Selection via DNA in livestock

Question 1

what are the trait types

Answer 1

qualitative and quantitative

Question 2

indirect and direct DNA tests

Answer 2

-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

Question 3

linkage

Answer 3

-recombination (crossover) more likely between gene mutation and marker
-marker is segregating with the trait and muation

Question 4

what are the two types of linkage tests

Answer 4

biallelic markers or multialleic markers

Question 5

bialleic marker

Answer 5

-(ie SNP) in or close to mutation
-only need to test the individual

Question 6

multallelic markers

Answer 6

(i.e microsatellites) near mutation
-need to test parents

Question 7

polymerase chain reaction

Answer 7

-small starting material to amplify DNA
-denature using heat
-primers
-DNA polymerases extends the sequence
-repeated 30x

Question 8

DNA extraction

Answer 8

-PCR amplifies DNA form a small amount of starting material
-hair roots
-straw of semen
-blood
-embryo
-milk
-tooth pulp

Question 9

central dogma of molecular biology

Answer 9

DNA replication
DNA
(reverse transcrip) transcription
mRNA (rna replication)
translation
protein

Question 10

what does genomic DNA include

Answer 10

exons and introns

Question 11

how is protein made

Answer 11

DNA: double stranded
-transcription of coding genes
RNA: single stranded
-spicing introns leaving exons
messenger RNA
-translation
amino acid chain
-folding
protein

Question 12

mutation detection

Answer 12

compares DNA sequence (chromatography) among many animals

Question 13

affects of amino acid changes…

Answer 13

-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?

Question 14

mutations in coding sequence

Answer 14

-start with wild type
-synonymous: silent
-non-synonomous:
-missence mutation
-nonsence mutation
-frame shift mutation

Question 15

how many precent of DNA actually codes for something

Answer 15

2%

Question 16

silent mutation

Answer 16

-third position of codons often
-AA does not change

Question 17

missence mutation

Answer 17

-AA changes
-impairs or abolishes protein function

Question 18

leptin mutation

Answer 18

-missence mutation
-arganine (basic) to cysteine (polar)
-creates disulphide bridges

Question 19

non sence mutation

Answer 19

-change in nucleotide results in AA change to a stop codon
-premature stop codon causes a truncated protein

Question 20

frame shift mutation

Answer 20

-insertion or deletion of nucleotides
-causes a “frame shift” in the DNA sequence
-prematue stop codon (truncated protein)

Question 21

inframe insertion or deletion

Answer 21

adds or removes multiple proteins to sequence

Question 22

mutations in the non-coding sequence. including effects of mutation in regulatory region, spice site, suppressor region

Answer 22

-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

Question 23

fishy egg taint

Answer 23

-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

Question 24

APAF1

Answer 24

-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

Question 25

bulldog dwarfism in dexters

Answer 25

-gene aggrecan
-results in premature stop codon position 914 (normally 2327 aa)
-two copies result in fetal death
-single copie results in dwarfism

Question 26

double muscling

Answer 26

-gene myostatin (GDF8)
-muscling hypertrophy or double muscling especially in hindquarters
-reduced body fat and intramuscular
-different mutations depending on the breed

Question 27

double muscling history

Answer 27

-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