analysis of genetic control of fruit size in apple using ... · pdf filediameter, height x x x...

Analysis of genetic control of fruit

size in apple using both multiple,

pedigree-related and single full-

sib familiesHélène MURANTY, François LAURENS, Marco C.A.M. BINK ,

Eric van de WEG

Hélène MURANTY RGC8 21-23 June 2016

• Fruit size = appearance + yield component

• QTL for marker-assisted selection

– large population precise location

– large diversity consistency across genetic backgrounds

Pedigree-based analysis

• Bink et al 2002, 2008, 2014

• Rosyara et al 2013

• Fresnedo-Ramírez et al 2015, 2016

• Roach et al 2016

• Allard et al 2016

2

Introduction


2

33Hélène MURANTY RGC8 21-23 June 2016

3

reference cross pop

size

fruit trait linkage group

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

Liebhard et al

(2003)

Discovery × Fiesta 251 weight

X X X X X X X X

Kenis et al (2008) Telamon × Braeburn 199 /

165

weight,

diameter, heightX X X X X X X

Devoghalaere et al

(2012)

Royal Gala ×

Braeburn

572

weight X X X X X XStarkrimson ×

Granny Smith

123

Chang et al (2014) Jonathan × Golden

Delicious

144 /

140

weight,

diameter, lengthX X X X

Costa (2015)

Fuji × Delearly 86

size, weight,

diameter, heightX X X X X X X

Fuji × Cripps Pink 73

Golden Delicious ×

Scarlet

185

Golden Delicious ×

Braeburn

75

Previous studies

4RGC8 21-23 June 2016Hélène MURANTY

GoldenDel

AntonovkaOB

F_B8_34.16

Clochard

Winesap

F_Delicious

F2_26829-2-2

EsopSpitz

F_Jonathan

Prima

GranSmith

Cox

McIntosh

F_Melba

JerseyBla

F_IngMarie

F_Lobo

F_LadyWill

DrOldenbu

F_JamesGr

WorcPearm

BeautBath

BVIII_34.16

F_X-4355

Chantecler

Delicious

PRI14-126

PRI14-152

Jonathan

Wines_Prima

Wagenerap

Coop-17

Rubinette

RomBeauty

X-6823

RallsJan

F_Wealthy

Melba

Macoun

F_Alwa

IngMarie

Lobo

F_Priscilla-NL

LadyWill

Alkmene

Clivia

JamesGr

Telamon

F_Braeburn

67-47

BX44.14

Discovery

Z185

PRI612-1

Idared

PRI672-3

ReiDuMans

X-3259

Crandall

F_O53T136

X-6679

KidsOrRed

Fuji

PRI668-100

Wealthy

F_Linda

Priam

Alwa

Melrose

D1955-44-220

Elstar

D3_DLO

Priscilla-NL

PinkLady

Pinova

Lambourne

Braeburn

Rewena

Pirol

Reanda

JoPr

DiPr

X-4355

Florina

X-3177

X-6799

O53T136

Gala

X-2771

RedWinter

Linda

Primula

PRI1661-2

F_Enterprise

X-4638

PRI54-12

D1972-10-33

D1973-01-41

Sampion

FuPi

TeBr

RePir

AlPi

PiRea

X-6820

X-6681

Baujade

TN_R10A8

X-6564

Galarina

X-3143

X-3263

RedWinterX3177

Fantazja

U1065

Enterprise

X-6808

Dorianne

Ligol

Liberty

D1980-15-25

FuGa

GaCr

GaPi

PiGa

AlSz

Generos

X-6683

X-6398

X-3305

X-6417

X-3318

Sawa

12_O

GaEn

12_K

I_CC

12_I

LiAl

MeLi

DLO-12

12_E

I_M

I_W

12_N

12_P

12_B

12_L

I_BB

12_F

12_J

I_J

Sa10

founders parents related FS families supplementary FS familiesintermediate ancestors separate FS families

HiDRAS

Material

26 related

families

2 families

phenotyped

separately

Phenotypes


HiDRAS

• 6 sites

• 30 control varieties

• 3 harvests (2003 2005)

• fruit size scored on a 1-5 scale

• well-shaped distributions

Phenotypes


HiDRAS

• 6 sites


• 3 harvests (2003 2005)


DLO-12 • 2 harvests (2006 – 2007)

• fruit weight


• moderate to high correlations

between years

Phenotypes


HiDRAS

• 6 sites


• 3 harvests (2003 2005)


DLO-12 • 2 harvests (2006 – 2007)

• fruit weight

Te x Br • 3 harvests (2004 2006)

• fruit weight

• fruit height (H) and diameter (D)


