An introduction to quantitative genetics

Dan Chitwood

(with slides from Julin Maloof)

March 16, 2015

What is a QTL?

• QTL– Quantitative Trait Locus– A genetic locus that contributes to quantitative

variation in a trait

• What is a quantitative trait? What contributes to the concept of “trait?”– Genes?– Environment?– Cross/allele/species background?– The researcher?

Is hypocotyl length a quantitative trait? No?

Qualitative: can classifyas tall or shortWT phyB

Is hypocotyl length a quantitative trait? Yes?

Segregation Ler x Cvi RIL

Quantitative: must measure (quantify) differences

What causes quantitative segregation?

• Signal to noise (allelic effect versus unexplained variance, environment, error)

• Multiple genes segregating, smaller effects (polygenic traits)

What causes quantitative segregation?

• Signal to noise (allelic effect versus unexplained variance, environment, error)

• Multiple genes segregating, smaller effects (polygenic traits)

allele effect = 3 allele effect = 2

Two Loci

+

Why study development with QTL?

• Micro-evolution– what makes two strains/populations/species

different?

– (Teosinte/Maize; Mimmulus; etc)

• Plant Breeding– Fruit shattering

– Flowering

– etc.

• Human Disease

• Different spectrum of loci than available through forward genetics

Single marker regression

• Simplified version:

– Phenotype all individuals

QTL mapping: Single marker regression

Marker “A” is linked to a hypocotyl QTL Marker “C” is unlinked

• Simplified version: – Phenotype all individuals– Genotype all individuals– Look for correlation

QTL mapping: Single marker regression

-Repeat, analyzing correlation to trait for 100s of makers

-Limitations:

-Confounding: can not separate QTL effect (size) and location of the QTL (relative to the marker).

-Does not account for effect of other contributing loci/markers

QTL mapping: Single marker regression

y = m*x + bhyp = m*gtB + mean + erroris m not equal to 0? If so, then we have a QTL

QTL mapping: Single marker regression

y = m*x + bhyp = m*gtB + mean + erroris m not equal to 0? If so, then we have a QTL

QTL mapping: Single marker regression

Simple interval mapping

QTL mapping: recombinationincreases variance

• The QTL “Q” may be some distance from marker “B”

• Parent genotypes: B-Q and b-q

• Progeny genotypes: B-Q, b-q, B-q, b-Q

• genotype at QTL: Q or q

• Solution:– Interval mapping

Simple Interval Mapping(SIM; Lander and Botstein)

• Evaluate intervals between markers rather than markers themselves

• Conceptually:

– Parents: B-Q-D and b-q-d

– Progeny:

• B-Q-D and b-q-d

• b-q-D b-Q-D B-Q-d B-q-d

• very rare: B-q-D b-Q-d

– Use B-D and b-d to estimate allelic effect size of QTL

– Use recombinants to estimate whether QTL is closer to B or D

– LOD score: Likelihood of linkage. Log10 of ratio of likelihood of linkage / likelihood unlinked

Simple Interval Mapping(SIM; Lander and Botstein)

• Evaluate intervals between markers rather than markers themselves

• In reality– The position of the QTL in the interval is evaluated by maximum likelihood.

– At each position in the interval an iterative algorithm is used to determine the most likely model given the data.

– The likelihood of a model with the QTL is compared to the null model (no QTL).

– These two likelihoods are compared to give a LOD score

• LOD score = log10(Likelihood with QTL/Likelihood no QTL)– what does a LOD score of 2 indicate?

Composite interval mapping

QTL mapping: other loci increase variance

QTL mapping: other loci increase variance

Problem with SIM: Linked and unlinked QTL affect the analysis

QTL mapping: composite interval mapping (Zeng; Jansen and Stam)

Simplifying and ignoring the “interval” issue:hyp = mean + m1*gtB + m2*gtA* + error

Composite IntervalPartial CIMSimple Interval Mapping

Zeng, Genetics, 1994

Comparison of QTL methods

Practicalities of QTL experiments

Practicalities—Backcross Population

Practicalities—F2 population

Practicalities:RIL population

Practicalities: experimental design

Design:

Randomization,

Replication,

Measurer effects,

Positional effects,

Environmental effects

y = m*x + bhyp = m*gtB +mean + erroris m not equal to 0? If so, then we have a QTL

QTL mapping: Single marker regression

J. MaloofPhotos: Charlie Rick, TGRC

Solanum pennellii(Peruvian desert)

Solanum lycopersicum(cultivated)

Desert tomato

Cactus

Single marker regression, sort of:Tomato introgression lines

Single marker regression, sort of:Tomato introgression lines

X

Backcross,marker-assisted selection

Self

…

Look forphenotypicdifferences

S. lycopersicum (domesticated)

S. pennellii (desert)

Single marker regression, sort of:Tomato introgression lines

Ravi KumarAashish RanjanMike Covington

RNA-Seq (genic polymorphisms) RESCAN (genic/non-genic polymorphisms)

Genotyping using next-generation sequencing

Kumar et al., Front. Plant Sci. 2012

A precise genetic map of thetomato introgression lines

Chitwood et al., Plant Cell (2013)

A precise genetic map of thetomato introgression lines

Chitwood et al., Plant Cell (2013)

Detecting subtle change takes field space andgenerates large phenomic datasets . . .

