This document summarizes research exploring phenotypic and genetic diversity in peach. Over 1580 accessions were studied across multiple locations in Europe and China. Phenotypic data was collected over several years and correlated between locations. Genetic analysis using a 9K SNP chip identified 473 clones and grouped accessions into occidental breeding, occidental non-breeding, oriental, and admixed categories. Genome-wide association studies identified major genes and QTLs associated with traits like acidity, melting behavior, and fruit flesh color.

1. YOUR LOGO
Exploring and exploiting
phenotypic and genetic diversity in
peach: identification of major genes and
QTLs by GWAS.
XIV EUCARPIA symposium on Fruit Breeding
and Genetics.
Maria José Aranzana

2. YOUR LOGO
Exploring and exploiting
phenotypic and genetic diversity in
peach: identification of major genes and
QTLs by GWAS.
XIV EUCARPIA symposium on Fruit Breeding
and Genetics.
Maria José Aranzana

3. YOUR LOGO
Partners involved
Ignazio Verde
Sabrina Micalli
Valeria Aramini
M.Teresa Dettori
Daniele Bassi
Laura Rossini
Igor Pacheco
Stefano Foschi
Alessandra Estella
Nelso Nazzicari
Andrea Caprera
Michela Troggio
Elisa Banchi
Pere Arús
Maria José Aranzana
Diego Micheletti
José Ramón Hernández
Ignasi Iglesias
Quim Carbó
Sanshan Gao
Xionwei Li
Li-rong Wang
Rui-juan Ma
Teresa Barreneche
Thierry Pascal
Bénédicte Quilot
Patrick Lambert
François Laurens

4. YOUR LOGO
Partners involved
Ignazio Verde
Sabrina Micalli
Valeria Aramini
M.Teresa Dettori
Daniele Bassi
Laura Rossini
Igor Pacheco
Stefano Foschi
Alessandra Estella
Nelso Nazzicari
Andrea Caprera
Michela Troggio
Elisa Banchi
Sanshan Gao
Xionwei Li
Li-rong Wang
Rui-juan Ma
Teresa Barreneche
Thierry Pascal
Bénédicte Quilot
Patrick Lambert
François Laurens
Pere Arús
Maria José Aranzana
Diego Micheletti
José Ramón Hernández
Ignasi Iglesias
Quim Carbó

5. YOUR LOGO
• Select those more interesting accessions within each
germplasm collection (200-300)
Exploring phenotypic diversity in peach
Approach
INRA UNIMI
CRA-RomeIRTA
ZJU
(China)

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• Select those more interesting accessions within each
germplasm collection (200-300)
Italy
France
Spain
China
• Collect all phenotypic information acquired for years
• Design the template of a common database for
available and common scales for new data
Approach
Exploring phenotypic diversity in peach

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1580 accessions:
• Local
• Old (founders)
• Commercial from breeding
programs
• Few non-persica
Exploring phenotypic diversity in peach
Common accessions with phenotypic
data between locations

8. YOUR LOGO
Numberofaccessionswithphenotypicdata
UMIL
ZJU
CRA
INRA
IRTA (1) IRTA
(2)
Years
Data available for
several years in
many of the
accessions
Exploring phenotypic diversity in peach

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Exploring phenotypic diversity in peach
Distribution of data on qualitative traits

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(r2= 0.60- 0.80) (r2= 0.97-0.98)
Exploring phenotypic diversity in peach
Data correlation between years

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(r2= 0.38- 0.68)
Data correlation between years
Exploring phenotypic diversity in peach

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Mean # days to full blossom IRTA-Mas Badia
Mean#daystofull
blossomIRTA-Gimenells
Mean # days to ripen IRTA-Mas Badia
Mean#daysto
ripenIRTA-Gimenells
Mean ºBRIX IRTA-Mas Badia
MeanºBRIXIRTA-
Gimenells
MeanacidityIRTA-
Gimenells
Mean acidity IRTA-Mas Badia
y = 47.4 + 0.39 x
r2= 0.18
y = 3.9 + 1.04 x
r2= 0.91
y = 6.5 + 0.49 x
r2= 0.39
y = 13.43 + 1.2 x
r2= 0.77
Exploring phenotypic diversity in peach
Data correlation between locations

