Animal Breeding

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Phenotype

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Measured level of performance for a trait. Genotype + Environment

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Breeding Value

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Value as a genetic parent. Value of additive genes to progeny. Ave transmissable genetic effect for a trait. Can't be measured directly, but can be predicted by own and relatives' performance. Expressed as deviation from the average.

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Genetic variance

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sigma squared / std dev squared. Variability in the breeding value in a population for a trait. Higher the further from the mean it is.

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Correlation

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Measure of the strength of the relationship between 2 variables. From -1 to +1.

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Phenotypic Correlation

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Strength of relationship between performance in one trait and performance in another

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Genotypic Correlation

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Strength of relationship between breeding values. Caused by pleiotropy and genetic linkage

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Selection

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Method to make long-term change. Selecting genetic parents to reach the breeding goal/objective.

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Types of mating systems

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Inbreeding, crossbreeding, complementary, corrective mating

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Epistasis

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When an allele effects another at a different loci. Dog coat color for example.

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Sex-limited inheritance

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When the expression of a gene is limited to one sex. e.g. Milk yield or scrotal circumference

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Sex-influenced inheritance

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When the expression of a gene is different for each sex. e.g. scurs, muscles, etc.

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Ways to change gene frequency

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Random genetic drift, mutation, migration, selection (natural or artificial)

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Random genetic drift

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Occurs when the population mates randomly. Can be avoided by increasing the population size and controlling mating

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Mutation

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Biochemical change in DNA. Uncontrollable and too rare to affect most breeding programs

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Migration

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When a new genotype enters the population. Happens in nature or by bringing in new animals to your herd

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Heritability

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A percent from 0 to 1 of the genotype predicted to be passed on to progeny. Inversely proportional to heterosis: traits with high heritability will have low heterosis (like growth) and vice versa. Not a fixed percent because it can be affected by environment. Only additive genes.

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Repeatability

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The consistency of a trait. Correlation between repeated records of same animal. Used to predict its future performance. If a trait has high enough repeatability, you only need to use a single record to predict instead of multiple. Rarely negative, but from -1 to +1. Includes non-additive

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Producing Ability

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Performance potential of a trait. Genotype + Permanent Environment. MPPA used to predict future performance

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Response to Selection

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Change in mean performance of the POPULATION resulting from selection per generation. Directly proportional to selection intensity, accuracy, and genetic variation. Inversely proportional to generation interval.

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Selection Accuracy

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Relationship between the predicted breeding value and the true breeding value. Square root of heritability. Depends on number of records, heritability, contemporary groups, environment.

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Generation Interval (L)

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Time taken to replace all parents with offspring. Approx = (age @ 1st offspring + age @ last offspring)/2 OR = sum of age of parent @ each offspring's birth/2

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Hardy-Weinburg Equilibrium

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p squared + 2pq + q squared . A genotype frequency will not change in a population assuming it's large, with random mating, no migration/mutation, equal fitness & fertility, same amount of males and females breeding. Used to predict offspring's gene frequency using the parents' frequency.

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Allele & gene frequency

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From 0 to 1 of how common allele is in a population. Changed by random genetic drift, mutation, migration, or selection. All frequencies added together must equal 1.

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Crossbreeding

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Mating two different breeds. Increases heterosis, can create a new breed. Reduces herd uniformity, difficult to maintain max heterosis, hard to manage programs and do genetic evaluations.

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Individual heterosis

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Heterosis that influences animal's own performance

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Maternal heterosis

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Advantage of crossbred mother over a purebred mother. Influences maternal female traits

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Paternal heterosis

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Rare. Influences sire traits

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3 breed cross

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One parent is crossbred AB and another is purebred C

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Backcrossing

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Crossing two crossbreds F1 and F1 to get F2. Halves heterosis each time you do it.

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Two-way rotational cross

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AxB=AB. ABxA=A(AB). A(AB)xB=B(A(AB)). Etc.

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Inbreeding

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Breeding individuals with a close genotype (relatives). Creates inbreeding depression that increases each generation you inbreed. Increases herd uniformity, identifies deleterious genes, and can cross two inbreds to get heterosis.

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Inbreeding coefficient

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Probability that 2 alleles at any locus are identical by descent. Delta F = 1/2Ne

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Linebreeding

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Breeding one sire with his offspring, and then with their offspring, and so on. Slow form of cloning. Maintains degree of relatedness without too many adverse effects of inbreeding.

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Robert Bakewell

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"Father of modern animal husbandry." Improved Leicester sheep (and created New Leicester breed) and Longhorn cattle. Used linebreeding. Let out his rams for breeding, observed which had the best progeny, then bred those for his own herd.

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Tandem Selection

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Selecting only 1 trait for one generation, and then selecting a different trait the next gen. Useful when you urgently need to improve 1 trait and the other traits only need minor improvement. But the traits cannot be negatively correlated or they will undo each other.

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Independent Culling Levels

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When selecting for more than 1 trait at a time, it's the minimum standard for performance. If an animal doesn't meet the standard it is not bred. Used by breeders informally to check for "functional defects" before breeding. Efficient if defects are rare. Used when it's too expensive to measure a trait on all the animals.

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Selection Index

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Score of genetic merit of an animal based on its own records or relatives' records. Like a GPA, animal can compensate for poor performance in one trait by excelling in another. Traits weighted by economic importance.

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BLUP

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Best Linear Unbiased Prediction. Created by Charles Henderson.

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Genomic Selection

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Selection based on genetic markers. Can calculate Genetic-estimated Breeding Value. Can select and breed animals right away instead of waiting to see how their progeny do. Disadvantage is less reliability because the bulls are changed so often.

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Direct markers

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When the gene itself is the marker for genomic selection. Rare. This becomes Genotype-Assisted Selection. Gets a better Response to Selection, helps sort progeny.

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Indirect markers

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When a closely linked gene is the marker for selection. Using SNPs and reference population. Becomes Marker-Assisted Selection

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Reference population

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A population with a known genotype used to find associated genotypes on the SNP chip, then used to estimate GBV for animals with unknown genotype.

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Team Reliability

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1-(1-ave reliability of individuals/# of total animals)

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Complete dominance

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When the Yy is expressed the same as YY

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Partial/Incomplete dominance

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When Yy is almost midway between YY and yy, but looks closer to YY. For example, red + white flowers = pink flowers

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Codominance/No dominance

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When Yy is exactly halfway between YY and yy. Red + white flowers = Red and white flowers

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Overdominance

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When Yy expression is outside what YY or yy look like, but still is closer to YY. Example with sickle cell anemia. YY has no sickle cell or malaria resistance. yy has sickle cell, but has malaria resistance as well. Yy has no sickle cell but has resistance, so it's superior.