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Plant & Animal Genetics
MBG*2400 University of Guelph
109
Microbiology
Undergraduate 2
12/07/2014

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Cards

Term
Additive genetic component (σA)
Definition
A component of genotype. A measure of the sum of effects of allels working together. The only component that is inherited.
Term
Allele
Definition
Different versions of a loci. A dominant allele is represented by a capital letter and the recessive by a lower case letter.
Term
Anonymous marker panel approach
Definition
An approach to QTL detection. A panel of markers is developed. Then multiple markers are used to scan a region, chromosome, or genome. Uses high density marker panels.
Term
ANOVA
Definition

ANalysis Of the phenotypic VAriance

A regression based method of testing for significance. If Pr>F is less than 0.05, there is significance.

Term
Artifical selection
Definition
Selection controlled by humans. Goal oriented towards an animals' appearance, use, productivity, or even just whimsy.
Term
Avian sex determination
Definition

Male birds have two Z chromosomes: ZZ

Female birds have one Z chromosome: Z_ (sometimes written as Zw

Term
Biddability
Definition
A CARAT trait for guide dogs. How well a dog does the bidding of a human.
Term
Binary trait
Definition
A threshold trait with two classes. A yes/no situation. Example: diabetes.
Term
Bottleneck
Definition
Moderate pressure natural selection. Cheetahs had a large bottleneck 10 - 15 thousand years ago. Cheetahs are all closely related.
Term
Calving ease
Definition
A quantitative trait. Categorized into unassisted, easy pull, hard pull, and surgical.
Term
Candidate gene approach
Definition
An approach to QTL detection. A gene is selected for physiological or biochemical reasons, and the polymorphism is detected within the gene. One at a time, selective, and targeted searching. Carefuly organized and tedious.
Term
CARAT traits
Definition
Traits that are looked for in service dogs. Determined using a series of 36 tests. Dogs are scored by their performance.
Term
Confidence with other dogs
Definition

A CARAT trait for service dogs.

h2 = 0.26

Term
Confidence with people
Definition

A CARAT trait for service dogs

h2 = 0.17

Term
Conformation final score
Definition

A phenotype looked for in cattle. Includes rump, feet, and legs.

h2 = 0.21

Term
Counting method
Definition
A method of calculating allele frequency. The genotypes of individuals are counted up, and the alleles counted. Population must be small enough to ount and the genotype of all individuals must be known.
Term
Cross country
Definition

A racing event for horses with fixed obstacles. Success in this competition is a hertiable trait.

h2 = 0.41

Term
Cross-dressing roosters
Definition
An example of sex-limited inheritance. All hens show characteristic hen feathering. Cocks with a dominant H allele (HH or Hh) show hen feathering. Homozygous recessive cocks (hh) show characteristic cock feathering.
Term
Cull
Definition
The genetic equivalent of death in artificial selection. It may be slaughter, neutering, or preventing that animal from breeding.
Term
Cut-off point (t)
Definition

aka Truncation point

In quantitative trait selection, the point in the phenotypic sliding range where individuals survive or are culled.

Term
Detection of carriers
Definition

Calculating the probability that a dominant phenotype individual is heterozygous without a test cross, where the individual mates randomly.

P = [f(AA) + 0.75f(Aa) + 0.5f(aa)]n

Term
Dominance genetic component (σD)
Definition
A component of genotype. A measure of combined dominance effects of individual loci.
Term
Draft horse
Definition
The genetic differences between large horses and small horses is one section of the genome.
Term
Drip loss
Definition
The loss of water from meat while in storage. If it is really bad, the meat can become concave. It is a heritable trait in pigs.
Term
Easy pull
Definition
A class of calving ease. Cow needs a small amount of assistance in birth.
Term
Environment (σE)
Definition
A component of phenotype. The conditions in which the genotype is expressed. Changes to this factor (altering diet, habitat, et cetera) are reversible.
Term
Epistasis
Definition
When alleles at one locus effect the expression of alleles at a different locus. Example: a white cat has a genotype of W_, and a genotype of ww allows other colour patterns to express.
Term
Evolution
Definition
Subtle pressure of natural selection.
Term
Extinction
Definition
Massive pressure natural selection.
Term
Fat percentage
Definition

