Term
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Definition
| Represents marker alleles at a marker locus. |
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Term
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Definition
| A component of genotype. The goal is to determine it as accurately as possible. A measure of the sum of effects of individual alleles. Genes working together. The only component of genotype passed on in genetics. |
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Term
| Anonymous marker panel approach |
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Definition
| A common way to develop marker locations in QTL detection. Develop a panel of multiple markers, and scan the region, chromosome, or genome. |
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Term
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Definition
| A method of calculating heritability. There are three cases: half sibs, full sibs, and full and half sibs. |
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Term
| Average allele effect (α) |
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Definition
| Originally called allele substitution effect. The difference between α1 and α2. A population concept. Measure the average allele effect within a population. Can infer the effect of an alelel for an individual after measuring it in the population. The average affect on the phenotype of an allele at this locus. Not a molecular genetics concept; the term was invented before transgenics. Animals must be genotyped to determine α, or we can measure the average value of an individual's progeny. Based on the amount by which it differs from the midpoint of all alleles, and the number of alleles. More common alleles have greater impact on phenotype. |
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Definition
| A supersonic fighter jet designed by Canadians. |
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Definition
| Slope of the offspring-parent regression. |
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Definition
Tests outbred populations. An ANOVA/regression based model. Simlpe t-test average.
Trait phenotype = mean + genotype + residual |
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Definition
| Quantitative traits include growth rate and calving ease. |
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Term
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Definition
| Before Europeans came to North America, there were more bison than there are cows in North America today. So it is unlikely that cattle are generating significant amounts of greenhouse gasses. |
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Definition
| Interactions are not independent. A group of loci that have interactions with each other. |
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Term
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Definition
| The sum of allele effects for a genotype. Depends on allele frequencies and range of phenotypes associated with each genotype. Average BV is always 0, since the population mean is removed in calculations. If both homozygotes have the same proportion in the population, their breeding values are the same. Used in dairy breeding. Select animals with the highest breeding values. Represents the proportion of the animal's genome which is passed on. Used to predict phenotypes of the next generation. |
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Term
| Broad sense heritability (H2) |
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Definition
| Proportion of total variance that is genetic. |
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Term
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Definition
| A common way to develop marker locations in QTL detection. Select a gene for physiological or biochemical reasons, identify it as a polymorphism within the gene. One at a time, select and target. |
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Term
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Definition
| Have a short generation time, so often mass selection is used in breeding programs. Colour of the egg has no effect on its quality. |
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Term
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Definition
| When the heterozygote phenotype is an intermediate of both homozygous phenotypes. |
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Definition
| An ancestor which is an ancestor to both parents of an individual. Must have at least two descendants. |
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Term
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Definition
| Similarity to the ideal individual of the variety. Looks at height, muscle structure, and bone structure. |
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Term
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Definition
| Response when we select for another trait. Happens when traits are controlled by some of the same loci. Useful for predicting responses for traits which are hard to measure. Example: height and weight. |
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Definition
| Increases additive variance. Breeding with individuals from other populations. Produces heterozygous hybrids. |
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Definition
Karyotype
Locates genes on chromosomes using FISH. Anchors linkage maps. |
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Term
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Definition
| Quantitative traits include milk yield, protein yield, and conformation. |
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Term
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Definition
| A gene which cost $5 million to sequence. It was on chromosome 14. A polymorphism in the non-coding region, slowing transcription of all alleles. |
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Definition
| Prof. Robinson's old Norfolk terrier. He was not aggresive enough to compete in agility competitions. |
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Definition
| Response when we select for a trait. |
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Term
| Diurnal height difference |
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Definition
| People are taller in the mornings. Remove this effect by measuring everyone's height at the same time of day. |
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Term
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Definition
| Quantitative traits include conformation and trainability. |
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Definition
| A component of genotype. Specific to the animal, and is not passed on. A measure of the combined dominance effects of individual loci. |
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Definition
A really good name for a donkey farm that also has beehives.
*HINT* = this will be the bonus question |
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Term
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Definition
| Prof. Robinson's old Norfolk terrier. Short for "dilemma". |
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Term
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Definition
A component of phenotype. Has significant influence on phenotype. Make muleiple measurements of the phenotype to determine if it is permanent or temporary. All individuals in an area may be affected by one environmental factor.
