05 di pierro
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YOUR LOGO
Construction and Application
of a Multi-parental High Density
SNP Linkage Map of Apple Erica A. Di Pierro, Luca Gianfranceschi, Johannes W. Kruisselbrink, Marco C.A.M. Bink, Roeland E. Voorrips,
Mario Di Guardo, Herma Koehorst van Putten, Sara Longhi, Luca Bianco, Michela Troggio, Diego Micheletti,
Riccardo Velasco, Larisa Gustavsson, Stefano Tartarini, Giulia Pagliarani, Hélène Muranty, François Laurens,
Eric van de Weg
YOUR LOGO
WHY THE NEED FOR A VERY RELIABLE GENETIC MAP IN APPLE?
YOUR LOGO
Very final goal
THE NEED FOR A VERY RELIABLE GENETIC MAP IN APPLE
YOUR LOGO
➧Reliable and consistent assessment of correlation trait ↔ molecular marker
• Discovery & Characterization
• Validation– Reproducibility on multiple families, pedigrees
NEEDS FOR SUCCESSFUL MAB STRATEGIES
YOUR LOGO
➧Reliable and consistent assessment of correlation trait ↔ molecular marker
• Discovery & Characterization
• Validation– Reproducibility on multiple families, pedigrees
NEEDS FOR SUCCESSFUL MAB STRATEGIES
➧Power and accurateness of QTL mapping and PBA approaches
YOUR LOGO
➧Reliable and consistent assessment of correlation trait ↔ molecular marker
• Discovery & Characterization
• Validation– Reproducibility on multiple families, pedigrees
NEEDS FOR SUCCESSFUL MAB STRATEGIES
➧Power and accurateness of QTL mapping and PBA analysis
• Correct linkage group (LG) assignment• Correct markers succession within LG
YOUR LOGO
➧Approaches reducing size data sets
• High-density SNP arrays
• Computer memory limitations, increase computation time
• Genotyping by SNP haplotypes
– Use as multi-allelic markers, more informative than single di-allelic SNPs
NEEDS FOR SUCCESSFUL MAB STRATEGIES
YOUR LOGO
➧Approaches reducing size data sets
• High-density SNP arrays
• Computer memory limitations, increase computation time
• Genotyping by SNP haplotypes
– Use as multi-allelic markers, more informative than single di-allelic SNPs
NEEDS FOR SUCCESSFUL MAB STRATEGIES
YOUR LOGO
➧NEED
THE NEED FOR A VERY RELIABLE GENETIC MAP IN APPLE
YOUR LOGO
➧NEED
➧APPROACH
THE NEED FOR A VERY RELIABLE GENETIC MAP IN APPLE
YOUR LOGO
1. HIGH DENSITY SNPs ARRAY:
Illumina Infinium 20 K SNPs array Luca Bianco et al. 2014
FUNDAMENTAL TOOLS
YOUR LOGO
1. HIGH DENSITY SNPs ARRAY:
Illumina Infinium 20 K SNPs array Luca Bianco et al. 2014
2. RELIABLE CALLS OF INFORMATIVE SNP
ASSIsT software Mario Di Guardo et al.
FUNDAMENTAL TOOLS
YOUR LOGO
1. HIGH DENSITY SNPs ARRAY:
Illumina Infinium 20 K SNPs array Luca Bianco et al. 2014
2. RELIABLE CALLS OF INFORMATIVE SNP
ASSIsT software Mario Di Guardo et al.
