Animal Genetics Exam 1

What is genetics

The study for heredity, or the study of how different characteristics/traits of animals are inherited or transmitted from generation to generation. This can be using one mutation in a single gene or using few number of genes

Genetic improvement through what? What two evaluations to improve genetics? What are these evaluations based on? What year did we switch evaluation systems?

Selection (Selective breeding)

Genetics evaluation: (pedigree + phenotypes) → genetic evaluation system based on (EBVs) before 2009

Genomics evaluation: uses DNA, genotypes and phenotype → genomic evaluation system used GBVs look for positive values after 2009

What is Selective breeding? What is the best animal? Ranking? Genetic Value?

Select the best animal for breeding to get the next generation

Best animal is the animal that meets the breeding objectives or goals, rank the animals based on their genetic values Aka estimated breeding values (EBVs) or Genomic breeding values (GBVs)

What are the breeding objectives?

1. The main goal of the genetic improvement

2. Traits of economic values (ex milk yield)

What genetics and genomic tools and investments do we use to from current animal to animal that meets our breeding objectives

Sources of info to measure traits?

Then evaluate breeding objectives via?

1. Measure traits: pedigree, DNA testing

   • Info from: genomics, proteomics, metabolomics, transcriptomics, meta-genomics & meta-transcriptions → micro biome

2. Genetic & Genomic Evaluations (EBVs or GBVs)

3. Reproductive technology (AI & ET)

Evaluate breeding objectives comparing EBVs or GBVs and alternative strategies

Why do Sudan, Tanaka and etc have low milk yield? Why is U.S. milk yield so high?

Because they don’t have systematic recording system of phenotypes regarding milk production, first step of genetic improvement is measuring traits like phenotype, US has this recording system and genetic and genomic evaluation

Why is pregancy rates decrease as milk yield increases? Why does the daughter pregnancy rates increase after 2003?

Reverse relationships between high milk production and fertility

If the cow produces lots of milk fertility will decrease because of enegry allocated to produces milk.

Pregnancy rates were not originally in the breeding objectives until 2003, they started to put daughter Pregnancy rates in their breeding objectives.

Why is there less beef cattle but more beef production?

We can produce more beef with less animals, the beef cattle production system is efficient, we produce more beef from less number of cattle

Progeny Tetsing

Evaluation the bull based on their progeny

What is King?

Phenotype

Who is the Old father of all animal breeding? What did he do

Robert Bakewell (1725-1795)

Introduced a systematic recording of performance

What is the phenotype formula?

P = G + E + G*E

P: phenotype

G: genotype

E: Environment

G*E: Interaction between G and E

Example of phenotype formula

Black coat color = genotype [BB] + E (excellent) + G*E (zero effect)

If environment is hot then they may not produce well

What is a genotype?

Combination of the two alleles in specific position on the genome

What is a trait

An observable or measurable characteristic of an animal,

 OR characteristics that you can observe or measure

 Examples: coat color, birth weight, 305-day milk production or type

classification, behavior traits (e.g. a reduced fear of humans and overall

tameness in dogs, temperament in dairy cattle )

What is a Phenotype (Performance level)?

An observed category or measured level of performance for a trait of an

individual,

 Examples: black and red coat color, 80 lb birth weight, 25,000lb /305-day

milk production record, type classification score(1-9).

What is a Genotype?

The genetic make up of an individual (all of the genes), but also more

narrowly describes the combination of alleles at a locus or loci for an

individual e.g. AA, AB, BB for one gene

What is the breeding objectives?

general goal for a breeding program, a notion of what

constitutes the best (most desirable) animal (traits and their economical weights)

Which is a chromosome?

A, B is a replicated chromosome

Genetics: study of?genetic evaluation consists of? Marker assisted selection?

The study of heredity (i.e. Inheritance). Or study how different

characteristics/traits of animals are inherited or transmitted from

generation to generation. This can be using one mutation in a single gene

or using few number of genes.

 Requires relatively simple statistical models and lab techniques

 Genetic Evaluation: (pedigree + phenotypes) + few genetic variants

(marker assisted selection: MAS).

Genomics: study of? Requires? Genetic evaluation

Study of all and organism genes (genome)

Offers opportunities to study complex, difficult to measure, low heritability, late in life traits, etc

Requires advanced data analyst if techniques & stat model, high performance computing vacillations (HPC) aka super computers, AI, machine learning, big data sets and sophisticated lab instruments (sequencing platforms)

Genetic Evaluation: genomic selection (phenotypes + DNA/+pedigree) → GBVS → evaluate (feed intake/efficiency, carcass traits)

DNA testing consist of three things

Applications of genomics?

What is ISAG? What do they do to do what?