Environment = Permanent + Temporary |
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Term
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Definition
| May change the way alleles are expressed. |
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Term
| False Discovery Rate (FDR) |
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Definition
| The probability that a hypothesis is right. Usually set at 5% threshold for analysis. Derived by sampling variance. Where the line goes above the FRD line, there are QTLs. |
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Term
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Definition
| A small number of loci with large individual effects. More interest in each individual locus. Selection alters frequencies at specific loci in larger increments. Phenotype depends on genotype and environment. |
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Term
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Definition
| The only type of animal which does not have paternal hierarchy. |
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Definition
| Locates specific genes in a karyotype. Create a probe with a fluorescent protein attached to it. |
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Term
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Definition
| All the wool removed from a sheep in the spring. It grows back in time for winter. |
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Term
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Definition
Case 3
An ANOVA method of calculating heritability. Each sire is mated to d dams, and there are n progeny per dam.
h2 = (2(σ2s + σ2dam)) / (σ2e + σ2s + σ2dam) |
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Term
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Definition
| Share half of their genomes, but there is a chance that they have inherited the same alleles at some loci, producing dominance. |
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Term
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Definition
Case 2
An ANOVA method of calculating heritability. Each sire is mated to 1 dam, and there are n progeny per dam. Applies to litter-bearing species.
h2 = 2σ2sire / (σ2sire + σ2e) |
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Term
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Definition
| Separates DNA pieces. An older method of genotyping. Not useful for genotyping large populations. |
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Term
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Definition
| The amount of time for one generation. Average age of parents when offspring are born. In cattle, 4 - 7 years. In poultry, less than a year. In pigs, 1 - 2 years. In humans, 25 - 35 years. |
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Term
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Definition
| The change in genotypic variance. Normally no progress in DD, because it depends on frequency of heterozygotes. All progress is usually in BV, if selection is for one allele. Always in relation to generation 0. |
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Term
| Genetic response for length of time (ΔR) |
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Definition
| The genetic response for the length of time required for one generation. |
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Term
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Definition
A component of phenotype.
Genotype = Additive + Dominance + Interaction |
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Term
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Definition
Breeding value plus dominance deviation.
G = A + D |
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Term
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Definition
Frequency of genotypes added up to one, and each breeding value or dominance deviation is already deviated from a mean of zero.
GV = BV + DD |
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Term
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Definition
| Individual locus genotyping. Can be done using PCR. |
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Term
| Haldane's Mapping function |
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Definition
Assumes no interference between loci.
C = ½ (1 - e-2m) |
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Term
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Definition
Case 1
An ANOVA method of calculating heritability. Each sire is mated to n dams, and there are 1 offspring per dam. Applies to single-birth species.
h2 = 4σ2sire / (σ2sire + σ2e) |
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Term
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Definition
| A unit of measurement equal to 4 inches. The height of the ground to a horse's withers is its height, usually measured in hands. |
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Term
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Definition
| Found in gametes. One allele per loci. Only the addirive part of the genotype. A summary of many markers. Part of the analysis of markers. |
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Term
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Definition
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Term
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Definition
Normal heritability
Proportion of total variance that is additive genetic. Half is transmitted from parent to offspring. Indicates the degree of genetic resesmblance between relatives and generations. Helps define how much genetic change would result from selection. Two methods of estimation: regression of Offspring (y) on Parent (x), and ANOVA analysis of phenotypes of specific relatives. To increase heritability, measure phenotype more accurately to reduce σE2, or increase additive variance by cross-breeding. Systematic changes due to environmental trends, inbreeding dpression, random shift, or small populations can affect estimates of heritability. Has no units: it is a ratio of two variances. Typically ranges from 0 to 0.5. If greater than 0.5, there is probably something affecting the result. |
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Term
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Definition
| Cross-breeding. Erases all accumulated homozygosity. |
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Term
| High density marker panel |
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Definition
| Photo-etched glass slides with "velcro" tags that grab matching DNA. Repeats 50 thousand to a million times! Grabbed DNA lights up spots to reveal the genotype. A canine chip has 38,000 genes. |
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Term
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Definition
| Over 35%. Includes size, stature, and fatness. |
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Term
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Definition
| The offspring of a donkey jenny bred to a stallion. Mitochondrial DNA is that of a donkey. |
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Term
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Definition
| A breed of dairy cattle. Average fat yield is 3.6 - 3.7%. The top 100 Holstein bulls are deemed so based on MAS genotyping. |
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Term
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Definition
| Quantitative traits include racing speed and temperament. |
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Term
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Definition
A combination of infinitesimal and finite locus models. Looks at individual loci, and quantitative approach. A few loci of large effect and many loci of small effect. Looks at allele frequencies, and contributions of each individual loci. Phenotype is a combination of expression of large effect of few individual loci and small effect of many loci.
