Understanding the genetic architecture of apple phytochemicals, and their interplay with conventional selection traits, is critical for the development of new apple cultivars with enhanced health benefits. Apple accessions (n = 344) used for this genome-wide association study (GWAS) represented the wide diversity of metabolic profiles in the domesticated and wild Malus genepools. Fruit samples were phenotyped for 34 metabolites, including a stable vitamin C glycoside ‘ascorbic acid 2-β-glucoside’ (AA-2βG), and the accessions were genotyped using the Apple 20K SNP Array. Several fruit quality traits, including red skin over-colour (OCOL), were also assessed. Wild Malus accessions showed at least 2-fold higher average content of several metabolites (e.g. ascorbic acid, chlorogenic acid, phloridzin, and trilobatin) than M. domestica accessions. Several new genomic regions and potential candidate genes underpinning the genetic diversity of apple phytochemicals were identified. The percentage of phenotypic variance explained by the best SNP ranged between 3% and 21% for the different metabolites. Novel association signals for OCOL in the syntenic regions on chromosomes 13 and 16 suggested that whole genome duplication has played a role in the evolution of apple red skin colour. Genetic correlations between phytochemicals and sensory traits were moderate. This study will assist in the selection of Malus accessions with specific phytochemical profiles to establish innovative genomics-based breeding strategies for the development of apple cultivars with enhanced nutritional value.

中文翻译：

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GWAS 为苹果植物化学物质产生和红色皮肤颜色的遗传机制提供了新的见解

了解苹果植物化学物质的遗传结构及其与传统选择性状的相互作用，对于开发具有增强健康益处的新苹果品种至关重要。用于这项全基因组关联研究 (GWAS) 的苹果种质 (n = 344) 代表了驯化和野生海棠基因库中代谢谱的广泛多样性。对水果样品进行了 34 种代谢物的表型分析，包括稳定的维生素 C 糖苷“抗坏血酸 2-β-葡萄糖苷”(AA-2βG)，并使用 Apple 20K SNP 阵列对这些种质进行了基因分型。还评估了几种水果品质性状，包括红皮泛色 (OCOL)。野生海棠种质的几种代谢物（例如抗坏血酸、绿原酸、根皮苷和三叶苷）的平均含量至少比家养海棠种质高 2 倍。确定了支持苹果植物化学物质遗传多样性的几个新基因组区域和潜在候选基因。对于不同的代谢物，由最佳 SNP 解释的表型变异百分比介于 3% 和 21% 之间。13 号和 16 号染色体同线区 OCOL 的新关联信号表明，全基因组复制在苹果红皮肤颜色的进化中发挥了作用。植物化学物质和感官性状之间的遗传相关性是中等的。本研究将协助选择具有特定植物化学特征的苹果种质，以建立创新的基于基因组学的育种策略，以开发具有更高营养价值的苹果品种。