WP4: Exploring the phenotypic and genetic diversity in European
apple and peach germplasm collections and its exploitation...
Main objectives of WP 4
 Improve the knowledge of genetic and phenotypic variability in
apple and peach European collecti...
Results achieved since the beginning
of the project
 Description of phenotypic variability in apple
and peach germplasm c...
UK; 2237
FR; 1054
BE; 1314
CZ; 256
IT; 421 SWE;195
Selection of accessions in
germplasm collections
UK
310
FR
274
BE
296
C...
GROUP LABEL DESCRIPTOR PRIORITY
DI1Canker
Tree-twigs - Susceptibility to NECTRIA
CANKER (1-9)
Partial
DI1Mildew
Leave & tw...
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 infor...
Results: phenotypic variability in apple
and peach germplasm collections
PEACH
Data entries per partner
0
500
1000
1500
20...
• Analysis of the distribution of traits variability per collection
Results: phenotypic variability in apple
and peach ger...
Results achieved since the beginning
of the project
 Description of phenotypic variability in apple
and peach germplasm c...
Results: peach variability, population
structure and LD analysis
1,296 peach
accessions
CRA-Rome
178
UNIMI
140
INRA
343
IR...
Results: peach variability, population
structure and LD analysis
- ~20% of accessions were clones (98% of identical genoty...
Results: peach variability, population
structure and LD analysis
Most representative K is 3:
• Occidental breeding materia...
Results: peach variability, population
structure and LD analysis
Occidental breeding material Occidental old / non breedin...
Results achieved since the beginning
of the project
 Description of phenotypic variability in apple
and peach germplasm c...
Results: apple genetic variability and
population structure
CH03g12z4.0
Hi02c0725.0
HB11AG38.0
CHVf156.0
CH05g0877.0
LG01
...
Results: apple genetic variability and
population structure
Nb of
genotypes
Nb of
accessions
Belgium 190 209
CZ 120 132
Fr...
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 g...
Population structure
K = 3
K = 2
Diversity – Tree distribution
(1230 genotypes)
Exemple of European Core Collection
(384 accessions)
Publications
• Meeting presentations
– Application of high throughput genotyping techniques in peach germplasm and breedin...
Publications plan for 2013
Genetic variability in a wide germplasm of
domesticated peach through high throughput
genotypin...
Main challenges for 2013
Task 4.1.- Description of phenotypic variability
 Phenotypic data already in a web database
Sea...
Main challenges for 2013
Task 4.2.- apple and peach core collections
peach cc set and analyzed with 9K SNPs
apple cc set...
Main challenges for 2013: chose
genotyping strategy in apple
• Test of SNP genotyping, 48 old apple accessions
with Illumi...
Task 4.3.- Acquiring new phenotypic data
Collect second year of phenotypic data
Main challenges for 2013: chose
genotyping...
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)
D...
Interactions between your WP and the
rest of the project
• Interactions planned with other WPs of the project:
– From your...
Agenda for WP4 session: EDIFICI
POLIVALENT 2.03 room
• Acquiring new phenotypic data (2013) (20´)
– Feedback of 2012 pheno...
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05 wp4 progresses&results-20130221

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05 wp4 progresses&results-20130221

  1. 1. 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
  2. 2. 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
  3. 3. 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
  4. 4. UK; 2237 FR; 1054 BE; 1314 CZ; 256 IT; 421 SWE;195 Selection of accessions in germplasm collections UK 310 FR 274 BE 296 CZ 253 IT 232 SWE 195 5,477 accessions in germplasm collections 1,560 accessions with phenotypic observations APPLE Removing synonyms and triploids IT-RO; 943 IT-MI; 575 FR; 764 ISP; 303 CH; 300 2,885 accessions in germplasm collections 1,296 accessions with phenotypic observations Removing synonyms and selecting diversity PEACH IT-RO 178 IT-MI 140 FR 343 SP 353 CH 282
  5. 5. 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) PartialFL1 = 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) PartialFR3 = FRUIT KEEPING & PICKING PERIODS FR3PeriodPicking Fruit Harvest Maturity (1-9) New FR4Size Fruit Size (Diameter mm) CommonFR4 = FRUIT INSTRUMENTAL CHARACTERISATION FR4Weight Fruit Weight Average (g) Common TR1Architecture Tree – Global Architecture PartialTR1 = 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
  6. 6. Results: phenotypic variability in apple and peach germplasm collections APPLE Data entries per partners and years
  7. 7. 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 .
