ANSC 305 Exam 2

Relationship coefficient

*The expected fraction of the DNA that two animals have in common due to common and (or) direct ancestry

Parameter space: 0 (not related) -1 (complete relationship/clone)

Rxy & Range of fraction of DNA

Parent/Progeny 0.5 (No variation)

Half siblings 0.25 (0-0.5)

Full siblings 0.5 (0(Parents passed on different genes to each progeny)-1 (identical twins))

Grandparent/kid 0.25 (0-0.5)

3/4 siblings 0.3125 (0-1)

Rxy Range of fraction of DNA

Parent/Progeny 0.5 No variation

Half siblings 0.25 0-0.5

Full siblings 0.5 0-1

Grandparent/kid 0.25 0-0.5

3/4 siblings 0.3125 0-1

Standard error (parent-offspring)

*Measure of precision of the relationship coefficient (measure of variability)

Rxy +/- Srxy Represents an interval w/ 0.68 probability that the true amount of DNA shared due to common and/or direct ancestry lies within

Diploid chromosome numbers

Cattle= 60 (n=30)

Sheep= 54 (n=27)

Pigs= 38 (n=19)

Goats= 60 (n=30)

Horses= 64 (n=32)

Additive relationship (axy)

*Measures the fraction of identical alleles shared by two individuals (on both chromosomes) that were inherited from common ancestors when averaged across all possible segregation outcomes

Inbreeding coefficient

*The fraction of DNA (pairs of genes) that will be homozygous (identical by descent) that would be heterozygous in a non-inbred individual of the population

Parameter space

Rxy: 0-1

Fx: 0-1

axy: 0-2

Regression: -infinity, infinity

Correlation coefficient (denominator of Rxy): 0-1 (standardized axy)

Probability: 0-1

Contribution

Arrow diagram process

1. Confirm or rule out direct ancestry for the two individuals

2. Identify common ancestor(s)

3. Establish inbreeding status of common ancestor(s)

4. Identify pathways of relatedness and the record the number of meiotic segregations (n) (any anc can only appear once)

5. Calculate pathway contributions

6. Square each pathway`s contribution (for standard error)

7. Sum pathway contributions= additive covariance and put in numerator of relationship coefficient

8. For each animal in the relationship coefficient, calculate 1+Fa and put the square root of their product in the denominator of the relationship coefficient

9. Calculate the standard error of the relationship coefficient as the square root of the sum of the squared contributions divided by 2 times the number of haploid chromosomes

Qualitatively inherited characters

Those where differences among animals are due to differences in genotype at one or two loci

Ex: Coat color, horned/polled, genetic disease

Probability

Parameter space: 0 (will not occur)-1 (100% chance it will occur)

*Frequencies as estimates of probability

-Allele frequencies

-Genotype frequencies

-Transmission probabilities

What genotypes are possible for a single locus with 2 alleles A & a?

-For Dominance genetic action, selection can be against the A or a

-For additive genetic action (dilution gene in cattle, can result in 3 distinct phenotypes), selection can be against either allele

Dominance Genetic action

-Dominance can be responsible for trait variation of qualitatively inherited characters

Wild-type allele

(+ or A) and recessive (a)

-Sometimes the recessive allele (aa) is considered the mutant (from the wild type) allele

-Recessive alleles are sometimes deleterious or even lethal

Lethal recessive

*homozygous lethal recessive alleles result in spontaneous abortion or the affected animal does not live long enough after birth to pass on genes

Deleterious recessive alleles

Gradation of harmfulness (persist in populations despite natural selection)

Selection against a recessive allele

1. Cull homozygous recessives (aa)

-You can see the difference between homozygous recessive and dominant or lethals use natural selection to get rid of recessives for us

2. Cull known heterozygotes (Aa)

-Can only tell from genetic testing, pedigree info, or progeny info

3. Breeding decisions based on pedigree/progeny info

4. Conduct informal/formal progeny test

5. Use progeny test info

6. Use Po and LOC to calculate P(HD|CT)

7. Use P(HD|CT) as Po values for selection and additional progeny testing decisions

P0

*Probability that breeding prospects are AA (homozygous dominant) using pedigree information (before progeny info is available)

-Progeny information supplements pedigree information

-Probabilities of being homozygous dominant P(AA) can be used as selection criteria and deciding on progeny testing

Progeny test information used to:

