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Genome wide association study of two phenology traits (flowering time and maturity date) in apple

Helene Muranty 1 Jorge Urrestarazu 1 Caroline Denancé 1 Diane Leforestier 1 Elisa Ravon 1 Arnaud Guyader 1 Rémi Guisnel 1 Laurence Feugey 1 Stefano Tartarini Luca Dondini Roberto Gregori Marc Lateur Patrick Houben Jiri Sedlak Frantisek Paprstein Matthew Ordidge Hilde Nybom Larisa Garkava-Gustavsson Michela Troggio 2 Luca Bianco 2 Riccardo Velasco 2 Charles Poncet 3 Anthony Théron Marco Bink Francois Laurens 1 Charles-Eric Durel 1
1 IRHS - Institut de Recherche en Horticulture et Semences
2 FEM - Fondazione Edmund Mach - Edmund Mach Foundation [Italie]
3 GDEC - Génétique Diversité et Ecophysiologie des Céréales
Abstract :

The aim of Genome Wide Association Studies (GWAS) is to identify markers in tight linkage disequilibrium with loci controlling quantitative trait variation. These markers can then be used in marker-assisted selection (MAS) in fruit crops such as apple. The GWAS approach involves both phenotyping of a large population of mostly unrelated individuals for the traits of interest, and genotyping at high marker density. In the EU-FP7 project FruitBreedomics, almost 1,200 European diploid dessert apple accessions (old and/or local cultivars) from six germplasm collections were genotyped with the Affymetrix Axiom_Apple480K array (487,000 SNPs). Phenotypic data on a large number of traits have been gathered during the project. Here we focus on flowering period and harvesting date. Knowledge of the genetic control of these traits is necessary to develop cultivars that can face the challenges imposed by global climate change and to target cultivar development as a function of a prolonged vegetation period in the production regions. Different models were tested, including control for effects of population structure and relatedness between cultivars. The full model, controlling for both structure and relatedness, was shown to be the most appropriate to avoid spurious marker-trait associations. When analyzing data over all collections, one significant marker-trait association was obtained for each trait, on chromosomes 9 and 3, for flowering period and harvesting date, respectively. Thereby, genomic locations previously identified in bi-parental populations could now be confirmed for a genetically diverse germplasm.

Keywords : germplasm collections Malus × domestica Marker-assisted selection
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https://hal.univ-angers.fr/hal-02516683
Contributeur : Okina Université d'Angers <>
Soumis le : mardi 24 mars 2020 - 03:33:06
Dernière modification le : mercredi 25 mars 2020 - 01:41:43

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UNIV-ANGERS | INRA | UNAM | IRHS | PRES_CLERMONT | GDEC

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Helene Muranty, Jorge Urrestarazu, Caroline Denancé, Diane Leforestier, Elisa Ravon, et al.. Genome wide association study of two phenology traits (flowering time and maturity date) in apple. Acta Horticulturae, International Society for Horticultural Science, 2017, 1172, pp.411-418. ⟨10.17660/ActaHortic.2017.1172.78⟩. ⟨hal-02516683⟩

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