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