Understanding the genetic architecture of fruit quality traits is crucial to target breeding of apple (Malus domestica L.) cultivars. We linked genotype and phenotype information by combining genotyping‐by‐sequencing (GBS) generated single nucleotide polymorphism (SNP) markers with fruit flavor volatile data, sugar and acid content, and historical trait data from a gene bank collection. Using gas chromatography–mass spectrometry (GC‐MS) analysis of apple juice samples, we identified 49 fruit volatile organic compounds (VOCs). We found a very variable content of VOCs, especially for the esters, among 149 apple cultivars. We identified convincing associations for the acetate esters especially butyl acetate and hexyl acetate on chromosome 2 in a region of several alcohol acyl‐transferases including AAT1. For sucrose content and for fructose and sucrose in percentage of total sugars, we revealed significant SNP associations. Here, we suggest a vacuolar invertase close to significant SNPs for this association as candidate gene. Harvest date was in strong SNP association with a NAC transcription factor gene and sequencing identified two haplotypes associated with harvest date. The study shows that SNP marker characterization of a gene bank collection can be successfully combined with new and historical trait data for association studies. Suggested candidate genes may contribute to an improved understanding of the genetic basis for important traits and simultaneously provide tools for targeted breeding using marker‐assisted selection (MAS).

中文翻译：

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苹果的全基因组关联研究揭示了香气挥发物，糖成分和收获日期的基因座。

了解的果实品质性状遗传结构是目标苹果育种（关键海棠斯蒂卡L.）品种。我们通过将基因分型（GBS）产生的单核苷酸多态性（SNP）标记与水果风味挥发性数据，糖和酸含量以及基因库收集的历史性状数据结合起来，将基因型和表型信息联系起来。使用苹果汁样品的气相色谱-质谱（GC-MS）分析，我们确定了49种水果挥发性有机化合物（VOC）。我们发现149个苹果品种中VOC的含量变化很大，尤其是酯类。我们确定了令人信服的联想，特别是乙酸酯，尤其是乙酸丁酯和乙酸己酯在2号染色体上的几个醇酰基转移酶（包括AAT1）区域中。对于蔗糖含量以及果糖和蔗糖占总糖的百分比，我们发现了显着的SNP关联。这里，我们建议液泡转化酶接近于重要的SNPs作为候选基因。收获日期与NAC转录因子基因有很强的SNP关联，测序确定了与收获日期相关的两个单倍型。研究表明，基因库集合的SNP标记特征可以与新的和历史的特征数据成功结合起来进行关联研究。建议的候选基因可能有助于增进对重要性状的遗传基础的理解，并同时提供使用标记辅助选择（MAS）进行定向育种的工具。研究表明，基因库集合的SNP标记表征可以成功地与新的和历史的特征数据结合起来进行关联研究。建议的候选基因可能有助于增进对重要性状的遗传基础的理解，并同时提供使用标记辅助选择（MAS）进行定向育种的工具。研究表明，基因库集合的SNP标记特征可以与新的和历史的特征数据成功结合起来进行关联研究。建议的候选基因可能有助于增进对重要性状的遗传基础的理解，并同时提供使用标记辅助选择（MAS）进行定向育种的工具。