Field Aggie Stadium

Medical Center

Detecting subtle change takes field space andgenerates large phenomic datasets . . .

Detecting subtle change takes field space andgenerates large phenomic datasets . . .

Detecting subtle change takes field space andgenerates large phenomic datasets . . .

A QTLNetwork . . .

IntrogressionLines

Classic examples ofQTL experiments

Doebley et al. Genetics 1995

Crop Domestication

Crop Domestication

tb1-ref tb1-refA158 A158

Doebley et al. The evolution of apical dominance in maize. Nature 1997

A. Mimulus lewisii--Bee PollinatedC. Mimulus cardinalis--Humingbird Pollinated

Schemske and Bradshaw, PNAS 1999

Pollination Syndromes

Variation in F2Schemske and BradshawPNAS 1999

M. lewisii M. cardinalisF1 Hybrid

F2

• Measure visitation rates in F2 population

• Look for correlation between floral QTL and visitation

• One QTL increases carotenoids -> decreases bee visitation 80%

• Another QTL increases nectar 3-fold, double hummingbird visits (indpendent of color)

Which Traits affect pollinator visitation?

Genetics of Reproductive Isolation

• 12 Traits…47 QTL

• 9/12 Traits had “major” QTL

• Therefore, major QTL can play a role in speciation.

– Contrasts with a very polygenic, additive small effect loci view of evolution

Genetics of Reproductive Isolation

Kuhlemeier Lab

Genetics of Reproductive Isolation

Hoballah et al. Plant Cell 2007

Genetics of Reproductive Isolation

Hoballah et al. Plant Cell 2007

Frary et al. Science 2000

Crop Breeding

S. pimpinellifolium S. lycopersicum

Transgenic forS. pennellii fw2.2candidate

Fruit Weight

• Cross wild to domesticated

• 11 fruit mass QTL

• fw2.2 largest effect, modifying fruit size up to 30%

• Create NIL and backcross

• Large allele in domesticated partially recessive

• Transgenics with wild allele have smaller fruit

• Structural homology to ras oncogene

Developmental effect of fw2.2?

• What makes 2 alleles different?

• Expression: temporal expression different

• Phenotypic effect: Reduced cell division in carpels

Real QTL effects are often “wimpy”

--ie, polygenic, small effects

--Contrasts with tb1 and pollinator shifts

Drastic differences in fruit and leaf phenotypesbetween wild and domesticated tomato species

How do we measure leaf shape?Elliptical Fourier Shape Descriptors

How do we measure leaf shape?Elliptical Fourier Shape Descriptors

-2 SD +2 SD Overlay

PC144.4%

S.penn(desert)

S.lyco(dom.)

How do we measure shape?Elliptical Fourier Shape Descriptors

-2 SD +2 SD Overlay

PC144.4%

PC213.0%

How do we measure shape?Elliptical Fourier Shape Descriptors

-2 SD +2 SD Overlay

PC144.4%

PC213.0%

PC36.9%

PC46.6%

PC54.1%

-5.00E-02

-4.00E-02

-3.00E-02

-2.00E-02

-1.00E-02

0.00E+00

1.00E-02

2.00E-02

3.00E-02

4.00E-02

5.00E-02

-0.55 -0.45 -0.35 -0.25 -0.15 -0.05 0.05

S.lyco(dom.)

The genetic basis of natural variationin leaflet morphology: an example

PC1

PC2

-5.00E-02

-4.00E-02

-3.00E-02

-2.00E-02

-1.00E-02

0.00E+00

1.00E-02

2.00E-02

3.00E-02

4.00E-02

5.00E-02

-0.55 -0.45 -0.35 -0.25 -0.15 -0.05 0.05

S.penn(desert)

IL4-3

S.lyco(dom.)

PC1

PC2

The genetic basis of natural variationin leaflet morphology: an example

-5.00E-02

-4.00E-02

-3.00E-02

-2.00E-02

-1.00E-02

0.00E+00

1.00E-02

2.00E-02

3.00E-02

4.00E-02

5.00E-02

-0.55 -0.45 -0.35 -0.25 -0.15 -0.05 0.05

S.penn(desert)

IL4-3

S.lyco(dom.)

PC1

PC2

The genetic basis of natural variationin leaflet morphology: an example

How to explain shapedifferences between tomatoes?

--Polygenic trait or epistasis

-5.00E-02

-4.00E-02

-3.00E-02

-2.00E-02

-1.00E-02

0.00E+00

1.00E-02

2.00E-02

3.00E-02

4.00E-02

5.00E-02

-0.55 -0.45 -0.35 -0.25 -0.15 -0.05 0.05

S.penn(desert)

IL4-3

S.lyco(dom.)

PC1

PC2

The genetic basis of natural variationin leaflet morphology: an example

How to explain shapedifferences between tomatoes?

--Polygenic trait or epistasis--Additive effects?

