Livestock and Poultry Breeding Notes PDF

**DEPARTMENT OF ANIMAL GENETICS AND BREEDING** LIVESTOCK AND POULTRY BREEDING CLASSROOM NOTES ------------------------------------- PREPARED BY: Dr. Deepti Kiran Barwa ------------------------------------- **\ ** **INTRODUCTION** Animal Breeding is the application of genetics and physiology of reproduction to animal improvement. Animal Breeding started with domestication. Firstly breeding was controlled by nature. Nature selects those which can survive in that type of nature i.e. known as survival for fittest. But after domestication human started breeding of those individuals by which it can get more production, for which it can be made easy to domesticate them like quite temperament. **History of Breeding:** Robert Bakewell (1725-1795) known as Father of Animal Breeding. He concentrated on producing farm animals with increased efficiency. He laid the foundation of pure breed for shire horses, Leghorn cattle, and Leicester sheep. He likes to records of the offspring and keeping the sons of the best males. In 1775 Collings brothers copied Robert Bakewell and laid foundation for the Shorthorn cattle. His principle was of mating best females with the best males. This lead to close inbreeding and due to this he had fertility troubles with his animals. This all happen with Robert Bakewell due to lack of a theory explaining inheritance, because of which animal breeding slowed down for many year. But soon after Gregor John Mendel (1822-1884) -- "Father of Genetics" gave first rule of genetic inheritance once again animal breeding fasten. But Mendel's rules worked well for discrete traits like yellow or green colour but traits like milk production or body weight which showed a continuous variation follow different inheritance rules. Then one Biometrician Karl Pearson (1857-1936) developed statistical method and rejected Mendel's rules saying that Mendel's rule is applicable in special case for discrete characters not to all. But Mendel suggested that the simple rules of inheritance could not be applied to continuous variation but in this case many inheritance factors might act simultaneously producing all intermediate indistinguishable classes after then a bitter dispute started about the mechanisms of inheritance and it goes on until Fisher (1890-1962) used statistical methods to reconcile Mendel's law of inheritance with the continuous variation observed by biometricians. This led to mile stone of a new branch called quantitative genetics. This new science had still to be applied to animal breeding. This task was accomplished by Lush (1896-1982). Lush defined concepts like heritability and proposed methods of selection including the information of relatives, weighed it according to the genetic contribution predicted by Mendel's rule and quantitative genetics. So, J.L. Lush also known as Father of Modern Animal Breeding. Fisher and Hazel developed indexes of selection for several traits and applied them to animal breeding using family information and weighted traits of economic interest. This indexes could not be used any farm or any season or parity. All this environmental factors affect the genetic values of animals. Several methods were developed to pre-correct the data before genetic analysis was made, but, it was Henderson (1911-1989) who proposed a method for integrating the genetic values and the environmental ones in the same statistical model. This method is called BLUP (Best Linear Unbiassed Prediction) is the standard method in animal breeding evaluation. BLUP needs the variance components for predicting the genetic values. To estimate them is a difficult task, because data come from different farms and different environments and they should be corrected as before. Paterson and Thompson showed how to correct for the environmental effects and how to estimate the genetic variance components at the same time. Their method is called REML (Residual or Restricted Maximum Likelihood) Then came the Bayesian method introduced by Daniel Gianola- this method use probabilities and leads to complicated integrals. To overcome this problem new numerical method called Monte Carlo Markov Chins method allowed use of Bayesian method in development and extension of them in animal breeding. In India there was no livestock census available till 1920. There were no record/herd or registry books available even many breeds evolved. ICAR started herd books for the first time in India for Red Sindhi and Sahiwal breeds of cattle in 1941. Subsequently herd books were also established for Hariana, Murrah, Gir, Kankrej, Tharparkar, Kangayam and Ongole breeds. In 2010 cloned a buffalo calf named "Shresth" at NDRI, Karnal India. According to 19^th^ livestock census total livestock population in India is 512.05 million, cattle is 151.17 million which is 37.28% of total livestock and buffalo is 108.70 million i.e. 21.23% of total livestock. In Chhattisgarh total livestock is 150.40 lakh and total bovine population is 112.03 lakh. There are 40 cattle, 13 buffalo, 26 goat, 42 sheep, 06 pig, 17 chicken, 06 horses and 09 camel breeds giving a total to 159 total registered breed. The overall contribution of livestock sectos in total GDP is nearly 4.11% during 2012-13. Realizing the importance of the livestock, the Governement of India under the Ministry of Agriculture has created an autonomous body namely ICAR (Indian Council of Agriculture Research) to conduct research on various aspects of livestock production and health. There are 10 research institutes directly under the control of ICAR. 1. National Bureau of Animal Genetics Resources (NBAGR) Karnal, Haryana. 2. Central Sheep and Wool Research Institute (CSWRI) Avikanagar, Rajasthan. 3. Central Institute for Research on Buffaloes, Hissar, Haryana. 4. Central Institute for Research on Goat, Makdoom, U.P. 5. Central Avian Research Institute (CARI), Izatnagar, Uttranchal. 6. National Equine Research Centre, Hissar, Haryana. 7. National Camel Research Centre, Bikaner, Rajasthan 8. Indian Grass land and forage Research Institute, Jhansi, U.P. 9. ICAR North Eastern Hill Complex, Shillong, Meghalaya. 10. National Research Centre on Yak, Dirang, Arunachal Pradesh. **Selection** The purpose of animal breeding is not to genetically improve individual animals but to improve future generation of the animal population. The method used by the breeder to make long-term change in animals is called Selection. Selection is the process in which certain individuals in a population are given an opportunity to produce offspring while others are denied this opportunity. It means choosing of best parents for the production of best progeny. According to J. L. Lush- "Selection is differential rate of reproduction". It means those which are selected their rate of reproduction are high and those which are not selected have no or low rate of reproduction. **Objective of selection:** The main of objective of selection is to improve the progeny by selecting parents. On the basis of objective selection can also be define as a tool to make improvement in the progeny generation or as tool for improvement of genetics of livestock. **Genetic Effect of Selection:** Selection does not create any new gene it only increases the frequency of desirable gene and decreases the frequency of undesirable gene. Since the selected individuals can transmit only sample halves of genes they have to their offspring, so if animals with better quality genes possessed are selected then the offspring will also posses the same. If the frequency of desirable gene is increased, the proportion of individuals homozygous for that desirable gene is also increased. The changes thus obtained in gene frequency due to selection are permanent even if selection ceases thereafter. Selection is of two types namely: 1. Natural Selection 2. Artificial Selection **Natural Selection:** The main force of natural selection is the survival of fittest in a particular environment. In nature, the individuals best adapted to their environment survived and produced the large number of offspring. This natural selection acts through the variations produced by mutation and recombination of genetic factors and eliminates unsuccessful genetic combination and allows nature's successful experiments to multiply. Natural selection operates through differences of fertility among the parents and viability or mortality among progeny. These are the two tools in nature to make selection. In natural selection there is a tendency to eliminate the defective or detrimental genes that have arisen through mutation. **Artificial Selection:** It is the selection practiced by man. This can also be defined as the efforts of man to increase the frequency of desirable genes or combination of genes in his herd/flock by saving those individuals with superior performance or that have the ability to produce superior performing offspring when mated with individuals from other lines or breeds. The simplest form of selection is to choose individuals on the basis of their own phenotypic values. The net value of an individual depends on several traits. Hence, it is necessary to apply selection simultaneously to all traits of economic importance. The traits to be selected depend upon their genetic significance and economic value. Genetic significance means how they responding to selection. Genetic significance depends on (1) Heritability, (2) Correlation or association of the trait with other. Once the decision is taken upon is how the selection should be applied on these traits in order to achieve the maximum improvement of overall economic value. The aids available to estimate the breeding value of an animal is through the phenotype of an animal or its relatives. Grand Sire Sire Progeny Individual Ancestor Grand Dam Grand Sire Dam Grand Dam Collateral Relatives (Brother, Sister, Cousins) **INDIVIDUAL SELECTION** **Or** **MASS SELECTION** Individual selection is the selection in which basis of selection is strictly based on animal's own performance. Here the best individual is selected from within a group of animals of similar age and in same environment i.e. comparison should be done within environment. Individual selection is also known as Mass Selection or Truncation selection. When selection is done in group it is called Mass selection. In this a truncation point or standard value of a particular trait is set and on the basis of which individual animals are selected or rejected. If the individual performance is above the set value it is selected and below these criteria animals are culled or rejected. **Breeding value/Additive Genetic Value:** The first component of the genotypic value is the additive genetic value or breeding value. This is caused by individual effects of genes or the additive gene action. The average effect of gene is fixed and transmitted in the progeny as such. Therefore this portion of genotypic value is a fixed effect in itself and is heritable. The breeding value is defined as the sum of average effects of genes carried by an individual. **Genetic Basis:** In individual selection, selection is done on the basis of phenotypic value. This phenotypic value is due to breeding value. Individual having better phenotypic value will also have high breeding value. Progeny coming from these selected parents will also have better breeding value and phenotypic value and this will give population with better breeding value. **Process of selection:** In mass selection the replacement value varies with species i.e. the herd size should not be decrease -- this is the criteria for how much percentage of animal in a herd are to be culled -- In dairy cattle 10 -- 30% per year are culled. For example: Records of milk yield is available and a list in deceasing order and see where the 70% of animal which are to be kept and below this i.e. 30% in list is culled. Another selection can be based on truncation point and is selected on the basis of truncation point. If single record of each animal's performance is available then the breeding value for a given trait is calculated as: EBV = P + h^2^ (P~i~ - P ) If multiple records are available - EBV = P + nh^2^ (P~i~ - P ) 1 + (n - 1) r P - Population average, h^2^ - heritability, P~i~ - Average performance of an individual n -- Number of records, r - repeatability **Accuracy of Individual selection:** Accuracy is correlation between phenotypic value and breeding value of an individual. Accuracy depends on heritability. If heritability is high accuracy is high. Therefore individual selection is best method of selection. Accuracy = √h^2^ = h Merits: 1. Procedure is simple. 