ISAG: International Society for Animal genetics

Use SNP chip panel to do percentage traits, correct pedigree, breed composition, hybrid vigor, heterosis

QTL mapping: what is it? What does it stand for?

Process of detecting the genes controlling the difference between the animals in the trait of interest

QTL: quantitative traits loci

Genetic disorders/lethal haplotypes

Mono genetics traits Ex: BLAD in cattle

F2 phenotype ration: consist of

Dominance and lethal mutation

Locus/loci

The site on a chromosome/genome where a gene, mutation or genetic Ariana’s are located. ANy of the alleles of a gene, mutation, or genetic variants can be present.

Ex: A gene point mutation: (SNP): single nucleotide polymorphis

(INDELS) insertion/deletion, less than 1,000 nucleotide

(CNV): copy number variants, >1000 nucleotides

Allele: what is it? Labels? Form of a?

Different forms of mutation/genetic variation/gene possible in a physic al position on the genome

Can be labeled A, a, etc or actual sequence at SNp position

The dominat alley is capital and recessive isnt, we dont always know which is dominants

Allele is a form of gene

Gene

The unit of inheritance that occupies a specific locus on a chromosome and that conveys a set of DNA sequences that are required to produce a polypeptide or RNA

Genotype

Combination of alleles at a locus or loci for an individual

Homozygous Vs Heterozygote

Combo of the same alleles at a locus Vs combo of the different alleles at a locus

DNA is the molecule ___(1)____ for creating all __(2)__ and ___(3)__ molecules needed to maintain homeostasis

1) cookbook

2) proteins

3) RNA molecules

The genetic code is made up of distinct __(1)__ molecules or pairs of molecules (1 from data and 1 from mom) called ___(2)__

1) DNA

2) chromosomes

Ex: bovine genome, these would be like 60 chapters in the master protein cookbook

DNA Structure

Karyotyping, different in composition of chromosomes?

Examining chromosomes (karotypes)

The female and male karyotypes where the only difference is the composition of the sex chromosomes, females XX and males XY

DNA doesnt have U, U only in RNA, it has T instead

E. TAACGGAG

B. DNA

SNP: stands for? What is it? Use what to determine which alleles animals has for a certain SNP? Based on __(1)_ for a group of indivuals for a given locus

SNP: single nucleotide polymorphism

Substitution of a single nuclei de that occurs at a specific position in the genome where the minor allele frqrcuny is more than 1%. Using sequencing or genotype assays it is possible to determine which Allen’s (genotype) animals have for a particular SNP locus

SNP is detected based on genotypeing of a group indivuals for a given locus

Term for a population not individual animal

If a minor alleles frequency is less than 1% then it’s called?

Rare mutation

Genotypes: pool of ?

Total genetic makeup of the animals (pool of alleles)

What is the blending inheritance theory? Was it valid?

The progeny inherits any traits as the Avery of the parents values of that characteristics

After a few generations all indivuals will have a blend phenotype

It was invalid (obsolete) theory

Dismissed and replaced by Mendel’s laws

Mendelian Inheritance: father of? Focused on how many pea plants traits? Two principles? Publishes is work and?

Gregor Mendel: father of modern genetics

Worked on: mice, meteorology, astronomy and honeybees

Focused on pea plants 7 traits

Described inheritance

Generalized two principles: Law of Segregation and Law of Indpendnet Assortments

Published work in 1866, nobody cared

Then in Spring 1900, 3 different people published rediscovering his principles in 3 months

What is the law of segregation?

Allergic pairs segregate (separate) during gametic formation and the paired condition is restored by random fashion of gametes at fertilization

Monogenic traits, Quantitative traits

Monogenic traits: trait that are controlled by one gene

Quantitative traits: are controlled by many genes

Mendel defined concepts: genes, two alleles from each parents, allergic separation, complete dominance

Genes: come at diffferent forms which are called alleles

For each inherited trait, a diploid organism has two alleles one from each parents, is that correct for all traits?

Since allergic pairs segregate from each other during the production of gametes (meiosis, sperm or egg carry only one allele

When two alleles are different one is expressed and the other masked (complete dominance effect) exceptions?

For all the inherited traits in a diploid organism, they are controlled by one locus that has two alleles; one from each parent. True or fals

False, not all inherited traits are controlled by a single locus

According to Mendel’s Law of Segregation, during meiosis the two alleles at a locus separate (segregate), so each gamete (sperm or egg) receives two alleles for that gene

False

Principle of Segregation: population average of allele frequency

f(Bb) = ___+ ___ = ?

The genotype French of the progeny is always determined by?

f(Bb) = f(bB) + f(Bb) = 0.5

The genotype frequency of the progeny is always determined by the frequency of the parental gametes

What can mess up the classic 1:2:1 phenotype ratio? (Within the same locus allergic interactions? Or how do alleles behave within the same locus?

