04 wp3 progresses&results-20130221

WP3

Results achieved since the beginning of the project and plans for 2013

Main objectives of WP3

1. Extend software for pedigree based QTL analyses

2. Discovery of QTL for fruit quality traits and disease resistance.

3. Validation of QTL-alleles over climatic regions and harvest dates

4. Assessment of genetic diversity as exploited within European breeding programs

Results: PBA software – T3.1

Intro:

• FlexQTLTM software

– Used to search for markers linked to traits.

– Designed for low marker densities

• SSR, AFLP...

• High densities (SNP): computation time too long

Needs:

– Approaches reducing computation time

Results: FlexQTLTM

Approaches:

• More efficient algorithm implemented: -25%

• Option to sample marker info less frequently: -10x

• Windows -> version Linux platform : - 5x

Results: PBA –software II

Intro-II

• SNP calling is performed using Genome Studio software

• Easily creates > million data points

• Issue: preparation of input data files for PBA software

Approach

• Script developed that converts Genome Studio output to a Pedimap (FlexQTLTM) input file

Intro III • Visual interpretation easier than inspection of

large tables

Approach • Important QTL results are presented in figures

– R-scripts have been added or improved for • Trace plots of QTL positions along the genome • Bin-wise posterior probabilities of QTL • Posterior mean estimates of QTL effects • Posterior probabilities of QTL genotypes of individuals

Results: PBA –software III

Intro IV

• FlexQTLTM results are presented in a large series of output files. Not user friendly for occasional users.

Approach

• A Interface is under development. Test version is un use.

PBA – software: Visual FlexQTL

PBA – software: Visual FlexQTL

PBA-Software: Integrated maps

Intro V • QTL mapping requires markers to be in correct order.

– LG, succession in within Linkage group

– Physical map not adequate: ± 15% SNP misplaced

Need – Markers correctly positioned on linkage map

Approach – Protocols developed for the generation of integrated

genetic linkage maps over multiple families

PBA-software

Summary - Better adopted to high marker densities

- Reductions in computation time

- Additional new functionalities

- Increased user friendliness - Interface

Acknowledgements • RosBREED project

– USDA-SCRI

– www.RosBREED.org Amy Iezzoni

Cameron Peace

Results: Training on PBA software – T3.7

Workshop

• Aim: Intro to FlexQTLTM & Pedimap

• Participants: Partners WP3-Peach

• Date: Feb 17-18, 2013

• Instructors: IRTA: Diego Micheletti

DLO: Marco Bink

Eric van de Weg

Results: Discovery QTL T3.2-T3.2 Background

1. Fruit related Traits – Maturity time

– Fruit Size

– Flesh color

– Firm/soft melting

– Flesh adherence,

– Titrable acidity

– Total sugar

– Flowering time

– Flowering intensity

– White anthers

– Monilinia resistance

3. Phenotypic data

– Historic: EU-Projects, National projects

2. Segregating germplasm

– 18 families , ±1500 individuals

– 5 breeding programs, 3 countries

4. Marker Data: next slide

Peach

3. Phenotypic data

– New : – 2011 & 2012 season

– Uploaded to DataBase

Results

Peach – Marker data

• 9K SNP array

• Filtered for robust SNP

• Marker maps generated for each family

Genotyping performance

• Assayed SNPs = 8144

• Polymorphic: 67.1%

– Robust and informative 53.8%

– Null Allele/preferencial annealing 2.9%

– Paralogous regions 10.1%

• Non-Polymorphic 32.9%

– False SNP 9.6%

– Failed 23.3%

Genetic mapping

• Comparison of the genetic map of chromosome 3 for two crosses – Belbinette x Nectalady

– (IF7319828 x P. ferganensis) x IF7310828

• High colinearity between genetic map and genome No need to create an integrated genetic for the PBA

PBA Preliminary results Peach

FlexQTL confirms known QTLs both for Flowering intensity & time

Peaks in Green

FlexQTL gives some evidence for additional minor QTL

peaks in black

G 8 Flowering Time

G 4 Flower intensity

Fruit Quality – Taste

• Firmness • Juiciness

• Crispness • Total Sugar • Acidity

– Storability – Shelf life – Harvest date – Fruit size – Skin Color Resistance to Nectria

Apple

1. Fruit Quality Traits: > 10

3. Phenotypic data

– HiDRAS

• 3 Years, Multiple time moments

– Harvest, Storage 2 & 4M

– Shelf Life: 2wks - 2M storage

– National projects

2. Segregating germplasm

24 families , ±1600 individuals

6 breeding programs, 6 countries

4. Genotyping: next slide

Results: Discovery QTL T3.2-T3.2

Results

Background

Genotyping

• Infinium 20K SNP

– Available Jan 16, First 2x96 individuals tested Jan 19 • Jonathan x Prima

– High quality data!