2. Individual selection is based on performance of individual and it records are most easily available. Limitation: Individual selection has some shortcomings which are as follows: 1. Several important traits including milk production egg production are expressed only by females. Thus, selection of breeding males cannot be based on their own performance. 2. Performance records for milk and egg production and other traits that are expressed only after certain age or sexual maturity for such traits based on individual performance cannot be performed. For example selection for milk yield or age at first calving is to be done of a one year old calf so selection cannot be done as this performance occur later in life. 3. In case in which heritability is low. Individual merit is poor indicator of breeding value. 4. Selection for carcass traits cannot be made because carcass traits are the trait that can be measured only after death. Ex. Dressing Percentage = Dressed body weight x 100 Dressed body weight can be obtained after the death of an individual after death selection cannot be performed. **PEDIGREE SELECTION** A pedigree is simply a record of ancestor. Here individual is selected on the basis of performance of individual's parents and grandparents or ancestors. But this performance should be in term of herd average or relative performance or deviation from their contemporaries i.e. performance must be deviation from the population. **Genetic Basis:** Each animal in the pedigree gets half its genetic makeup from its parents. Parents having better phenotypic value will have better breeding value and parents having better breeding value will have progeny of better breeding value and so will have better phenotypic value. **Procedure:** 1. If selection of a bulls (male animal) is to be done than the selection is done on the basis of phenotypic value of his mother and on this basis male animal is either selected or culled. 2. On the basis of expected breeding value of individual which is half of expected breeding value of his mother. **Accuracy of pedigree selection:** It is the correlation between phenotypic value of either of the parent and breeding value of the individual under selection (Source to target). **0.5/R** **A~O~** R -- Coefficient of relationship between the ancestor and individual. P~P~ -- Phenotypic value of the parent A~P~ -- Breeding value of parent A~O~ -- Breeding value of progeny So, Accuracy = Rh R depends on source or relatives if it is a parents then R= 0.5 Relative accuracy of pedigree selection = [Accuracy of pedigree selection] Accuracy of individual selection = Rh / h If either of the parents is the basis of selection then, R = 0.5 Then, relative accuracy of pedigree selection is 0.5 or 50%. It means the selection based on pedigree selection is 50% accurate than the individual selection. Merit: 1. Young animal can be selected. 2. Selection can be done for carcass trait. 3. Selection for sex limited trait can done 4. Selection for low heritable trait can be performed. Demerit: 1. Sometime required records of pedigree is not available not in the form of deviation from population mean. 2. Even if records are available not in the form of deviation from population mean. 3. Sampling nature of inheritance: Progenies from same parents are not genotypically alike. In this type of selection we assume that all the progeny are same. Parents transfer a sample of their genes to a progeny and other sample to other progeny. **COLLATERAL/ FAMILY SELECTION** There are two type of collateral relative, they are -- 1. Direct relatives -- Relatives that are contributing directly to the individual, they all come in direct relation i.e. Father, Mother, Grand Father, Grand Mother. Grand Father Grand Mother Father Mother Individual 2. Collateral Relatives -- Individual sharing the parentage or ancestor in common. Sire Sire Dam Offspring~1~ Offspring~2~ Offspring~1~ Offspring~2~ **Half -- Sib Full - Sib** They are neither ancestors nor descendents. Because of their common ancestry, they would have some genes in common and there by some performance in common. Family in Animal Breeding includes full-sib and half-sib families. **Genetic Basis:** Full sib or half sib share common parent, so they would have some genes in common. If the record or performance of one Individual is known and is better than it is necessarily have trait which will be better in the other individual too having common parent. In short if the performance of one progeny is known that trait will also be transfer to other progeny (Half-sib). **Procedure:** If the records of the individual are included in the family average and used as a criterion for selection, it is known as family selection. If the individual's records are not included in arriving at the average, then it is known as sib selection. When selection is carried out for market weight in swine, the market weights of all males and females in the family are considered in the calculation of family average. But when selection is carried out for fertility traits and milk yield, the performance of males cannot be included but they are selected on the basis of sib's average (Sib selection). PBV = P + nh^2^ ( F - P ) 1 + (n - 1) t Where, n -- no. of family members whose records are available t -- intraclass correlation F -- family average P -- population average t = ¼ h^2^ (half sib) t = ½ h^2^ (full sib) **Accuracy:** = √ nh^2^ 1 + (n -1) t = h √ n 1 + (n -1) t Relative accuracy = [Accuracy of family selection] Accuracy of individual selection The accuracy of selection increases as the records on a large number of half sibs. Merits: Young animal can be selected. 1. Selection can be done for carcass trait. 2. Selection for sex limited trait can done 3. Selection for low heritable trait can be performed 4. When h^2^ is low and numbers of records from family are more, family selection is good. Demerits: 1. Availability of records of family members may not be available. 2. Sampling nature of inheritance. **PROGENY TESTING** Progeny testing is the selection of individual which is based on the performance of his progeny. It is a technique generally used for males because they are responsible for more progeny in their lifetime than any one female, so bulls are also known as half of the herd. A set of progeny is generated and on the basis of their performance sire is selected and the future progenies from selected sire will be better. Pedigree tells what the individual ought to be, Individuality tells what the individual seems to be but progeny testing tells what the individual is. **Genetic Basis:** As each offspring represent a sample half of the genes of each parent and this is a sample half of the parent breeding value. Different genes are transmitted by a parent to its different progenies due to segregation of genes during gamete formation and the probability to receive exactly the same set of genes by its progenies is very low specially for polygenic traits. Therefore, the estimation of breeding value of an individual based on one or few progenies may be misleading. Moreover the polygenic traits are influenced by environmental factors and the different progenies of the same parent do not get same environment. Thus the environmental factors cause differences in the performance of different progenies. Therefore these two factors segregation of genes and environmental factors which produces deviation in the breeding value of a parent are to be balanced out by estimating the breeding value on any progenies. **Method of Progeny testing:** Young bulls born of superior parents are mated to number of females and only one offspring per female is used. For making selection of sex limited trait only offspring of particular sex will be recorded and for the growth traits records of both male and female offspring are taken. The performance of the offspring (halfsibs) is used to evaluate the bulls by suitable statistical technique called sire index. D1 P1 S1 D2 P2 D3 P3 D4 P4 For sex limited traits like milk yield only female S2 D5 P5 offspring performance will be recorded and for D6 P6 growth traits performance of both male and female offspring are recorded. D7 P5 S3 D8 P6 \| D9 P7 \| \| So on.... **Progeny Testing Programme:** A certain number of young sires produced using the very best dams and sires are put under test. Adequate numbers of test doses of bulls put to test are distributed in selected herds to ensure that at least 100 complete first lactation records of daughters per bull are available for estimating breeding values of bulls with a very high reliability. On the basis of daughter's milk yield bulls are selected; these top ranking bulls are crossed with selected cows which are elite cows and are selected among the daughters. The very best 1-10% of progeny tested bulls and the very best 1 to 10% of recorded cows are used for producing the next generation of young bulls. The young bulls are again put to test and the cycle is repeated. Before going to next progeny testing cycle male calves have to undergo parentage and genetic disease testing along with libido and semen quality checking which is known as initial selection. All these young bulls are reared strictly in same environmental and managemental conditions. **Progeny Testing Programme** **Requirements:** 1. Randomization: Dam should be distributed randomly to each sire from population. For example -- 5 bulls 100 cows from 500 no. of cows. 2. Replication: Sufficient number of progeny from each sire must be produced (at least 25) for the selection to be accurate. 3. Local control: Other factors such as breed, parity which may affect the genetic potential of the progeny must be same. Progeny of bulls must be borned at same season and duration and raised under similar set of managemental and feeding condition to minimize the influence of other factors. 4. Test as many sires as possible minimum 5 -- 10 sires. 5. No progeny should be culled until the end of the test. 6. Sire under test should be raised and compared under similar environmental condition. The breeding value of bull based on the progeny performance -- 1 + (n - 1) t t -- intraclass correlation among progeny t = ¼ h^2^ (half sib) R -- Coefficient of relationship between individual and his progeny i.e. 0.5 4 + (n - 1) h^2^ 4 + (n - 1) h^2^ Where, n -- no. of family members whose records are available P~i~ -- Average performance of the progenies of individual sire P~c~ --Average performance of contemporary progenies If the progeny testing is based on one progeny accuracy is equal to selection based one parent or one full sib which is equal to 0.5h. If progeny testing based on 5 progeny then accuracy is equal to individual selection for moderate heritable trait. If progeny number increases more than 5 progeny accuracy tends toward 100% accurate for any value of h^2^. Thus, progeny test gives higher accuracy than any other selection criteria. Merits: 1. It is the most accurate method for evaluating dairy sires. 