What is a QTL?What are QTL?

Current methods for QTL Single Marker Methods (Student, 17??)

t-tests

Interval Mapping Method (Lander and Botstein, Genetics 1989)

Mapping: estimate genetic maps Locating QTL: based on genetic map

Composite Interval Mapping (Jansen 1993; Zeng 1993, 1994; Genetics)

Locating QTL: based on genetic map

Understanding variability... what causes it? can we account for it?

Making predictions where there is uncertainty...

Drawing conclusions from incomplete information...

Statistical Genetics/Genomics

microarray

QTL

protein

microarray

quantitative

expression

trait mapping (QTL)

RW Doerge; Nature Reviews Genetics.2002. 3:43-52

Metabolism under phenotype

• Keurentjes, J.J.B. et al. Nat. Genet. 38, 842–849 (2006). | Article |

• Clusters of metabolite level traits are controlled by pleiotropic QTL

…the big picture

There are “genes” or “regions’’ of DNA associated with traits, diseases, resistances of interest.

yield in corn oil content in soybean sugars of tomato multiple sclerosis in human

Statistical Genetics aims to understand these genomic regions

Quantitative Trait Loci (QTL): genomic regions associated with a quantitative trait of interest.

Complex traits: are controlled by many QTL, often behaving differently in changing environments and under different conditions.

…example

Major Quantitative Trait Locus

Doebley & Stec (1991) Genetics

QTL mapping of many traits in the same RILs

Annual Review of Plant BiologyVol. 55: 141-172 (Volume publication date June 2004)

(doi:10.1146/annurev.arplant.55.031903.141605)

First published online as a Review in Advance on December 12, 2003 NATURALLY OCCURRING GENETIC VARIATION IN

ARABIDOPSIS THALIANAMaarten Koornneef,1 Carlos Alonso-Blanco,2 and Dick

Vreugdenhil3

Cloned QTL in ArabidopsisLocus Trait Molecular function

Functional polymorphism

Functional alteration References

CAL Inflorescence morphology MADS TF SNP Altered protein (66)

FRI Flowering Unknown INDELs (1-345 bp) Truncated protein

(43, 58, 79)

FLC Flowering MADS TF INDELs (1.2 to 4.2 kb)

Expression level

(43, 109)

EDI Flowering CRY2 photoreceptor SNP AA substitution (37)

PHYA Hypocotyl length PHYA photoreceptor SNP AA substitution (99)

PHYD Flowering/hypocotyl length

PHYD photoreceptor INDEL (14 bp) Truncated protein

(12)

AOP2 Glucosinolate biosynthesis

2-oxoglutarate-dioxygenase

INDEL (5 bp) Expression level

(71)

AOP3 Glucosinolate biosynthesis

2-oxoglutarate-dioxygenase

Unknown Expression level

(71)

ESP Glucosinolate hydrolysis Epithiospecifier protein

INDELs, SNP Expression level

(87)

MAM1 Glucosinolate biosynthesis

Methylthioalkylmalate synthase

INDELs, (several kb)

Deleted gene (80)

MAM2 Glucosinolates/insect resistance

Methylthioalkylmalate synthase

INDELs, (several kb)

Deleted gene (80)

RTM1 Virus resistance Jacalin-like protein SNP Truncated protein

(30)

RPS2 Resistance to pseudomonas

LRR protein INDEL (10 bp), SNP Truncated protein

(111)

RPM1 Resistance to pseudomonas

LRR protein INDEL (2.8 kb) Deleted gene (150)

Experimental Populations for QTL Study

Backcross 1 Backcross 2

RW Doerge; Nature Reviews Genetics.2002. 3:43-52

Estimated Genetic Map(framework for QTL mapping)

Chromosome 11 mouseRW Doerge; Nature Reviews Genetics.2002. 3:43-52; Butterfield et al., 1999; Journal of Immunology

Single Marker Analysis

Using a recombinant inbred (RI) or backcross population there are two possible alleles at each marker and, two genotypic classes per marker

RI: M1/M1 and M2/M2 Backcross: M1/M1 and M1/M2

Each individual: genotypic and phenotypic data

consider: marker M and trait Y every marker has 2 states:

homozygous 1: M1/M1 heterozygous 2: M1/M2

using a simple t-test

split individuals into marker classes calculate

sample means and variances on Y

test for differences in means

…diamonds are the single markers

RW Doerge. Nature Reviews Genetics.2002. 3:43-52

…take advantage of marker order Interval Mapping

Marker M: alleles M1 and M2

Marker N: alleles N1 and N2

Distance between M and R defined by recombination r the values of r is estimated and known M-------r--------N

Use the additional information from knowing ‘r’ to locate QTL

Lander and Bostein. 1989. Genetics

M NQ Q

r

Locate QTL by stepping through the interval defined by M and N

1r 2r1r 2r

• With arrays markers are no longer limiting

• >10k SFPs

Composite Interval MappingMultiple QTL Mapping (MQM)

• Y=x*b* + X B +E

• Y is a quantitative trait (gene expression) vector, i=1,…,n• b* effects of the putative QTL being tested • x* is an indicator variable specifying the probability of an

individual being in the different genotypic classes for the supposed QTL, depending on the flanking markers which define the interval.

• B is the vector of effects of selected markers fitted in the model

• X is the design matrix for the selected markers

• E is the error vector

cofactors

Zeng 1993, 1994; Jansen 1993; Genetics

interval mapping

QTL mapping methodology

Churchill & Doerge 1994

interval mapping

composite interval mapping

permutation threshold

single marker

Fisher 1935; Thoday 1961; Lander and Botstein 1989; Zeng 1994;

Overall Summary QTL methodology

Detect and locate QTL

Locating QTL depends on genetic map Many statistical and genetic issues

Permutation thresholds are specific to experiment

eQTL utilize expression data as quantitative traits to map expression variation molecular dissection of complex traits