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Saturating the Prunus (stone fruits) genome with candidate genes for fruit quality

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Abstract

To identify genes involved in the expression of a trait using the candidate gene (CG) approach, the genome positions of the maximum number of genes which potentially cause the observed phenotypic variability needs to be known. This position is compared with that of major genes or quantitative trait loci (QTL) for this character, with the co-location of the CG and major gene or QTL indicating a possible cause and effect relationship. In the present study we selected 273 sequences from expressed sequence tag collections, corresponding to CGs from metabolic pathways affecting fruit growth and maturity, texture, sugar and organic acid content, aroma and color, and mapped them in the Prunus reference map (T × E) based on an interspecific almond × peach F2 population. We used the bin-mapping approach, where only eight plants, six of the T × E progeny plus one of the parents and the F1 hybrid, are used to determine the position of a marker. This strategy was very efficient, with 206 CGs mapped, based mainly on the segregation of one or more single-nucleotide polymorphisms. These CGs were located throughout the Prunus genome and are a resource for genetic analysis in stone fruit (peach, plum, apricot and cherry) and almond. Co-locations between CGs and major genes or QTL responsible for natural variability of fruit quality characters in Prunus were identified using the available information on their positions.

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Acknowledgments

This study was supported in part by the ISAFRUIT Integrated Project. The ISAFRUIT Project is funded by the European Commission under Thematic Priority 5 – Food Quality and Safety of the 6th Framework Programme of RTD (Contract No. FP6-FOOD-CT-2006-016279). Disclaimer: Opinions expressed in this publication may not be regarded as stating an official position of the European Commission.

Funding from the Zhejiang University group comes from the China Natural Science Foundation (30771496). The group of IRTA is a member of the CONSOLIDER Center for Basic Genomics and Agro-food Orientation (CSD2007-00036) funded by the Spanish Ministry of Science and Innovation.

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Authors and Affiliations

  1. IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB, Carretera de Cabrils Km 2, 08348, Cabrils, Barcelona, Spain

    Eudald Illa, Iban Eduardo, Pere Arús & Werner Howad

  2. Parco Tecnologico Padano, Via Einstein, Località Cascina Codazza, 26900, Lodi, Italy

    Iban Eduardo, Francesca Barale, Carlo Pozzi, Laura Rossini & Alberto Vecchietti

  3. INRA-UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, 84000 BP 94, 84143, Montfavet, France

    Jean Marc Audergon, Patrick Lambert & Jean-Luc Poëssel

  4. INRA-UR419, Unité de Recherches sur les Espèces Fruitières, BP 81, 33140, Villenave d’Ornon, France

    Elisabeth Dirlewanger & Loick Le Dantec

  5. Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang University, 310058, Hangzhou, People’s Republic of China

    Xiongwei Li & Zhongshan Gao

  6. INRA-UMR619 Fruit Biology, BP 81, 33140, Villenave d’Ornon, FR, France

    Annick Moing

  7. Dipartimento di Produzione Vegetale, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy

    Laura Rossini

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  1. Eudald Illa
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  2. Iban Eduardo
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  3. Jean Marc Audergon
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  4. Francesca Barale
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  5. Elisabeth Dirlewanger
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  6. Xiongwei Li
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  7. Annick Moing
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  8. Patrick Lambert
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  9. Loick Le Dantec
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  10. Zhongshan Gao
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  11. Jean-Luc Poëssel
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  12. Carlo Pozzi
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  13. Laura Rossini
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  14. Alberto Vecchietti
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  15. Pere Arús
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  16. Werner Howad
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Corresponding author

Correspondence to Werner Howad.

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Eudald Illa and Iban Eduardo contributed equally to this paper.

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11032_2010_9518_MOESM1_ESM.xls

Supplementary Table 1: Features of 273 candidate genes involved in fruit quality and their primer sequences. (XLS 2226 kb)

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Illa, E., Eduardo, I., Audergon, J.M. et al. Saturating the Prunus (stone fruits) genome with candidate genes for fruit quality. Mol Breeding 28, 667–682 (2011). https://doi.org/10.1007/s11032-010-9518-x

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