The Mariana Trench remarkable geological features on Earth.pptx
15 pascal
1. FruitBreedomics - WP1 - T1.3
Pilot studies on peach for
fruit quality and resistance traits
J.B. Mauroux 1, V. Diévart 1, C. Tuéro 1, L. Maillard 2, A. Maillard 2, M.J. Aranzana 3, I.
Batlle 3, J.C. Marcaillou 4, O. Carrillo-Mendoza 4, D. Bassi 5, I. Pacheco5 , S. Foschi 5
and T. Pascal 1
Bologna, June 18th 2015
2. Pilot Studies on Peach for Fruit Quality and Resistance Traits
Objective, works and partners
Objective: verify MASS efficiency
Works
- public & private partners provide populations (1500 trees/partner) with combinations of
genes/traits previously listed,
- screen these populations with SNPs markers associated to the genes/traits, by using the
genotyping pipeline implemented, to predict the corresponding phenotypes,
- evaluate the power of the markers by comparing the observed phenotypes of individuals,
previously got, with the predicted phenotypes given by markers.
Partners
public research institutes
private breeding compagnies
- Inst. Nationale de la Recherche Agronomique (INRA, France)
- Inst. de Recerca i Tecnologia Agroalimentariès (IRTA, Spain)
- University of Milan (UMIL, Italy)
- Agro Sélection Fruit (ASF, France)
- Rústicas Del Guadalquivir (RDG, Spain)
- Daniele Neri Vivai (DNV, Italy)
INRA
ASF
IRTA
RDG
UMIL
DNV
3. List of traits/genes
Fruit quality traits :
1. peach/nectarine ( locus)
2. white/yellow flesh ( locus)
3. non-flat/flat ( locus)
4. acid/sub-acid ( locus)
5. melting/non-melting ( locus)
Two complementary approaches to identify candidate markers
from ISPC 9K SNP array (1-7 SNPs/locus)
by genetic mapping
G
Y
D
Fm
Resistance traits
6. resistance to the green peach aphid ( loci)
7. resistance to powdery mildew ( loci)Vr1/Vr2
Rm1/Rm2
Pilot Studies on Peach for Fruit Quality and Resistance Traits
Studied traits/loci for MASS purposes
S*
by GWA studies Y, G, S* & D loci (IRTA)
Y
Fm
D
G
Vr1/Vr2
Rm1/Rm2
LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8
S*
4. Populations provided by partner (public & private) with combinations of genes/traits
Pilot Studies on Peach for Fruit Quality and Resistance Traits
Studied traits/partner
G Y D Fm Vr1/Vr2Rm1/Rm2S*
Resistance traitsF
6. KASP™ (Kompetitive allele specific PCR) is a cost-effective and robust technology to perform
high- throughput genotyping with a low number of molecular markers
the selected company (LGC Genomics) provided boxes, the know-how to make the leaf
collection by the use of specific punchers, and how to deliver the collected samples
LGC Genomics has done both the DNA extraction and genotyping, as well as the design and
synthesis of primers. Genotypic data were provided in Excel™ files
freeze-dried leaves had to be preferably delivered to the company in a 96-well format but it was
also possible to send fresh material if packed in plastic bag as indicated by the company
Pilot Studies on Peach for Fruit Quality and Resistance Traits
Genotyping technology: KASPtm
plate plan
7. Sample taking done by all project partners
in greenhouse (INRA) in orchard (all partners)
Markers validation by INRA, IRTA and UMIL
a) data analysis (parents + progenies)
- check the polymorphism of markers
- verify the right allele/trait association
- predict the phenotypes
b) prediction efficiency of markers calculated by
comparing the observed phenotype of individuals
with the predicted phenotype given by markers
Pilot Studies on Peach for Fruit Quality and Resistance Traits
Pipeline used … mainly 4 steps
packaged samples
parents + progenies
Genotyping done by LGC Genomics
