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


Input fileSimple to generate & manageRequired: Targeted individual & its parents

Example: Florina & its Progenitors


Input fileSimple to generate & manageRequired: Targeted individual & its parentsOptional: Traits, Nuisances Example: Florina & its Progenitors


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


Type 1: OverviewFounders that contributed to the targeted individualFlorina, which are its Progenitors ?


Type 2: Names only Founders that contributed to the targeted individualFlorina, which is its Offspring?


Type 3: Names only + phenotypicvalues

Starting pointFull sib FamiliesSelectionsCultivarsDesign of genetic experimentsType of offspring?Color name-boxes:


3. Names only + phenotypic valuesTreeNot Available: lostTree & NAType of offspring?Color name-boxes:Design of genetic experiments


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


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


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


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 !


Use:Validation of parentagesValidation TTT germplasmOrigin / introgression chromosome segmentsFounderHomolog with important gene & position locus

1. Successful introgression2. Little linkage drag


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


17/08/201515

Use:Validation of parentagesValidation TTT germplasmOrigin/introgression chrom. segmentsFounder composition of modern cvs

F2-26829-2-2Golden DeliciousGolden DeliciousDeliciousCox


Pedimap & Breeding decissionsHeading for maximum diversity, which would be the best parent to combine with Galarina?


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?)


ConclusionFunctionalityPedimap supports visual presentation of PedigreesIncluding phenotypic values & marker genotypesUse: clarifies Genetic structures in breeding germplasmInheritance patterns


Generation ViewsViews simple to generate & manageInterface, user-friendlyManual & Additional documentation


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


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


Videos FB-Pedimap workshopPBA workshop, MSU JUNE 10 23


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


AcknowledgementsDeveloper: Dr. Roeland VoorripsWageningen URPBA workshop, MSU JUNE 10 25

ProjectsEU-HiDRAS : Software & ManualUSDA-SCRI RosBREED: Scientific paper


Questions?

Thanks


19 van de weg

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