3. RELIABLE SINGLE FAMILY MAPS FOR 21 FAMILIES (ca. 1600 individuals)
FUNDAMENTAL TOOLS
YOUR LOGO
1. SNPs ORGANIZED in Focal Points (FPs)• Exploiting FPs design introduced in Chagné et al. 2012
and Bianco et al. 2014
STRATEGY STEPS
YOUR LOGO
1. SNPs ORGANIZED in Focal Points (FPs)• Exploiting FPs design introduced in Chagné et al. 2012
and Bianco et al. 2014
2. INNOVATIVE MAPPING APPROACH• FPs strategy• Backcross strategy in outcrossing species and data
integration across families prior to map construction
STRATEGY STEPS
YOUR LOGO
1. SNPs ORGANIZED in Focal Points (FPs)• Exploiting FPs design introduced in Chagné et al. 2012
and Bianco et al. 2014
2. INNOVATIVE MAPPING APPROACH• FPs strategy• Backcross strategy in outcrossing species and data
integration across families prior to map construction
3. SOFTWARE DEVELOPMENT FOR DATA INTEGRATION AND CONVERSION (FP-mapper by J. Kruisselbrink)
STRATEGY STEPS
YOUR LOGO
➧Focal Points design
Regions of max 10kb having up to 10 SNPs
➝ Suitable for building stable multi-allelic SNP-haplotypes
➝ Distribution across genome
1. SNPs ORGANIZED IN FPs
YOUR LOGO
➧Focal Points design
Regions of max 10kb having up to 10 SNPs
➝ Suitable for building stable multi-allelic SNP-haplotypes
➝ Distribution across genome
1. SNPs ORGANIZED IN FPs
SNP name FP segr phase segr phase segr phase
SNP_028768 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa <aaxab> {-0} -- aa ab ab -- aa ab ab
SNP_028769 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
SNP_028770 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa -- -- -- -- -- -- -- --
SNP_028771 FP_60 <abxab> {00} ab -- bb -- ab bb ab ab <abxaa> {0-} aa -- -- aa ab aa -- aa <aaxab> {-0} aa aa ab ab ab aa ab ab
SNP_028772 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <abxaa> {0-} aa aa aa aa ab aa aa aa <abxab> {10} ab ab ab ab bb aa ab ab
SNP_028773 FP_60 <aaxab> {-0} aa aa ab -- ab ab ab aa -- -- -- -- -- -- -- -- <abxab> {10} -- -- ab ab bb aa ab ab
Pop 1 Pop 2 Pop 3
YOUR LOGO
➧Focal Points design
Regions of max 10kb having up to 10 SNPs
➝ Suitable for building stable multi-allelic SNP-haplotypes
➝ Distribution across genome
1. SNPs ORGANIZED IN FPs
SNP name FP segr phase segr phase segr phase
SNP_028768 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa <aaxab> {-0} -- aa ab ab -- aa ab ab
SNP_028769 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
SNP_028770 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa -- -- -- -- -- -- -- --
SNP_028771 FP_60 <abxab> {00} ab -- bb -- ab bb ab ab <abxaa> {0-} aa -- -- aa ab aa -- aa <aaxab> {-0} aa aa ab ab ab aa ab ab
SNP_028772 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <abxaa> {0-} aa aa aa aa ab aa aa aa <abxab> {10} ab ab ab ab bb aa ab ab
SNP_028773 FP_60 <aaxab> {-0} aa aa ab -- ab ab ab aa -- -- -- -- -- -- -- -- <abxab> {10} -- -- ab ab bb aa ab ab
Pop 1 Pop 2 Pop 3
YOUR LOGO
➧Focal Points design
Regions of max 10kb having up to 10 SNPs
➝ Suitable for building stable multi-allelic SNP-haplotypes
➝ Distribution across genome
1. SNPs ORGANIZED IN FPs
SNP name FP segr phase segr phase segr phase
SNP_028768 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa <aaxab> {-0} -- aa ab ab -- aa ab ab
SNP_028769 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