• moderate to high correlations

between years

• high correlation between diameter

and weight within year


Marker data

20K SNP array (Bianco et al 2014)

genetic mapping in 20 FS families

focal point mapping across families(E. di Piero et al, in prep.)

haploblock markers building

scrutinizing for Mendelian

inconsistencies

scrutinizing for double

recombinants

null-allelesadditional SNP at the probe setparalogous loci


Marker data

20K SNP array (Bianco et al 2014)

genetic mapping in 20 FS families

focal point mapping across families(E. di Piero et al, in prep.)

haploblock markers building

scrutinizing for Mendelian

inconsistencies

scrutinizing for double

recombinants

1112 haploblocks,

1281 cM

1.2 cM between adjacent HB

with ~7 K robust markers

null-allelesadditional SNP at the probe setparalogous loci

• Phenotypic analysis

• Pedigree-based QTL mapping : FlexQTL (Bink et al, 2014)

– transmission of alleles through generations (IBD)

– Bayesian method for QTL mapping

• Bayes factor: test statistic to infer which model is more likely,

e.g. 1 QTL vs. 0 QTL

• Report QTL for Bayes factor ≥ 5

– additive QTL effects

RGC8 21-23 June 2016Hélène MURANTY

Data analysis

𝑌~𝑠𝑖𝑡𝑒 × 𝑦𝑒𝑎𝑟 + 𝑔𝑒𝑛𝑜𝑡𝑦𝑝𝑒

adjusted means

10


QTL location, at chromosome level

Fruit size Fruit weight

pre

vio

us

stu

die

s

HiDRAS DLO-12 TeBr

3 yrs 2003 2004 2005 2006 2007 2004 2005 2006

# indiv. 1059 678 623 677 220 164 105 96 111

LG1 30.2 29.9 9.3 3.4 2

LG2 5.8 1

LG9 7.1 10.6 1

LG10 4.6 8.8 5.3 2

LG11 10.9 3.9 3

LG12 10.2 8.2 5.3 4.6 1

LG14 8.6 10.1 0

LG15 8.6 5.8 5

LG16 7.7 9.1 2

LG17 4.2 10.6 3

Bayes factor

1 QTL vs. 0 QTL

Some QTL stable over years within datasets

Most QTL specific of each dataset, except LG12

2 year-specific QTL on LG15

12Hélène MURANTY RGC8 21-23 June 2016

Fruit size Fruit weight

HiDRAS DLO-12 TeBr

3 yrs 2003 2004 2005 2006 2007 2004 2005 2006

# indiv. 1059 678 623 677 220 164 105 96 111

LG1 25% 19% 9% 5%

LG2 9%

LG9 7% 15%

LG10 13% 21% 15%

LG11 5% 2%

LG12 3% 5% 6% 8%

LG14 9% 18%

LG15 14% 15%

LG16 7% 12%

LG17 3% 14%

Part of variance explained by QTL

Moderate to small effect QTL

Q-haplotype q-haplotype

He

tero

zyg

ote

sQ

q Dorianne, X-6808, X-

6564, X-3305, Galarina,

X-6683, RedWinterX3177,

X-3263, X-6679, X-6681,

X-3259, X-6398

2-2-2-Q-2-2-2

2-2-2-Q-2-4-2

2-2-2-Q-2-4-3

2-4-2-Q-4-4-2

4-4-2-Q-2-4-2

4-4-2-Q-4-4-2

5-4-2-Q-4-4-2

7-6-2-Q-2-2-2

13-9-3-q-8-3-3

2-14-3-q-8-3-3

Pirol, Sampion2-2-2-Q-2-4-2

4-4-2-Q-4-4-22-2-2-q-2-9-2

RGC8 21-23 June 2016Hélène MURANTY

LG1: Rvi6 region

13

HB-01-1HB-01-2HB-01-2bHB-01-3HB-01-3bHB-01-4HB-01-4bHB-01-5HB-01-5bHB-01-6HB-01-7HB-01-8HB-01-9HB-01-10HB-01-11HB-01-12HB-01-13HB-01-13bHB-01-14HB-01-15HB-01-16HB-01-17HB-01-17bHB-01-18HB-01-19HB-01-20HB-01-21HB-01-22HB-01-23HB-01-23bHB-01-24HB-01-25HB-01-25bHB-01-26HB-01-27HB-01-28HB-01-28bHB-01-29