13. YOUR LOGO
Exploring and exploiting
phenotypic and genetic diversity in peach:
identification of major genes and QTLs by
GWAS.
XIV EUCARPIA symposium on Fruit Breeding
and Genetics.
Maria José Aranzana

14. YOUR LOGO
• 1580 accessions geotyped with the 9K SNP chip
No Call <5%, three
genotypes
Null allele or preferential
annealing
Duplicated sequences/genes
FalseSNPs
Failed
Exploring genetic diversity in peach
4330
53%
25%

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115
28
17
4 2 2 2 2 0 1
2 3 4 5 6 7 8 9 10 11
# accessions with identical genotype (clones)
• SNPs identified 473 clones
(173 groups with 2 or more
clons)
Exploring genetic diversity in peach

16. YOUR LOGO
115
28
17
4 2 2 2 2 0 1
2 3 4 5 6 7 8 9 10 11
# accessions with identical genotype
• SNPs identified 473 clones
(173 groups with 2 or more
clons)
• 92% of accessions with the
same name where identical
Exploring genetic diversity in peach

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Exploring genetic diversity in peach
Oriental
(Chinese)
Occidenal
Breeding
Occidental
non-breeding
Occidenal
Breeding
Occidental
non-breeding
Oriental
(Chinese)

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Exploring genetic diversity in peach
Occ Breed
Occ non-Breed
Oriental
Admixed
Minor allele Frequency

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Exploring genetic diversity in peach
1.4 Mb 1 Mb
1.8 Mb 0.8 Mb
Occidental
Breeding
Occidental
Local
varieties
Oriental
Occidental varieties show SNPs in LD in the
flesh color (Y) region
Chromosome 1
Occidental
Breeding
Occidental
Local
Oriental Admixed
Linkage disequilibrium (LD)

20. YOUR LOGO
Exploring and exploiting
phenotypic and genetic diversity in peach:
identification of major genes and QTLs by
GWAS.
XIV EUCARPIA symposium on Fruit Breeding
and Genetics.
Maria José Aranzana

21. YOUR LOGO
Exploiting genetic diversity in peach: GWAS
Sub-acid
Peach/nectarine
Melting/non-melting
Leaf gland
White/yellow fruit flesh
Flat/round fruit
Flower type

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0 200 400 600 800 1000
Hap97
Hap98
Hap36
Hap5
Acid
Subacid
 23 SNPs associated
 Region 1.8 Mb
 99 haplotypes
 4 haplotypes associated
Exploiting genetic diversity in peach: GWAS

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 21 SNPs associated
 Region of 5.2 Mb
 152 haplotypes
 6 haplotypes associated
Exploiting genetic diversity in peach: GWAS
 3 causal alleles
 SSR
 TE
 SNP

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152 haplotypes
6 significant haplotypes
Ho
0.76
1.00
0.86
1.00
0.92
1.00
SSR
+TE
Set of SNPs associated in haplotypes tested in
WP1-pilot studies
Exploiting genetic diversity in peach: GWAS

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China
Exploiting genetic diversity in peach: GWAS

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Spain
Exploiting genetic diversity in peach: GWAS

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Ignazio Verde
Sabrina Micalli
Valeria Aramini
M.Teresa Dettori
Daniele Bassi
Laura Rossini
Igor Pacheco
Stefano Foschi
Alessandra Estella
Nelso Nazzicari
Andrea Caprera
Michela Troggio
Elisa Banchi
Pere Arús
Maria José Aranzana
Diego Micheletti
José Ramón Hernández
Ignasi Iglesias
Quim Carbó
Sanshan Gao
Xionwei Li
Li-rong Wang
Rui-juan Ma
Teresa Barreneche
Thierry Pascal
Bénédicte Quilot
Patrick Lambert
François Laurens
Thanks for your attention