SNP_028770 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa -- -- -- -- -- -- -- --
SNP_028771 FP_60 <abxab> {00} ab -- bb -- ab bb ab ab <abxaa> {0-} aa -- -- aa ab aa -- aa <aaxab> {-0} aa aa ab ab ab aa ab ab
SNP_028772 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <abxaa> {0-} aa aa aa aa ab aa aa aa <abxab> {10} ab ab ab ab bb aa ab ab
SNP_028773 FP_60 <aaxab> {-0} aa aa ab -- ab ab ab aa -- -- -- -- -- -- -- -- <abxab> {10} -- -- ab ab bb aa ab ab
Pop 1 Pop 2 Pop 3
YOUR LOGO
➧Focal Points design
Regions of max 10kb having up to 10 SNPs
➝ Suitable for building stable multi-allelic SNP-haplotypes
➝ Distribution across genome
1. SNPs ORGANIZED IN FPs
SNP name FP segr phase segr phase segr phase
SNP_028768 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa <aaxab> {-0} -- aa ab ab -- aa ab ab
SNP_028769 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
SNP_028770 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa -- -- -- -- -- -- -- --
SNP_028771 FP_60 <abxab> {00} ab -- bb -- ab bb ab ab <abxaa> {0-} aa -- -- aa ab aa -- aa <aaxab> {-0} aa aa ab ab ab aa ab ab
SNP_028772 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <abxaa> {0-} aa aa aa aa ab aa aa aa <abxab> {10} ab ab ab ab bb aa ab ab
SNP_028773 FP_60 <aaxab> {-0} aa aa ab -- ab ab ab aa -- -- -- -- -- -- -- -- <abxab> {10} -- -- ab ab bb aa ab ab
Pop 1 Pop 2 Pop 3
YOUR LOGO
2. NEW MAPPING APPROACH: FPs STRATEGY
➧FPs strategy
SNP name FP segr phase segr phase segr phase
SNP_028768 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa <aaxab> {-0} -- aa ab ab -- aa ab ab
SNP_028769 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
SNP_028770 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa -- -- -- -- -- -- -- --
SNP_028771 FP_60 <abxab> {00} ab -- bb -- ab bb ab ab <abxaa> {0-} aa -- -- aa ab aa -- aa <aaxab> {-0} aa aa ab ab ab aa ab ab
SNP_028772 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <abxaa> {0-} aa aa aa aa ab aa aa aa <abxab> {10} ab ab ab ab bb aa ab ab
SNP_028773 FP_60 <aaxab> {-0} aa aa ab -- ab ab ab aa -- -- -- -- -- -- -- -- <abxab> {10} -- -- ab ab bb aa ab ab
Pop 1 Pop 2 Pop 3
FP-mapper by J. Kruisselbrink
YOUR LOGO
2. NEW MAPPING APPROACH: FPs STRATEGY
➧FPs strategy
SNP name FP segr phase segr phase segr phase
SNP_028768 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa <aaxab> {-0} -- aa ab ab -- aa ab ab
SNP_028769 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
SNP_028770 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa -- -- -- -- -- -- -- --
SNP_028771 FP_60 <abxab> {00} ab -- bb -- ab bb ab ab <abxaa> {0-} aa -- -- aa ab aa -- aa <aaxab> {-0} aa aa ab ab ab aa ab ab
SNP_028772 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <abxaa> {0-} aa aa aa aa ab aa aa aa <abxab> {10} ab ab ab ab bb aa ab ab
SNP_028773 FP_60 <aaxab> {-0} aa aa ab -- ab ab ab aa -- -- -- -- -- -- -- -- <abxab> {10} -- -- ab ab bb aa ab ab
Pop 1 Pop 2 Pop 3
FP-mapper by J. Kruisselbrink
• Stable SNP haplotypes
YOUR LOGO
2. NEW MAPPING APPROACH: FPs STRATEGY
➧FPs strategy
SNP name FP segr phase segr phase segr phase
SNP_028768 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa <aaxab> {-0} -- aa ab ab -- aa ab ab
SNP_028769 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