QTL Advances

The Punctate phenotype:An example of bulk-segregant approaches

with next-generation sequencing

S. pennellii, low magnification S. penn., high magnification

The Punctate locus lies on chromosome 10

S. lycopersicumIL10-3, chrom. 10

The Punctate locus lies on chromosome 10

IL10-3, chrom. 10

The Punctate locus lies on chromosome 10

IL10-3, chrom. 10

Chromosomes1 2 3 4 5 6 7 8 9 10 11 12

Chromosome 10

The Punctate locus lies on chromosome 10

IL10-3, chrom. 10

Chromosomes1 2 3 4 5 6 7 8 9 10 11 12

Chromosome 10

2.65 Mbp; ~300 genes

X

…

S. lycopersicum (domesticated)

S. pennellii (desert)

BackcrossedIntrogression Lines (BILs)

Backcrosses

Self

BIL-460

BIL-430

BIL-263

BIL-274

BIL-202

BIL-040

BIL-218

BIL-176

BIL-466

BIL-405

BIL-057

BIL-194

BIL-376

BIL-232

BIL-127

BIL-347

1 2 3 4 5 6 7 8 9 10 11 12Chromosome

Genotypes of Punctate BILs share chrom. 10 region

Aashish Ranjan

BIL-224

BIL-067

BIL-039

BIL-215

BIL-176

BIL-031

BIL-427

BIL-007

BIL-003

BIL-289

BIL-422

BIL-433

BIL-066

BIL-439

BIL-275

BIL-360

BIL-046

Genotypes of Punctate BILs share chrom. 10 region

1 2 3 4 5 6 7 8 9 10 11 12Chromosome

Aashish Ranjan

On the Pn interval are four related MYBs,one of which is is Anthocyanin 1 (ANT1)

“MYB250” ANT1 “MYB270” Heavy metal-associateddomain gene

“MYB290”

S. lycopersicum:

Aashish Ranjan

This et al. TAG 2007Foumier-Level et al. Genetics 2009

. . . but berry color in grape is also causedby a set of tandemly duplicated MYBs!

MYBA2 MYBA1V. vinifera:

MYBA3

Relatedness of Vitis, Solanum, andArabidopsis MYBs

Relatedness of Vitis, Solanum, andArabidopsis MYBs

V. vinifera (Grape)

S. lycopersicum (Tomato)

Arabidopsis

Quattrocchio et al. Plant Cell 2006

The Arabidopsis MYB homolog also affects trichome pigmentation

Dissertation of Antonio Gonzalez

35S:MYB114

MYB113 MYB114 PAP2/MYB90

Arabidopsis

Evolution at work:from berries to trichomes

V. vinifera (Grape)

S. lycopersicum (Tomato)Arabidopsis

• 4,523 eQTL for 4,066 genes

A QTLNetwork . . .

IntrogressionLines

IL4-3

Gene expression as phenotype: eQTL, cis- and trans-relationships, and transcriptional networks

IL4-3:I

II

III

IV

VVIVII

VIII

IX

X

XIXII

S. pennellii (desert)

S. lycopersicum (domesticated)

Gene expression as phenotype: eQTL, cis- and trans-relationships, and transcriptional networks

S. pennellii (desert)

S. lycopersicum (domesticated)

IL4-3:

IV

Differentially expressed:IL4-3 <-> S. lycopersicum

cis- regulation

Gene expression as phenotype: eQTL, cis- and trans-relationships, and transcriptional networks

S. pennellii (desert)

S. lycopersicum (domesticated)

IL4-3:

IV

Differentially expressed:IL4-3 <-> S. lycopersicum

cis- regulation

trans-regulation

Adaxial Abaxial

S. ly

co.

(do

mes

tica

ted

)S.

pen

n.

(de

sert

)

Another phenotype of IL4-3:Increased pavement cell size

Pavement cellsize:

The molecular mechanismsunderlying cellular natural variation

Histone H3A, Histone H3B, Histone H2B, MCM3, MCM4,

MCM5,ssDNA replication binding

protein,Cyclin B1, Cyclin B2,

CDC20

Up-regulatedgenes:

The molecular mechanismsunderlying cellular natural variation

Histone H3A, Histone H3B, Histone H2B, MCM3, MCM4,

MCM5,ssDNA replication binding

protein,Cyclin B1, Cyclin B2,

CDC20

Cell cycle

Up-regulatedgenes:

Sig. GO terms,trans-regulatedgenes:

The molecular mechanismsunderlying cellular natural variation

Histone H3A, Histone H3B, Histone H2B, MCM3, MCM4,

MCM5,ssDNA replication binding

protein,Cyclin B1, Cyclin B2,

CDC20

Cell cycle

E2F binding

site

Up-regulatedgenes:

Sig. GO terms,trans-regulatedgenes:

Promoter motifs,trans-regulatedgenes

CDS

E2F promotes endoreduplication

G1

SG2

M

E2F

Mitosis

Endocycle

E2F promotes endoreduplication

0

0.5

1

1.5

2

2.5

3

3.5

4

4.5

SKP2A expression is reducedin S. penn. and IL4-3

G1

SG2

M

SKP2A E2F

Mitosis

Endocycle

Exp

ress

ion

leve

l

Lauren Headland