2. Selection can be done for carcass trait. 3. Selection for sex limited trait can done 4. Selection for low heritable trait can be performed. 5. To test for recessive gene. Limitation/Demerit: 1. It takes long time for the animal to be evaluated as maturity is in 3^1/2^ years and breeding takes 1year so total 4 years and sexual maturity of progeny and for production again 4 year. Individual to be selected takes 8year. 2. Progeny testing is a expensive storage of sufficient number of semen and keeping progeny for long period is expensive. 3. Progeny testing is effective on adequate number of progeny. 4. Small herd size also limits the progeny testing programme. 5. Lack of proper infrastructure: For 5 bulls to be tested 125 total progeny female will be required. So total 30progeny for each bull if mortality occur. There must be 60 calving so that minimum 25 female progeny can come. So A.I. must be done in 100no. of cows (AI = 50%) so for 5 bull to be tested 500 cows must be present in a farm so, if 10 bulls are to be tested 1000 cows are needed which is difficult to accumulate in an organized farm. So the progeny testing are extended in field condition. Progeny testing is of 3 types: 1. Single herd progeny testing -- Progeny testing in single herd is a problem as discussed in limitation 2. Associated herd or multiple herd progeny testing: Different herd are associated and semen of bulls under test is distributed to them. 3. Field progeny testing: If a large numbers of animals spread over many villages and these villages have facilities to get AI services, progeny testing is a practical and the best option for achieving genetic improvement in the breed. 1. Tandem selection 2. Independent culling level method 3. Total score or Selection Index **TANDEM SELECTION** Word "Tandem" means one after another. In tandem selection, improvement is practiced for single trait at a time until a desirable level of improvement is achieved, then second trait is considered for improvement and so on for third. The efficiency of this method is dependent on the genetic relationships among the traits. If the two traits are favourably or positively correlated, selection for the first trait will also automatically improve the other trait and vice versa. ![Tandem method](media/image2.jpeg) Here, the trait A was improved quickly in one generation, whereas B took more time (two generations) and C took very much longer (few generations). A remains stable when worked on B, and both A and B remained stable when worked on C. Therefore the traits are assumed to be independent. On the other hand if they are not independent, then the situation could be seen by the dotted lines A^'^ whereas B went up, A came down i.e. See-saw effect caused by a genetic antagonism between them. The efficiency depends on genetic correlation between traits. For example -- First milk fat is selected and then making selection for milk production. Merit: 1. It is a simple and straight forward method. Demerit: 1. It takes very long time because improvement with respect to single trait may take several generations so improvement for other traits may involve many generation of selection. Example: If a trait improves in 3 generation and each generation comes in 3 years, then for improvement of 3 traits will take 9 generation which means 27 years. During this long duration goal of selection may change, management may change and breeder may get frustrated. 2. Genetic parameter i.e. correlation between traits is not taken into account because of negative correlation the made in first trait may get nullified with the progress in second trait. **INDEPENDENT CULLING LEVEL METHOD** In this more than two traits are taken simultaneously at a time. A minimum standard is set for each of the n numbers of traits and all individual below that level for any one trait are culled without regard to their merit for other traits. It is like an examination system with different pass marks for each subject but if the student fails one subject than be fails the lot. There is no compensation for poor performance in one trait by brilliance in another. Example- Three traits are taken milk yield, fat percent and age at first calving and standard is set for each i.e. 1700kg, 4.5% and 3years respectively. A cow is having 2500kg milk yield, 4.0% milk fat and 2.8year age at first calving; this cow will be culled as it fails to pass minimum criteria for milk fat inspite of excelling in milk production. Merit: 1. Selection based on independent culling method is easy to perform but becomes complicated when more traits are considered. 2. Since all the traits are taken simultaneously it takes less time. 3. This method is most useful when traits are reduced to minimum and where culling is done at different stages in an animal's life. Example: at birth selection for birth weight and genital anomalies, at 1 -2 years of age : selection for growth rate and any structural deformities, 3 -- 4 year of age: selection for Age at first calving and age at puberty, at 4 -- 5 year of age: fertility, milk yield and fat percent. Demerit: 1. Genetic parameter is not considered. 2. Even in slight deficiency with respect to one trait will not be compensated by excellence with respect to other trait. 3. Equal weightage is given to all the traits. 4. With the increase of number of traits under selection selected animal number decreases, selection intensity is reduced. **TOTAL SCORE METHOD / SELECTION INDEX** All the desired traits are taken together for selection. A selection Index is simply means of putting a lot of different information into one value. Using this information net merit of an individual is estimated. The individual with highest score are kept for breeding purpose. The traits to be considered in selection may not be equally important economically, some kind of weighing is required. The amount of weight given to each trait depends on its relative economic values and genetic parameters (heritability, genetic and phenotypic correlation between different traits). Depending on relative economic value and genetic parameters different weights are given to each trait and different traits are combined in the form of linear equation so as to give aggregate genetic worth of each individual under selection. The individual specification for a number of traits can vary greatly and is combined into one value for the animal called a **Total score or an Index.** **I = b~1~x~1~ + b~2~x~2~ + b~3~x~3~ + \_ \_ \_ \_ \_ \_ \_ \_ \_ + b~n~x~n~** **Where,** **I = Index value** **x~1~ ,x~2~,x~3~ \_ \_ \_ \_ \_,x~n~ are phenotypic values for the different traits these phenotypic values are deviation from population mean.** **b~1,~b~2~,b~3~, \_ \_ \_ \_ \_ ,b~n~ are weights given to each of the traits. In statistical terms the b's are multiple regression coefficients.** **Here, the high merit in one trait can certainly be used to make up for the deficiency in other. The aim in computing an index is to estimate in which various traits are appropriately weighted to give the best prediction of the animal's breeding value i.e. what it will produce when it breeds.** **There is a set of procedure to find out the weights to be given to each trait and that procedure is known as Construction of Selection Index. To do this requires a considerable amount of data such as:** 1. **Heritability of the trait** 2. **Phenotypic variance or standard deviation** 3. **Phenotypic correlation** 4. **Genetic correlation** 5. **Relative economic value of the trait** **The relative economic value often causes confusion because it is not based on the actual prices in use at one particular time, but rather the relationship between the prices of the components over a period of time. The relation between prices in the past is used to predict their relationship in the future.** **Merit:** 1. **Genetic parameters are considered.** 2. **Different weightage is given to different traits depending on their economic value.** 3. **Excellence of one trait can be used for makeup of deficiency of other trait if the trait is economically important.** 4. **Less time is required as numbers of traits are selected.** **Demerit:** 1. **Relative economic value of trait varies from time to time and in different locality. So selection index** has to be constructed and modified from time to time. 2. Genetic and phenotypic parameter is difficult to find when the numbers of traits exceed three or more. 3. An index constructed for one herd cannot be applied to other because genetic and phenotypic parameter differs in different population and different management practices. **RESPONSE TO SELECTION / GENTIC GAIN** Selection is choosing the best individuals in a population to be the parents of the next generation or progeny generation. We make selection in parent generation and response or result of selection is realized in progeny generation is called response to selection, symbolized by "R". Genetic gain can also be defined as increment or change in the mean value of progeny generation as a result of selection made in parent generation is called response to selection or genetic gain. The response to selection is the difference of mean phenotypic value between the offspring of the selected parents and the whole of the parental generation before selection; this is known as realized response to selection. R = [\$\\overline{O}\$]{.math.inline} + [\$\\overline{P}\$]{.math.inline} [\$\\overline{O}\$]{.math.inline} is mean of the offspring [\$\\overline{P}\\ \$]{.math.inline} is mean of population before selection R is realized response of selection When response is estimated in coming progeny on the basis of heritability and selection differential it is known as predicted or expected response to selection. R = h^2^ x ([\$\\overline{P}\$]{.math.inline}~s~ + [\$\\overline{P}\$]{.math.inline}) [\$\\overline{P}\$]{.math.inline} is mean of selected parents [\$\\overline{P}\$]{.math.inline} is population mean before selection Selection differential is the difference between the mean of the selected parent and the mean of the population before selection. Expected response depends on heritability and selection differential. This is response per generation. Response per year = h^2^ x [\$\\frac{\\overline{\\mathrm{\\text{Ps}}}\\mathrm{\\ \\ \\ \\ +}\\text{\\ \\ \\ \\ \\ \\ }\\overline{\\mathrm{P}}}{\\mathrm{\\text{Generation\\ Interval}}}\$]{.math.inline} Generation interval is the time period between two successive generations with respect to the same stage of life cycle. Selection differential can also be expressed in standard unit i.e. selection differential divided by phenotypic standard deviation. [\$\\frac{S}{\\ \\sigma p}\$]{.math.inline} = i (Intensity of selection) Intensity of selection is also known as standardized selection differential as it tell number of σp by which the mean of the selected parent is above the population mean before selection. Selection intensity is the mean deviation of the selected individuals in units of standard deviation. The intensity of selection is symbolized by "i". R = h^2^ x i x σp R = [\$\\frac{\\sigma\_{G}\^{2}}{\\sigma\_{P}\^{2}}\$]{.math.inline} x i x σp R = [\$\\frac{\\sigma\_{G}\^{2}}{\\sigma\_{P}\^{}}\$]{.math.inline} x i R = h x i x [*σ*~*G*~]{.math.inline} h is accuracy i is intensity of