1. 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

8. 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.

9. 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.

10. Generating the Backcross
Cast/EiJ x C57BL/6J
F1 x Cast/EiJ
BC1s
Backcross progeny have on average:
75% CE, 25% B6 alleles 50% C/C, 50% C/B genotypes for all loci
C57BL/6J (B6)
Cast/EiJ (CE)

13. Some types of detectable variation
RFLPs (Restriction fragment length polymorphisms)
VNTRs (Variable nucleotide tandem repeats) = minisatellites
Microsatellites
SNPs (Single nucleotide polymorphisms)

14. Microsatellite Analysis by PCR

15. Genotyping Extract DNA from brain, liver or tail
Genotype mice using markers distributed throughout genome (10 cM resolution)
Use microsatellite repeats
CACACACACACACACAC CE GTGTGTGTGTGTGTGTG
CACACACACACACACACACACACACACACA B6 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
Using primers flanking the repeat region gives PCR products of different size

16. Genotyping D1Mit119 Chr 1, 10 cM D14Mit169 Chr 14, 54 cM

17. Genetic Map of Markers used in Analysis

18. Genome-Wide Scan for QTL
Black = Max likelihood (EM algorithm) Blue = Haley-Knott regression

21. QTL-analysis in Recombinant Inbred (RI) Strains of Mice
Generation of C57BL/6J X DBA/2J (BXD-RI) Strains