WP4: Exploring the phenotypic and genetic diversity in European apple and peach germplasm collections and its exploitation by association genetics approach

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

Maria José Aranzana + all WP4 partners

Main objectives of WP 4

Improve the knowledge of genetic and phenotypic variability in apple and peach European collections

Identify genomic regions contributing to the genetic control of major horticultural traits through genome-wide association genetics (LD mapping)

In combination with WP3, supply WP1 with tightly linked molecular markers for implementation into the MAB pipeline

Results achieved since the beginning of the project

Description of phenotypic variability in apple and peach germplasm collections

• Peach genetic variability, population structure and LD analysis

• Apple genetic variability and population structure

UK; 2237

FR; 1054

BE; 1314

CZ; 256

IT; 421 SWE;195

Selection of accessions in germplasm collections

UK310

FR274

BE296

CZ253

IT 232

SWE195

5,477 accessions in

germplasm collections

1,560

accessions with

phenotypic

observations

APPLE

Removing synonyms and triploids

IT-RO; 943

IT-MI; 575FR; 764

ISP; 303CH; 300

2,885 accessions in

germplasm collections

1,296 accessions

with phenotypic

observations

Removing synonyms and selecting

diversity

PEACH

IT-RO178

IT-MI140

FR343

SP353

CH 282

GROUP LABEL DESCRIPTOR PRIORITY

DI1Canker Tree-twigs - Susceptibility to NECTRIA CANKER (1-9)

Partial

DI1Mildew Leave & twigs - Global Susceptibility to POWDERY MILDEW (1-9)

Partial

DI1ScabFruit Fruit – Global Susceptibility to SCAB (1-9) Partial

DI1 = FUNGI DISEASE

DI1ScabLeaf Leaf – Global Susceptibility to SCAB (1-9) Partial

FL1Class Flowering Period (1-9) Common

FL1Intensity Flowering Intensity (1-9) Partial FL1 = FLOWERING PHENOLOGY

FL1Regularity Relative regularity of flowering - Biennal Habit (1-9)

Add

FR1OverColorAmount Fruit Global amount of over colour (1-9) Common

FR1Size Fruit Size (1-9) Common

FR1RibApex Fruit Crowning apex (1-9) Partial

FR1RussetAmount Fruit Global Amount russet (1-9) New

FR1Shape Fruit Basic Global shape (1-4) Common

FR1ShapeRatio Fruit Global shape (RATIO Heigt / Width) Partial

FR1 = FRUIT CHARACTERISATION

FR1StalkLength Fruit Stalk Length (1-9) Partial

FR2Acid Fruit Sensory Acidity (1-9) Partial

FR2AcidSugarRatio Fruit Sensory Flesh Balance Sweet/acid New

FR2Bitter Fruit Sensory Flesh Bitterness (1#9) Partial

FR2Crunch Fruit Crispness (1-9) New

FR2Firm Fruit Sensory flesh Firmness (1-9) New

FR2Granular Fruit Sensory flesh Texture (1-9) Common

FR2Juice Fruit Sensory Juiciness (1-9) New

FR2Mealy Flesh mealiness Add

FR2Sugar Fruit Sensory Sweetness (1-9) Partial

FR2TasteGlobal Fruit – Sensory Global eating quality (1-9) Common

FR2 = FRUIT TASTE

FR2TasteMaturity Assessment of the optimal ripening stage of the fruits when picked and/or tasted

New

FR3PeriodKeeping Global Period of Fruit Keeping ability (1-9) Partial FR3 = FRUIT KEEPING & PICKING

PERIODS FR3PeriodPicking Fruit Harvest Maturity (1-9) New

FR4Size Fruit Size (Diameter mm) Common FR4 = FRUIT INSTRUMENTAL

CHARACTERISATION FR4Weight Fruit Weight Average (g) Common

TR1Architecture Tree – Global Architecture Partial TR1 = TREE CHARACTERISATION TR1BearingHabit Tree Type of fruiting (1-4) (Lespinasse) Partial