selection [*σ*~*G*~]{.math.inline} is genetic variation of trait or genetic variation Factor affecting response to selection: 1. Heritability: It is the term used to describe the strength of inheritance of a character i.e. whether it is likely to be passed on to the next generation or not. If the h^2^ is high, the genetic gain will also be more, because the environmental variation will be less. 2. Selection differential: It is the superiority of the selected parents over the mean of the population before selection. There should be variation i.e. genetic variation. The selection differential is reduced if the population is uniform as few animal are far enough above or below the mean to make any impact by selecting the best and culling the worst. Selection differential can be calculated for both the parent. Example: Selection Differential of Male -- Mean of selected males -- 2kg/day Overall herd mean - 0.25kg/day Selection differential = 2 - 0.25 = 1.72kg/day Selection Differential of female Mean of selected females - 0.75kg/day Overall herd mean - 0.25kg.day Selection differential = 0.75 -- 0.25 = 0.50kg/day Mean selection differential = [\$\\frac{1.75\\ \\ + \\ \\ 0.50}{2}\$]{.math.inline} = 1.13kg/day Now, in second condition when in a herd there is not enough cows to replace to kept up the numbers in herd, in that case all the females will be retained. Then, the mean selection differential will be -- = [\$\\frac{1.75\\ \\ + \\ \\ 0}{2}\$]{.math.inline} = [\$\\frac{1.75\\ \\ }{2}\$]{.math.inline} = 0.88kg/day +-----------------------+-----------------------+-----------------------+ | **Species** | **Percentage of | | | | animals to be | | | | selected** | | +=======================+=======================+=======================+ | | **Females** | **Males** | +-----------------------+-----------------------+-----------------------+ | Dairy cattle | 4 - 5 | 50 - 60 | +-----------------------+-----------------------+-----------------------+ | Beef cattle | 4 - 5 | 40 - 50 | +-----------------------+-----------------------+-----------------------+ | Sheep | 2 - 4 | 45 - 55 | +-----------------------+-----------------------+-----------------------+ | Swine | 1 - 2 | 10 - 15 | +-----------------------+-----------------------+-----------------------+ | Chicken | 1 - 2 | 10 - 15 | +-----------------------+-----------------------+-----------------------+ | Horse | 2 - 4 | 40. \- 50 | +-----------------------+-----------------------+-----------------------+ 3. Generation Interval: This is the time interval between generations and is defined as the average age of the parents when the offspring is born. This varies between species and selection procedure. Management practices for early breeding in females reduces GI and breeding practices like progeny testing increases the GI. To ensure rapid progress the aim is to keep the generation interval short. This is dependent on sexual maturity and duration how long it take to get sufficient data. Ex. Waiting for complete first lactation milk yield of daughter before a bull is used in herd. X Maximum gain/year = For situation of low h^2^ and long G.I. = x The average generation intervals for different species are: **Species** **Generation Interval (in years)** -------------- ------------------------------------ ------------- ------------- **Males** **Females** **Average** Dairy cattle 3 - 4 4.5 - 6.0 4 - 5 Beef cattle 3 - 4 4.5 - 6.0 4 - 5 Sheep 2 - 3 4.0 - 4.5 3 - 4 Swine 1.5 - 2 1.5 - 2.0 1.5 - 2.0 Chicken 1 - 1.5 1 - 1.5 1.0 - 1.5 Horse 8 - 12 8 - 12 8 - 12 4. Intensity of selection: The intensity of selection depend on the proportion of the population selected when the selected individual number is less in population intensity is more and if large number of individual are selected from a population intensity is less. Response will be high when selected individual is less. **SYSTEMS OF BREEDING** There are only two ways in which the breeder can change the genetic properties of the population. - By selection: Choice of individuals to be used as parents. - By controlled mating: Controlled mating of selected parents. Although selection is the most important method for increasing the frequency of desired genes, same genetic control over the population is provided by the mating system. Mating animals which are alike in pedigree or visible characters tend to increase the homozygosity. Mating unlike individuals will increase heterozygosity. - **Inbreeding **is a system of mating where by the mates are more closely related than the average members of the population. - **Grading:** is the practice of using registered sires of a given breed on scrub or native females generation after generation. - **Crossbreeding **is the mating of pure bred animals from two different breeds. - **Out crossing** is the mating of animals of the same breed but with no traceable relationship for several generations back in the pedigree. - **Mating system based on phenotypic resemblance or dissimilarity** Mating system based on phenotypic resemblance. This is also known as assortative mating. In this system mates are chosen on the basis of external appearance in a particular character. - **Assortative mating:** Mating based on phenotypic resemblance or dissimilarity. - **Positive assortative:** Mating of phenotypically similar individuals (i.e like with like mating). - Eg. Mating biggest with biggest ; Mating smallest with smallest. - **Negative assortative mating** - Mating between dissimilar individuals. - Breeding best to worst. Positive assortative mating tends to create more genetic, phenotypic variation than would be found in comparable with random mating population,in the population undergoing the assortative mating (Mating high X high, low X low) tends to spread the distribution away from the centre towards the extreme. So, the phenotypic variation caused by the assortative mating normally considered as draw back. However increase in genetic variation can be beneficial from the selection point of view. Greater the genetic variation faster the genetic change. Eg. To increase dairy milk yield, mating the high producing cows to bulls with highest predicted performance. Negative assortative mating or disassortative mating is mating like with unlike. Best X Worst Tall X Dwarf. Negative assortative mating tends to decrease the variation. That is intermediate types are produced due to mating of such individuals. It is not good strategy if we want to speed up directional genetic change. It reduces genetic variation, decrease response to selection. Eg. In layers Rooster having high breeding value for egg size mated with hen with small size eggs. **Properties of assortative mating** Sewall Wright (1921) studied and formulated same properties - With complete + ve assortative mating complete homozygosity of population is obtained but slowly - Assortative mating based on external resemblance may had a population of genetic composition may different from that reached by inbreeding based on genetic relationship. Eg. Metric character depend on 2 pair of genes with additive and equal effects, assortative mating lead to 2 extreme types AABB, aabb But close inbreeding leads to AABB, aaBB, Aabb, aabb (4) phenotypes. **MATING BASED ON GENETIC RELATIONSHIP** **Mating based on genetic relationship** Eg. Mating Brother x Sister Parent x Offspring It takes into account of the relationship of mates. This mating exerts its influence on all the characters simultaneously. The coefficient of relationship between parent and offspring is half. So when mated, the relationship exerts its influence on milk production, age at first calving and other characters. **Mating system can be classified into two major groups.** - So far, we have studied how the breeder selects the parents for the next generation. The next step is to decide how to breed them. Systems of breeding do not create new genes. They sort out available genes into new patterns. Success in animal breeding depends on the proportion of favourable genes present in the foundation stock. Genes that are not present in the foundation stock can be found in other populations or strains or breeds and can be introduced through crosses. Systems of breeding are classified as follows. Matting Mating system based on genetic relationship is divided into 1. Inbreeding 2. Out breeding Inbreeding is defined as mating of animals more closely related to each other than the average relationship with in the population concerned. Inbreeding includes matings like parent -- offspring, brother --sister, eg. Brother, half sister and among cousins and other collateral relatives. **Inbreeding** Inbreeding is classified into two types 1. Close inbreeding 2. Line breeding **Out breeding** It** ** is a form breeding where the mates are chosen on the basis of not being related. 1. Out crossing 2. Top crossing 3. Line crossing 4. Grading 5. Crossbreeding 6. Species hybridization - Out crossing: It is usually applies only to matings with in a pure breeds. In two herds or flocks within the same breed or separated for 4 or 5 generations and the sire from one herd or flock is used in the another herd their amounts to out crossing. - Top crossing : This is a system of crossing which is normally used with in pure breeds; It refers to the use of highly inbred male with females of base population or non-inbred population. Top cross in dairy cattle usually refers to the last sire in a pedigree. Top crossing also refers to the continued use of sires to different families with in a breed. - Line crossing : It usually refers to crossing of inbred lines within a specific breed. It takes advantage of both increased homozygosity with in a line and difference between lines. - Grading: It is the continuous use of sire of one pure breed starting with foundation of which were of another breed or non descriptive animals. - Cross breeding: It is the mating of two individuals from different breeds. Breeds represent tremendous resources of varying genetic material - Species hybridisation:** **By crossing of two different species is called species hybridization. The mule is a good example of a commercially important species hybrid. Mare x Jackal ass = Mule. **INBREEDING** nbreeding is the mating between animals, which are more closely, related each other than the average relationship between all individuals in a population or inbreeding is mating between animals related by ancestors. When the animals are considered as closely related when they have one or more common ancestors in common, in the first 4 to 6 generations of their pedigree. Example: Sire-daughter, Son-daughter or Brother-sister. In general, inbreeding refers to close breeding. Inbreeding is classified into two types - Close Inbreeding:** **Such as mating between sibs or between parents and progeny in order to achieve inbred lines with relatively high degree of homogenisity. In most of the time we use full sib mating method. The same effect can be achieved by consistently back crossing the progeny to the younger parents. Half sib mating is much slower, rich in homozygosity but it is also less risky. - Line breeding: It is a system of mating in which the relationships of an individual or individuals are kept as close as possible to some ancestor. In general line breeding is a milder form of inbreeding. As a general rule sire is not mated to its daughters but half sib matings are made among the offspring of the particular sire. Line breeding was used extensively in the past in development of British breeds of cattle such as Angus, Hereford and Shorthorn. The following points should be remembered while practicing line breeding, - Line