a) DNA extraction b) SNP genotyping
genotypic data
(Excel file)
traits
genotypic
information,
pedigree
…
Phenotyping of progenies
done by all breeders for tested traits
8. Predictions efficiency for the resistance to the green peach aphid on INRA-Av populations
Comparison: observed / predicted phenotypes
Pilot Studies on Peach for Fruit Quality and Resistance Traits
Results checking efficiency of the MASS
Predictions efficiency for fruit quality traits on IRTA, RDG and ASF populations
G
Y
D
S*
- still in process for powdery mildew resistance
- markers still in development …
IRTA RDG ASF
Trait
IRTA_pop1
IRTA_pop2
IRTA_pop3
IRTA_pop4
IRTA_pop5
IRTA_pop6
IRTA_pop7
IRTA_pop8
IRTA_pop9
IRTA_pop10
IRTA_pop11
IRTA_pop12
IRTA_pop13
Average
RDG_pop1
RDG_pop2
RDG_pop3
RDG_pop4
RDG_pop5
RDG_pop6
RDG_pop7
RDG_pop8
RDG_pop9
RDG_pop10
RDG_pop11
RDG_pop12
Average
ASF_pop1
ASF_pop2
ASF_pop3
ASF_pop4
ASF_pop5
ASF_pop6
ASF_pop7
Average
- - 94 100 94 92 100 - - 96 97 - - 96 % 98 - - - - - 100 - BC 86 94 - 95 % 100 89 - 95 96 … … 95 %
100 80 97 98 92 97 89 85 97 95 86 95 98 93 % 90 87 93 93 95 - - - 98 83 93 92 92 % 89 88 81 87 95 … … 88 %
- NP - NP NP NP - - - NP NP 100 NP - - NP 94 - NP - 90 92 98 93 98 96 94 % NP NP 95 - NP … … -
- 88 - 99 - - - - - 99 - - 99 96 % - - - - - - - - 100 NP - - - 100 - - 96 99 … … 98 %
… data not still verified
- no segregation of the trait
the phenotypes can be predicted on 50% of the offsprings
NP no polymorphic markers
BC bad configuration of markers (the heterozygote parent for the trait has the same dominant and recessive allele for the marker)
Trait
INRA_pop1
INRA_pop2
INRA_pop3
INRA_pop4
INRA_pop5
INRA_pop6
INRA_pop7
INRA_pop8
Average
100 88 90 78 93 89 96 92 91 %
9. - good efficiency of the MASS controlled as part of pilot studies on peach …
- compare cost/efficiency between TSS and MASS
- finalize the phenotypic & genotypic data analysis engaged
- archive all acquired information (phenotypic & genotypic data)
- pursue the objective to get more of diagnostic markers for easier DNA
tests
-continue to share this MASS approach with the more larger community
of fruit breeders, both public than private
Pilot Studies on Peach for Fruit Quality and Resistance Traits
Conclusion and perspectives
10. THANKS ! Main contributors:
ASF: Laurence & Arsène Maillard
DNV: Daniele Neri, Stefano Foschi
RDG: Jean-Clément Marcaillou, Omar Carrillo-Mendoza
INRA: Jehan-Baptiste Mauroux, Thierry Pascal
IRTA: Maria-José Aranzana, Ignasi Battle
UMIL: Daniele Bassi, Igor Pacheco Cruz
FruitBreedomics - WP1 - T1.3
Pilot Studies on Peach for Fruit Quality and Resistance Traits
Editor's Notes
Partners involved in the peach pilot studies:
Public institutes were responsible for the coaching of their respective private partners
→ A list of traits/genes has been established (T1.2) during the kick-off meeting of the project which takes account of the needs expressed by stakeholders (T1.1)
→ Two complementary approaches were used to identify candidate markers coming from ISPC 9K SNP array (1-7SNPs/locus) for Marker-assisted selection purposes
by DNA tests
The 96 wells have to be sealed with a membrane allowing the circulation of air, the so sealed 96 well have to be placed in a plastic bag containing a paper bag filled with silica gel, and the plastic bag has to be hermetically closed removing as much as possible air. In this way the leaf discs will dry. From this material DNA will be extracted. The company proved to be able to test both young and old leaves.
for predict the phenotypes of offsprings based on the SNP markers,
