Genetics

Explain how dairy bull progeny testing schemes work in nz

-LIC wants a minimum of 70 daughters per bull spread over many farms. Sire proving scheme (where the progeny testing takes place) - there will be an exam question on this -because of importance of accurate data contracted herds are used for progeny testing- extremely important as such a small amount of sires are used through ai. -LIC contracts 400 herds (130,000 cows) collectively called the sire proving scheme -most of these herds are high performing and hold many top BV cows -All daughters are treated the same and there is no differential culling All daughters are: -herd tested -weighted (estimate of feed efficiency) -management traits (e.g. milking speed) are scored by milkers working with the daughetrs in the milking parlour -conformational traits such as teat placement are scored by trained inspectors -the management and conformation traits are collectively called Traits other than production (TOP) -bulls are also DNA tested to prove parentage and to search for recessive conditions such as BLAD -DNa tests are also available for production genes

Describe how genetic improvement is generated in the new Zealand dairy or sheep industry

-Open, dispersed, nucleus with sire referencing to link herds -80% bred to AI -Need to consider the below for each of the 4 pathways 1. selection intesnsity 2. selection accuracy 3. variation (ignore- assumed to be unchanged) 4. Generation interval Cow to cow. (minor contribution to delta G) 1. Very low selection intensity - only pathway under farmer control 2. Based on several records so relative accuracy. 4. L= 5 years Cow to Bull pathway The highest BV cows are contracted to produce bull calves - At least 2 generations of recorded pedigree to the same breed -Milk tested and inspected for conformation 1. Selection intensity high. 30k elidgible, 650 used. 2. Based on one lactation 4. L= 4 years Bull to cow/ Bull to Bull pathway. -300 Bulls generated for progeny testing -LIC wants a minimum of 70 daugheters per bull spread over many farms. 1. 6 bulls selected for the bull to bull patway. 15 selected for bull to cow so high selection intensity. .9+ 2. Selection accuracy is extremely high 4. L= 6 years for bull to bull. L= 7 years for bull to cow. Breeding value/breeding worth -BW/BV set to 0 for an average cow born in 2000 -Bull bv= ancestry information + progeny test information (+dna) -cow bv= ancestry information + own information BW= EV(milk) BV (milk) + EV(fat)BV(fat) +

4. Describe the circumstances under which indirection selection might be used

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Discuss for at least one animal disease/infection how the use of molecular genetic techniques might result in the production of superior vaccines

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Discuss the current breed composition of the national sheep flock and beef and dairy cattle herds.

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Facial eczema- present only in nz: an example of polygenic resistance to infectious diseases -Caused by saprophytic fungus pithomyces chartarum- lives on dead grass. It likes warm and moist conditions such as January- may. -ingested spores release a toxin, sporidesmin. Sporidesmin affects liver, resulting in accumulation of chlorophyll metabolites that in turn leads to photosensitivity. Sheep, cattle and deer are affected. -severe loss in production and can result in death -animal welfare issue -heritability of genetic variation is high = .4 to .6 Initial selection for reistant animals was by progeny testing based on liver damage. This was expensive. Subsequently, liver enzyme GGT had been identified as a reliable measure of liver damage -GGt levels can be used to identify susceptible/resistant animals However this test requires prior exposure of the animals to sproidesmin. This is now widely employed by commercial ram breeders High GGT= more susceptible. Liver enzyme levels go up when liver is damaged.

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KNOW TANDEM REPEATS ETC- EXAM QUESTION ON THIS.

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discuss with examples how recombinant dna techniques would be useful in improving animal health.

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What advice would you offer to a client who has asked your opinion on breeding from an animal they suspect to be carrying an undesirable gene.