HB-01-30

HB-01-31HB-01-31b HB-01-32HB-01-32b

HB-01-32cHB-01-33HB-01-34HB-01-35

0

20

40

60

FS

-3yrs

FS

-200

3

FS

-200

4

FS

-200

5

1

13 different haplotypes in the 9 qq parents

7 different haplotypes in the 5 QQ parents

9.1 cM

Cox

4 54 42 2

12 49 42 2

D3_DLO

* ** *2 24 203 53 3

McIntosh

2 22 22 22 22 52 3

IngMarie

5 44 42 24 124 92 2

Lobo

2 42 42 22 45 183 4

Elstar

4 44 42 24 124 92 2

Priscilla-NL

2 52 92 32 85 43 2

D1972-10-33

* *4 292 2* ** *2 3

D1980-15-25

2 529 92 3

20 85 43 2

GoldenDel

2 42 42 22 44 42 2

Clochard

5 42 42 22 45 43 2

F2_26829-2-2

13 49 53 28 73 43 2

X-6823

2 42 42 22 44 42 2

PRI14-152

2 132 92 34 84 32 3

PRI672-3

13 49 23 28 23 43 2

X-4638

4 134 92 34 84 32 3

Dorianne

4 134 92 34 84 32 3


Rvi6 region: linkage drag or effect of R gene ?

Rvi6

Soriano et al (2009)

Rvi69.1 cM

2.5 cM

Cox

4 54 42 2

12 49 42 2

D3_DLO

* ** *2 24 203 53 3

McIntosh

2 22 22 22 22 52 3

IngMarie

5 44 42 24 124 92 2

Lobo

2 42 42 22 45 183 4

Elstar

4 44 42 24 124 92 2

Priscilla-NL

2 52 92 32 85 43 2

D1972-10-33

* *4 292 2* ** *2 3

D1980-15-25

2 529 92 3

20 85 43 2

GoldenDel

2 42 42 22 44 42 2

Clochard

5 42 42 22 45 43 2

F2_26829-2-2

13 49 53 28 73 43 2

X-6823

2 42 42 22 44 42 2

PRI14-152

2 132 92 34 84 32 3

PRI672-3

13 49 23 28 23 43 2

X-4638

4 134 92 34 84 32 3

Dorianne

4 134 92 34 84 32 3


Rvi6 region: linkage drag or effect of R gene ?

Rvi6

Soriano et al (2009)

Rvi6Vd3

Vd3

Parent D1980-15-25 segregates for

Rvi6 but not for fruit weight

linkage drag9.1 cM

2.5 cM


HB-12-1

HB-12-1bHB-12-2

HB-12-3 HB-12-4

HB-12-5

HB-12-6 HB-12-7

HB-12-8HB-12-9HB-12-10HB-12-10bHB-12-11HB-12-12HB-12-13HB-12-14HB-12-15HB-12-15bHB-12-16HB-12-16bHB-12-17HB-12-18HB-12-18bHB-12-19HB-12-19bHB-12-19cHB-12-20HB-12-20bHB-12-21HB-12-21bHB-12-22HB-12-23HB-12-24HB-12-25 HB-12-26HB-12-26bHB-12-27HB-12-28HB-12-28bHB-12-28cHB-12-28dHB-12-29 HB-12-30HB-12-30bHB-12-31HB-12-32HB-12-32bHB-12-33HB-12-33bHB-12-33cHB-12-33dHB-12-33eHB-12-33f HB-12-34HB-12-35

HB-12-35bHB-12-35cHB-12-36HB-12-37

HB-12-37bHB-12-38

HB-12-39HB-12-39b

HB-12-40HB-12-41HB-12-41b

20

40

60

FS

-HiD

RA

S-3

yrs

FW

-DLO

-12-2

006

FW

-DLO

-12-2

007

12LG12: a q allele coming from Golden Delicious

FS-3yrs

FW-2006

FW-2007

GoldenDel Clochard RomBeauty EsopSpitz F_Jonathan F_O53T136 F2_26829-2-2 Cox F_IngMarie Coop-17

Jonathan PRI14-152 X-6823 IngMarie Chantecler

Crandall PRI672-3 D1955-44-220 Elstar X-3259

O53T136 X-4638 D1973-01-41

TN_R10A8 X-6808 Dorianne

X-6417

DLO-12

Conclusion

• QTL spread over 10 chromosomes

• Stable over years and year-specific QTL

• Moderate to small effects

• Many regions too wide for MAS (except on LG1

and LG14)

• Use recombinants in Rvi6 region to reduce

linkage drag


17

Acknowledgements


Genotypic data M. Troggio, E. Banchi

Y. Noordijk

Phenotypic data

HiDRAS project

IsaFruit project

HiDRAS

Genetic mapping H. Koehorst- van Putten

M. di Guardo, S. Longhi

F. Costa, G. Pagliarani, T.

Letschka, L. Lozano-Luis

S. Tartarini, E. di Pierro,

L. Gianfranceschi

Haploblock building J. Kruisselbrink

Telamon x Braeburn pop° M. Davey, W. Keulemans

Thank you for

listening

analysis of genetic control of fruit size in apple using ... · pdf filediameter, height x x x...

Documents