SNP_028770 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa -- -- -- -- -- -- -- --
SNP_028771 FP_60 <abxab> {00} ab -- bb -- ab bb ab ab <abxaa> {0-} aa -- -- aa ab aa -- aa <aaxab> {-0} aa aa ab ab ab aa ab ab
SNP_028772 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <abxaa> {0-} aa aa aa aa ab aa aa aa <abxab> {10} ab ab ab ab bb aa ab ab
SNP_028773 FP_60 <aaxab> {-0} aa aa ab -- ab ab ab aa -- -- -- -- -- -- -- -- <abxab> {10} -- -- ab ab bb aa ab ab
Pop 1 Pop 2 Pop 3
Female meiosis ab aa ab ab aa ab ab ab aa aa aa aa ab aa aa aa ab ab aa aa ab aa aa aa
Male meiosis aa aa ab ab ab ab ab aa aa ab ab ab ab ab ab aa aa aa ab ab ab aa ab ab
FP-mapper by J. Kruisselbrink
• Stable SNP haplotypes• Haplotype data integration
bi-parental genotypes split into single parent datasets
YOUR LOGO
2. NEW MAPPING APPROACH: FPs STRATEGY
➧FPs strategy
SNP name FP segr phase segr phase segr phase
SNP_028768 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa <aaxab> {-0} -- aa ab ab -- aa ab ab
SNP_028769 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
SNP_028770 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa -- -- -- -- -- -- -- --
SNP_028771 FP_60 <abxab> {00} ab -- bb -- ab bb ab ab <abxaa> {0-} aa -- -- aa ab aa -- aa <aaxab> {-0} aa aa ab ab ab aa ab ab
SNP_028772 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <abxaa> {0-} aa aa aa aa ab aa aa aa <abxab> {10} ab ab ab ab bb aa ab ab
SNP_028773 FP_60 <aaxab> {-0} aa aa ab -- ab ab ab aa -- -- -- -- -- -- -- -- <abxab> {10} -- -- ab ab bb aa ab ab
Pop 1 Pop 2 Pop 3
Female meiosis ab aa ab ab aa ab ab ab aa aa aa aa ab aa aa aa ab ab aa aa ab aa aa aa
Male meiosis aa aa ab ab ab ab ab aa aa ab ab ab ab ab ab aa aa aa ab ab ab aa ab ab
FP-mapper by J. Kruisselbrink
• Stable SNP haplotypes• Haplotype data integration
bi-parental genotypes split into single parent datasets
• Missing values reduction
YOUR LOGO
2. NEW MAPPING APPROACH: FPs STRATEGY
➧FPs strategy
SNP name FP segr phase segr phase segr phase
SNP_028768 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa <aaxab> {-0} -- aa ab ab -- aa ab ab
SNP_028769 FP_60 <abxaa> {1-} ab aa ab ab aa ab ab ab -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
SNP_028770 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <aaxab> {-0} aa ab ab ab ab ab ab aa -- -- -- -- -- -- -- --
SNP_028771 FP_60 <abxab> {00} ab -- bb -- ab bb ab ab <abxaa> {0-} aa -- -- aa ab aa -- aa <aaxab> {-0} aa aa ab ab ab aa ab ab
SNP_028772 FP_60 <abxab> {00} ab aa bb bb ab bb ab ab <abxaa> {0-} aa aa aa aa ab aa aa aa <abxab> {10} ab ab ab ab bb aa ab ab
SNP_028773 FP_60 <aaxab> {-0} aa aa ab -- ab ab ab aa -- -- -- -- -- -- -- -- <abxab> {10} -- -- ab ab bb aa ab ab
Pop 1 Pop 2 Pop 3
Female meiosis ab aa ab ab aa ab ab ab aa aa aa aa ab aa aa aa ab ab aa aa ab aa aa aa
Male meiosis aa aa ab ab ab ab ab aa aa ab ab ab ab ab ab aa aa aa ab ab ab aa ab ab
FP-mapper by J. Kruisselbrink
• Stable SNP haplotypes• Haplotype data integration
bi-parental genotypes split into single parent datasets
• Missing values reduction
YOUR LOGO
2.NEW MAPPING APPROACH: BACKCROSS STRATEGY
➧Backcross strategy and data integration across families (FP-mapper by J. Kruisselbrink)
Female meiosis ab aa ab ab aa ab ab ab aa aa aa aa ab aa aa aa ab ab aa aa ab aa aa aa