TR2 = FRUIT CROPPING

TR2Prod1year Relative Fruit setting (1-9) – Year by year Add

Results: phenotypic variability in apple and peach germplasm collections

0

5000

10000

15000

20000

25000

READING INRA CRA-W RBIPH UNIBO

Fruit & Tree

Period of flowering

Disease susceptibility

APPLE

• 1,264 accessions with observations

• 81,206 informative data entries in the

phenotypic database

Results: phenotypic variability in apple and peach germplasm collections

APPLE

Data entries per partners and years

Results: phenotypic variability in apple and peach germplasm collections

• 998 accessions with observations

• 37,818 informative data entries in the

phenotypic database

PEACH

CRA-Rome UMIL IRTA INRA ZJU

vigor x x - - x

tree habit x x - - x

gland type x x - - x

flower type x x - - x

male sterility - x - x x

beginning of flowering date x - x x x

beginning of flowering description - - - - x

full blossom date - x x x x

full blossom description - - x - x

flower density x x x x x

beginning of ripening date x x x - x

beginning of ripening description - - x - x

yield x x - - x

fruit size x x - x x

fruit size weight x - x x -

fruit pubescence x x x x x

fruit shape x x x x x

fruit flesh color x x x x x

fruit hue of overcolor x x - - x

fruit extent of overcolor x x - x x

sugar content brix - - x x x

sugar content taste data - x - - -

acidity - - x x -

acidity taste description - x - - x

acidity taste scale - x - - -

flesh firmness x x - x x

texture x x - - x

stony hard - x - - x

adherence of stone to flesh x x - x x

PRODUCTION

FRUIT QUALITY

VEGETATIVE TRAITS

FLOWER TRAITS

FRUIT MORPHOLOGY

FLOWERING

MATURITY

0

1000

2000

3000

4000

5000

6000

CRA-Rome UNIMI INRA IRTA ZJU

Vegetative traits

Flower Traits

Flowering period

Maturity

Production

Fruit Morphology

Fruit Quality

.

Results: phenotypic variability in apple and peach germplasm collections

PEACH

Data entries per partner

0

500

1000

1500

2000

2500

3000

3500

1985

1986

1987

1988

1989

1990

1991

1992

1993

1994

1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

2011

Years with phenotypic observations

Nu

mb

er

of

data

en

trie

s

CRA-Rome

UNIMI

INRA

IRTA

ZJU

• Analysis of the distribution of traits variability per collection

Results: phenotypic variability in apple and peach germplasm collections

Days to full blossom Days to ripen

Sugar content Acidity

Results achieved since the beginning of the project

Description of phenotypic variability in apple and peach germplasm collections

Peach genetic variability, population structure and LD analysis

• Apple genetic variability and population structure

Results: peach variability, population structure and LD analysis

1,296 peach

accessions

CRA-Rome

178

UNIMI

140

INRA

343

IRTA

353

ZJU

282Genotyped with the 9K IPSC SNPs chip:

8,144 SNPs identified through the re-

sequencing of ca. 50 prunus

accessions

SNP genotyping

Good437954%

Null allele2423%

Lack of one

homozygous827

10%

To check

200%

Monomorphic

77810%

Failed189823%

Results: peach variability, population structure and LD analysis

- ~20% of accessions were clones (98% of identical genotype)

- Average observed heterozygosity 30% (Min 0.3% and Max 68%)

- Average inbreeding coefficient (F): 0.27 (first cousin)

Results: peach variability, population structure and LD analysis

Most representative K is 3:

• Occidental breeding material (352 accessions)

• Chinese / oriental material (58 accessions)

• Occidental old / non breeding material (165 accessions)

• Admixed accessions [Q < 0.8] (665 accessions)

Results: peach variability, population structure and LD analysis

Occidental breeding material Occidental old / non breeding material

Chinese / oriental material Admixed accessions [Q < 0.8]

LD 1Mbp

Results achieved since the beginning of the project

Description of phenotypic variability in apple and peach germplasm collections

Peach genetic variability, population structure and LD analysis

Apple genetic variability and population structure

Results: apple genetic variability and population structure

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CH02c0642.0

CH05e0351.0

CH03d0167.0

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CH03d0167.0

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LG03

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LG03

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LG04

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CH05d0232.0

Hi07b0255.0

CH02c02b73.0

LG04

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CH02a0890.0

CH04e03108.0

LG05

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CH04e03108.0

LG05

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CH03d0723.0

CH03d1240.0

CH05a0578.0

LG06

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CH03d1240.0

CH05a0578.0

LG06

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CH04e0535.0

Ms06c0954.0

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LG07

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LG08

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CH01h0259.0

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LG09

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CH01d03z89.0

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CH05a0447.0

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In red : 8 common SSR In purple : 4 additional SSR genotyped on the 1000 acc.

SSR Genotyping

SSR data already available on Collections : UNIBO : 11 SSR INRA : 24 SSR (29) Reading/Brogdale : 12 SSR

SSR data newly acquired on Collections : CRA-W : 12 SSR RBIPH : 12 SSR USL-Baslgard : 12 SSR + adjusting SSR allele sizes between INRA/UNIBO/Reading

READING

310

INRA

274

CRA-W

296

RBIPH

253

UNIBO

232

Balsgard

195

Results: apple genetic variability and population structure

Nb of genotypes

Nb of accessions

Belgium 190 209

CZ 120 132

France 225 225

Italy 167 184

Sweden 158 160

UK 271 271

2 countries 78 171

3 countries 20 72

4 countries 12 58

1241 1482

0

1

2

3

4

5

6

7

8

1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73 76 79 82 85 88 91 94 97 100 103 106 109