breeding should be practiced in purebred population of high degree of excellence, after identifying outstanding individuals. - Line breeding is probably most useful when an out standing sire is dead or not available for breeding purpose. - To form new breeds, line breeding can be advocated. **Disadvantage of line breeding** - Line breeding tends to make gene good or bad, homozygous rapidly. Hence choosing of a ancestor (sire) to line breed is very important. Those that are definitely superior should alone be selected. Beside rigid selection, culling of undesirable recessive is highly essential. Line breeding should be practised only in herds distinctly superior to the general average of the breed. **GENETIC EFFECTS OF INBREEDING** Inbreeding makes more pairs of genes in the population homozygous irrespective of the type of gene action involved. The consequences of homozygosity are: - Inbreeding does not increased the number of recessive alleles in a population; but merely brings to light through increased homozygosity. - Inbreeding fixes characters in an inbred population through increased homozygosity whether the effects are favorable or unfavorable. - As a result of homozygosity, the offsprings of inbred parents are more likely to receive the same genes from their parents than of offspring of non-inbred parents. This is another way of saying that inbred parents are more likely to be pre-potent than non-inbred parents. - If overdominance exists (Aa is superior than AA or aa), inbreeding decreases the overdominance by changing the Aa genotype to AA and aa. **PHENOTYPIC EFFECTS OF INBREEDING** When the animals are homozygous for a no. of traits, the regularity of inheritance is assured (i.e it fixes the characteristics). Inbreeding reduces vigour is called inbreeding depression. Increased inbreeding results in - Reduced fertility, - Reduced mothering ability, - Reduced viability and growth rate - Inbreeding if accompanied by selection may increase the phenotypic uniformity. **PREPOTENCY** - Prepotency is the ability of the individual to stamp its characteristic on its offspring to such an extent that they resemble their parents more closely than in usual. It is the property of the characteristic and not the individual breed or sex. When two individuals are mated one may have more influence than the other on offspring. Similarly some lines and breeds are more pre-potent than others. However prepotency can't be passed on from one generation to another unless it is possessed by both sires and dams. - A high degree of homozygosity and possession of a high per cent of dominant genes are the inherent qualities that will enable an animal to stamp its own characteristic on majority of its offspring. A perfectly homozygous animals produce only one kind of gametes and all the offspring will receive exactly the same gene from each. Any genetic difference between the offspring would depend entirely on the halving process and on number of different genes received from the other parent. If the parent is homozygous for several dominant gene all the offspring will resemble it irrespective of what they received from other parent. Here prepotency is the maximum. **Measure of prepotency** - In breeding and increasing of homozygosity is the only means of mating animals prepotent for characteristics. The more the animals are inbred the more they become homozygous for a number of genes. The inbreeding coefficient then is the best estimation of animal's prepotency. Prepotency however is not transmissible from parent to offspring. **Development of Strain** - A strain could be defined as a group of birds or animals which have been closed for outside breeding and the herd or flock has been randomly mated with intense selection for a particular trait or traits for 5 generations and give a name. The description of the strain should always followed by a economic trait. This is considerably milder form of inbreeding in which strain forms. When the population of animals closed for outside breeding, the population becomes closed flock. Estimate the genetic parameters, once the average performance of the closed flock are known, rigid selection is followed to improve particular trait in subsequent generations. The selected strain should have superior breeding quality. In breeding point of view are more or less isolated from each other. Since the populations are close from the entry of new animals, homozygosity increases as a result of small population size. The superior strain formed within the breed could cross among them for exploiting heterosis or hybrid vigour. **Development of Line** - The line can be defined as a collection of animals, as a result of inbreeding or more closely related to each other than the individuals in the strain. The line should be always qualified by inbreeding coefficient. From the strain, the birds are chosen at random. Full sib or half sib matings are taken for successive generations. The progeny has a co-efficient of inbreeding for excess of 50%. Then perform selection among the population and fix a particular trait in that line which is homozygous for a particular trait. **Uses of Inbreeding** In spite of certain obvious disadvantages of inbreeding, there are certain instances where it may be used as advantage of livestock production. - The most practical use of inbreeding is to develop strains and lines that can be used for crossing purposes to exploit heterosis. - Inbreeding may be used to determine the actual genetic worth of an individual, is done by mating to a sire with 25 to 35 daughters before it is used extensively in AI programme. - Inbreeding could be used as a practical way to select against the recessive genes of economic importance. Such inbreeding brings out the hidden recessive genes both recessive homozygous and heterozygous parents can be identified and culled. - Inbreeding may be used to form distinct families with in a breed especially the selection is practiced along with it. - To maintain genetic purity and thereby to increase prepotency - To eliminate undesirable recessives. When a sire is mated to 20 of its daughters and does not produce any recessive characters in the offspring, it may concluded that the sire is not heterozygous for recessive characters. - To develop inbred lines. - To regroup the genetic material - To produce uniform progeny - To determine the type of gene action. If inbreeding effects are large, the type of gene action is non -- additive: if inbreeding effects are small , then the type of action is additive. **Disadvantages of Inbreeding** - Undesirable traits appear with increasing frequency as intensity of inbreeding increases (lethal and sub lethal). - Growth rates in farm animals reduced by inbreeding. - Inbreeding reduces the reproductive efficiency. - Reduced vigour lower vitality due to inbreeding depression **Inbreeding depression** The most striking observed consequence of inbreeding is the inbreeding depression. It is the reduction in the mean phenotypic value shown by characters connected with reproductive capacity or physiological efficiency. In general inbreeding tends to reduce the fitness. Thus, characters that form an important component of fitness, such as litter size show reduction on inbreeding. Whereas characters that are not closely related with fitness show little or no change. Inbreeding depression for a single locus can be expressed as follows. **MF = Mo - 2dpqF and for all loci concerned** it is, **MF = Mo - 2 F pqd** Where, Mo - Mean value of a population for a particular character before inbreeding. MF - Mean value of the population for a particular character after inbreeding. F - Inbreeding co.efficient d - dominance, i.e heterozygote does not have a value average to that of homozygote p - Frequency of one allele q - Frequency of other allele Therefore, inbreeding depression is -- 2F pqd which depends on dominance (d), inbreeding coefficient (F) and relative frequencies of alleles (p & q). Genes are at intermediate frequency at the beginning of breeding show highest depression. Economic traits like reproductive viability, milk yield and growth rate show inbreeding depression. Characters like fat % and back fat thickness do not show much inbreeding depression. **Inbreeding is to be practised only when** - the herd is better than the average. I.e when the frequency of desirable genes are more - the herd has an outstanding sire - the breeder knows the merits and demerits of inbreeding - the herd is not maintained for commercial purpose. **MEASUREMENT OF COEFFICIENT OF RELATIONSHIP** The relationship between two animals is expressed as coefficient of relationship, symbolised by "R ". It measures the probable portion of genes that are the same for two individuals due to their common ancestors, over and above the base population. **Relationship may be two kinds.** 1. Direct 2. Collateral - Direct relationship: You are directly related to your father or mother. You and your father have 505 common genes and you and your mother have 505 common genes. - Collateral relationship: You and your cousin's are collateral relatives because you both have some common ancestors. You and your cousin have the same grand parents C and D. The important step in measurement of relationship is the number of generations between the animals studied and that common ancestor. The formula for relationship between individual X and Y is **R~xy~ =∑ \[(1/2) ^n+n' ^\]** Where **∑ **= summation ½ = Halving of inheritance in each generation n = No. of generations between X and the common ancestor or the no. of times the halving process has undergone between X and common ancestor n' = No. of generations between Y and the common ancestor or the no. of times the halving process has undergone between Y and common ancestor. **INBREEDING DEPRESSION** - A degree in the performance of inbred mostly in traits like fertility, survivability and reduction in overall performance noticed in inbred is called inbreeding depression. It is a manifestation of poor gene combination value, which is direct result of increase homozygosity. Decline in performance of inbred over the mean of their parents is also called inbreeding depression. Decline is more pronounced in traits which are close to reproduction or fitness. - Eg. Reduction in growth rate, reduced No. of ova, increase in early embryonic mortality, increase in mortality. **COEFFICIENT OF INBREEDING** ![Inbreeding-coefficient](media/image4.jpeg) **OUT BREEDING** Out breeding is the mating of animals which are less closely related to each other than the average of the population. Its general effects are the opposite of those of inbreeding. Out breeding increases the heterozygosity of the individual. The maximum practical usefulness of out breeding systems is the production of animals for market. Out breeding systems are broadly classified as follows: 1. Out crossing 2. Top crossing 3. Line crossing 4. Grading 5. Crossbreeding 6. Species hybridization **OUT CROSSING** Out crossing usually applies only to mating within a pure breed. If two lines or flocks within the same breed are separated for four or five generations and the sire from one herd is used in another herd that amounts to out crossing. The use of out crossing in purebreds are - When there is lack of selection response due to reduced genetic variability. - To reduce inbreeding in a closed population. - To introduce new genes with reference - colour, horn type, etc. **TOP CROSSING** This is a system of crossing which is normally used within pure breeds. Top crossing refers to the use of highly inbred males to the females of the base population or non-inbred