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Review Article|01 Mar 2018|OPEN
An integrated approach for increasing breeding efficiency in apple and peach in Europe
François Laurens1, María José Aranzana2,3, Pere Arús2,3, Daniele Bassi4, Marco Bink5,16, Joan Bonany6, Andrea Caprera7, Luca Corelli-Grappadelli8, Evelyne Costes9, Charles-Eric Durel10, Jehan-Baptiste Mauroux11, Hélène Muranty1, Nelson Nazzicari7, Thierry Pascal10, Andrea Patocchi10, Andreas Peil12, Bénédicte Quilot-Turion11, Laura Rossini4,7, Alessandra Stella7, Michela Troggio13, Riccardo Velasco13,14 & Eric van de Weg15
1IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé 49071, France
2IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
3Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
4Università degli Studi di Milano - DiSAA, Via Celoria 2, Milan 20133, Italy
5Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
6IRTAMas Badia, Mas Badia, La Tallada 17134, Spain
7Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi 26900, Italy
8Dipartimento di Scienze Agrarie, Alma Mater Studiorum - Università di Bologna, Bologna, Italy
9UMR AGAP, INRA, Montpellier 34398, France
10GAFL, INRA, Montfavet 84143, France
11Agroscope, Research Division Plant Breeding, Schloss 1, Wädenswil 8820, Switzerland
12Julius Kühn-Institute (JKI); Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, Dresden 01326, Germany
13Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
14CREA-VE, Center of Viticulture and Enology, via XXVIII Aprile 26, Conegliano (TV) 31015, Italy
15Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O.Box 386, Wageningen 6700AJ, The Netherlands
16Hendrix Genetics Research, Technology & Services, Boxmeer 5830 AC, The Netherlands

Horticulture Research 5,
Article number: 11 (2018)
doi: 10.1038/hortres.2018.11
Views: 563

Received: 05 Dec 2017
Revised: 06 Dec 2017
Accepted: 23 Dec 2017
Published online: 01 Mar 2018

Abstract

Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond.