: The phenotype of the heterozygous progeny is greater than either parent.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Advantages and disadvantages of inbreeding a-Advantages of inbreeding 1. Obtaining uniform families within the herd through increasing the similarity of genes. 2. The possibility of identifying undesirable recessive genes (phenotypically) in the original genotypes, and its easy to exclude the animals that carry these recessive genes. 3. Producing genetically divergent lines to be used in hybridization processes to benefit in the hybrid vigor.  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Advantages and disadvantages of inbreeding b- Disadvantages of inbreeding 1. Increase of homozygosity. 2. Appearance of lethal alleles. 3. Reduction in hybrid vigor. 4. Reduction in reproductive ability. 5. Segregation of population in distinct lines. 6. Reduction in yield (production traits).  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Population mean at inbreeding ▪ In the case of random matting (no inbreeding) F=0 Mo (original)= a (p-q)+2dpq  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Population mean at inbreeding ▪ In the case of partial inbreeding 1> F> 0 MF (partial inbreeding)= a (p-q)+2dpq (1-F)  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Population mean at inbreeding ▪ In the case of full inbreeding F=1 MF (full inbreeding)= a (p-q)  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding References ▪ https://jvanderw.une.edu.au/gene251-351_lec5.pdf ▪ https://www.icbf.com/wp-content/uploads/2015/11/breeding-value.pdf ▪ https://sciencenotes.org/wp-content/uploads/2021/11/Genotype-vs-Phenotype.png ▪ https://www.uaex.uada.edu/publications/pdf/FSA-3068.pdf ▪ https://emphasis.plant-phenotyping.eu/about/plant-phenotyping ▪ https://www.cambridge.org/core/services/aop-cambridge ▪ https://www.youtube.com/watch?app=desktop&v=mw3365ulV8Q  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding References ▪ core/content/view/26DFA92B3BA3EA92CD76847BFA21C5C8/S0016672300022825a.pdf/divclass-title- a-note-on-fisher-s-average-effect-and-average-excess-div.pdf ▪ https://iastate.pressbooks.pub/cropgenetics/chapter/inbreeding-and-heterosis-2/ ▪ Beavis, W., L. Merrick, K. Meade, A. Campbell, D. Muenchrath, and S. Fei. (2023). Inheritance of quantitative traits. In W. P. Suza, & K. R. Lamkey (Eds.), Crop Genetics. Iowa State University Digital Press. DOI: 10.31274/isudp.2023.130 ▪ Merrick, L., W. Beavis, J. Edwards, T. Lübberstedt, A. Campbell, D. Muenchrath, and S. Fei. (2023). Inbreeding and heterosis. In W. P. Suza, & K. R. Lamkey (Eds.), Crop Genetics. Iowa State University Digital Press. DOI: 10.31274/isudp.2023.130  Sixth lecture Quantitative Genetics Breeding Values & Population mean at inbreeding Any Question ?