1. identify and cull heterozygotes (carriers)

2. Calculate the level of confidence (LOC) for tested animals that are not detected as carriers

Carrier

*Individual that is heterozygous (Aa)

-Informal/Formal progeny testing can identify carriers

P(AA) with no progeny info

-Phenotypically dominant

-Ps and Pd are probabilities that the sire and dam of a given animal are homozygous dominant

-Ps and Pd are independent

Level of confidence (in results of progeny test)

*Probability of detection (not a clean test) of heterozygote in a progeny test

Ex: LOC=0.81 81% probability an Aa parent would have produced greater than/equal to 1 aa progeny if mated to the same test mates

-Independent test mates

-Passes the test if phenotypically dominant animal only produced phenotypically dominant progeny

-large pi: multiply parentheses (for each test mate) and subtract product from 1

-n: number of test mates(# of parentheses; Increasing # of progeny/ test mates statistically makes test better)

-mi: number of progeny produced by mating with the ith test mate

-P__: probability of being the subscripted genotype

P(HD|CT)

*Probability of AA conditional on previous info and on a "clean test" (no aa progeny)

-Parameter space 0-1 (probability)

Probability Example

-Black bull

-Before test info: Both parents were known carriers of the red allele

-Bull bred to 2 red calves (assume each produced 1 offspring)

-P0= (1+0+0+0)/(3+0+0-0) or from punnet square (1/4)/(3/4)= 1/3 (33% chance the bull is heterozygous dominant before info)

-LOC= 1- ((0+ 0(3/4)^1+ 1(1/2)^1)(0+ 0(3/4)^1+ 1(1/2)^1))= 3/4 (75% confident that the bull would have produced a homozygous recessive calf if he was heterozygous)

-P(HD|CT)= (1/3)/(1-(3/4)(1-(1/3))= 2/3 (67% chance he is homozygous dominant)

Snorter Dwarfism

Breed affected: Hereford

Appearance: Shorter body & head (skull deformed) than normal calf, potbelly, snorting when breathing

-Prone to bloat bc/ of difficulty breathing & belching

-Originated from sire Kansas lad--> traced to his offspring St. Louis Lad--> defect spread widely from popular sire WHR Royal Domino 51st

-Recessive allele

Test: N/A

Comprest Herefords

Breed affected: Hereford

Appearance: 2 frame scores smaller than normal calves (~4 in.)

-Due to dominant gene (may be carrier of snorter gene)

-Originated w/ Comprest Conqueror

Test: N/A

Crooked-legged Dwarfism

Breed affected: Hereford

Appearance: Smaller than Snorter affected cattle & have crooked legs

-Due to crossing of 2 comprest herefords (contains both comprest & snorter alleles)

Test: N/A

Needle-nose Dwarfism

Breed affected: Hereford

Appearance: Small head w/ pointed (elongated) nose & stunted body (BW=15lbs)

-Highly inbred calves

-Calves don't live past a year bc/ they can't chew their cud

-Lethal recessive

Test: N/A

Idiopathic Epilepsy (Shaker claves)

Breed affected: Hereford

Appearance: Neurological disorder causing seizures

-recessive lethal

Test: DNA test

Results: IEF or IEC

Hydrocephalus

Breed affected: Hereford

Appearance: Very pronounced head from fluid build up (internal), bulging forehead

-recessive lethal

-Resulted from selection against snorters

Test: N/A

Dexter cattle

Breed affected: Dexter

Appearance: Shorter than normal cattle (Dexter breed already short)

-Heterozygotes are slightly shorter than normal calves

Test: N/A

Bulldog Dwarfism

Breed affected: Dexter

Appearance: Bulldog face w/ small severely deformed body

-Lethal recessive from breeding of 2 affected (aa) Dexters

Test: N/A

Double Muscling

Breed affected: Originated in Charolais & Belgium Blue (present in all breeds now)

Appearance: Myostatin mutation causes muscle enlargement w/ large grooves btw, causes structural problems (Females have small vulva/uterus, Males have small testis)

-Heterozygotes display some muscling (not completely recessive, intermediate)

Test: N/A

Palate-Pastern Syndrome

Breed affected: Charolais

Appearance: Cleft pallet & deformed pasterns (tendons contracted)

-recessive lethal (calf dies from being unable to suckle)

Test: N/A

Curly Calf Syndrome (Arthrogryposis Multiplex)