– High number of polymorphic markers

Genotyping: 1st SNP results

• High number of polymorphic markers

• 70% (1820/2598) excluded: same segregation pattern

• 700 – 800 Unique segregation patterns, ±45/LG

• ± 3 SNP / Focal Point

Jonathan #

# Left

Prima #

# Left

J+P #

J+P # Left

Total Filtered 3000 2958 2400

Similarity -JM -1549 1409

Ungrouped -33 1376

Excluded 1081 -271 1105

Similarity map -317 764 -303 764

Unique patterns 764 802

Mapped easily

J1 P1 J2 P2 J3 P3 J4 P4 J5 P5 J6 P6 J7 P7 J8 P8 J9 P9 J10 P10 J11 P11 J12 P12 J13 P13 J14 P14 J15 P15 J16 P16 J17 P17

0

5

10

15

20

25

30

35

40

45

50

55

60

65

70

75

80

85

90

95

100

105 Some ends of chromosomes need to be checked +P7

Graphical genotyping: Error added

• Graphical genotyping: High quality maps!

Results genetic diversity EU breeding programs T3.4

• Peach:

– SSR study

– Presentation Maria Jose – Stakeholdersday

• Apple – Results for 2 breeding programs (Y1)

– Y2: No activities

– Urgent need to progress

Publications Peach: Planned

Title WP Responsible Participants

Application of PBA in peach: PBA to identify

major genes* 3 IRTA All WP3-Peach

Genetic diversity as exploited in

EU apple and peach breeding. 3 DLO DLO+IRTA

AG and PBA: characters related to climate

change *(blooming/flowering/maturity) 3-4 INRA tbd

AG? and PBA to detect QTLs of characters

related to disease resistance 3-4 INRA tbd

AG and PBA to detect QTLs of characters

related to fruit quality 3-4 UNIMI-CRA tbd

Publications Apple: Published

1. Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array.

– 2012, BMC Genomics 25;13:203.

– Antanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ

2. PEDIMAP: Software for the visualization of genetic and phenotypic data in pedigrees.

– 2012, Journal of Heredity.

– Voorrips RE, Bink MCAM, Van de Weg WE

Publications Apple: Planned ‘13 - ‘14

1. Procedures for construction of Integrated Genetic linkage using multiple families. – Jansen et al. – DLO, IASMA, PFR

2. Procedures for filtering and calling of SNP markers. – DiGuardo et al. – DLO, IASMA

3. Integrated genetic linkage map of apple using ± 24 families. – DiGuardo et al. – DLO, IASMA, .....?

4. QTLs for Nectria resistance in apple – Koehorst et al. – DLO, IASMA

Main challenges for 013 - Peach

Extend PBA to the 18 subpopulations (starting from March)

– Normalization of phenotypic data from 5 different location in Europe:

• INRA - Avignon (F), INRA- Bordeaux (F), IRTA (E), CRA-FRU (I), and University of Milan (I)

Evaluation of the construction of SNP haplotypes (to use as

multi-allelic markers, more informative than single SNPs)

Correction of the genetic/physic position of some misplaced SNPs

Main challenges for 2013 - Apple

1. Apple: Integrated genetic linkage map – Needed to get started with QTL analyses

2. Development of a sustained/ ‘agreed’ vision on type and format of QTL & marker of use to breeders – Joined activity WP1.5, WP3, WP7

3. Involve stakeholders in validation of QTL in their breeding germplasm.

4. Report on the delivery of genetic diversity in Breeding programs

Interactions between WP3 ↔ other WP

• Interactions needed with other WPs: – WP1: Keep informed on discovery Fruit quality QTL – WP4: Comparison on marker-trait-associations – WP5: Phenotyping protocols + Phenotypic data – WP6: SNP genotyping, Genetic <> Physical map – WP7: Development conceptual model for WP3 data – WP8: Organization of PBA workshop for stakeholders – WP9: management of the project, reports

• Interactions planned with other projects or stakeholders of the project – RosBREED – Apple Breeders