A phenotype in cows.

h2 = 0.5

Term
Fat yield
Definition

A phenotype in cows.

h2 = 0.34

Term
Feet and legs conformation
Definition

A phenotype in cattle

h2 = 0.12

Term
Fertility
Definition

A phenotype in cattle

h2 = 0.07

Term
Fitness (w)
Definition
The suitability of an animal's phenotype to its environment, be that a natural or artificial environment. Expressed as a fraction representing how many of the individuals with that phenotype will reproduce.
Term
Gaited horse
Definition
A horse with a particular way of running where the horse's back does not move up and down as much. There is genetic basis for this phenotype.
Term
Genotype (σG)
Definition

A component of phenotype. Many loci contribute to it. Changes to this factor (breeding), are permanent.

σGσAσDσI

Term
Genotyping
Definition
Determining the genotypes of individuals. The challenge is to decrease the cost per genome, and increase the number of loci. Can be expensive.
Term
Gold/silver chicken sexing
Definition
A method of maxing determining the sex of chicks easier. A silver hen (S_) is crossed with a gold cock (gg). All the female chicks will be gold (g_) and all the male chicks will be silver (Sg).
Term
Hard pull
Definition
A class of calving ease. Cow needs a large amount of assistance in birth.
Term
Hardy-Weinberg equilibrium
Definition

Population must be large with random mating, and lack migration, mutation, and selection. All allele and genotypic frequencies remain constant

1 = p2 + 2pq + q2

Term
Herd life
Definition

A phenotype in cattle

h2 = 0.1

Term
Heritability (h2)
Definition

The portion of total variance that is additive genetic. Half is transmitted to offspring

h2σA2 / σP2

Term
High density marker panel
Definition
A device used in anonymous marker panel approach of QTL detection. Photo etches 50,000 - 1,000,000 markers onto a glass slide, building "velcro" tags that "grab" matching DNA. The grabbed areas light up, thus genotyping the individual. A thousand times cheaper, and faster than PCR method.
Term
Highland cattle
Definition
A cattle breed bred to survive harsh environments. Smaller size, thicker coat. Can survive rough conditions on marginal feed.
Term
Holstein
Definition
A cattle breed bred for high milk production. Require high quality feed to produce milk at the rate they do. Prevalent in the dairy industry.
Term
Horned/polled sheep
Definition
An example of sex-limited inheritance. Homozygous deominant (PP) sheep are horned. Homozygous recessive (rr) sheep are polled. Heterozygous ewes (Pp) are polled, and heterozygous rams (Pp) are horned.
Term
i
Definition

i = S / σP

Depends on the proportion of the population selected in quantitative trait selection. Use the standard distribution curve table to find values based on the S value (portion of the population that is selected).

Term
Inheritance
Definition
A factor affecting QTL detection. Crosses of divergent lines (looking for multi-modal distribution), offspring-parent resemblance (deviation from the parent average), and segregation analysis (expected inheritance using pedigree).
Term
Imprinting
Definition
Genes expressed only if they are inherited from a particular parent (from the mother or father). One of the parent's genes is destined to be inactive because of their sex.
Term
Interaction genetic component (σI)
Definition

aka Epistasis

A componenet of genotype. A measure of the combined interactions between loci.