population. Top cross usually refers to the best sire in a pedigree. Top crossing also refers to the continued use of sires to different families within a pure bred, same breed or different breed. **LINE CROSSING** - Line crossing usually refers to crossing of inbred lines within a specific breed. Line crossing takes advantage of both increased homozygosity within a line and the difference between lines. Line crossing - Line crossing is mainly done to exploit heterosis or hybrid vigour. **BACK CROSSING** - It is the mating of a cross bred animal back to one of the pure parent races, which were used to produce it. It is commonly used in genetic studies, but not widely used by breeders. When one of the parents possess all or most of the recessive traits, the back cross permits a surer analysis of the genetic situation than the F~2~ does. - A heterozygous individual of F~1~ when crossed with a homozygous recessive parent the offspring group themselves into a phenotypic ratio of 1:1. On the other hand if the F~1 ~individual is crossed with the homozygous dominant parent then all the offspring will be phenotypically alike. **GRADING / GRADINGUP** - Grading up is the continual use of sires of one pure breed starting with foundation females which were of another breed or no particular breed at all (Non-descript or Mongrel). Marked improvement in crosses if sires from a particular breed (A) are repeatedly back crossed to another breed / non-descript animals (B). Five generations are sufficient to raise the level of inheritance of breed A to 96.9% (0.969) in the fifth generation. After five generations of repeated back crossing to a particular breed, the animals after the end of fifth generation become eligible to be registered as purebred. **Generation** **Level of pure bred blood of sire used %** -------------------- --------------------------------------------- Foundation stock 0 First generation 50 Second generation 75 Third generation 87.5 Fourth generation 93.75 Fifh generation 96.875 Sixth generation 98.4375 Seventh generation 99.23875 **CROSS BREEDING** - Cross breeding is mating of two individuals from different breeds. Breed represents tremendous resources of varying genetic material. Cross breeding is done. Cross breeding is done to exploit hybrid vigor or heterosis and to sell the crossbred to market. Every time, the parental breeds have to be crossed for producing market animal. - Crossbreeding has been used in recent years to establish a broad genetic base in the development of new breeds or synthetics: one or two crosses between the two or more populations are made in order to produce a single population of animals containing genes from each of the population involved. Once a synthetic has been formed then the main aim is to improve it as rapidly as possible by selection within it. For example: Santa Gertrudis, The Jamaica Hope, the Norwegian Red and White, the Australian Milking Zebu, Hissardale, Karan Swiss, Sunandhini, Taylor breed. The main guidelines to be followed in crossing to produce a synthetic are: - Ensure that the animals used in the original crossings have been intensely selected in terms of relevant characters; it is of no use starting a synthetic with inferior animals. - Maximise variance in breeding values amongst the foundation animals in the synthetics using as many unrelated animals as possible from each of the contributing populations. **SPECIES HYBRIDISATION** Hybrids can occur where the species are closely related for the egg and sperm to result in a viable embryo. Where the two species are very closely related, the hybrids may even been partially or fully fertile. Some hybrids are bred for curiosity or public display, others are bred by researchers involved in genetic researcher and a few occur naturally. Chimeras are not the same as hybrids. Hybrids have intermediate features and each cell is a mix of chromosomes from the parental species. Chimeras are a mix of genetically different cells to form a mosaic animal. **Crossing the species boundary** - Speciation (one species evolving into two) is usually a slow process. It is generally accepted that different species usually cannot mate and reproduce - this is called \"**reproductive isolation**\". The exception was closely related species which can produce hybrids, although those hybrids have reduced fertility. - Sometimes, one species can split into two through **behavioural isolation**. Some individuals develop behaviour patterns which limit their choice of mates e.g. they might be attracted to certain colours or might be active at different times of day. Though they are fully capable of interbreeding with the other group, their different behaviours keep them apart. If their habitat became permanently overcast, those behaviour barriers would break down and they would interbreed freely; their hybrids might become new species. - Another way reproductive isolation occurs is when fragments of DNA accidentally jump from one chromosome to another in an individual i.e., **chromosomal translocation**. The mutant individuals cannot reproduce except with other mutant individuals - not much good unless the individual has mutant siblings to mate with! There are also \"**master genes**\" which govern general body plan (**Hox genes**) and those which switch other genes on and off. A small mutation to a master gene can mean a sudden big change to the individuals that inherit that mutation. Sometimes, those radical mutations can \"undo\" generations of evolution so that two unrelated species can mate with each other and produce fertile young (only seen in micro-organisms). - In mammals, hybrid **White-Tail/Mule Deer** don\'t inherit either parent\'s escape strategy (White Deer dash. Mule Deer bound) and are easier prey than the pure-bred parents. Another example is seen in **Galapagos Finches**. Healthy Galapagos Finch hybrids are relatively common, but their beaks are intermediate in shape and less efficient feeding tools than the specialised beaks of the parental species so they lose out in the competition for food. **Mechanisms for keeping species separate** - **Physical separation: **the species live in different geographic locations or occupy different ecological niches in the same location and so never have the chance to meet each other. \ **Temporal isolation:** the species that mate during different seasons or different time of day and cannot breed together. - **Behavioral isolation: **members of different species may meet each other, but do not mate because neither performs the correct mating ritual. Imprinting by fostering the young of one species on a female of the other species can overcome this in some cases. - **Mechanical isolation: **copulation may be impossible because of incompatible size and shape of the reproductive organs. - **Morphological isolation: **copulation may be impossible because of the difference in body size or shape. - **Gametic isolation: **the sperm and egg may not fuse and hence fertilization cannot occur; if it does occur then the embryo fails to get past the first few cell division. **Haldan\'s rule** - **Haldane\'s Rule** states that in animal species whose gender is determined by sex chromosomes, when in the first cross offspring of two different animal species, one of the sexes is absent, rare or sterile, that sex is the heterogametic sex. The \"heterogametic sex\" is the one with two different sex chromosomes (e.g. X and Y); usually the male. The \"homogametic sex\" has two copies of one type of sex chromosome (e.g. X and X) and is usually the female. - **Haldane\'s Rule for Hybrid Sterility** states that a race of animals could diverge enough to be considered separate species, but could still mate to produce healthy hybrid offspring in a normal ratio of males and females. If any of the hybrid offspring were sterile, the sterile offspring would be the heterogametic offspring (males). If the heterogametic offspring was fertile, it produced the normal 50:50 ratio of X and Y sperm. - **Haldane\'s Rule for Hybrid Inviability** states that if the divergence between the species became large enough to generate genic differences, but not to prevent mating, then parental gene products may fail to co-operate during development of the embryo, resulting in hybrid inviability (the hybrids are aborted, stillborn or don\'t survive to maturity). In this case, the male to female ratio of hybrid offspring is skewed with more homogametic offspring while the heterogametic offspring (males) are absent or rare. By crossing two different species, sometimes we get good individuals. The mule is a good example of a commercially important species hybrid. Mare x Jackal ass = Mule, She ass x stallion -- Hinny. Male Mules are always sterile as for as it yet known. A few cases of fertile mare mule have however reported, but they are very rare. Hinny is generally inferior to Mule as a worth animals. Hinny is also sterile. Horse having 32 pairs and Ass 31 pairs. Mules comes to possess 63 chromosomes in all. The mare mules have given birth to mule foal and horse foal when bred to Jack and stallion respectively. The inference is that the mare follicles occassionally produce an egg containing nothing but horse chromosomes, and all of the Ass chromosomes have been extruded in the polar body. The fertile mare mules essentially function as mare as far as the genetics of the egg is concerned. If all the horse chromosome where extruded in the polar body the Mules will function genetically as assess. But no case of this sort has been reported. Pure breeding of Mules as such also theoretically impossible. - **European cattle and American Bison **when crossed produce sterile Males and Fertile females. By Back crossing the females to Bison and Cattle attempts are being made to form a new breed of cattle called **cattallo**. - **Male Jackals **only mate with domestic bitches if the Jackal pups are raised by a domestic bitch (to become imprinted on dogs). There is a psychological barrier, but the offspring are fertile (pre-zygotic barrier, but no post-zygotic barrier). - **Lions and Tigers **must overcome behavioural (courtship) barriers, but produce fertile female offspring and sterile male offspring (pre-zygotic and post-zygotic barriers). **Lions and leopards** have some physical barriers (size), but these are overcome if the lioness lies on her side to let the leopard mount her; the male **Leopons** are sterile, though female offspring are fertile (pre-zygotic and post-zygotic barriers). In these cases, pre-zygotic barriers are overcome by rearing the two species together (in whales and dolphins this occurs naturally). Some cases seem to need additional rules! In **Beefalo,** Domestic cows may have an immune response against Bison/Cow hybrid calves - this is a physiological barrier, but does not prevent conception. Bison cows don\'t have this immune response against hybrid calves and hybrid Beefalo males can be fertile. In some hybrids of domestic cats with small wildcats, a proportion of hybrid males are claimed to be *partially* fertile (incomplete post-zygotic barrier?) and though the hybrid females are fertile they may not successfully raise their young - a psychological barrier, but one which does not prevent mating/conception. By crossing the two different species, sometimes good, visible individuals are produced. The mule is a good example of species hybridisation. Several other species hybrids have been produced. Some of them are **S.No.