Breed affected: Angus

Appearance: Deformed limbs (very rigid, fixed joints-->lead to dystocia) & spine (twisted), appear thin from limited muscle development

-recessive lethal

Test: DNA test

results: AMF (free) or AMC (carrier)

Neuropathic Hydrocephalus

Breed affected: Angus

Appearance: Head the size of a basketball/volleyball from fluid accumulation (external), cleft palate w/ malformed skull & spine

-recessive lethal

Test: DNA test

results: NHF (free) or NHC (carrier)

Fawn Calf Syndrome (Contractural Arachnodactyly)

Breed affected: Angus

Appearance: Spine is slightly arched, BW is normal, but slightly taller & slender w/ legs causing limited range of motion (walks like deer)

-Recessive

Test: DNA test

results: CAF (free), CAA (affected)*cannot register*, or CAC (carrier)

Developmental Duplication

Breed affected: Angus

Appearance: Born w/ additional limbs from the neck/shoulder area

-Recessive (calves can live if removed, death occurs from birthing difficulties)

Test: DNA test

Results: DDF (free), DDC (carrier), or DDA (affected) *can't register*

Osteopetrosis (Marble bone disease)

Breed affected: Angus/Red Angus (primarily)

Appearance: Born premature (2-4 wks) w/ short lower jaw and bones lacking marrow (break easily)

-recessive lethal

Test: DNA test

Results: OSF or OSC

Itty Bitty Calves

Breed affected: Angus

Appearance: Calves are proportioned normally, but are extremely small

-recessive lethal (die bc/ cannot chew cud)

-May be the same as miniature Charolais cross calves

Test: N/A

Tibial Hemimelia Syndrome (TH)

Breed affected: Shorthorn (show industry has spread to other breeds)

Appearance: Twisted legs w/ fused joints, large abdominal hernias, and skull deformity (visible spinal cord)

-recessive lethal

Test: Molecular test

Pulmonary Hypoplasia with Anasarca

Breed affected: All show breeds

Appearance: Fluid accumulation in skin and body (causes dystocia from added weight, kills dam 50% of time) w/ underdeveloped/absence of lungs

-lethal recessive

Test: Molecular test

Callipyge

Breed affected: All sheep breeds

Appearance: Double muscling

-gene not expressed until 3-4 wks old

-No intermediate

Test: N/A

Impressive Syndrome (hyperkalemic periodic paralysis)

Breed affected: Quarter horse

Appearance: Double muscling

-Are stress prone & have uncontrollable shaking that leads to paralysis

-Dominant (present in heterozygotes)

-Originated from Impressive sire

Test: Molecular test

HERDA (hereditary equine regional dermal asthenia)

Breed affected: Quarter horses

Appearance: Collagen defect causes lack of adhesion btw/ skin and body

-Can live 2-4 years

-becomes present typically when breaking to ride

-Originated with Poco bueno

-recessive

Test: Molecular

Dwarfism in Friesians

Breed affected: Friesian

Appearance: Stunted growth

-recessive

Test: N/A

Hydrocephalus in Friesians

Breed affected: Friesian

Appearance: fluid accumulation in the head

-recessive lethal

Test: N/A

Syndactyly (mule foot)

Breed affected: Originated in Chianina (now in all breeds)

Appearance: One or more hooves are solid in structure (one toe instead of split)

-Begins with right front foot (1 foot most common) then moves counterclockwise if multiple are affected

-Recessive

Test: N/A

Spider Lamb Syndrome

Breed affected: Suffolk (hamps & dorsets have been affected from cross breeding)

Appearance: Legs are severely deformed

-Originated from Walking Tall

-recessive lethal

Test: Molecular

Results: NN (free), NS (carrier), or SS (affected)

Lethal White Foal Syndrome in Frame Overos

Breed affected: Frame overos

Appearance: white foal w/ deformity in GI tract (kills foal)

-dominant (Ff --> normal genotype, FF--> affected)

Test: N/A

Brain hernia

Breed affected: All pigs

Appearance: large hernia in the skull

-lethal recessive (some have lived for studies)

Test: N/A

Recessive Dwarfism in Texel Sheep

Breed affected: Texel sheep

Appearance: stunted growth & deformed legs

-recessive

Test: N/A

Parrot Mouth Dwarfism

Breed affected: Southdown

Appearance: top jaw longer (overshot) & stunted growth

-lethal recessive (die at 1-2 months)

