Animal Breeding and Genetics

1. Animal Breeding and Genetics Instructor: Dr. Jihad Abdallah Genetic Model for Quantitative Traits

2. Simply Inherited and Polygenic Traits • Simply inherited traits: traits affected by one or few genes (coat color, presence of horns, genetic defects like spider syndrome in sheep). • Phenotypes of simply inherited traits are placed into categories (qualitative or categorical traits) • Very little affected by the environment.

3. Polygenic traits: are traits affected by many genes (no single gene having an overriding effect) like growth rate, milk production, birth weight, etc. • Generally described in numbers. • Typically quantitative or continuous in their expression (an exception is Dystocia which is affected by many genes but pohenotype is described in categories) • Polygenic traits are affected by the environment.

4. Polygenic traits: are traits affected by many genes (no single gene having an overriding effect) like growth rate, milk production, birth weight, etc. • Generally described in numbers. • Typically quantitative or continuous in their expression (an exception is Dystocia which is affected by many genes but pohenotype is described in categories) • Polygenic traits are affected by the environment.

5. The basic model for quantitative traits • P = µ + G + E • P = phenotypic value of an animal for a given trait. • µ = population mean or average phenotypic value for the trait of all animals in the population. • G = the genotypic value of the animal for the trait. • E = the effect of the environmental factors on the phenotype of the animal. • G and E are expressed as deviations from the mean of the population. Therefore, the mean of G in the population and the mean of E is equal to zero.

6. Genotypic Value • Genotypic value is the overall effect of all the genes carried by the animal (singly and in combination) on the phenotype of the animal for the trait. • Unlike the phenotypic value, G is not directly measurable. • The genotypic value is the sum of two values: breeding value (BV) and Gene Combination Value (GCV). G = BV + GCV

7. Breeding value • Breeding value (also called the additive genetic value) is the part of genotypic value that can be transmitted from parents to offspring. It is the sum of the effects of individual genes (called independent gene effects or additive gene effects) independent of the effects of dominance and epistasis. • Breeding value is considered as a parental value (the value of an individual as a contributor of genes to the next generation). • Before we select animals to be parents of the next generation, we first estimate their breeding values and choose those with the best breeding values.

8. Example: assume that a trait is affected by 5 loci and the independent (additive) gene effects for the 10 genes (alleles) at the 5 loci are as given in the table. The breeding value is the sum of these effects.

9. An individual only transmits a sample composed of half of its genes to each of its offspring; this half is a random half of its genes. Progeny difference (PD) or transmitting ability (TA) are used in practice by some countries to rank animals. • PD = TA = ½ BV • Progeny difference and transmitting ability are practical concepts. These are defined as the expected difference between the mean performance of the progeny of a parent and the mean performance of the progeny of all the parents in the population: • PDi = TAi = µ offspring of parent i – µ offspring of all parents

10. Progeny difference and transmitting ability are not directly measurable but can be predicted using performance data. • The predicted value for PD is called EPD (expected progeny difference) • The predicted value for TA is called PTA (predicted transmitting ability). • Both terms mean the same thing but EPD is used in beef cattle, swine and sheep breeding while PTA is used in dairy cattle breeding.

11. The breeding value of an offspring can be viewed as the sum of the additive effects of the genes inherited from the sire (father) and the additive effects of the genes inherited from the dam (mother).

12. For example, if the estimated BV of a sire for weaning weight is + 2.5 kg and the estimated BV of the dam is + 1.5 kg, then the average expected BV of their offspring is equal to (2.5 + 1.5)/2= +2 kg. That is, we expect the average of offspring of these sire and dam to be 2 kg heavier at weaning than the average of all offspring in the population. Therefore, if the population mean of weaning weight is 18 kg then the average phenotype of the offspring of these sire and dam is 18 + 2 = 20 kg.

13. Gene Combination Value (GCV) • GCV is the part of the genotypic value that is due to gene combination effects (dominance and epistasis). • Because individual genes and not gene combinations survive segregation and independent assortment during meiosis, GCV can not be transmitted from parent to offspring and therefore it is not important in selection.

14. Example: suppose that a locus affects litter size in swine with two alleles T and t and T is completely dominant over t. The independent effects are +0.1 pigs for T and – 0.1 pigs for t.

15. Producing Ability (PA) • For repeated traits (traits for which the animal have more than one performance record during its lifetime) the producing ability is very important • Producing ability represents the performance potential of an animal for a repeated trait (the ability of the animal to repeat its performance in future records). Producing ability is a function of all those factors which permanently affect the performance potential of the animal: • The genotypic value and its components (BV and GCV) which are determined at conception and remain with the animal during his whole life. • Some environmental factors which permanently affect the performance of the animal.

16. Examples of permanent environmental effects (Ep): - Nutrition at early stages of development affects the ability of beef and dairy cows to produce milk permanently. - A permanent problem in the udder will affect milk production during all productive life of the cow or ewe. • The environmental effects which do not affect performance permanently are called temporary environmental effects (Et). Examples on these include forage quality, weather conditions and some management practices. These factors vary from season to season or year to year and so they do not influence different records in the same way.

17. The producing ability is a combination of genetic and permanent environmental effects: PA = G + Ep  PA = BV + GCV + Ep • The average of PA is 0 across the population because it is expressed as a deviation from the mean. • The genetic model for repeated traits is: P = µ + BV + GCV + Ep + Et

18. Example: two records of 305-d milk production (in lbs) for two cows: PA for cow 1 = 1500 – 1000 + 2500 = 3000 lb PA for cow 2 = 1000 + 500 – 4500 = -3000 lb If we were to cull (discard) one of these cows we will cull cow 2.

19. Importance of producing ability • It is important to commercial producers as a measure of productive capacity. Typically dairy farmers feed their cows according to their producing ability. • Therefore, prediction of PA is quite useful in practice. The predicted value of PA is called Most probable Producing Ability (MPPA). • P = µ + MPPA is a prediction of the animal’s next record.