** **Hybrids** **Sire** **Dam** **Remarks** ----------- --------------- ------------------------------ ------------------------------------------ --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1 Hinny Stallion Jennet It is inferior to mule as a work animal and is also sterile 2 Zebroid Zebra Horse Popular in tropics -- docile -- better disease and heat resistance 3 Cattalo Cattle Bison Bison is known as American buffalo. Males are sterile and females are fertile. domestic bull/Bison cow crossings have a lower infant mortality rate (cow immune systems can reject hybrid calves) 4 Beefalo American Bison Domestic Cattle Beefalo have been back-crossed to Bison and to domestic cattle; some of these resemble pied Bison with smooth coats and a maned hump. The aim is to produce high protein, low fat and low cholesterol beef on animals which have \"less hump and more rump\". Although Bison bull/domestic cow crossings are more usual, 5 Pien niu Cattle Yak Found in Tibet. 6 Goep Goat Sheep Sheep and goat are not so closely related. When crosses are made between them fertilization sometimes takes place. However the embroys die before parturition and are resorbed or aborted. 7 Zubron Domestic cattle Wisent (European Bison,*Bison bonasus*). Zubron was considered as a possible replacement for domestic cattle as they were durable and resistant to many cattle diseases. They also thrived on poor pasture, in harsh weather and with minimal husbandry. First generation Zubron males are infertile and cannot be used for breeding, but the females are fertile and may be bred back (back-crossed) to either Wisent or to domestic bulls. Males from these back-crosses are fertile. 8 Yakalo Bison (American \"Buffalo\") Domestic Tibetan Yak In Nepal, Yak/Cow hybrids are bred using Yak bulls on domestic cows or, less often, domestic bulls on Yak cows. The Yak-Cow females are fertile, the males are sterile and the meat is considered superior to beef. In Nepalese, the hybrid is called a Khainag or Dzo (male)/Dzomo (female). A Dzomo crossed with either a domestic bull or yak bull results in an Ortoom (three-quarter-bred) and an Ortoom crossed with a domestic bull or yak bull results in a Usanguzee (one eighth bred). 9 Geep Goat embryo Sheep embryo Although often cited as a hybrid, the famous \"Geep\" is not a true goat/sheep hybrid, but was a laboratory experiment which fused a sheep embryo with a goat embryo (a type of animal called a chimera). The geep is a mosaic of mismatched goat and sheep parts; the parts which grew from the sheep embryo are woolly while those which grew from the goat embryo are hairy. Each set of cells kept their own species identity instead of being intermediate in type. It could be fertile, but will produce either goats or sheep depending on whether its reproductive organs grew from the goat embryo or from the sheep embryo. 10 Cama Camel Llama Llama is a hybrid 11 Iron Age Pigs American wild hogs Tamworth pigs Resemble early domestic pigs **CROSS BREEDING** - Cross breeding is mating of two individuals from different breeds. Various breeds represent tremendous resources of varying genetic material. Cross breeding is done for any one of the following reasons. - Complimentarity of different breeds. - Cross breeding is done to exploit hybrid vigor or heterosis. - Every time, the parental breeds have to be crossed. - Wide genetic base for producing synthetics. ![Threeway-rotational\_cross](media/image6.jpeg) **HETEROSIS OR HYBRID VIGOUR** Crosses of animals from different strains or lines of the same breed, from different breeds or from different species, result in offspring whose level of production is above that of the average of the parents. The increased production may be due to increased fertility, increased pre and post natal viability, faster and more efficient growth, improved mothering ability etc. The increased level of performance as compared to the average of the parents is known as heterosis or hybrid vigour. The heterosis can be either positive or negative. Heterosis is the phenomenon in which progeny of crosses between inbred lines or purebred populations exceed the average of the two parental populations. It is just the opposite of inbreeding depression. Heterosis can be measured by using the formula **Heterosis (H) = \[ (Mean of F~1~ offspring) - (Mean of parents) /Mean of Parents \] x 100** Example: The mean litter size at weaning in pigs Breed A = 7.0 Breed B = 8.0 Mean of A & B = 7.5 F~1~ offspring = 8.5 Heterosis = (8.5 - 7.5) / 7.5 = 1.0/7.5 = 0.13333 = 13.33% Various types of heterosis are recognised in breeding. - Parental heterosis (maternal and paternal) - Individual heterosis referring to the non-parental performance. - Heterosis is due to non-additive gene action. **Genetic basis of heterosis** The theories put forward to explain heterosis are - Dominance Theory : It postulates that the parental lines are homozygous dominant for different loci -- when crossed produces progeny with dominant gene at all loci. - Overdominance Theory : It postulates that the heterozygote is superior to either homozygotes (parents). - Epistasis Theory : It postulates that gene interactions are responsible. But in practice the heterosis is due to combination of dominance, overdominance and epistasis in any proportion. However, the contribution of epistasis to heterosis is negligible in crossbred of domestic animals. Generally all the quantitative characters are governed by many genes and no animal is likely to carry all of them in homozygous dominant state. In living organisms, dominant genes are more often favourable than the recessive genes. Crossing of two different lines or breeds has a greater chance of contributing different dominant genes to the progeny. Different breed crossing Since the offspring carries more dominant genes than the parents, it will be more vigourous or productive. All the recessives (aa bb dd ee) except 'cc' are masked by the dominant alleles. The degree of heterosis depends on the no. of dominant genes present in the crossbred individual. Maximum heterosis could be obtained if animals carrying all desirable homozygous dominant genes are used for crossing. It would never be possible to have such animals. Eg. Two animals heterozygous for 'n' pairs of genes can produce 3ⁿ types of offspring. If only seven pairs of genes are heterozygous, 3^7^ or 2187 types of offspring. If 10 pairs of genes are heterozygous, 3^10^ or 59049 types of offspring are possible. As the quantitative traits are polygenic in nature and the animals produce only a few offspring, it is not possible to produce animals with perfect combination even after many generations of selection. The chance is further reduced by other genetic factors like undesirable recessives, linkage between desirable and undesirable genes and by non-genetic factors like environment. **Formulae H~F1~ = dy^2^ and H~F2 ~= 1/2 dy^2^** **BREEDING FOR HETEROSIS** To exploit heterosis, lines or breeds with good nicking ability or combining ability are crossed. The combining ability can be determined only by test crosses. A breeder attempting to produce lines which will combine well with each other has to produce large no. of lines. Then he can test them in crosses and find those which give best results. This idea is expensive, time consuming and uncertain. As a general rule the lines or breeds totally unrelated give better heterosis in crosses. There are two types of combining ability - General combining ability (GCA) is the mean performance of F1 expressed as a deviation from the mean of all crosses and it is due to additive genetic variance. - Specific combining ability (SCA) is the superiority of a particular cross over the average GCA of the two lines and it is due to non-additive genetic variance. **CAUSES OF HETEROSIS** - Difference in gene frequency between two population for several generations. - Dominance, overdominance and epistasis. Complementarity is the second reason for cross breeding. This refers to the additional profitability obtained from crossing two populations resulting not from heterosis but from the manner in which two or more characters complement each other. E.g. Crossing Angus carcass quality with Zebu Brahman (adaptability). Complementarity is not heterosis. Complementarity is due to additive gene action. If there is complementarity, the crossbred progeny are in midway between these two breeds. Traits which show heterosis would rank above the average of parental breeds in the crossbred progeny and often would be superior to either. **SYSTEMS OF UTILIZATION OF HETEROSIS** Heterosis is a phenomenon in which the crosses of unrelated individuals often result in progeny with increased vigour, much above their parents. - The progeny may be from the crossing of strains, varieties or species. - Hybrid vigour includes hardiness, greater viability, faster growth rate, greater milk producing ability, fertility etc. - One of the best-known examples for hybrid vigour is MULE, which is proven for hard work in extreme climatic conditions. **GENETIC BASIS OF HETEROSIS** - Heterosis is caused by heterozygosity of genes involving non-additive effects, which mainly includes dominanace, over dominance and epistasis. **Dominance** - When several pairs of genes control one trait, one breed could be homozygous dominant for several pairs and homozygous recessive for another pair (AA BB CC dd) and another breed could be homozygous recessive for respective several pairs and homozygous dominant for respective another pair(aa BB CC DD). Assume that the recessive genotype contributes 1 unit and dominant genotype contributes 2 units of phenotypic values. If these two breeds are crossed: ![Dominance](media/image8.jpeg) - This hybrid will be superior to either parent because of presence of at least one dominant gene in all pairs of genes which affect the particular trait. **Over dominance** - For some pairs of genes, the heterozygotes may be more vigorous than either of homozygotes. Here heterozygosity produces hybrid vigour. Consider the same illustration given for dominance producing heterosis. Assume that recessive, heterozygous and homozgous genotypes contribute 1, 2 and 1.5 units of phenotypic values. Over dominance - The F1 hybrid generation, phenotypic variability is generally much less than that exhibited by the inbred parental lines or strains or breeds. This shows that heterozygotes are less influenced by environmental factors than the homozygotes. This phenomenon is termed as "buffering", which means that the organisms' development is highly regulated by genetics. Another term often used in this connection is "homeostasis", which means the steady stse in the development of the organism within a normal range of environmental fluctuations. **Epistasis** - To a lesser degree, interallelic interaction or epistasis can account for heterosis. In dominance and over dominance, the heterosis is due to the interaction of genes that are alleles. In epistasis, the interaction is between pairs of genes that are not alleles. ![Epistasis](media/image10.jpeg) - Contribution of AaBb results in an interaction such that the presence of both A and B gives a phenotype larger or in other words more desirable than would be expected from average phenotypes of AAbb or aaBB. **Application of heterosis in animal breeding** - Not all traits in farm animals are affected to the same degree by heterosis. Those traits expressed early in life, such as survival and growth rate to weaning seem to be affected most. Feed-lot performance as measured by rate and efficiency of gain after weaning is moderately affected. Heterosis has very little effect on carcass traits. Traits, which show the greatest degree of heterosis are the same ones which show the greatest adverse effects when inbreeding is practiced. Highly heritable