R = h2 + BV |
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Term
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Definition
| There are health problems, leading to fertility issues. Has less impact in litter-bearing species. |
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Term
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Definition
| When the heterozygote phenotype is an intermediate of both homozygotes, but closer to one of the homozygous phenotypes. |
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Term
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Definition
| If all loci involved in genetic variation are independent of each other, then BV, ETA, σ2A, and σ2D, at the phenotypic level are the sum of effects at individual loci. Occurs if the loci are unlinked, or have no interactions. |
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Term
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Definition
| Analyze the effect of an individual locus on phenotype. Assume the locus works in conjunction with polygenes. Look at the allele effects individually: additive and dominance effects. Determine the incremental contributions of a locus to the value of an individual's genotype. Determine the incremental contribtions of this individual as a parent of the next generation. |
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Term
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Definition
A large number of loci with small individual effects. Doesn't worry about each individual locus. Selection alters frequencies at many loci in small increments. Phenotype depends on genotype and the environment.
R = Sh2 |
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Term
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Definition
| A species with few or no crossover events in its entire genome. |
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Term
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Definition
| A Canadian invention, developed by scientists Banting and Best. |
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Term
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Definition
Epistasis
A component of genotype. Specific to the animal, and is not passed on. A measure of the combined interaction of all loci. |
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Term
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Definition
| Two loci close together have less likelihood of recombination. |
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Term
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Definition
| A breed of dairy cattle. Average fat yield is 4.5%. |
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Term
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Definition
Allows for some interference between loci; non-random recombination. More conservative than Haldane's mapping function.
C = 0.5(e4m - 1) / (e4m + 1) |
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Term
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Definition
| Prof. Robinson's old Norfolk terrier. Won agility competitions and was very intelligent. |
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Term
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Definition
| A breed of chicken. Lays white eggs. |
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Term
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Definition
Linkage groups based on lists of linked genes. Linear oder, and statistical differences. Determine differences between markers by pairwise distances. Based on statistics, assuming constant recombination rate across the map. Accuracy is affected by things that affect crossover rates: location on a chromosome (telomeres and centromeres have lower crossover rates), sex, and species. The computer arranges markers by linkage disequilibrium, looking at recombination rates.
1. Genotype multiple markers on the same chromosome.
2. Calculate all possible pair-wise distances.
3. Determine marker order based on distances. |
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Term
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Definition
| Dependent on the average for the breed, and the individual. There are may factors that affect litter size. In pigs, NCOA1 can increase litter size. |
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Term
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Definition
| 0% - 15%. Includes health, reproduction, fitness, behaviour. |
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Term
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Definition
| Represents marker loci. It is located inside the coding region, so that it is present when the gene is coded correctly. |
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Term
| Marker assisted selection (MAS) |
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Definition
| A new technology. Only 5% of big effect loci can be found with statistical significance. Genotyping individuals for many loci to calculate breeding value. Uses marker loci. The marker genotype is used to select individuals with the best linked QTL alleles. Used for traits wih low heritablity, sex-limited traits, traits that require the animal to die to be measured, and traits expressed later in life. Increases genetic progress with intensity, accuracy, variation, and time. Results vary; there may be less response or up to 50% in response. A 2 - 5% cost for hte same response; uses resources better, measures phenotypes only in the best potential candidates, and reduces generation interval. Standard procedure in major livestock species: dairy, beef, pigs. Can cost $100 - $300 per animal. Scientists must continue to find markers for selection purposes. |
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Term
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Definition
| A permanent environmental impact that causes damage to the udder, affecting milk yield for the cow's entire life. |
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Term
| Maximum likelihood based model |
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Definition
| Tests outbred populations. Calculate the most likely of the value of each allele given the observed phenotypes. |