Test: N/A

Ancon Dwarfism

Breed affected: Cheviots

Appearance: Deformed, short legs that turn out

-Heterozygotes are normal

Test: N/A

Dwarfism in Finewool Sheep

Breed affected: Rambouillet, Booroola-Merino

Appearance: Short, crooked legs that turn in

Test: N/A

Pig Genotypes

Hampshire: EE dd KK I^l I^l

Duroc: ee dd KK ii

Yorkshire: E^p E^p DD KK II

Landrace: E^p E^p DD KK II

Chester White: E^p E^P DD KK II

Spot: E^p E^p DD KK ii

Poland China: E^p E^p DD kk ii

Berkshire: E^p E^p DD kk ii

Hog Color Genetics flow chart

Set-up:

1. Start w/ I

2. E

3. D

4. K

Rules to remember:

II (always white), I__(predominantly white),

I^l__ (something w/ a belt), ii (back to base color)

E__ (Black or Blue butt), E^p (black spots), ee (non-black base color)

DD (white), Dd (sandy), dd (red) (dilution of red, not black)

K (ONLY applies to E^p) kk (w/ ii results in black w/ 6 white points)

Dominance:

I> I^l >i

E> E^p > e

D,d (no dominance, hetero intermediate)

K> k

British Beef cattle breeds

Angus: Black, polled, Scotland, most # of registrations, marbling standard

Hereford: Red w/ white face, horned or polled, England, cancer eye (select for pigmentation)

Continental European beef cattle breeds

Charolais: White, horned, in France, but many in US are polled, France

Simmental: Originally light red and white, but many are black in US, horned or polled, Switzerland, dual purpose

Limousin: Originally red, but many are black in the US, horned or polled, France

Bos Indicus and Bos Indicus influenced beef cattle

Brahman: Bos Indicus breed, gray or red, most are horned, US origin from cattle that originated in India

Beefmaster: 1/2 Brahman 1/4 Hereford 1/4 Shorthorn, various colors, horned or polled, France

Santa Gertrudis: 3/8 Brahman 5/8 Shorthorn, red, horned or polled, US

Dairy cattle

Holstein: Black & white spotted, horned, Holland, Highest milk pro, highest pop. worldwide

Jersey: Brown or brown & white spotted, most are horned, Jersey Island (btw/ England & France), most milk fat

Finewool sheep

Rambouillet: White faced (white all over), rams horned & ewes have scurs or knobs, France

Medium wool sheep

Suffolk: Black faced w/ no wool cap, polled, England

Hampshire: Black faced w/ white wool cap & leg wool, polled, England

Hair sheep

Dorper: Either black headed or white (white head & body), composite of Dorset & Black headed Persian, most are polled, but many rams have scurs and some have horns, South Africa

Hair goats (fiber)

Angora: White, horned, produce mohair (do not produce cashmere), area that is now Turkey

Meat goats

Boer: Red headed, horned, South Africa **For all practical purposes, all goats are horned**

Terminal Sire type hog breeds

Duroc: Red, heavily muscled, down ears, US

Hampshire: Black belted, heavy muscled, up ears, US

Pietrain: White w/ dull black spots, usually w/ part of the black spots covered w/ white hair, extremely heavy muscled, up ears, Belgium

Maternal Hog breeds

Yorkshire: White, up ears, US, but largely of english origin

Landrace: White, large down ears, Denmark

Meishan: Black w/ white on the legs & often on the nose, large down ears, fat, have large litters, Meishan prefecture of China

Light horse breeds

Quarter horse: Various colors, including bay, sorrel, brown, black, gray, dun, palomino, buckskin, and grullo, speed at short distances, cow work, US

Thoroughbred: Various colors, including bay, chestnut, brown, gray, and black (rare), speed at intermediate distances, England

Arabian: Same colors as Thoroughbred, endurance, intelligence, Arabian peninsula

Appaloosa: Same traits and base colors as the Quarter horse w/ one of the leopard patterns, US

Paint: Same traits and base colors as the Quarter horse w/ one of the paint patterns, US

Draft horse breeds

Clydesdale: Bay, black, brown, or chestnut, w/ white on the face & legs, feathering (long hair) on the lower legs, heavy draft, Scotland

Percheron: Usually black or gray, but some bays & sorrels, no feathering, heavy draft, France