thomas hunt
used fruit flies to demonstrate that linked genes must be real physical objects that are located proximity on the same chromosome
bateson et al.
crossed homozygous pea plants (performed a typical dihybrid cross between one pure line with purple flowers and long pollen grains and a second pure line with red flowers and round pollen grains) and discovered genes display partial linkage
morgan
discovered eye-color trait in fruit flies was connected with the sex factor (In order to get white-eyed females, he crossed males w/daughters) (originally no white eyes females)
linkage equilibrium
if the occurrence of an allele at one locus is independent of the presence or absence of an allele at a second locus
loci on difference chromosomes
behave independently and thus are in linkage equilibrium
linkage disequilibrium
if the occurrence os an allele at one locus is nonrandomly associated with the presence or absence of an allele at a second locus
two different loci close together on the same chromosome
can be randomly linked
degree of linkage of different locu depends on
the distance between them
single nucleotide polymorphism (SNP)
is a variation at a single position in a DNA sequences among individuals
if more than 1% of a population does not carry the same nucleotide at a specific position in the DNA sequence then ___
this variation can be classified as a SNP
if SNP occurs within a gene
then the gene is describe as having more than one allele
SNPs can be used as
markers to detect the presence of disease-risk alleles
supergene
group of functionally related genes close enough together to segregate as a unit (a supergene is a group of genes that are inherited together as a unit, often with a lot of other noncoding DNA)
QTL analysis links
traits with genes
QTL
analysis method that links two types of information of phenotypic data and genotypic data in an attempt to explain genetic variation in complex traits
QTL analysis requirements
-two or more strains of organisms that differ genetically with regard to the trait of interest
-genetic markers that distinguish between these parental lines (favorable)
several types of markers are used as well as
SNPs, SSRs or microsatellites, RFLPS, and transposable elements position
to carry out QTL analysis,
the parental strains are croossed, resulting in heterozygous (F1) then crossed
markers that are gentically linked to a QTL influencing the trait of interest will
segregate ore frequently with traits values whereas unlinked markers will not show significant association with phenotype
QTL analysis can help researches identify
genes contributing to variation in several different traits
Hoeksra el al QTL analysis of coat color in mice
after crossing, correlation with alleles were found in two loci associated with coloration. Agouti (strongest correlation with coat color) and Mc1r
Mc1r
encodes that triggers the production of pigment (dark pigment)
Agouti
production of light pigment (by encoding a receptor that shuts down the Mc1r receptor
Expression of Agouti during development influences
coat color
Genetic manipulation of dark mice makes them
lighter
the members of the F1 generation would be invariant and would have an intermediate phenotype
the F2 generation would be variable
regulatory genes
genes that code for transcription factors
genome wide association (GWA)
mapping involves scanning through genomes of many different individuals w/or w/o focal trait of interest, to search for markers associated with expression of that trait
GWA studies
produce many unlinked individual genes but riddled with large expected numbers of false positives
GWAS contribute ot the
phenotype of interest
GWA scan for
genetic loci associated with disease risk
genetic and evironmental influences on phenotype
Vp = VG + VE
several complex traits in the fruit fly Drosophila melanogaster has revealed
that many genes influence longevity and significant-by-environment effect have also been reported for life span
phenotypic plasticity
a single genotype produces different phenotypes depending on the environment
snowshoe hares exhibit
phenotypic platicity
reaction norm can
predict response to environment
reaction norm
refers to the pattern of phenotypic expression of a single genotype across a range of environment
all genotypes may not respond to the
environment in the same way
phenotypic plasticity
in Caenorhabditis elegans
QTL analysis shows
chromosome IV is strongly associated with levels of plasticity in fertility
plasticity can
evolve
QTL and GWA
identifies regions of the genome associated with phenotypic variation
differences in phenotypic plasticity may be heritable and adaptive phenotypic plasticity can therefore evolve
may be heritable and adaptive phenotypic plasticity can therefore evolve