Male meiosis aa aa ab ab ab ab ab aa aa ab ab ab ab ab ab aa aa aa ab ab ab aa ab ab
Segr Pop 1 Pop 2 Pop 3
YOUR LOGO
2.NEW MAPPING APPROACH: BACKCROSS STRATEGY
➧Backcross strategy and data integration across families (FP-mapper by J. Kruisselbrink)
FP_60 unique marker
Female meiosis ab aa ab ab aa ab ab ab aa aa aa aa ab aa aa aa ab ab aa aa ab aa aa aa
Male meiosis aa aa ab ab ab ab ab aa aa ab ab ab ab ab ab aa aa aa ab ab ab aa ab ab
Segr Pop 1 Pop 2 Pop 3
Merging single parent datasets in a single backcross-type population ➝ Twice the individual of the original population ➝ 3200 meiosis
YOUR LOGO
2.NEW MAPPING APPROACH: BACKCROSS STRATEGY
➧Backcross strategy and data integration across families (FP-mapper by J. Kruisselbrink)
FP_60 unique marker
Female meiosis ab aa ab ab aa ab ab ab aa aa aa aa ab aa aa aa ab ab aa aa ab aa aa aa
Male meiosis aa aa ab ab ab ab ab aa aa ab ab ab ab ab ab aa aa aa ab ab ab aa ab ab
Segr Pop 1 Pop 2 Pop 3
Merging single parent datasets in a single backcross-type population ➝ Twice the individual of the original population ➝ 3200 meiosis
YOUR LOGO
ADVANTAGES
YOUR LOGO
ADVANTAGES
YOUR LOGO
Families Individuals:
Focal Points (FPs):Total SNPs: Average SNPs/FP: Average mv%/FP:
Average distance: cMmax d. (LG6) : cMmin d. (many LGs): cMTotal Map Length: cM
21~1600
~3000~15000
~5~40
0.403.300.00
~1267
HIGH DENSITY FPs GENETIC MAPJoin Map (V4.1)
YOUR LOGO
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
HIGH DENSITY FPs GENETIC MAP Join Map (V4.1)
YOUR LOGO
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
HIGH DENSITY FPs GENETIC MAP Join Map (V4.1)
63 cM
112 cM
YOUR LOGO
LG 3
Join Map (V4.1) Test for alternative positions (1000 iterations)
0%
50%
100%
o ROBUSTNESS OF MARKERS POSITIONSQUALITY OF THE MAP
THE PROBABILITY OF EACH MARKER (FP) TO BE ASSIGNED TO ITS POSITION IN THE MAP
YOUR LOGO
Join Map (V4.1) Estimated Plausible Positions
0%
50%
100%
THE PROBABILITY OF EACH MARKER (FP) TO BE ASSIGNED TO ITS POSITION IN THE MAP
0%
50%
100%
LG 3
QUALITY OF THE MAPo ROBUSTNESS OF MARKERS POSITIONS
YOUR LOGO
Join Map (V4.1) Estimated Plausible Positions
0%
50%
100%
THE PROBABILITY OF EACH MARKER (FP) TO BE ASSIGNED TO ITS POSITION IN THE MAP
LG 3
0%
50%
100%
LG3_FP_1140
o ROBUSTNESS OF MARKERS POSITIONSQUALITY OF THE MAP
YOUR LOGO
0%
50%
100%
THE PROBABILITY OF EACH MARKER (FP) TO BE ASSIGNED TO ITS POSITION IN THE MAP
Join Map (V4.1) Test for alternative positions (1000 iterations)
LG 3
QUALITY OF THE MAPo ROBUSTNESS OF MARKERS POSITIONS
YOUR LOGO
IMPACTS
YOUR LOGO
IMPACTS
• MARKERS TO BE MAPPED ON THE CORRECT LG
• MARKER POSITIONING through FPs VALIDATION
YOUR LOGO
IMPACTS
• Special approach elaborated by Voorrips et al. see POSTER SESSION
YOUR LOGO
BABAB BABAB
BABAB BBBAB
Hap
loty
pe
24
BABAAAABAA
Hap
loty
pe
12
Hap
loty
pe
13
10 SNP markers
HAPLOTYPINGSpecial approach elaborated by Voorrips et al. see POSTER SESSION
Joint genotypes of multiple successive SNPs
• single multi-allelic marker
YOUR LOGO
BABAB BABAB
BABAB BBBAB
Hap
loty
pe
24
BABAAAABAA
Hap
loty
pe
12
Hap
loty
pe
13
LG1HaploBlock 2
10 SNP markers
HAPLOTYPINGSpecial approach elaborated by Voorrips et al. see POSTER SESSION
Joint genotypes of multiple successive SNP
• single multi-allelic marker