Dominance: the degree to which alleles at a locus mask one another in a diploid organism

Lethal haplotypes: genotypes, mutations, SNPs

We observed the phenotype of the heterozygote to detect the degree level of dominance

Identify what kind of dominance each image is?

Incomplete/Co-Dominance

Identify what kind of dominance each image is?

Complete Dominance of A allele

Identify what kind of dominance each image is?

Complete Dominance of T allele

(T levels equal)

Identify what kind of dominance each image is?

Over Dominance of T allele

Identify what kind of dominance each image is?

Partial Dominance of T allele

Complete Dominance:

One allele (domaintt) completely mask another allele (recessive)

In this case heterozygous genotypes (heterozygotes) have the phenotypes of the dominant homozygote (resemble 1 parents in F1)

In F2 the phenotypic ratio is not 1:2:1

Examples of Domainat/Recssive Allelels:

Polled dominant (PP) / Horned recessive (pp)

• Black color (BB) / Red color (bb)

• White head (WW)/ Other colored head (ww)

• Normal size / Dwarf

• Normal / Most genetic defects

– Complex Vertebral Malformation (CVM)

– Bovine Leukocyte Adhesion Deficiency (BLAD),

– Mule Foot, Limber leg, etc.

– Severe combined immunodeficiency (SCID) in horses

– Hyperkalemic Periodic Paralysis (HYPP) in Horses

– Cystic fibrosis (CFTR) human

-Sickle cell in human

What does T, P, PC and I in front of alleles mean, ex: TP, PP, PC, I

T stands for tested free of trait, TP = tested free of polled, so that animal is horned

PP = tested homozygous trait (polled)

PC = polled carrier

I (Indeterminate): polled status cant be definitely determined

What are the 7 traits studied by Mendel?

1) Flower color (white or purple)

2) Seed color (yellow or green)

3) Seed shape (round or wrinkled)

4) Pod color (green or yellow)

5) pod shape (inflated or constricted)

6) Flower shape (axial or terminal)

Incomplete dominance (haploinsufficiency?)

What is heterozygote?

Heterozygote is blend of phenotypes of homozygote

The offspring show 3rd phenotype

In F2 heterozygote has distinct phenotype so 1:2:1 ratio holds

Incomplete dominance:

Ex 1: In Andalusian chicken (P) black + white = F1, F1 → ?

Ex 2: Myostatin gene (MSTN) in Belgian Blue and Piedmontes what kind of mutation? Effect in equinome speed test?

Ex: 1 BB + WW = BW (blue chicken), F2: 1 BB : 2 BW : 1 WW

Ex 2: A depletion of 11 bp nucleotides in the third exon causes a loss of 102 amino acids due to frame shift, leads to faster horses

Codominance: alleles form? Ratio?

Ex 1: shorthorn cattle R + W = RW (roan) → ? RR : ?RW : ?WW

Both Allie’s show in a complete form

In F2 1:2:1 ratio holds

F2 ½ red, ½ roan and ¼ white

Ex 2: Beta casein in Milk of Dairy Cattle: 2 version of beta casein, what is it? Located?

2 version of beta casein: A1 and A2

Is a protein that makes up around 30% of all milk proteins, located on BTA 6, milk containing A1 or A1/A2 B-CN variates, the B-casomorphin 7-peptide (BCM-7) is release upon digestion and during cheese manufacturing and ripening

Beta casein gene → alleles forms → A1 (protein digested) and A2 (zero ?

Factors affecting F2 phenotype ratio, Dominance:

Dominance: The interaction between the two alleles in a single locus, one gene, one mutation. Does reflect any interaction between genes or loci

Factors affecting F2 phenotype ratio: Lethal Mutations (Complete Dominance)(JNS, stands for?) Embryonic lethal meaning?

Ex: JNS → Jersey cattle, J- dominant, healthy, j → recssive, (JNS)

JNS: Jersey Neuropathy with Splayed Forelimbs

Jj x Jj = 25% JJ, 25% Jj (carrier), 25% jj (JNS) big issue

Incomplete Domiance: lethal white Overo (LWO) in horses

A mutation in the endothelin receptors B (EDNRB) gene causes LWO

O is a dominant and a lethal allele, O/O indvuials die

N/N color normal, n/O overo pattern, O/O: lethal white syndrome, incomplete colon and ability to defecate which leads to death or euthanasia

Why is White Lethal Overo incomplete dominance and not co-dominance.

Because for codimance each allele express itself

But this is incomplete domaine because one allele express isn’t self with the normal protein but the second allele doesnt express itself with the normal protein so the class for the n/O the normal allele is expressed but the lethal O allele isnt expressed so the n/O is fine. The overo lethal white gene is not a gene that control coat color but the gene affects melanocytes influencing coat color causes a spotted pattern

Lethal Mutations: Problmes with AI when? What to do if you have carriers?