Duplicates - diploids Belgium Czech_Republic France Italy Sweden United_Kingdom

Diploids

Results: apple genetic variability and population structure Diversity –

Geographic origin

Results: apple genetic variability and population structure Diversity –

Partner’s collection

Position of WP3 parents in the overall diversity

WP3 parents cover well the most frequent variability

WP4 based on large genetic diversity while WP3 in breeding material

Population structure

K = 3

K = 2

0 0.5

Diversity – Tree distribution (1230 genotypes)

0 0.5

Exemple of European Core Collection

(384 accessions)

Publications

• Meeting presentations – Application of high throughput genotyping techniques in peach germplasm and breeding lines

within the FruitBreedomics project (Micheletti D., Arús P., Barreneche T., Bassi D., Dirlewanger E., Gao Z., Lambert P., Laurens F., Pascal T., Quilot B., Rossini L., Troggio M., Van de Weg E., Verde I. and Aranzana MJ). Poster. PAG 2012

– Genetic variability in a wide germplasm of domesticated peach through high throughput genotyping. Diego Micheletti, Valeria Aramini, Pere Arus, Elisa Banchi, Teresa Barreneche, Daniele Bassi , Elisabeth Dirlewanger, Zhongshan Gao, Laura Gazza, Patrick Lambert, François Laurens, Xiongwei, Thierry Pascal, Bénédicte Quilot-Turion, Laura Rossini, Michela Troggio, Ignazio Verde, Maria Jose Aranzana. Oral presentation. PAG 2013

– Genetic variability description in a wide germplasm of Peach through High Throughput Genotyping within Fruitbreedomics. Diego Micheletti,Valeria Aramini, Pere Arús, Elisa Banchi, Teresa Barreneche,Daniele Bassi, Elisabeth Dirlewanger, Zhongshan Gao, Laura Gazza , Patrick Lambert, François Laurens, Xiongwei Li, Thierry Pascal, Bénédicte Quilot-TurionLaura Rossini, Michela Troggio, Ignazio Verde, Maria José Aranzana . Oral presentation. RGC6 2012

Publications plan for 2013

Genetic variability in a wide germplasm of domesticated peach through high throughput genotyping. (D.4.2).

Main challenges for 2013

Task 4.1.- Description of phenotypic variability

Phenotypic data already in a web database

Search queries and statistical analysis tools in

the database to be defined (jointly with WP1 and

WP3 and done by WP7)

Main challenges for 2013

Task 4.2.- apple and peach core collections

peach cc set and analyzed with 9K SNPs

apple cc set and analyzed with SSRs

Apple SNP genotyping:

• LD decays fast in apple thousands of NSPs needed

• Which genotyping method???

•SNP chip

•Genotyping by sequence

Main challenges for 2013: chose genotyping strategy in apple

• Test of SNP genotyping, 48 old apple accessions with Illumina SNP Chip

Good1036357%

Null allele1101%

Lack of one homozygous; low frequency; missing data

587033%

Monomorphic14918%

Failed1851%

20K apple SNP Chip

14 apple accessions re-sequenced

2.6 million SNPs found 750 K valid

18,019 SNPs selected (16.3K new and

3.7K from previous chip)

Genetic interval 1cM

LD decay at 55 Kb!!

Task 4.3.- Acquiring new phenotypic data

Collect second year of phenotypic data

Main challenges for 2013: chose genotyping strategy in apple

Action Plan for 2013

WHAT WHO HOW DEADLINE

Deliverables and milestones for the next 12 months

D4.2.- Database uploaded with already available phenotypic data (M24)

D4.3.- Submit a manuscript of: (M30)

• Allelic diversity, population structure and LD in peach

• Construction of apple CC

MS15.- SNP SSR data available in the database for apple cultivars (M18)

MS16.- Peach SNP data available in the database (M24)

MS17.- Apple SNP data available in the database (M33)

MS18.- One year of phenotypic and genome-wide data in the database (M36)

Interactions between your WP and the rest of the project

• Interactions planned with other WPs of the project:

– From your WP:

• WP1: provide SNPs linked to monogenic traits

• WP3: share QTLs information for comparison

• WP7: genetic information needs to be included in the database; search toolbox and statistics of phenotypic information

– To your WP:

• WP3: share QTLs information for comparison

• WP7: release of

Agenda for WP4 session: EDIFICI

POLIVALENT 2.03 room

• Acquiring new phenotypic data (2013) (20´)

– Feedback of 2012 phenotyping

– Problems to solve?

• Apple core collection. Prospects for the paper (15´)

• Draft of variability and LD paper on peach (15´)

• Discussion on the best strategy for apple SNP genotyping (30´)

• Action plan (10´)