1. Determine if it is even under genetic influence. There is tendency to assign all problems to genetics Ask/enquire -the web -your professional connections (he is one of them) -other breeders -literature -researchers 2. Test mating. Ethical issue for especially companion animals. What do you do with all the offspring you generate? Euthinase.. 3. Breed to non related-carefully chosen individual 4. Biochemical tets biochemical test:few genes are totally recessive in their expression. While the observable effects we can see by looking at the animal may be recessive, the biochemical or physiological pathways that contribute to what we observe may not be recessive. So at a more basic level he may be able to differentiate between heterozygous and homozygous individuals. So we tested the levels of each of the enzyme activity in the animals. Ones with lower levels of activity had one copy of the gene. For this case. examine at the macro level: recessive enzyme level: codiminance 5. Gene probes Gene probes: directly identify the different alleles at a particular locus. 6. Cost, time vs benefits. 7. Do not breed from its offspring. pleiotropy: Pleiotropy occurs when one gene has more than one observable effect. So in this case the two affects are 1. Shortened tail and 2. Death (crushing of organs) MM is normal Mm is manx. (mm) is lethal. Cat tails

List three things that should be reflected in the relative economic value of a trait included in a selection index

1. Future value of traits 2. Should reflect the timing and the number of expressions of the trait 4. Reflect appropriate emphasis of the trait

List four functions of the nz angus cattle breed society

1. Maintain breed purity (ensure adequate pedigree records are kept) 2. Promote the interests of the breed e.g. eat angus 3. Promote performance recording 4. Encourage genetic imporvement toward some objective 5. Ensure conformity to a breed type

SIMPLE MENDELIAN INHERITANCE.

1. Mannosidosis - nearly 3k angus calves affected annually in nz - lethal nervous disease - caused by a defective gene coding for lysosomal enzyme a-mannosidase - heterozygotes were normal, recessive homozygotes however lack the enzyme - individuals lacking the enzyme would die within the first year due to accumulation of an oligosaccharide containing mannose and glucosamine - initial control by test mating of potential heterozygous sires to heterozygous cows. 1 out of 4 progeny would be affected if the sire is heterozygous - however selection to eliminate a gene at low frequencies is ineffective. - Breakthrough achieved when a professor showed the enzyme levels in carriers would be half that of normal animals. - Therefore heterozygotes were identified by a blood test for a-mannosidase and eliminated from the reproductive pool. 2. Bovine leukocyte adhesion deficiency - occurs in Holstein-freisian cattle -shows simple mendelian inheritance -immunodeficiency: accepted calves susceptiable to several infections - die within 2-4 months of age -A PCR-RFLP test was developed. Since then carrier bulls and cows identified and culled 3. PROgressive retinal atrophy 4. Severe combined immunodeficiency 5. Spider lamb syndrome - either abnormal at birth or normal at birth but develop into spiderlamb at 2-6 weeks of age - failure to slow down the lengthening of long bones in the foetus - homozygous recessive condition- simple mendelian inheritance

What factors determine how accurate a breeding value is?

1. The smaller the prediction error variance (PEV), the more accurate the prediction -The greater the RTI, the more accurate the prediction 3. Depends on a) number of phenotyic records the bv is based on b) source of phenotypic records the bv is based on.

What is a selection objective

A list of traits to be improved and their relative importance. Chosen by ****know for exam 1. IMpact on profitability (in the future) 2. Heritability (but even low heritable traits may be included if they are of high enough importance The more traits you include, the slower the prgress -if correlations are unfavourable, you may need to include these too

Define the term breeding value

A measure of the genetic merit of the animal, describing value of its genes when passed on to progeny. The sum of additive values of the alleles carried by the individual that affect the quantitative trait.

Discuss the advantages and disadvantages of progeny testing

Advantages 1. Increases corrleation between true and predicted genetic merit 2. More accurate than individual selection 3. Increases accuracy with increased number of progeny 4. Reudces environmental factor if the progeny are spread out Disadvantages 1. Need multiple progeny 2. Increased cost (need to test progeny even for unsuccessful) 3. Increases L

For a genetic disease explain how moleuclar techniques would enable to reduce the incidence of the disease in herds/flocks. Write an account on the inheritance of a disease of yoru choice and suggest a breeding plan that can be employed by commercial breeders to minimise its incidence.

