Selection via DNA in livestock Flashcards
what are the trait types
qualitative and quantitative
indirect and direct DNA tests
-markers: used to select for traits
-single nucleotide polymorphism (SNP) is a variation in the DNA
-microsatellites (repeated elements)
-SNP may be: close to or in the gene (marker)
-actual causative mutation
linkage
-recombination (crossover) more likely between gene mutation and marker
-marker is segregating with the trait and muation
what are the two types of linkage tests
biallelic markers or multialleic markers
bialleic marker
-(ie SNP) in or close to mutation
-only need to test the individual
multallelic markers
(i.e microsatellites) near mutation
-need to test parents
polymerase chain reaction
-small starting material to amplify DNA
-denature using heat
-primers
-DNA polymerases extends the sequence
-repeated 30x
DNA extraction
-PCR amplifies DNA form a small amount of starting material
-hair roots
-straw of semen
-blood
-embryo
-milk
-tooth pulp
central dogma of molecular biology
DNA replication
DNA
(reverse transcrip) transcription
mRNA (rna replication)
translation
protein
what does genomic DNA include
exons and introns
how is protein made
DNA: double stranded
-transcription of coding genes
RNA: single stranded
-spicing introns leaving exons
messenger RNA
-translation
amino acid chain
-folding
protein
mutation detection
compares DNA sequence (chromatography) among many animals
affects of amino acid changes…
-check if amino acid is changes
-not all mutants have functional effects
-stop codon is always significant
-cysteine changes usually significant
-amino acids are 4 groups- does group change?
mutations in coding sequence
-start with wild type
-synonymous: silent
-non-synonomous:
-missence mutation
-nonsence mutation
-frame shift mutation
how many precent of DNA actually codes for something
2%
silent mutation
-third position of codons often
-AA does not change
missence mutation
-AA changes
-impairs or abolishes protein function
leptin mutation
-missence mutation
-arganine (basic) to cysteine (polar)
-creates disulphide bridges
non sence mutation
-change in nucleotide results in AA change to a stop codon
-premature stop codon causes a truncated protein
frame shift mutation
-insertion or deletion of nucleotides
-causes a “frame shift” in the DNA sequence
-prematue stop codon (truncated protein)
inframe insertion or deletion
adds or removes multiple proteins to sequence
mutations in the non-coding sequence. including effects of mutation in regulatory region, spice site, suppressor region
-may or may not have effect on phenotype in non-coding regions
-mutation in regulatory region:
-turn on a gene and cause protein to be produced in wrong place or at the wrong time
-can reduce or eliminate the production of an important protein when needed
-mutation in splice site:
-mRNA may not spice correctly
-mutation in an enhancer or suppressor region:
-reduces or increases the amount of protein
fishy egg taint
-FMO3 (detoxifying liver enzyme)
-A to T SNP in exon 7
-causes Thr to Ser at aa 329
-but it occurs in highly conserved motif
-loss of enzyme function
APAF1
-Holstein bull- one of the most prolific bulls born in 1966 accounts for 14% of current us holstein population
-introduced a recessive mutation in APAF1 gene to population
-causes embryonic and fetal mortality
-cytosine to thymine nucleotide change results in glutamine to stop amino acid change
bulldog dwarfism in dexters
-gene aggrecan
-results in premature stop codon position 914 (normally 2327 aa)
-two copies result in fetal death
-single copie results in dwarfism
double muscling
-gene myostatin (GDF8)
-muscling hypertrophy or double muscling especially in hindquarters
-reduced body fat and intramuscular
-different mutations depending on the breed
double muscling history
-identified as autosomal recessive in 1970
-mapped to chromosome 2 in 1995
-mouse gene found 1996 on “equivalent” chromosome
-mouse gene used to find cattle gene 1997
-7 different mutations identified in different cattle breeds in coding sequence
-identified in goats, dogs, humans
