13 aranzana

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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

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Partners involved

Ignazio VerdeSabrina Micalli Valeria AraminiM.Teresa Dettori

Daniele BassiLaura RossiniIgor PachecoStefano Foschi

Alessandra EstellaNelso NazzicariAndrea Caprera

Michela TroggioElisa Banchi

Pere ArúsMaria José AranzanaDiego MichelettiJosé Ramón Hernández Ignasi IglesiasQuim Carbó

Sanshan Gao Xionwei LiLi-rong WangRui-juan Ma

Teresa BarrenecheThierry PascalBénédicte QuilotPatrick LambertFrançois Laurens

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Partners involved








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• Select those more interesting accessions within each germplasm collection (200-300)

Exploring phenotypic diversity in peach

Approach

INRA UNIMICRA-RomeIRTA

ZJU(China)

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• Select those more interesting accessions within each germplasm collection (200-300)

ItalyFranceSpainChina

• Collect all phenotypic information acquired for years• Design the template of a common database for

available and common scales for new data

Approach


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1580 accessions:• Local• Old (founders)• Commercial from breeding

programs• Few non-persica

Exploring phenotypic diversity in peachCommon accessions with phenotypic data between

locations

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Num

ber o

f acc

essio

ns w

ith p

heno

typi

c da

ta UMIL

ZJU

CRA

INRA

IRTA (1) IRTA (2)

Years

Data available for several years in many of the accessions


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Distribution of data on qualitative traits

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(r2= 0.60- 0.80) (r2= 0.97-0.98)


Data correlation between years

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(r2= 0.38- 0.68)

Data correlation between years


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Mean # days to full blossom IRTA-Mas Badia

Mea

n #

days

to fu

ll bl

osso

m IR

TA-G

imen

ells

Mean # days to ripen IRTA-Mas Badia

Mea

n #

days

to

ripen

IRTA

-Gim

enel

ls

Mean ºBRIX IRTA-Mas Badia

Mea

n ºB

RIX

IRTA

-Gi

men

ells

Mea

n ac

idity

IRTA

-Gi

men

ells

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 peachData correlation between

locations

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• 1580 accessions geotyped with the 9K SNP chip

No Call <5%, three genotypesNull allele or preferential annealingDuplicated sequences/genes

False SNPs

Failed

Exploring genetic diversity in peach

433053%

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)


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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

• SNPs identified 473 clones (173 groups with 2 or more clons)• 92% of accessions with the same name where identical


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Oriental (Chinese)

Occidenal Breeding

Occidental non-breeding

Occidenal Breeding

Occidental non-breeding

Oriental (Chinese)

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Occ BreedOcc non-BreedOrientalAdmixed

Minor allele Frequency

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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)

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Exploiting genetic diversity in peach: GWASSub-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

AcidSubacid

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


3 causal alleles SSR TE SNP

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152 haplotypes

6 significant haplotypes

Ho0.761.000.861.000.921.00

SSR

+TE

Set of SNPs associated in haplotypes tested in WP1-pilot studies


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ChinaExploiting genetic diversity in peach: GWAS

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Spain


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Thanks for your attention

13 aranzana

Science