• converted into haploblocks
YOUR LOGO
Joint genotypes of multiple successive SNP
• single multi-allelic marker
• converted into haploblocks
• allow exploring entire allelic variation
BABAB BABAB
BABAB BBBAB
Hap
loty
pe
24
BABAAAABAA
Hap
loty
pe
12
Hap
loty
pe
13
LG1HaploBlock 2
3 haplotype variants
10 SNP markers
HAPLOTYPINGSpecial approach elaborated by Voorrips et al. see POSTER SESSION
YOUR LOGO
➧ Flow of haplotype alleles along pedigrees
– LG1 apple, region flanking the Vf gene for scab resistance
– Pedigree 1 commercial cv:
• Galarina Vf-resistant
HAPLOTYPINGSpecial approach elaborated by Voorrips et al. see POSTER SESSION
YOUR LOGO
➧ Single HaploBlocklocus / marker
• 5 generations
• Flow of Haplotype 13
Delicious
11 128 42 23 2
GoldenDel
2 42 42 43 2
F2_26829-2-2
13 49 58 73 3
Jonathan
5 24 24 23 2
Cox
4 54 412 42 3
PRI14-126
4 134 94 82 3
KidsOrRed
11 58 42 43 3
PRI612-1
12 134 92 82 2
Gala
5 44 44 23 3
Florina
13 29 28 *2 2
Galarina
13 59 48 42 3
4 55 213 42 411 12
11 54 13
12 13 5 4
13 2
13 5
HAPLOTYPE FLOW
YOUR LOGO
HAPLOTYPE FLOW
➧ Single HaploBlocklocus / marker
• 5 generations
• Flow of Haplotype 13
Delicious
11 128 42 23 2
GoldenDel
2 42 42 43 2
F2_26829-2-2
13 49 58 73 3
Jonathan
5 24 24 23 2
Cox
4 54 412 42 3
PRI14-126
4 134 94 82 3
KidsOrRed
11 58 42 43 3
PRI612-1
12 134 92 82 2
Gala
5 44 44 23 3
Florina
13 29 28 *2 2
Galarina
13 59 48 42 3
4 55 213 42 411 12
11 54 13
12 13 5 4
13 2
13 5
YOUR LOGO
HAPLOTYPE FLOW
➧ Single HaploBlocklocus / marker
• 5 generations
• Flow of Haplotype 13
Delicious
11 128 42 23 2
GoldenDel
2 42 42 43 2
F2_26829-2-2
13 49 58 73 3
Jonathan
5 24 24 23 2
Cox
4 54 412 42 3
PRI14-126
4 134 94 82 3
KidsOrRed
11 58 42 43 3
PRI612-1
12 134 92 82 2
Gala
5 44 44 23 3
Florina
13 29 28 *2 2
Galarina
13 59 48 42 3
4 55 213 42 411 12
11 54 13
12 13 5 4
13 2
13 5
YOUR LOGO
HAPLOTYPE FLOW
➧ Single HaploBlocklocus / marker
• 5 generations
• Flow of Haplotype 13
Delicious
11 128 42 23 2
GoldenDel
2 42 42 43 2
F2_26829-2-2
13 49 58 73 3
Jonathan
5 24 24 23 2
Cox
4 54 412 42 3
PRI14-126
4 134 94 82 3
KidsOrRed
11 58 42 43 3
PRI612-1
12 134 92 82 2
Gala
5 44 44 23 3
Florina
13 29 28 *2 2
Galarina
13 59 48 42 3
4 55 213 42 411 12
11 54 13
12 13 5 4
13 2
13 5
YOUR LOGO
HAPLOTYPE FLOW
➧ Single HaploBlocklocus / marker
• 5 generations
• Flow of Haplotype 13 came from F2-26829:Vf-resistant
selection, 2nd generation from M.foribunda 821
Delicious
11 128 42 23 2
GoldenDel
2 42 42 43 2
F2_26829-2-2
13 49 58 73 3
Jonathan
5 24 24 23 2
Cox
4 54 412 42 3
PRI14-126
4 134 94 82 3
KidsOrRed
11 58 42 43 3
PRI612-1
12 134 92 82 2
Gala
5 44 44 23 3
Florina
13 29 28 *2 2
Galarina
13 59 48 42 3
4 55 213 42 411 12
11 54 13
12 13 5 4
13 2
13 5
YOUR LOGO
Delicious
11 128 42 23 2
GoldenDel
2 42 42 43 2
F2_26829-2-2
13 49 58 73 3
Jonathan
5 24 24 23 2
Cox
4 54 412 42 3
PRI14-126
4 134 94 82 3
KidsOrRed
11 58 42 43 3
PRI612-1
12 134 92 82 2
Gala
5 44 44 23 3
Florina
13 29 28 *2 2
Galarina
13 59 48 42 3
4 55 213 42 411 12
11 54 13
12 13 5 4
13 2
13 5
HAPLOTYPE FLOW
➧ Single HaploBlocklocus / marker
• 5 generations
• Flow of Haplotype 13 came from F2-26829:Vf-resistant
selection, 2nd generation from M.foribunda 821
• Flow of Haplotype 5 came from Cox
YOUR LOGO
HAPLOTYPE FLOW
➧ Multiple HaploBlocks
• Consistent flow
