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Transcript of 19 van de weg
Pedimap: Graphical presentation of genetic information in pedigrees
PBA workshop, MSU JUNE 10 1Eric van de WegFruit Breedomics, stakeholders day Feb 11 2014, Zurich
PEDIMAP software: Visual presentation of PedigreesTo clarify genetic structure in breeding germplasm & to clarify inheritance patternsEric van de WegFruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Pedimap software: IntroductionTool to present pedigree relationshipsUseful to present / clarify:Genetic structures in breeding germplasmInheritance patternsEasy in use: Graphical User Interface
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Input fileSimple to generate & manageRequired: Targeted individual & its parents
Example: Florina & its Progenitors
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Input fileSimple to generate & manageRequired: Targeted individual & its parentsOptional: Traits, Nuisances Example: Florina & its Progenitors
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Pedimap software: Type of ViewsDifferent Type of graphs different goals OverviewNames onlyNames + Phenotypic traitNames + Marker genotypesNames + IBD probabilities
Examples on applicationsPBA workshop, MSU JUNE 10 5
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
Type 1: OverviewFounders that contributed to the targeted individualFlorina, which are its Progenitors ?
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Type 2: Names only Founders that contributed to the targeted individualFlorina, which is its Offspring?
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Type 3: Names only + phenotypicvalues
Starting pointFull sib FamiliesSelectionsCultivarsDesign of genetic experimentsType of offspring?Color name-boxes:
Fruit Breedomics day , EUCARPIA 2015 Bologna, Jun 18
3. Names only + phenotypic valuesTreeNot Available: lostTree & NAType of offspring?Color name-boxes:Design of genetic experiments
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3. Names only + Phenotypes, Limited # classesPBA workshop, MSU JUNE 10 10
Winter hardiness 4x garden rose
UnknownInheritance patterns ?Color name-boxes according to phenotypic value
Limited x Limited Better
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3. Names only + Phenotypes, continuous scale
Fuji
X-3143
X-6564
Galarina
X-3263
X-3318
12_F13
12_F41
12_J16
12_J28
12_J29
I_J44
I_J50
I_J56
Very firm
SoftQuite softFirmIntermediateQuite softSoftFirmness-QTL pyramid along successive generationsFruit firmness of appleInheritance patterns ?Color name-boxes
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4. Names + Marker genotypesParentage & DNA sample True To Type?2 homologs4 loci (SSR)
Delicious229202120116152143null99
Cox212212116122143null9775
KidsOrRed229212120116152143null75
Delicious229202120116152143null99
Cox212212116122143null9775
KidsOrRed229212120116152143null75
Manual analyses: Pedigree records & DNAs are OK
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B. Names + Identity By Descent (IBD) probabilitiesMarker alleles coloured according to origin (founder)Based on IBD data as coming from the FlexQTLTM software Chromosome fragments: where do they come from? Where do they go to?
Delicious229202120116152143null99
Cox212212116122143null9775
GoldenDel2292141161161521437999
KidsOrRed229212120116152143null75
Gala2122291161161431527579
IngMarie212218122116null1439795
Elstar2292181161161521439997
F_IngMarie218999116122143null95999
Rubens2292291161161431527599
Rubens: Top segment homozygous for Golden Deliciouss Homologe-1Homozygous through IBD !
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Use:Validation of parentagesValidation TTT germplasmOrigin / introgression chromosome segmentsFounderHomolog with important gene & position locus
1. Successful introgression2. Little linkage drag
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IBD probabilities: explanationLinkage group inherited frommother fatherColor indicates founder from which allele is inherited
Locus positionsWidth indicates probability of founder alleles
Elise
Locus10
Locus25
Locus310
Locus415
Locus520
Was de-activated in previous slide except for the targeted locus
Previous slide: only targeted founder-haplotype was coloured, all others were set at grey
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17/08/201515
Use:Validation of parentagesValidation TTT germplasmOrigin/introgression chrom. segmentsFounder composition of modern cvs
F2-26829-2-2Golden DeliciousGolden DeliciousDeliciousCox
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Pedimap & Breeding decissionsHeading for maximum diversity, which would be the best parent to combine with Galarina?
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Reminder Pedimap is on visualisation, No statistical or genetic analysesNo data manipulationIdentity By Descent data come from the FlexQTLTM software For apple, SNP & IBD data are coming public available for few hundred cultivars & breeding selections through the FruitBreedomics website/data base (spring 2016?)
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ConclusionFunctionalityPedimap supports visual presentation of PedigreesIncluding phenotypic values & marker genotypesUse: clarifies Genetic structures in breeding germplasmInheritance patterns
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Generation ViewsViews simple to generate & manageInterface, user-friendlyManual & Additional documentation
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Availability & OperationFreewareSoftware link includes manual & examplesOperation: Windows
Developper Dr. Roeland VoorripsDownload from: http://www.wageningenur.nl/en/show/Pedimap.htm2 links: Software & License file requestLicense generated instantly, sent by email
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Documentation & useAdditional documentationPresentations & vimeos at the FruitBreedomics websitewww.fruitbreedomics.comVideos from a 1 day FruitBreedomics workshophttp://www.fruitbreedomics.com/index.php/media-center/learning-material-training-sessions/156-use-of-pedimap-software-in-breeding
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Videos FB-Pedimap workshopPBA workshop, MSU JUNE 10 23
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Documentation & useAdditional documentationPresentations & vimeos at the FruitBreedomics websitePublication in J HeredityVoorrips et al. 2012, 103:903-907, DOI 10.1093/jhered/ess060
Examples through scientific publicationsRosyara et al. 2013, Mol. Breed DOI 10.1007/s11032-013-9916-yBink et al. 2014, Theor Appl Genet. 127:1073-1090Van Dijk et al. 2014, BMC Pl Biol 14:55. doi:10.1186/1471-2229-14-55Soriano et al. 2014, Mol Breeding DOI 10.1007/s11032-014-0159-3
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AcknowledgementsDeveloper: Dr. Roeland VoorripsWageningen URPBA workshop, MSU JUNE 10 25
ProjectsEU-HiDRAS : Software & ManualUSDA-SCRI RosBREED: Scientific paper
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Questions?
Thanks
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