traits seem to be affected very little by heterosis; whereas, those which are lowly heritable are affected to a greater degree. For example, fertility and litter size in swine (heritability is 15 to 17%). - The degree of heterosis depends on degree of genetic diversity of the parents. Therefore, heterosis will be higher when breeds are crossed than lines within the breeds are crossed. Crossing breeds having greater differences in genetic backgrounds should give more heterosis than crossing breeds having similar genetic backgrounds. This is because unrelated parents are less likely than related parents to be homozygous for the same pairs of genes. - Heterosis is much employed to produce commercial stock where the individual merit is promoted, but the breeding value is lowered. - The successful exploitation of heterosis depends upon how superior the crosses are over the purebreds and whether it is worth considering the lowering the breeding value of the individual and cost of replacement of purebred stock. - For these reasons, it is commonly practiced in poultry, swine and sheep where the fertility is high and the cost of replacement of purebred stock is necessary **COMBINIG ABILITY** - At the present state of knowledge, performance of two or more breeds or lines in crosses is somewhat unpredictable. Some lines or breeds appear to \"combine well\" whereas others do not. This can be determined only by test crosses. There are two types of combining abilities viz., general combining ability (GCA) and specific combining ability (SCA). GCA is the mean performance of the F~1~ offspring of a line with other lines and it is due to additive genetic variance. SCA is the superiority of a particular cross over the average GCA of the two lines and it is due to non-additive genetic variance. GCA and SCA are expressed as variance and not as values. - To estimate the combining ability of two or more lines, "diallel mating system" is followed. In this system of crossing, all possible combinations of the lines are produced. This mating scheme allows estimating the performance of the individual combinations. The diagram below explains the diallel mating system and the combining abilities of four lines, x~1~, x~2~, x~3~ and x~4~. **Line** **x~1~** **x~2~** **x~3~** **x~4~** **GCA** ---------- ---------- ---------- ---------- ---------- --------- x~1~ x~1~x~1~ x~1~x~2~ x~1~x~3~ x~1~x~4~ x~1~ x~2~ x~2~x~1~ x~2~x~2~ x~2~x~3~ x~2~x~4~ x~2~ x~3~ x~3~x~1~ x~3~x~2~ x~3~x~3~ x~3~x~4~ x~3~ x~4~ x~4~x~1~ x~4~x~2~ x~4~x~3~ x~4~x~4~ x~4~ SCA: The diagonals elements In symbols, the performance of a combination of lines is composed as follows: **G~(x1x2)~ = GCA~(x1)~ + GCA~(x2)~ + SCA~(x1x2)~** where, G~(x1x2) ~denotes the genotypic value of the cross "x~1~x~2~". **SELECTION FOR GENERAL COMBINING ABILITY** For measuring the general combining ability, top crossing is followed. In top crossing, individuals from the inbred lines to be tested are crossed with individuals from the base population. The mean value of the progeny measures the general combining ability of the line because the gametes of individuals from the base population are genetically equivalent to the gametes of a random set of inbred lines derived without selection from the base population. This method is for comparing the general combining abilities of different lines and to choose the lines most likely to yield the best cross among all the crosses that would be made between the available lines. **SELECTION FOR GENERAL AND SPECIFIC COMBINING ABILITY** - The specific combining ability of a cross cannot be measured without making and testing that particular cross. To get SCA, two lines should be developed which differ in gene frequencies. Two methods of selection are available *viz.,*recurrent selection and reciprocal recurrent selection. - Both these systems involve progeny testing. Due to the increased generation intervals, this would be expected to result in slower progress than other breeding systems for characters moderate to high in heritability. They would be expected to be more useful than other breeding systems only if overdominance or other non-additive types of inter- or intra-allelic gene action are important in heterosis. **RECURRENT SELECTION** - The principle of recurrent selection is developed out of convergent improvement. In this a highly inbred line presumably homozygous at most loci is selected as a ***tester***. A large number of individuals are crossed with this line and their progeny are evaluated. Those giving best progeny are subsequently inter mated and a large number of their progeny are tested in the crosses on the inbred tester. The cycle is repeated over and over. This is done to take greater advantage of the interaction of genes and the resultant overdominance by selecting inbred lines during their developmental process for the purpose of better complementing each other. - The success depends on the ability of the breeder to accumulate a greater number of genes having additive effects in two different parental lines that interact to greater advantage. If heterosis is largely dependent upon overdominance, this procedure should result in the line selected on cross performance becoming homozygous for different alleles than the inbred used as the tester. In other words when tester is aa, the selected line would become AA; the tester is BB, the selected line becomes bb etc. - The application of recurrent selection to animal breeding appears to be more difficult than its application to plant breeding because - The overall effects of inbreeding are deleterious - The degree of fertility is lacking. It depends on survivability - More number of animals are required and it involves longer generation interval and make this selection **RECIPROCAL RECURRENT SELECTION** - It is a system of selection for increasing the combining ability of two or more lines or breeds that nick or combine well. Individuals in two lines are not completely homozygous in opposite ways for all pairs of genes but that one allele may be present at a high frequency in one line and at a low frequency in other line. Crossing the lines and selecting the individual to reproduce each pure line on the basis of the performance of their crossbred progeny make the two lines more homozygous in opposite direction. It is a method of selection between lines or families or breeds to take advantages of overdominance, dominance, epistasis, or only additive effects. - In farm animals, selection is usually carried out for more than one trait, since one trait may be affected mostly by non-additive gene action and another by additive gene action or both. Hence, it is to select and improve the best and mating the best to best followed by crossing the improved lines or breeds to take the advantage of hybrid vigour due to non-additive gene action. - Randomly selected representatives of each of the non-inbred strains are progeny tested in crosses with the other. Those individuals of each strain having the best cross progeny are then intermated to propagate their respective strains. Offspring from these within strain mating are again progeny tested in crosses with the other and the cycle repeated. Reciprocal recurrent selection - These systems are useful in breeds or strains in which their performance is already high for highly heritable traits and in which it is desired to improve the potential performance of their crosses for the low heritable traits related to fertility and liveability e.g. litter size and early growth rate in swine. **SIRE EVALUATION** - There is urgent need to increase the production in order to meet the demand for the exploding population. This could be achieved by applying various modern methodologies in selection and breeding of livestock. Increasing the productivity through genetic improvement requires adequate identification and intensive selection of genetically superior sires. About 93 per cent of the total herd improvement comes from breeding of young bulls from tested sires and only six per cent from selection of dams. With the advances in artificial insemination and cryopreservation of semen, a sire has a potential of serving 3/4^th^ million cows and producing 1/4^th^ million progenies. Thus, selection of bulls is of great importance in dairy herd improvement. - For maximising the genetic gain by sire selection, it is essential that the method of estimating breeding values of sires should be unbiased and efficient. The breeding value refers to the average genetic effect of the genes passed on by the individual to its offspring and is estimated to know whether the individual is genetically superior to other individuals or not for the trait concerned. - A sire's production transmitting ability can be estimated by mathematical means and expressed as a single figure known as sire index. In other words, an attempt to express what a sire would have produced, has he been a cow, is the sire index of that bull. **SIMPLE DAUGHTER AVERAGE INDEX** - The simplest way to evaluate a bull is by his daughter's production alone (Edward, 1932). The fault with this method is that it does not consider the probable contributions of the dam. It would be all right if all the bulls were bred to average group of cows. **S~I~ = D~i ~= (1 / m~i~ )Σ D~ij~** where, D~ij~ = yield of j^th^ daughter of the i^th^ sire m~i~ = number of dams mated to i^th^ sire - This index when used for ranking sires would be subject to bias if the levels of production of dams allotted to different sires were unequal. **EQUIPARENT / INTERMEDIATE / DAIRY BULL INDEX / YAPP'S INDEX** - This index (Yapp, 1925) is based on the principle that the two parents contribute equally to the genetic make up of the progeny. This index overestimates the breeding value of a sire mated to set of dams inferior on the average and underestimates if dams happen to be superior on the average to the general level of herd. S~I~ = 2D -- M where, D = average yield of daughters of the sire; M = average yield of dams mated to the sire - In Yapp's formula, the potential transmitting ability can be expressed in terms of 4% fat corrected milk. **MOUNT HOPE INDEX** Goodale (1927) proposed the index and he suggested that in matting between animals of unequal levels of milk production is on the average about 7 / 10 of the distance above the level of the lower parent. While butter fat production is about 4 / 10 of the distance above the lower level. To get this index, compute the average mature equivalent of milk production of the dams of these daughters and take the difference between these averages. - If the daughter's average exceeds the dam's average, add 3 /7 (0.4286) of the difference to the daughter's average to get the bull's milk index figure. - If the daughter's average is less than the dam's average, subtract 7 / 3 (2.333) of the difference to the daughter's average to get the bull's milk index figure. - If the daughter's butter fat average exceeds the dam's average, add three halves or 1.5 of the difference to the daughter's average to get the bull's butter fat index figure. - If the daughter's butter fat average is less than the dam's average, subtract 2 / 3 or 0.6667 of the difference to the daughter's average to get the bull's butter fat index figure. **Formula** - For milk yield - S = D + (D - M) x 3/7 if D\>M - S = D - (M - D) x 7/3 if M\>D - For Butter fat % - S = D + (D - M) x 3/2 if D\>M - S = D + (M - D) x 2/3 if M\>D **HEIZER\'S INDEX** - This index is used to determine the transmitting ability of individual bulls with regard to milk production. This method is bas

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