Facial eczema- present only in nz: an example of polygenic resistance to infectious diseases -Caused by saprophytic fungus pithomyces chartarum- lives on dead grass. It likes warm and moist conditions such as January- may. -ingested spores release a toxin. The toxin affects the liver, resulting in accumulation of chlorophyll metabolites that in turn leads to photosensitivity. Sheep, cattle and deer are affected. -severe loss in production and can result in death -animal welfare issue -heritability of genetic variation is high = .4 to .6 Initial selection for reistant animals was by progeny testing based on liver damage. This was expensive. Subsequently, liver enzyme GGT had been identified as a reliable measure of liver damage -GGt levels can be used to identify susceptible/resistant animals However this test requires prior exposure of the animals to sproidesmin. This is now widely employed by commercial ram breeders High GGT= more susceptible. Liver enzyme levels go up when liver is damaged. Measured by taking blood samples. So can identify susceptible animals/cull- take out of gene pool. especially used in ram selection. 1. Mannosidosis - nearly 3k angus calves affected annually in nz - lethal nervous disease - caused by a defective gene coding for lysosomal enzyme a-mannosidase - heterozygotes were normal, recessive homozygotes however lack the enzyme - individuals lacking the enzyme would die within the first year due to accumulation of an oligosaccharide containing mannose and glucosamine - initial control by test mating of potential heterozygous sires to heterozygous cows. 1 out of 4 progeny would be affected if the sire is heterozygous - however selection to eliminate a gene at low frequencies is ineffective. - Breakthrough achieved when a professor showed the enzyme levels in carriers would be half that of normal animals. - Therefore heterozygotes were identified by a blood test for a-mannosidase and eliminated from the reproductive pool.

Describe the functions of breed societies.

Functions of a breed society Maintain breed purity -Maintain a flock book -ensure adequate pedigree records are kept -ensure conformity to breed type Promote interests of breed e.g. eat angus pure. Promote performance recording. Try and get breeders to be measuring the animals so the breeding value for that animal actual has value.

Discuss the importance of knowing h2 traits to be selected

Heritability tells you how much genetic influence the trait is under. -If it has high heritability, you can make rapid progress through selection -if it has low heritability, progress will be slower but may still be worthwhile e.g. fertility -lower heritability indicates greater environmental variance therefore predictions of merit based on phenotype are less accurate. Before undertaking a breeding program on a trait, an animal breeder will require estimates of the extent of genetic variation and heritability of a trait Therefore important to know in choosing what trait you want to improve/make genetic improvement toward. /how long it will take. might need to try and increase the h2 for a trait?

polygenic disease

Hip dysplasia in dogs: a polygenic gene? -deformity of coxo-femoral joint during growth period which creates a poorly fitting hip joint - as the dog walks on this joint, arthritis sets in -ball and socket joint gets excessively shallow which restricts movement -potential dislocation leading to pain and animal welfare issues -hereditary condition: tends to occur in families of dogs however not a simple mendelian inheritance -complex trait involving both genetics and environment

Be able to define and calculate selection differentials.

I bar The merit of the individuals selected as parents relative to the merit of individuals available for selection in known as the selection differential. -Proportion of animals selected as parents Standardized selection differentiation (I bar) -measures how many standard deviations better than the population the selected parents are *Remember is the number you have selected is below 500, you have to -.25/s s= (number selected)

3. Explain what relative economic values are

It reflects the appropriate emphasis for each trait Can be hard to determine -Should reflect the FUTURE value of traits -should reflect the timing and number of expressions of the trait -ultimately relativity is most important

Explain the phenotypic consequences, together with underlying genetic mechanims resulting from breeding of individuals for several generations in small populations. also list the measures you would put in place to minimise untoward consequences.

