In order to better preserve and utilize tomato germplasm resources, a total of 484 tomato cultivated accessions were used to construct a core collection based on phenotypic traits and single-nucleotide polymorphisms (SNPs). First, 32 phenotypic traits were investigated and the genetic diversity of all accessions were analyzed. The results showed that the entire population has high genetic diversity, and there is correlation between most quantitative traits. According to two genetic distances, six sampling proportions, three sampling methods and eight clustering methods were used to construct core collections. The core collection with each strategy was evaluated by using four genetic parameters: the percentage of mean difference (MD), the percentage of variance difference (VD), the coincidence rate of range difference (CR), and the variation rate of coefficient of variation (VR). The best construction strategy was "Mahalanobis distance + 10 % + Preferred sampling + Weighted pair-group average method". In addition, all accessions were genotyped using 48 pairs of highly polymorphic primers, and population structure analysis showed that all accessions were divided into four subpopulations. The major allele frequency (MAF) and polymorphic information content (PIC) were calculated and compared, and it was found that the core collection constructed at a sampling ratio of 20 % was the most representative core collection. Finally, the core collection was constructed using the Core Hunter package of R 4.3.3. We constructed a core collection of 137 accessions using phenotypic traits and SNP markers, which provided an effective basis for the conservation and utilization of tomato germplasm resources.

中文翻译：

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基于表型性状和 SNP 标记的番茄 （Solanum lycopersicum） 种质核心集合的构建


为了更好地保存和利用番茄种质资源，共利用 484 份番茄栽培种质构建了基于表型性状和单核苷酸多态性 （SNP） 的核心种质。首先，调查 32 个表型性状，并分析所有种质的遗传多样性。结果表明，整个种群具有高度的遗传多样性，并且大多数数量性状之间存在相关性。根据 2 个遗传距离、6 个采样比例、3 种采样方法和 8 种聚类方法构建核心收藏。通过使用四个遗传参数评估每种策略的核心集合：平均差百分比 （MD） 、方差百分比 （VD） 、范围差异的符合率 （CR） 和变异系数 （VR） 的变异率。最好的构建策略是“马氏距离 + 10 % + 首选抽样 + 加权对组平均法”。此外，使用 48 对高度多态性引物对所有种质进行基因分型，种群结构分析显示所有种质分为 4 个亚群。计算和比较主要等位基因频率 （MAF） 和多态性信息含量 （PIC），发现以 20 % 采样率构建的核心集合是最具代表性的核心集合。最后，使用 R 4.3.3 的 Core Hunter 包构建了核心集合。利用表型性状和 SNP 标记构建了 137 份种质的核心种质，为番茄种质资源的保存和利用提供了有效依据。