  8. 8. 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 Numberofdataentries CRA-Rome UNIMI INRA IRTA ZJU
  9. 9. • 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
  10. 10. 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
  11. 11. Results: peach variability, population structure and LD analysis 1,296 peach accessions CRA-Rome 178 UNIMI 140 INRA 343 IRTA 353 ZJU 282 Genotyped with the 9K IPSC SNPs chip: 8,144 SNPs identified through the re- sequencing of ca. 50 prunus accessions SNP genotyping Good 4379 54% Nullallele 242 3% Lack of one homozygous 827 10% To check 20 0% Monomorphic 778 10% Failed 1898 23%
  12. 12. 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)
  13. 13. 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)
  14. 14. 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
  15. 15. 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
  16. 16. Results: apple genetic variability and population structure CH03g12z4.0 Hi02c0725.0 HB11AG38.0 CHVf156.0 CH05g0877.0 LG01 CH02f061.0 CN49313924.0 CH02c0642.0 CH05e0351.0 CH03d0167.0 LG02 CH03e033.0 CH03g0724.0 Hi03d0643.0 GD1255.0 AU22365776.0 Ms14h0394.0 CH03g12y111.0 LG03 NZ05g080.0 CH04e022.0 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 HB09TC9.0 CH03d0723.0 CH03d1240.0 CH05a0578.0 LG06 CN4447945.0 Hi03a1026.0 CH04e0535.0 Ms06c0954.0 Hi05b0974.0 LG07 CH01c0618.0 CH01f0933.0 CH01h1052.0 Hi23g1262.0 LG08 NH0029a12.0 CH01f03b24.0 Hi05e0742.0 CH01h0259.0 CN44454269.0 CH05d0873.0 LG09 CH03g12z4.0 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 AU22365776.0 Ms14h0394.0 CH03g12y111.0 LG03 CH03e033.0 CH03g0724.0 Hi03d0643.0 GD1255.0 AU22365776.0 Ms14h0394.0 CH03g12y111.0 LG03 NZ05g080.0 CH04e022.0 Hi23g0218.0 CH05d0232.0 Hi07b0255.0 CH02c02b73.0 LG04 NZ05g080.0 CH04e022.0 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 CN44454269.0 CH05d0873.0 LG09 NH0029a12.0 CH01f03b24.0 Hi05e0742.0 CH01h0259.0 CN44454269.0 CH05d0873.0 LG09 CH04c06z13.0 CH02b0714.0 CH02c1140.0 CH03d1150.0 CH04g09y64.0 CH02b03b81.0 Ms06g03104.0 LG10 CH04h020.0 Hi07d11x10.0 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 CH05h054.0 Hi04g0518.0 GD14740.0 NH009b70.0 LG13 CH05g07-10.0 CH01g0510.0 CH04c0719.0 U7894842.0 LG14 NZ02b018.0 CH03b0611.0 Hi03g0623.0 CH01d0837.0 Hi04c0555.0 CH02d1177.0 CH02c09110.0 LG15 CH02a038.0 CH05c0614.0 Hi04e0430.0 CH05a0447.0 CH04f1076.0 LG16 CH04c06y0.0 AT00017412.0 CH01h0125.0 Hi03c0535.0 Hi02f1255.0 Hi05c0674.0 CH05d0891.0 Hi07h02100.0 LG17 CH04c06z13.0 CH02b0714.0 CH02c1140.0 CH03d1150.0 CH04g09y64.0 CH02b03b81.0 Ms06g03104.0 LG10 CH04c06z13.0 CH02b0714.0 CH02c1140.0 CH03d1150.0 CH04g09y64.0 CH02b03b81.0 Ms06g03104.0 LG10 CH04h020.0 Hi07d11x10.0 CH02d0831.0 CH04a1246.0 Hi16d0255.0 CH04g0773.0 LG11 CH04h020.0 Hi07d11x10.0 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 CH05h054.0 Hi04g0518.0 GD14740.0 NH009b70.0 LG13 CH05h054.0 Hi04g0518.0 GD14740.0 NH009b70.0 LG13 CH05g07-10.0 CH01g0510.0 CH04c0719.0 U7894842.0 LG14 CH05g07-10.0 CH01g0510.0 CH04c0719.0 U7894842.0 LG14 NZ02b018.0 CH03b0611.0 Hi03g0623.0 CH01d0837.0 Hi04c0555.0 CH02d1177.0 CH02c09110.0 LG15 NZ02b018.0 CH03b0611.0 Hi03g0623.0 CH01d0837.0 Hi04c0555.0 CH02d1177.0 CH02c09110.0 LG15 CH02a038.0 CH05c0614.0 Hi04e0430.0 CH05a0447.0 CH04f1076.0 LG16 CH02a038.0 CH05c0614.0 Hi04e0430.0 CH05a0447.0 CH04f1076.0 LG16 CH04c06y0.0 AT00017412.0 CH01h0125.0 Hi03c0535.0 Hi02f1255.0 Hi05c0674.0 CH05d0891.0 Hi07h02100.0 LG17 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
  17. 17. 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 100103106109 Duplicates - diploids Belgium Czech_Republic France Italy Sweden United_Kingdom Diploids
  18. 18. Results: apple genetic variability and population structure Diversity – Geographic origin
  19. 19. Results: apple genetic variability and population structure Diversity – Partner’s collection
  20. 20. 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
  21. 21. Population structure K = 3 K = 2
  22. 22. Diversity – Tree distribution (1230 genotypes)
  23. 23. Exemple of European Core Collection (384 accessions)
  24. 24. 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
  25. 25. Publications plan for 2013 Genetic variability in a wide germplasm of domesticated peach through high throughput genotyping. (D.4.2).
  26. 26. 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)
  27. 27. 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
  28. 28. Main challenges for 2013: chose genotyping strategy in apple • Test of SNP genotyping, 48 old apple accessions with Illumina SNP Chip Good 10363 57% Null allele 110 1% Lack of one homozygous; low frequency; missing data 5870 33% Monomorphic 1491 8% Failed 185 1%  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!!
  29. 29. Task 4.3.- Acquiring new phenotypic data Collect second year of phenotypic data Main challenges for 2013: chose genotyping strategy in apple
  30. 30. Action Plan for 2013 WHAT WHO HOW DEADLINE
  31. 31. 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)
  32. 32. 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
  33. 33. 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´)
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