Delicious
11 128 42 23 2
GoldenDel
2 42 42 43 2
F2_26829-2-2
13 49 58 73 3
Jonathan
5 24 24 23 2
Cox
4 54 412 42 3
PRI14-126
4 134 94 82 3
KidsOrRed
11 58 42 43 3
PRI612-1
12 134 92 82 2
Gala
5 44 44 23 3
Florina
13 29 28 *2 2
Galarina
13 59 48 42 3
YOUR LOGO
HAPLOTYPE FLOW
➧ Multiple HaploBlocks
• Consistent flow
• Tracing recombination events
Delicious
11 128 42 23 2
GoldenDel
2 42 42 43 2
F2_26829-2-2
13 49 58 73 3
Jonathan
5 24 24 23 2
Cox
4 54 412 42 3
PRI14-126
4 134 94 82 3
KidsOrRed
11 58 42 43 3
PRI612-1
12 134 92 82 2
Gala
5 44 44 23 3
Florina
13 29 28 *2 2
Galarina
13 59 48 42 3
YOUR LOGO
HAPLOTYPE FLOW
➧ Multiple HaploBlocks
• Consistent flow
• Tracing recombination events
• Consistent results validated with SSR-Hidras data
Delicious
11 128 42 23 2
GoldenDel
2 42 42 43 2
F2_26829-2-2
13 49 58 73 3
Jonathan
5 24 24 23 2
Cox
4 54 412 42 3
PRI14-126
4 134 94 82 3
KidsOrRed
11 58 42 43 3
PRI612-1
12 134 92 82 2
Gala
5 44 44 23 3
Florina
13 29 28 *2 2
Galarina
13 59 48 42 3
YOUR LOGO
CONCLUSION
ACCURATE AND RELIABLE ORDER OF THE HIGHEST POSSIBLE NUMBER OF MARKER LOCI
YOUR LOGO
CONCLUSION
ACCURATE AND RELIABLE ORDER OF THE HIGHEST POSSIBLE NUMBER OF MARKER LOCI
ACKNOWLEDGEMENTS
Eric Van de WegJohannes KruisselbrinkHerma KoehorstSara Longhi
Stefano Tartarini
Giulia Pagliarani
Luca Gianfranceschi
Mario Di GuardoDiego MichelettiLuca BiancoMichela Troggio
Hélène MurantyLarisa Gustavsson
YOUR LOGO
THANKS FOR YOUR
ATTENTION !
YOUR LOGO
Roeland E. Voorrips
Marco C.A.M. Bink
Johannes W. Kruisselbrink
Herma J.J. Koehorst - van Putten
W. Eric Van de Weg
POSTER SESSION
YOUR LOGO
ADVANTAGES
➧Advantages of the FPs strategies
• Reduced number of missing values
• Increased robustness of marker scores
• Complete exploitation of genetic information
• Fully informative markers
YOUR LOGO
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
105
110
CORE DATASET in Black• at least 800 meiosis present• 25% of present data
in Violet• at least 300 meiosis present• 10% of present data
THE FINAL INTEGRATED GENETIC MAP
YOUR LOGO
➧Advantages of the backcross strategy
NEW MAPPING APPROACH
Standard outcrossers integrated map
• Integration of the 2 parental maps• Integration across families
Integration of DATASETS prior to map construction
Novel approach
VS
YOUR LOGO 63
HAPLOBLOCKS
HB 1
HB 2
HB 3
HB 4
HB 5
HB 6
HB 7
HB 8
Galarina Florina Gala • Tightly linked sets of SNPs
• Recombination occurs onlybetween haploblock and NOT WITHIN
multi-allelic markersbased on correctlyassigned haplotypes
Voorrips et al. POSTER SESSION
LG1
YOUR LOGO
➧Approaches reducing size data sets• High-density SNP arrays• Computer memory limitations, increase computation time• Genotyping by SNP haplotypes
– Use as multi-allelic markers, more informative than single di-allelic SNPs
NEEDS FOR SUCCESSFUL MAB STRATEGIES
Complexity of Apple Genome ➾ Apple Physical Map V2 with uncertainties
YOUR LOGO
NEXT STEP
➧PUBLICATION of the Integrated Genetic Map
➧ORIGINAL DATA will become publicly AVAILABLE on the FB-database
➝ Allow USERS to FURTHER IMPROVE REGION of INTEREST by
further DATA SCRUTINIZING
adding data (e.g. additional families)
➝ MOST RELIABLE marker-loci ORDER for the HIGHEST POSSIBLE NUMBER of MARKERS
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