Seedlessness has always been a valuable quality characteristic of edible grape varieties. Although the production of seedless grapes has been ongoing for decades, the genetic complexity of seedless grapes is not yet fully understood. Therefore, determining the genetic mechanisms and key regulatory genes of seedless grapes is of great significance for seedless grape breeding and meeting market demands. The emergence of high-throughput analysis software offers greater possibilities for mining genes related to plant organ development. Specifically, to mine a greater number of candidate genes related to grape seed traits, this study used the seed trait parameters analyzed by Tomato Analyzer as the target trait and then used a genome-wide association study (GWAS) to mine candidate genes. In the two-year analysis using principal component analysis (PCA), we extracted five principal components with a cumulative contribution rate of 96.586 %. The cumulative contribution rate for component 1 reached 87.352 %. Correlation analysis revealed correlation coefficients ranging from 0.54 to 0.98 among the seven basic traits. The GWAS results indicated that 370 SNP loci were significantly correlated with seed traits. These SNP loci were distributed on 18 chromosomes, except for chromosome 4, with most SNP loci distributed on chromosome 18. Based on the physical location of single nucleotide polymorphism (SNP) markers significantly associated with seed-related traits in the grape reference genome, candidate genes are screened within the range of linkage disequilibrium (LD) attenuation distance, both upstream and downstream of the significant SNP loci. These candidate genes were mainly transcription factor-related genes (VvMADS4 and VvMADS5), ubiquitin ligase-related genes (E3 ubiquitin ligase BIG BROTHER), serine/threonine protein kinase-related genes, and carbohydrate metabolism-related genes (Sucrose Synthase 2) and simultaneously controlled multiple (at least two or more) seed traits. These results indicate that seed traits are jointly regulated by some genes involved in seed morphology regulation. In this work, we identified new gene loci related to grape seed traits. Identifying molecular markers closely related to these seed traits is of great significance for breeding seedless grape varieties.

中文翻译：

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基于全基因组关联研究挖掘葡萄种子性状的候选基因


无核一直是食用葡萄品种的一个有价值的品质特征。尽管无核葡萄的生产已经持续了几十年，但无核葡萄的遗传复杂性尚未完全了解。因此，确定无核葡萄的遗传机制和关键调控基因对无核葡萄选育和满足市场需求具有重要意义。高通量分析软件的出现为挖掘与植物器官发育相关的基因提供了更大的可能性。具体来说，为了挖掘更多与葡萄种子性状相关的候选基因，本研究使用 Tomato Analyzer 分析的种子性状参数作为目标性状，然后使用全基因组关联研究 （GWAS） 来挖掘候选基因。在使用主成分分析 （PCA） 的两年分析中，我们提取了 5 个主成分，累积贡献率为 96.586 %。组件 1 的累计贡献率达到 87.352 %。相关性分析显示，7 个基本性状的相关系数在 0.54 到 0.98 之间。GWAS 结果表明，370 个 SNP 位点与种子性状显著相关。这些 SNP 位点分布在 18 条染色体上，除 4 号染色体外，大多数 SNP 位点分布在 18 号染色体上。基于葡萄参考基因组中与种子相关性状显著相关的单核苷酸多态性 （SNP） 标记的物理位置，在重要 SNP 位点的上游和下游的连锁不平衡 （LD） 衰减距离范围内筛选候选基因。 这些候选基因主要是转录因子相关基因 （VvMADS4 和 VvMADS5）、泛素连接酶相关基因 （E3 泛素连接酶 BIG BROTHER）、丝氨酸/苏氨酸蛋白激酶相关基因和碳水化合物代谢相关基因 （Sucrose Synthase 2），并同时控制多个 （至少两个或多个） 种子性状。这些结果表明，种子性状受一些参与种子形态调控的基因的共同调控。在这项工作中，我们确定了与葡萄种子性状相关的新基因位点。鉴定与这些种子性状密切相关的分子标记对于培育无核葡萄品种具有重要意义。