May become a breed problem particularly with AI: when line breeding (inbreeding), if breed numbers are small, use of limited # of bulls will have signficant impact in spreading the recessive allele

Carrier Detection: DNA testing, genotyping

Check pedigree when natural breedings

Dont cull, match carries with none carriers, only select non carriers for replacement/breeding, cull carriers

Embryonic lethal

The problem from the gene negatively impacts e,RBI’s development so the embryo dies, no offspring observed

Online Mendelian Inheritance in Animals (OMIA): what is is?

 How many species?

 From the summary table, how ma

OMIA is a catalogue of inherited disorders, other (single-locus) traits, and genes in many animal species.

727 species

6063 traits ?? Check this

Multiple Loci: Mendelian Law of Independent Assortment

=> Principle of independent assortment

Two independent loci will behave independently, and both follow the law

of segregation

extension of single locus case of the law of segregation.

If you have one parent that is heterozygotes at two loci so this parent will

produce gametes with __(1)___ frequency of the possible combinations of

alleles in these two loci

1) equal

Determine the gametes frequency produced by this cross given Allie’s controlling separate traits are segregate independently

[Yy] x [Rr]

We can use the multiplicity rule to predict the genotype frequency for any number of loci assuming these loci segregate independently

Rules of Multiplication, determine f of yyrr of cross YyRr x YyRr

You can use this rule to calculate the frequency of a specific genotype

o Examples:

• F(YyRr) =f(Yy) f(Rr) = ½ ½ = ¼

• F(YYRR) = f(YY) f(RR) = ¼ ¼ = 1/16

• F(yyrr) = f(yy) f(rr) = ¼ ¼ = 1/16

• F(YyRR) = = f(Yy) f(RR) = ½ ¼ = 1/8

Rule of Addition

 Used to calculate the frequency of multiple genotypes=> (i.e. genotype with similar phenotype)

 f(Yy) OR f(yY) = f(Yy) + f(yY) = ¼ + ¼ = ½

 f(YYRR) + f(YYRr) + f(YyRR) + f(YyRr)

What is the genotype frequency for the following:

 f(Yyrr) = ?

 f(YyRrZZ) = ?

f(Yyrr) = f(Yy) x f(rr) = (1/2)x(1/4) =1/8

f(YyRrZZ) = f(Yy) x f(Rr) x f(ZZ) = (1/2)x(1/2)x(1/4)

What can mess up the F2 ratio phenotypes? 2 main points, 4 examples

When 2 loci are not independent, F2 Ratios do NOT hold

=> Allelic Interaction between two or more loci

=> Factors affecting independence and F2 ratios

Pleiotropy:

One locus affects two or more traits .

Epistasis: Alleles at one locus affect the expression of alleles at a different

locus.

Linkage & Linkage Disequilibrium: Two or more loci are on the same chromosome.

Sex Linkage

What is Pleiotrophy? How does it work?

One locus, gene or mutations affects for than one trait. One of the main causes of genetic correlation between traits

Dominant W allele causes deafness and white cat = WW or Ww

How? melanocytes

 Fur pigment produced by melanocytes

 Inner ear also has melanocytes for electrical transmission to the

brain

 Defective melanocyte development means no pigment or electric

signals = white and deaf

Pleiotropic effects of myostatin locus P (msP) allele: Myostatin gene

Location? Deletion? Causes? Dominance type?

Myostatin gene (MSTN) in Belgian Blue and Piedmontese

Location: chromosome 2, MSTN has 1887 bp with three exons and two introns.

• A deletion of 11 bp nucleotides in the third exon causes a loss of 102 amino acids due to a frame-shift

• Absence of functional myostatin increases in all muscles up to 40%, and the gene is incomplete autosomal dominance.

Epistasis, identify the genes of the dad and mom

Alleles in one gene effect the expression of alleles in another gene

E with B = black

E with b = chocolate

e with B = yellow

e with b = liver color nose

Dad: EEBB x eeB(B or b)

Litters: all black no litter so no ee, all EeBB

Linkage: what is it? Disequilibrium

What is a spermatid?

 Linkage occurs when two loci are on the same chromosome.

 In this situation the two loci are not independent because of chromosome tend to segregate intact

Disequilibrium: is non random associations within the alleles in two loci or more the alleles are connected/linked the level of linkage depends on the distance between the loci. They do not segregate independently.

Linkage disequilibrium is one of the main causes of genetic correlation between traits

Ex; milk yield/fat yield gene and fertility/diseases near each other and affect each other/ genetic correlated