Citric acid (CA) plays a crucial role as a fruit flavor enhancer and serves as a mediator in multiple metabolic pathways in tomato fruit development. Understanding factors influencing CA metabolism is essential for enhancing fruit flavor and CA-mediated biological processes. The accumulation of CA, however, is influenced by a complex interplay of genetic and environmental factors, leading to challenges in accurately predicting and regulating its levels. In this study, we conducted a genome-wide association study (GWAS) on CA, employing six landmark models based on genome-wide variations including structural variants, insertions and deletions, and single nucleotide polymorphisms. The identification of 11 high-confidence candidate genes was further facilitated by leveraging linkage disequilibrium and causal variants associated with CA. The transcriptome data from candidate genes were examined, revealing higher correlations between the expression of certain candidate genes and changes in CA metabolism. Three CA-associated genes exerted a positive regulatory effect on CA accumulation, while the remaining genes exhibited negative impacts based on gene cluster and correlation analyses. The CA content of tomatoes is primarily influenced by improvement sweeps with minimal influence from domestication sweeps in the long-term breeding history, as evidenced by population differentiation and variants distribution. The presence of various causal variants within candidate genes is implicated in the heterogeneity of CA content observed among the tomato accessions. This observation suggests a potential correlation between the number of alternative alleles and CA content. This study offers significant function-based markers that can be utilized in marker-assisted breeding, thereby enhancing their value and applicability.

中文翻译：

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番茄柠檬酸的全基因组变异和最佳等位基因组合

柠檬酸 (CA) 作为水果风味增强剂发挥着至关重要的作用，并且是番茄果实发育过程中多种代谢途径的调节剂。了解影响 CA 代谢的因素对于增强水果风味和 CA 介导的生物过程至关重要。然而，CA 的积累受到遗传和环境因素复杂相互作用的影响，导致准确预测和调节其水平面临挑战。在这项研究中，我们对 CA 进行了全基因组关联研究 (GWAS)，采用了基于全基因组变异的六种标志性模型，包括结构变异、插入和缺失以及单核苷酸多态性。利用与 CA 相关的连锁不平衡和因果变异，进一步促进了 11 个高可信度候选基因的鉴定。对候选基因的转录组数据进行了检查，揭示了某些候选基因的表达与 CA 代谢变化之间存在更高的相关性。根据基因簇和相关性分析，三个 CA 相关基因对 CA 积累发挥积极的调节作用，而其余基因则表现出负面影响。在长期育种历史中，番茄的CA含量主要受改良扫除的影响，而驯化扫除的影响最小，如群体分化和变种分布所证明的那样。候选基因中各种因果变异的存在与番茄种质中观察到的 CA 含量的异质性有关。这一观察结果表明替代等位基因的数量和 CA 含量之间存在潜在的相关性。这项研究提供了重要的基于功能的标记，可用于标记辅助育种，从而提高其价值和适用性。