Mating of related individuals -Mating of individuals more closely related than the average of the population. -Inbreeding increases phenotypic resemblance. 1. increased homozygosity. This can be without change in gene frequency. 2. If there is dominance. The aa may be inferior. Inbreeding will cause a decrease in performance. 3. Alleles become "fixed". This causes decreased genetic variation. Phenotypic effects of inbreeding 1. Increased incidence of "throwbacks" aka atavism. (traits reappearing which had disappeared generations before.) 2. Inbreeding depression -decline in performance from mating related individuals -result in inbreeding where there is non-additive gene action (dominance, epistasis) 3. Expression of deleterious recessive alleles (due to recessive homozygosity) . Might result in prepotency. An individual is prepotent if the appearance of performance of his/her offspring is especially like her/his own. "an individual can stamp his features in the progeny at the expense of the other parent. Prepotency How to avoid inbreeding? 1. we need to bring in animals from outside populations a) regularly. (every year). b) We also must use different sources, so keep rotating the source of animals. -2. Keep ratio of males/females high -Conflict with selection intensity 3. Keep replacements from several families 4. Increase generation interval (this is another conflict) 5. Avoid mating close relatives (nothing closer than cousins) Advantages of inbreeding 1. To increase uniformity in a population. Uniformity within a breed e.g. coat colour. -Production of laboratory animals (better to have all uniform to compare treatments) 2. To study inheritance pattern of recessive traits e.g. spider syndrome, earlessness in lambs. E.g. using test crosses 3. To increase hybrid vigour. Cross two different inbred lines

1. Describe how tandem selection, independent culling levels and index selection are used to enable multiple trait selection

Multiple trait selection. Tandem selection 3 advantages and 3 disadvantages -make a list of the traits you want to select on -Rank them in order of importance -Select on them one at a time in the order youve ranked them, once youve selected on the last one start again on the first one. Advantages: 1. easy 2. make fast progress in first (most important trait) 3. Useful for traits that can only be measured sometimes e.g disease resistance. Disadvantages -Can take a long time to get through all the traits - how long do you spend on each one? -What if unfavourable traits are correlated Independent culling levels -Determine a threshold culling level for each trait -Cull any animal that fall below the threshold for any of the traits Advantages -allows selection on all traits at once -easy Disadvantages: -thresholds may have to be very low for some traits -it culls the worst rather than selects the best -what if two traits are unfavourably correlated -makes no allowance for an animal having outstanding merit in one category if it is below threshold in another Index selection. rev x bv -combines all the traits to be selected on into an equation for overall merit, with each trait weighted on its relative importance -gives a single value for each animal, can then rank on this index value and select best overall animals -an animal can be very good in one trait but weak in another trait and be selected -can be hard to determine -should reflect the future value of the traits: you are making decisions for the animals you want in the future.

What is heterosis? illustrate how different types of non additive gene action could contribute to heterosis. explain how sequential breeding can be employed to retain the heterosis observed in f1 hybrids to the greatest possible extent in the subsequent generations.

Overdominance: the phenotype of the heterozygote is superior to that of the homozygote. E.g. heterozygotes have a greater resistance to malaria than those with only normal red-blood cells. Codominance Heterosis is mostly due to nonadditive gene action. E.g. could be due to dominance. Or via overdominance (in which the heterozygote is better than the homozygotes - either aa or AA.) Epistasis can also result in heterosis. E.g. a homozygote masks a trait for another gene pair- but now youd get more heterozygotes so it wouldn't be masked. 3. Hybrid vigour or heterosis- increased mean performance of progeny in comparison to the mean performance of parents. -This is the most important effect of outbreeding -Increased heterozygosity at loci influencing a trait leads to 'gain in gene combination value' i.e. heterosis -It is the opposite of inbreeding depression. Defined as the deviation of the average of reciprocal crossbred progeny from the average of the parent breeds. sequential breeding- crisscrossing or roational crossing crisscrossing: systematic crossbreeding program with a sequence of two breeds e.g. ab x b then ab x a. -tries to retain the heterosis observed in the f1 -only purebred sires needed. -large variation between generations