Term
Johanna Rag Apple Pabst
Definition
A bull who is the ancestor of 99.5% of all Canadian Holsteins. Came from Quebec, but lived in Guelph.
Term
Large population
Definition
One of the requirements for Hardy-Weinberg equilibrium. Populations must be large enough to maintain Hardy-Weinberg equilibrium. Generally too arge to count all individuals.
Term
Lethal allele
Definition
An allele with an s value of 1. May actually be lethal to the animal, causing abortion or early death, or just that humans cull every single individual carrying the allele.
Term
Linkage
Definition
When two or more loci are on the same chromosome.
Term
Mammalian sex determination
Definition

Female mammals: XX

Male mammals: XY

Term
Marker
Definition
Unimportant polymorphisms that occur nearby to QTL, so recombine with the QTL. They often have no genotypic effect on the phenotype. Used to locate QTLs. If the marker and QTL are separated by recombination, then it is useless.
Term
Mass selection
Definition
Used when there are many progeny, such as in fish or poultry.
Term
Mean (X bar)
Definition

aka Average

X bar = (Σ xi) / n

Term
Meishan pig
Definition
A pig that produces very large litters up to 30 piglets! The large litter size is due to a single SNP in the NCOA1 gene.
Term
Melanocytes
Definition
Cells that produce fur pigments in cats. They also affect the electrical transmission of electrical signals from the ear to the brain. As a result, white cats are often also deaf. White cats are only deaf if they have blue eyes. If just one eye is blue, the cat is deaf on that side.
Term
Mendelian Genetics
Definition

aka Classic genetics

Crossing two heterozygoes (Aa x Aa) gives 1AA : 2Aa : 1aa

Term
Migration
Definition

One of the limits of the Hardy-Weinberg equilibrium. The alleles move from one population to another. May be due to climate change, human activities, or humans shipping germplasm. Depends on the immigration rate and the difference in allele frequencies betwen the populations.

P' = allele frequency in migrant population

M = percentage of population that are migrants

P' = p1 + m(p2 - p1)

Term
Milk yield
Definition

A phenotype in cows

h2 = 0.43

Term
Mutation
Definition
A limit on Hardy-Weinberg equilibrium. New alleles are created. Most mutations are recessive. If the mutation phenotype has fitness at or above that of the wild type, the mutation will not go away.
Term
Natural selection
Definition
Selection by the environment. Individuals must adapt to the environment or perish. Includes evolution, bottlenecks, and extinction.
Term
P
Definition
The selected portion of the parent population in quantitative trait selection.
Term
PCR
Definition

aka "genetic horserace"

Endonuclease cleaves DNA at specific sequenes and then is put in a gel to determine genotype. Slower and more expensive than high density marker panels.

Term
Persistence with other dogs
Definition

A CARAT trait.

h2 = 0.16

Term
Phenotypic variance (σP2)
Definition
σP= (σA2 + σD2 + σI2) + σE2
Term
Phenotype (σP)
Definition
Determined by a combination of genetics and environment.
Term
Phenotypic selection
Definition
Selection for quantitative traits. Selection based on phenotype. Indirectly influencing allele frequency. Tracking progress by change in phenotype.
Term
Pleiotropy
Definition
When one locus affects two or more traits. Example: white cats are often also deaf.
Term
Polymorphism
Definition
A differene in alleles. Example: SNPs.
Term
Population design
Definition
A factor affectin QTL detection. Inbred line crossing, and outbred populations.
Term
Proportion method
Definition

A method of calculating allele frequency. The genotypes of individuals are counted.

f(AA) = P

f(Aa) = H

f(aa) = Q

f(A) = P + 0.5H

f(a) = Q + 0.5H

Term
Protein percentage
Definition

A phenotype in cows

h2 = 0.5

Term
Protein yield
Definition

A phenotype in cows.

h2 = 0.4

Term
Qualitative trait
Definition
Controlled by one or few loci. Discrete phenotypes. Traits are selected with single locus selection. Easy to predict if the allele frequency is known. Genotype can be determined in a lab.
Term
Quantitative trait
Definition

aka Polygenic trait

Controlled by multiple loci, up to thousands. Most of the loci have small effects on the phenotype, so are difficult to pinpoint. Some of the loci may have a larger effect on phenotype, so may be located. Phenotypes occur on a continuous sliding scale. Include threshold traits. Traits are selected wth phenotypic selection.

