BACKGROUND Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~ 253 K SNPs) in order to reconstruct pedigrees. RESULTS Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as 'Ribston Pippin', 'White Transparent' and 'Braeburn' were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely 'Reinette Franche' and 'Margil', and one North-Eastern Europe cultivar from the 1700s, 'Alexander'. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the nineteenth century onwards. CONCLUSIONS The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection.

中文翻译：

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利用全基因组 SNP 数据重建苹果种质中的大型多代谱系。


背景技术苹果(Malus x Domestica Borkh.)是温带地区最重要的果树作物之一，具有巨大的经济和文化价值。苹果品种可以通过嫁接在植物收藏中保存几个世纪，其中一些品种被认为可以追溯到罗马时代。分子标记提供了一种重建谱系的方法，从而揭示了生物材料的近期迁移和贸易历史。本研究的目的是使用全基因组 SNP 数据（约 253 K SNP）来确定 1400 多个老苹果品种之间的关系，以重建谱系。结果使用简单的排除检验，基于计算孟德尔错误的数量，识别出1000多个亲子关系和295个完整的亲子家庭。此外，还确定了一对祖父母夫妇在 26 对亲子配对中缺少父母一方。在407个没有第二个确定父母的亲子关系中，有327个可以通过其中一个个体是一个完整家庭的后代或使用有关亲子关系或记录日期的历史数据来定位。诸如“Ribston Pippin”、“White透明”和“Braeburn”等标志性品种的亲本已被确定。整个谱系结合了所有已确定的关系，涵盖了七代，揭示了法国和英国起源的两个文艺复兴时期品种，即“Reinette Franche”和“Margil”，以及一个1700年代的东北欧品种“Alexander”的重大影响。相反，来自中世纪或罗马时代的几个较古老的品种在所研究的种质组中没有或只有单个可识别的后代。 人们发现了来自欧洲不同地区的品种之间频繁的杂交，特别是从十九世纪开始。结论 超过 1400 个苹果基因型的可用性，之前已根据遗传独特性进行了筛选，并提供了欧洲种质的广泛代表性，对于这一大型谱系重建的成功起到了重要作用。它启发了欧洲苹果品种的经验选择和近期育种的历史，并为加快未来的育种和选择提供了见解。