2. explain how information about the individual, its ancestors or progeny (or a combination of these) can be used to estimate a breeding value

Predicting genotype from phenotype We want the best predictor (l) for true merit (T) to minimise environmental noise. If you know the phenotype (deviation) and the relationship with the individual (indicates the proportion of genes in common), you can use the information to estimate genetic merit. Theh more losely related theanimals, the more useful the information. Parental records can allow you to select young animals which decreases L and increases genetic gain. Also for sex limiting traits and traits expressed later in life. However low accuracy, so rti lowers. INdividual records: -higher rti than parental. -can be expensive progeny -greatly increases L -high accuracy with lots of progeny.

Explain why the accuracy of a breeding value is important in the selection of livestock

RTI indicates how accurate selection based on the EBV will be The greater the RTI, the more likely the best animals selected on ebv are truly the best animals Greater accuracy means more genetic gain (include equation)

Why use indirect selection?

Selecting on one trait with the aim of improving genetic merit for a correlated trait useful for 1. sex limited traits (e.g. milk traits in bulls) 2. Traits that are measured late in life or require death e.g. carcass traits 3. Hard to measure traits e.g. age of pubserty 4. Traits that are only expressed sometimes e.g. facial eczma resistance

What does spreading the bulls over many farms also double as?

Sire referencing. By using a small team of the same sires across a number of flocks/herds, the progeny of these sires provide a benchmark against which to compare the progeny of home-bred sires. So this is different than the sire proving scheme.

2. be able to define and calculate generation intervals

The average age of the parents when the progeny are born!!! It indicates how long it takes you to turn over a generation

Define heritability

The proportion of phenotypic variance in a population that is due to genetic variation/that results from genetic differences among individuals. Heritability (proportion of variation due to genetic differences between animals) Need to know the formula for this!

Accuracy vs reliability

The sheep and beef industries use accuracy. these are true rti values the dairy presents reliability for breeding values this is the square of rt1

For a breed of your choice, define a selection objective and explain why the traits are included in the objective. For a livestock industry of your choice, outline a selection index that is used and justify the inclusion of the traits and the relative economic values assigned to them. ***will be in exam.

This index measures the expected ability of the cow or bull to breed replacements which are efficient converters of feed into profit. , the Dairy Board expects the relative value of fat to decrease compared to the value of protein 1. Protein has a weighing of 40% and an EV of 8.6. So for every 1kg increase in protein we expect an increase in ent farm income of 8.6 dollars. Moderately heritable trait. Why is protein given such a high economic value? It's the limiting component of what fontera is producing. 2. Milk is a moderately heritable trait. You should aim to increase or maintain milk breeding value over time. It has a weighting of 15% and an ev of -.094 dollars. 3. Liveweight. Weighting of 14$. ev of -1.5 dollars. 4. Milk fat. weighting of 12%. increase of 1.9 Milk fat has been going down because of consumer demand for lower fat products. 5. Fertility is a lowly heritable trait. weighting of 8%. ev of 3 dollars. so for every 1% increase in fertility we expect... Fertility is a big deal because if cow doesn't get pregnant= no milk produced= loss of profit. 6. Somatic cell score is a low to moderate heritable trait. ev of -31. weighting of 7%. should try and decrease due to correlation with mastitis. Farmers score two-year-old heifers for four traits relating to their adaptability to milking, shed temperament, milk speed and overall opinion. In all cases, more positive values are better

Describe how molecular genetic techniques can enhance the selection of new parents.

Tools for detecting variation at DNA level: PCR-RFPL -widely used in detecting genetic diseases -PCR amplification of a specific gene or gene region followed by restriction digestion -polymorphism recorded by gel electrophoresis -used to detect sequence variation or length variance within the gene. Can identify the carriers for genetic diseases that we cannot see phylogenetically

What is the vision of genomic selection and advantages?

