Complex Traits

• Most neurobehavioral traits are complex– Multifactorial– Polygenic– Multigenic

• QTL: quantitative trait locus– Region of a chromosome that contains a gene(s) with different

alleles that contributes quantitatively to the variance in a trait

Quantitative Trait Loci (QTL):the specific loci whose allelic differences are

responsible for the genetic variation in a quantitative trait (e.g. total sleep time)

Note: QTL does not refer to the sum total of all loci that influence a particular trait, only those

loci that are functionally polymorphic (with respect to the trait of interest) between the

parental strains. Mutagenesis and engineered KOs can artificially alter any gene, however, polymorphisms can represent more subtle

“natural” variations.

QTL Mapping• QTL mapping: identification of chromosomal regions containing

gene(s) that correlate with measured phenotypes

• Different methods– Single-marker analysis: compares phenotypic means of different

marker genotypes – Interval mapping: estimates position of QTL between two markers

using maximum likelihood– Composite Interval mapping: IM and multiple regression– Multiple QTL models

• QTL present when LOD score exceeds critical threshold– LOD = Log of the Odds = log10 (H1/H0) – often for single locus analysis, 3.0 is significant and 2.0 is

suggestive depending on sample size, number of markers, and other variables.

Generating the Backcross

Cast/EiJ x C57BL/6J

F1 x Cast/EiJ

BC1s

Backcross progeny have on average:

75% CE, 25% B6 alleles50% C/C, 50% C/B genotypes for all loci

C57BL/6J (B6)

Cast/EiJ (CE)

Some types of detectable variation

• RFLPs (Restriction fragment length polymorphisms)

• VNTRs (Variable nucleotide tandem repeats) = minisatellites

• Microsatellites

• SNPs (Single nucleotide polymorphisms)

Microsatellite Analysis by PCR

Genotyping

• Extract DNA from brain, liver or tail• Genotype mice using markers distributed throughout

genome (10 cM resolution)• Use microsatellite repeats

CACACACACACACACAC CEGTGTGTGTGTGTGTGTG

CACACACACACACACACACACACACACACA B6GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT

• Using primers flanking the repeat region gives PCR products of different size

GenotypingD1Mit119Chr 1, 10 cM

D12Mit141Chr 12, 55 cM

D14Mit169Chr 14, 54 cM

D18Mit122Chr 18, 31 cM

Genetic Map of Markers used in Analysis

Genome-Wide Scan for QTL

Black = Max likelihood (EM algorithm) Blue = Haley-Knott regression

QTL-analysis in Recombinant Inbred (RI) Strains of Mice

Generation of C57BL/6J X DBA/2J (BXD-RI) Strains