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Term
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Definition
| 15% - 35%. Includes milk yield, protien yield, growth rate, feed intake, trainability, fat yield, and speed. |
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Term
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Definition
| A pig breed. Produces many piglets, up to 32! A good fat source. There was an import of Meishan pigs to North America in the 1800s, so some of their genes are found in Western pig breeds. |
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Term
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Definition
| Produces additive genetic variation, producing progeny that are not identical. Recombination during meiosis prophase. Can estimate Mendelian sampling components for large groups of progeny. The difference between the genetic value and mean expectations. The reason that siblings are not identical; sampling of genes when gametes are produced. |
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Term
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Definition
| "Stutters" in the DNA. Used to be popular. Highly polymorphic, and expensive to locate. |
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Term
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Definition
| The average of the phenotypes of both parents. |
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Term
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Definition
| A quantitative trait in dair. Has doubled over the last 50 years. Factors that affect it include appetite, digestive efficiency, and udder size. If you feed a good cow poorly, milk yield will be low. Can be measured in only one sex. As milk yield increases, lifespan of the cows decreases. |
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Term
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Definition
| Inherited only from the mother. Part of the function for internal temperature. |
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Term
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Definition
| A method of calculating heritability. Accounts for related animals in the population structure. |
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Term
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Definition
| Figures out what genes are present. |
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Term
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Definition
| Used in parentage testing, pedigree verification, DNA fingerprinting, studying similarities, differences, and diversity. Used to map major genes with qualitative and quantitative effects, and in selection decisions based on genotypes to introgress genes into a population. Select a gene as a candidate for study, and sequence the information. Scatter markers across a chromosome/genome; anonymous markers (high density SNP panels), no presumed connection to any function or trait. Comparative studies using well-documented species and homology to look for markers known in other species in your species of interest. Rare for a marker to be in a coding region, usually in an intron or promoter region. If it is in the gene, it doesn't affec the expression. |
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Term
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Definition
| The distance of DNA at which there is an average of one recombination event per meiosis. The human and pig genomes have about 3,300 cM. |
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Term
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Definition
| The offspring of a mare bred to a donkey jack. Mitochondrial DNA is that of a horse. |
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Term
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Definition
| A gene with a polymorphism that distinguishes Mieshan pigs from Yorkshire pigs. Associated with a slight reduction in piglet birth weight. No significant association was found with litter size, but lighter piglets suggests a slight increase in litter size. The gene is required for ovulation. Located on the short arm of chromosome 3. Associated with oocyte number; upstream from a gene for estrogen. |
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Term
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Definition
| Produce small litters because the puppies are large in comparison to the mother. |
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Term
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Definition
| A small racehorse who sired many progeny. |
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Term
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Definition
| Inherited from the father and the mother. |
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Term
| Offspring/midparent regression |
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Definition
| A type of regression used to calculate heritability. |
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Term
| Offspring/parent regression |
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Definition
| A type of regresion used to calcualte heritability. |
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Term
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Definition
| When the heterozygote phenotype exceeds both of the homozygous phenotypes. |
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Term
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Definition
| When males are selected much more than females are. Due to AI or increased fertility. |
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Term
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Definition
| Detects a difference in DNA sequence for genotyping. Restriction endonucleases cleave the DNA at specific sequences. The DNA fragments are separated. Differences are coded as alleles. |
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Term
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Definition
| A component of environment. Specific to the animal, and is not passed on. |
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Term
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Definition
What we observe. A function of genetics and the environment.
