ANSC 313 mod 5

trait type: qualitative

no inbetween

ex: horns or polled

trait types: quantitative

• heritability

• markets

signle nucleotide polymorphism (SNP)

• variation in DNA

• change at 1 base pair

microsatellite short tandem repeat (STR)

• repeated elements

• Counts # of repeats

indirect test

• DNA linkage tests

• used when the causative mutation is not known

• tests for marker linked to the trait

• less accurate then direct tests

linkage

• marker is segregating with the trait or mutation

• recombination (crossover) is more likely between the mutation and marker the farther they are apart

linkage testing

• biallelic markers (SNP) in or close to a mutation

• mutliallelic markers (microsatellites) near mutation

polymerase chain reaction (PCR)

• amplifies a segment of DNA

• need very little starting material

• steps in the cycle (repeated 30 times): denaturation, annealing, extension

central dogma

DNA → RNA→ messenger RNA→ amino acid chain → protein

SNP in 3rd position of codon

least likely to change an amino acid

missense mutation

• changes amino acid

• impairs of abolishes protein function

• conservative: same class of amino acid

• non-conservative: changes class of amino acid

nonsense mutation

• premature stop codon

• causes truncated rpotein

silent mutation

• no change in amino acids

• also called synonymous

frameshift

• insertion or deletion of nucleotides

• shifts codons after it out of frame

• changes amino acids and/or premature stop codons

in-frame insertion or deletion

• mutliple of 3 nucleotides

• codons stay in fram (no shift)

non-coding mutations

• any mutation outside of exons

• may or may not affect phenotype

• mutation in regulatory region

• mutation in splice site

• mutation in an enhancer on suppressor region

PCR-RFLP

• PCR restriction fragment length polymorphism

• amplify segment surrounding SNP with PCR

• digest with a restriction enzyme that recognizes one allele but not the other

• cut fragment (allele 1) will be shorter than uncut fragment (allele 2)

• separate by size on an agarose gel using electrophoresis

real-time PCR genotyping

• use fluorescently-labeled probes specific to each genotype

• PCR amplication

• measured during or at end of PCR

• faste and less expensive than PCR-RFLP

• two main systems for SNP genotyping: KASP, TaqMan

SNP chip

• DNA microarrays that can genotype many SNPs at one time

• used to predict animal’s breeding value for traits of interests

• data from large training population

• complex stats analysis

• compare test animal genotype to test population results

purebred cattle sales advertise..

• colour genotype

• polled genotype

• genetic disease

• ingenity and tenderness of beef

• EPD and GE-EPD

igenity beef

• score of 1-10 in three indices

• maternal index

• production index

• terminal index

holstein canada - dairy cattle

• parentage verification

• milk components

• disease testing

• coat clour

• hgih density standar panel

pigs catalog traits

• coat color

• litter size

• weight gain

• fat content

• meat quality

quantitative trait loci (QTL) Mapping

• use DNA marker to find chromosomal regions associated with the trait

• look for genes within the identified regions

• need to genotype many individuals divergent for the trait

genome-wide associated study (GWAS)

• utilizes SNP chips to map traits

• very high resolution

• results typically displayed in a manhattan plot

positional candidate genes

• trait mapped to chromosomal region (GTL or GWAW)

• look for and investigate genes located in this area

• position in genome and how it corresponds with selected trait

functional candidate genes

• genes involved in functions associated with the trait

behaviour - phenotypic measurement

• movement mesuring device

• temperament

• habituation

DRD4

• positional and functional candidate genes

• associated with behaviour traits in ither species

leptin

• affects appetite and fat deposition

• called “obese” gene

• involved in appetite regulation

leptin genotype

• backfat thickness

• backdeposition

• yield grade

• milk producton

• frequency of T (fat) allele

trangenics

• genetically modified organism

• trandgenic organism

genetically modified organism

an organism in which new genetic material has been experimentally introduced into the germ cells

transgenic organism

organism which new genetic material from a different from a different species has been experimentally introduced into germ cells

for a transgene, DNA must be

• integrated

• transcribed

• translated

• expressed in correct tissue

• inherited by offspring

transgenic bacteria

• used to produced human proteins on a large scale for pharmaceuticals

• eukaryotic gene in a prokaryote

problems of eukaryotic genes in prokaryotes

• remove introns

• add signal sequence to secrete

• active protein

DNA construct

1. gene

2. promoter: signals attachment of RNA polymerase

3. optional additions: reporter gene, signal sequences

GFP reporter

• green fluorescent protein

• added to a construct as a reporter gene

transgenic plants

• longer lasting

• herbicide resistance

• insect resistance

transgenic animals methods:

• microinjection

• viral transfer (cell culture, retrovirus, nuclear transfer)

publiv perception on GMO and transgenics

• big hurdle in commmercializing these products

• less opposition to gene editing

CRISPR - Cas9

• clustered regularly interspaced short palindromic repeats

• detect and defend against viruses

• cleave DNA

ART

assisted reproduction technologies

AI

• most used in dairy cattle

• used for biosecurity/disease control

• prevent sinjury from natural service

• can be stored

• used for selective breeding

3 techniques of AI in dogs

• vagina insemination

• transcervical insemination

• surgical insemination

sexing semen

• sort semen by x and y

• flow cytometry

• available commercially

• lower fertility, higher cost

embryo transfer

• multiple ovulation embryo transfer

• superovulate donor cow

• inseminate

• collect embryos

• transfer to recipient cows

cloning

• embryo manipulation (splitting and sectioning)

• somatic cells (nuclear transfer)

embryo splitting

• also called artificial twinning

• remove cells from an embryo

• transfer each to an empty donor ZP

embryo sectioning

• morula or blastocyst

• cut embryos in half

• 2 identical embryos

nuclear transplant

• enucleate oocyte (haploid0

• diploid donor cell

• fuse

• transfer to recipient

nuclear transplant steps

1. oocyte/ovum, remove nuclear material

2. donor cell, blastomere

3. transfer donor into enucleated oocyte

4. fuse ooplasm and donor cell

why are nuclear transplant offpring not completely geneticlally similarnto mother

mitochondrial genomes are different

offspring get mitochondria from recipient ova

large offspring syndrome

• abnormally high fetal growth

• occurs with IVF and cloning

• improper gene imprinting