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
CH03g12z4.0
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LG02
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Hi03d0643.0
GD1255.0
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LG03
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LG04
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LG07
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CH01f0933.0
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LG08
NH0029a12.0
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CH01h0259.0
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LG09
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Hi02c0725.0
HB11AG38.0
CHVf156.0
CH05g0877.0
LG01
CH03g12z4.0
Hi02c0725.0
HB11AG38.0
CHVf156.0
CH05g0877.0
LG01
CH02f061.0
CN49313924.0
CH02c0642.0
CH05e0351.0
CH03d0167.0
LG02
CH02f061.0
CN49313924.0
CH02c0642.0
CH05e0351.0
CH03d0167.0
LG02
CH03e033.0
CH03g0724.0
Hi03d0643.0
GD1255.0
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Ms14h0394.0
CH03g12y111.0
LG03
CH03e033.0
CH03g0724.0
Hi03d0643.0
GD1255.0
AU22365776.0
Ms14h0394.0
CH03g12y111.0
LG03
NZ05g080.0CH04e022.0
Hi23g0218.0
CH05d0232.0
Hi07b0255.0
CH02c02b73.0
LG04
NZ05g080.0CH04e022.0
Hi23g0218.0
CH05d0232.0
Hi07b0255.0
CH02c02b73.0
LG04
Hi09b045.0
Hi04a0820.0
CH03a0934.0
CH05e0645.0
Hi04d0269.0
CH05f0681.0
CH02a0890.0
CH04e03108.0
LG05
Hi09b045.0
Hi04a0820.0
CH03a0934.0
CH05e0645.0
Hi04d0269.0
CH05f0681.0
CH02a0890.0
CH04e03108.0
LG05
HB09TC9.0
CH03d0723.0
CH03d1240.0
CH05a0578.0
LG06
HB09TC9.0
CH03d0723.0
CH03d1240.0
CH05a0578.0
LG06
CN4447945.0
Hi03a1026.0
CH04e0535.0
Ms06c0954.0
Hi05b0974.0
LG07
CN4447945.0
Hi03a1026.0
CH04e0535.0
Ms06c0954.0
Hi05b0974.0
LG07
CH01c0618.0
CH01f0933.0
CH01h1052.0
Hi23g1262.0
LG08
CH01c0618.0
CH01f0933.0
CH01h1052.0
Hi23g1262.0
LG08
NH0029a12.0
CH01f03b24.0
Hi05e0742.0
CH01h0259.0
CN44454269.0CH05d0873.0
LG09
NH0029a12.0
CH01f03b24.0
Hi05e0742.0
CH01h0259.0
CN44454269.0CH05d0873.0
LG09
CH04c06z13.0CH02b0714.0
CH02c1140.0
CH03d1150.0
CH04g09y64.0
CH02b03b81.0
Ms06g03104.0
LG10
CH04h020.0
Hi07d11x10.0
CH02d0831.0
CH04a1246.0
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CH04g0773.0
LG11
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NZ28f0429.0
CH01g1245.0
CH04d0251.0
CH01f0255.0
CH03c0261.0
Hi07f0176.0
CH01d03z89.0
LG12
CH05h054.0
Hi04g0518.0
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LG13
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CH01g0510.0
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CH01d0837.0
Hi04c0555.0
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CH02c09110.0
LG15
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CH05a0447.0
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CH01h0125.0
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CH05d0891.0
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CH02c1140.0
CH03d1150.0
CH04g09y64.0
CH02b03b81.0
Ms06g03104.0
LG10
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CH02c1140.0
CH03d1150.0
CH04g09y64.0
CH02b03b81.0
Ms06g03104.0
LG10
CH04h020.0
Hi07d11x10.0
CH02d0831.0
CH04a1246.0
Hi16d0255.0
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LG11
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CH02d0831.0
CH04a1246.0
Hi16d0255.0
CH04g0773.0
LG11
CH05d0413.0
NZ28f0429.0
CH01g1245.0
CH04d0251.0
CH01f0255.0
CH03c0261.0
Hi07f0176.0
CH01d03z89.0
LG12
CH05d0413.0
NZ28f0429.0
CH01g1245.0
CH04d0251.0
CH01f0255.0
CH03c0261.0
Hi07f0176.0
CH01d03z89.0
LG12
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Hi04g0518.0
GD14740.0
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LG13
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LG13
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CH01g0510.0
CH04c0719.0
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CH01g0510.0
CH04c0719.0
U7894842.0
LG14
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CH03b0611.0
Hi03g0623.0
CH01d0837.0
Hi04c0555.0
CH02d1177.0
CH02c09110.0
LG15
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Hi03g0623.0
CH01d0837.0
Hi04c0555.0
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CH05c0614.0
Hi04e0430.0
CH05a0447.0
CH04f1076.0
LG16
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CH05a0447.0
CH04f1076.0
LG16
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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´)