View
220
Download
1
Category
Preview:
Citation preview
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
Hélène MURANTY RGC8 21-23 June 2016
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
5RGC8 21-23 June 2016Hélène MURANTY
HiDRAS
• 6 sites
• 30 control varieties
• 3 harvests (2003 2005)
• fruit size scored on a 1-5 scale
• well-shaped distributions
Phenotypes
6RGC8 21-23 June 2016Hélène MURANTY
HiDRAS
• 6 sites
• 30 control varieties
• 3 harvests (2003 2005)
• fruit size scored on a 1-5 scale
DLO-12 • 2 harvests (2006 – 2007)
• fruit weight
• well-shaped distributions
• moderate to high correlations
between years
Phenotypes
7RGC8 21-23 June 2016Hélène MURANTY
HiDRAS
• 6 sites
• 30 control varieties
• 3 harvests (2003 2005)
• fruit size scored on a 1-5 scale
DLO-12 • 2 harvests (2006 – 2007)
• fruit weight
Te x Br • 3 harvests (2004 2006)
• fruit weight
• fruit height (H) and diameter (D)
• well-shaped distributions
• moderate to high correlations
between years
• high correlation between diameter
and weight within year
8RGC8 21-23 June 2016Hélène MURANTY
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
9RGC8 21-23 June 2016Hélène MURANTY
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
11RGC8 21-23 June 2016Hélène MURANTY
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
14RGC8 21-23 June 2016Hélène MURANTY
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
15RGC8 21-23 June 2016Hélène MURANTY
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
16RGC8 21-23 June 2016Hélène MURANTY
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
Hélène MURANTY RGC8 21-23 June 2016
17
Acknowledgements
18RGC8 21-23 June 2016Hélène MURANTY
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
Recommended