Term
Quantitative triat locus (QTL) detection
Definition
Finding polymorphisms in a genome that is associated with a distinctive difference in phenotype. Can be complicated. Often QTL are discovered using markers. Two methods: candidate genes, and anonymous markers. Affected by inheritance and population design.
Term
Race earnings
Definition

A phenotype in horses

h2 = 0.25

Term
Racing speed
Definition

A phenotype in horses

h2 = 0.25

Term
Random mating
Definition
One of the requirements for Hardy-Weinberg equilibrium. All allele frequencies remain constant. This generally excludes human populations because random mating is not socially acceptable in human societies.
Term
Red & White spotting
Definition
An example of sex-influenced inheritance in Shorthorn cattle. Homozygous dominant (RR) cattle have red and white spotting. Homozygous recessive (rr) cattle are white. Heterozygous (Rr) cows are red and white spotted, and heterozygous (Rr) bulls are white.
Term
Response (R)
Definition

In quantitative trait selection, the deviation of the progeny from the original population average

R = [average of offspring] - [average of parent population (including unselected)]

Term
Rump conformation
Definition

A phenotype in cattle

h2 = 0.23

Term
SAS analysis
Definition
A computer program that determines how well a model fits with the observed phenotypes. The smaller the Pr>F value, the more likely the model is valid.
Term
Secretariat
Definition
A racehorse who won races by a large margin. Lived in 1973. Turned out he was not above average in speed, but just looked fast compared to the other horses.
Term
Selection
Definition

A limit of Hardy-Weinberg equilibrium. The process which determines which individuals will become parents of the next generation. Includes natural and artificial selection. Allele frequencies are altered.

p1 = (p0(1 - s1q0) / (1 - 2s1p0q0 - s2p02)

Term
Selection differential (S)
Definition

In quantitative trait selection, the average of selected parents deviated from the population mean.

S = [average of selected parents] - [average of parent population]

Term
Selection pressure (s)
Definition
How many individuals in a phenotype survive and become parents.
Term
Sex-influenced inheritance
Definition
Heterozygoes express a different phenotype in males than in females.
Term
Sex-limited inheritance
Definition
Phenotypes can be observed only in one sex. Sexes may not even possess the necessary body parts for certain phenotypes.
Term
Sex linkage
Definition
When a gene is found on a sex chromosome.
Term
Show jumping
Definition

A phenotype in horses

h2 = 0.45

Term
Significance
Definition
When Pr>F is less than 0.05. The hypothesis will be incorrect 5% of the time.
Term
Single locus selection
Definition
Selection of qualitative traits. Selecting based on alleles. Directly influencing allele frequency. Track progress with allele frequency.
Term
Single nucleotide polymorphism (SNP)
Definition
Pronounced "snip". A single change of base in DNA.
Term
Social interactions with people
Definition

A CARAT trait for service dogs.

h2 = 0.47

Term
Standard deviation
Definition
The square root of variance.
Term
Surgical
Definition

aka Mal-presentation.

A class of calving ease. Cow needs surgery in birth. Calf pushed back, turned around, and then pushed out the right way.

Term
Test cross
Definition
Crossing a dominant phenotype indiviual with a recessive phenotype individual. If any of the offspring have the recessive phenotyp, the individual is heterozygous.
Term
Threshold trait
Definition
Quantitative traits that are categorized into discrete groups on the sliding scale. Includes calving ease and binary traits.
Term
Ultimate selection pressure
Definition
In qualitative trait selection, when one allele has a fitness level of zero in both homozygous and heterozygous forms. By the second generation, the allele frequency is zero.
Term
Unassisted
Definition
A class of calving ease. The cow gives birth without any human help.
Term
Variance (σ2)
Definition

The measure of diversity and variety in a phenotype. The square root of variance is standard deviation.

σ2 = (Σ (x - x bar)2) / (n - 1)

Term
Visual reactivity
Definition

A CARAT trait in service dogs.

h2 = 0.18

Term
Whining
Definition

An unwanted CARAT trait in service dogs.

h2 = 0.06

Term
Z
Definition
The height of the standard distribution curve at the cut-off point.
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