Vision: to select replacement nucleus animals using pedigree plus dna information (so they want to move away from the pedigree + progeny test) -reduce generation interval -reduce measurement effort -select difficult to measure traits -discard unwanted animals earlier -increase delta G by 40-70% -waas launched in spring 2008 Genomic selection- what is needed? -relationship between DNA markers and phenotype (linkage) -Current markers are SNPs -need accurate phenotypes on many relevant animals -DNA from high genetic merit animals -Lab for dna work -aduitable system to tract dna to animal -bioinformatics

What is additive gene action?

Where each allele contributes a fixed amount to the trait, and the genotype is the sum of all the effects.

What is rTI?

accuracy of selection When based on a single measurement of the animals own phenotype rTI= h

What is an antigen

antibody generating substance An antibody is an immunoglobulin froduced from activated B lymphocytes. A lymphocyte is a type of white blood cell. Role of immune response gnees in resitance/susceptibility to infectious diseases Innate immunity: polymorphisms of genes encoding receptors on sentinel cells (macrophages and dendritic cells) Aquired immunity Polymorphisms of genes endcoding class I and class II MHC molecules -The role of MHC gnes in disease resistance has been the subject of several investigations

One of your clients wants to start using crossbreeding in their beef herd. Discuss the potential oppurtunities and pitfalls that hte client should consider when deciding what sort of cross breeding system they might implement.

interse (synthetic breeds) -dont need to produce purebreeds -heterosis doesnt decrease after f1 backcrossing (fixed percentage crossing system)- used to grade up to new breeds -need to keep purebreeds -heterosis continues declinign -f1 cross you get full heterosis but expensive to keep purebreeds. 3 way cross maternal heterosis 4 way cross maternal paternal and individual heterosis. -best suited to fecund. sequential -crisscrossing/rotational

Review the historical development of sheep and cattle breeds in New Zealand.

just read the slides.

disease REISTANCE. mendelian.

neonatal diarrhea in piglets -mareks disease in poultry -scrapie in sheep 1. Neonatal diarrhea in piglets -caused by e.coli -some strains of e.coli have a surface antigen -Useful in attachment to intestinal wall -strains without surface antigen are not virulent The intestinal wall receptors in pigs are encoded by an autosomal gene pair SS- normal receptors Ss- normal ss-no receptor Therefore piglets with ss genotype are resistance to e.coli k88 strain since they can not bind to the intestinal wall 2. Scrapie in sheep -Scrapie is transmited by prions -prions are a non-traditonal infectious agent -prions act as templates and induce similar changes in hosts PrP genes -susceptibility of sheep to scrapie is determined by point mutations at three positions in sheep PrP gene -sheep with ARR/ARR genotype is mostly resistant 3. Mareks disease in poultry -highly contagious viral neoplastic disease in chickens -results in t cell lymphoma -mortality can be up to 100% post infection -two allele at B complex MHC strongly influence resistance or susceptibility B21= resistance B19= susceptible Upon divergent selection for 4 generations, incidence in resistance line was 7% and in susceptible line 94%

2. Explain what a genetic correlation is

rg(x,y). Is a measure of how changes in the genetic merit of one trait will affect the genetic merit for another trait.

A commercial farmer client wants to improve facial eczema resistance of their sheep flock. recommend on how they shoudl proceed without establishing a genetic selection program.

supplementing with zinc, Perhaps differential culling i.e. cull or don't keep offspring of any visibly affected? Id say that he could just bring in a whole new flock of "resistant" sheep; no selection... Further bring in ram that is known to be from a resistant line.. cull by eye

3. Define the term repeatability

t The proportion of phenotypic variance that is due to genetic and permanent environmental effects

Define the accuracy of a breeding value

the correlation between the true and index value.