Phenotype = Genotype + Environment |
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Term
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Definition
| Change in G and E. Assume no change in E, unless specified. Change in G is a change in GV. Always in relation to generation 0. |
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Term
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Definition
| Quantitative traits include litter size and growth rate. |
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Term
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Definition
| A breed of chicken. Lays cream eggs. |
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Term
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Definition
| It is good to have some structure in the population, which can be incorporated into analysis. |
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Term
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Definition
| Reversed DNA that sticks to sequences in teh genome. A slow, expensive method to genotype. |
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Term
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Definition
| Represents the QTL. In most cases we never know what it is. Expensive to sequence. |
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Term
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Definition
| Uses include medial research, livestock improvement, ecology and evolution studies, and companion animals. The goal is to find a polymorphism in the genome associated with a distinct difference in phenotype within the region of the genome that is used as a marker. Concept is simple, but execution can be complex. Molecular genetic tools are used. Genotyping individuals for the marker locus, develop a method to visualize the DNA sequence. Early work used blood groups and proteins, but this was limited by antibodies. Develoepd a primer and enzyme combination to identify the target sequences containing polymorphisms, and to cleave the DNA to visualize it as fregments with different molecular weight. The challenge is to increase the number of loci, and reduce cost per genotype. All methods come down to comparing individuals with MM to individuals with mm. If the QTL and marker are linked, the comparison is equivalent to comparign QQ with qq. Can be affected by inheritance and population design. |
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Term
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Definition
| Uses marker genotypes to select superior individuals. |
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Term
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Definition
| Can be quantified. Controlled by many loci. The degree of how loci affect phenotypes, and how they are inherited varies. Selection process is slower; not able to identify one good genotype. No specific gene or phenotype. Includes behaviour, and intelligence. Some are easier to measure, like milk yield. |
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Term
| Quantitative trait locus (QTL) |
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Definition
| A chromosome region controlling part of a trait. Not necessarily a gene. Most are discovered using markers. Usually an "unimportant" polymorphism. They normally do not genotype the QTL itself. |
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Term
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Definition
| Created statistical tests. |
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Term
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Definition
| Many factors affect this trait. A horse can have a good training experience that causes its racing speed to increase. |
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Term
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Definition
| Has differential recombination rates by sex. |
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Term
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Definition
| Generation response mean v.s cumulative selection differential. Classical selection experiments can estimate it. Another way to calculate heritabiltity. Add response over all generations, add selection overall generations, and find the ratio. It may take a long time to finish the experiment, and there may be problems with doing such long-term experiments. |
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Term
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Definition
| Occurs less in telomeres and centromeres. |
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Term
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Definition
| Determines how related two variables are. Includes offspring/parent and offspring/midparent. |
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Term
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Definition
| The chance of getting the same phenotype again from the same individual. The proportion of the phenotypic variance that is due to permanent effects unique to the individual. The same phenotype is expressed by the same animal. Can never be a negative number because it is based on variances. Range is 0 - 1. A value of 1 indicates that temporary factors have no effect; almost nothing has a repeatability of 1. A value of 0 indicates that there is no genetic influence at all; only environmental effect. Can use it to preduct future phenotype, based on past observations. |
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Term
| Response to selection (R) |
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Definition
| Deviation of progeny from the original population average. Units are the same as phenotype. To increase R, increase S or increase h2. Negative if the breeding program is trying to decrease phenotype. |
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Term
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Definition
| A breed of chicken. Lays brown eggs. Eggs are slightly larger. |
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Term
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Definition
| A horse that had huge stride length. A successful racehorse. |
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Term
| Selection differential (S) |
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Definition
| Average of selected parents, deviated from the population mean. Units are the same as phenotype. To increase S, select fewer individuals, but watch out for inbreeding. Use a standard normal distribution to find S for all possible situations. Negative if the breeding program is trying to decrease phenotype. Does not assume normality. |
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Term
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Definition
| Developed early methods for calculating relatedness. |
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Term
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Definition
| It is accounted for in offspring-parent regressiosn by using the midparent. |
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Term
| Single nucleotide polymorphism (SNP) |
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Definition
| A type of marker. The most popular, most common, least expensive marker. Used currently. It is correlated with phenotype, but may not cause the phenotype. |
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Term
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Definition
| A glass media with tiny "fingers" of DNA that attach to matching DNA, which show as fluorescent blue, yellow, or red spots. Can genotype 38,000 SNPs in one pass. |
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Term
| Standardized selected differential (i) |
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Definition
| Depends on proportion of population selected, if we standardize the distribution. Used to represent selection intensity. The mean value of p. Assumes normality. |
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Term
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Definition
| A trait which is hard to measure; cannot breed animals after you measure lifespan. A correlated response is measured. In cows this could be milk yield. |
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Term
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Definition
| Created in 1949, to calculate relatedness of many individuals. At the time there were no computers to use for this. |
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Term
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Definition
| A component of environment. |
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Term
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Definition
| Half the value of the breeding value. A measure of what is passed on to offspring. Used in beef breeding. |
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Term
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Definition
| The minimum phenotype in the selected group. |
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Term
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Definition
Large White
A common pig breed in the Western world. A good meat source. |
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