Laurens Francois, Aranzana Maria José, Arus Pere, Bassi Daniele, Bink Marco, Bonany Joan, Caprera Andrea, Corelli-Grappadelli Luca, Costes Evelyne, Durel Charles-Eric, Mauroux Jehan-Baptiste, Muranty Hélène, Nazzicari Nelson, Pascal Thierry, Patocchi Andrea, Peil Andreas, Quilot-Turion Bénédicte, Rossini Laura, Stella Alessandra, Troggio Michela, Velasco Riccardo, van de Weg Eric
IRHS, 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.
Hortic Res. 2018 Mar 1;5:11. doi: 10.1038/s41438-018-0016-3. eCollection 2018.
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.
尽管苹果和桃子的全基因组序列已可获取，但基因组学与育种之间仍存在相当大的差距。为了弥合这一差距，欧盟资助了“水果基因组学”项目（2011年3月至2015年8月），该项目涉及28个研究机构和私人公司。项目采用了三种互补方法：（i）工具和软件开发；（ii）考虑等位基因多样性来解读主要园艺性状的遗传控制；（iii）为育种者开发植物材料、工具和方法。项目取得了决定性突破，包括提供用于标记辅助育种的现成DNA诊断测试、开发苹果和桃子新的高密度SNP阵列、针对一些复杂性状的新表型方法、通过基于系谱分析（PBA）在育种种质中发现基因/QTL的软件。这导致通过PBA以及对几个欧洲基因库收集品进行全基因组关联研究（GWAS），发现了对园艺性状具有高度预测性的分子标记。“水果基因组学”项目还培育了聚合了多种抗性来源的预育种植物材料，以及能够支持育种者进行选择活动的软件。通过“水果基因组学”项目，苹果和桃子育种、遗传学、基因组学和生物信息学领域取得了重大进展，育种者、种质管理者和科学家将从中受益。该项目期间收集的大部分数据已存储在“水果基因组学”数据库中，并已向公众开放。本综述涵盖了这一重大项目所取得的科学发现，以及欧洲及其他地区苹果和桃子育种与基因组学的前景。
