Husk tomato is an annual vegetable crop grown for its fruits in Mexico, where it grows as weedy and wild. Eight races are recognized from wild (Wild and Milpero) and cultivated (Arandas, Manzano, Puebla, Rendidora, Salamanca, and Tamazula) conditions based on morphological and ecological traits. However, few studies have addressed the genetic diversity and divergence of all races. We aimed to (i) assess the genetic diversity and structure of 10 cultivars representing the recognized races of husk tomato and (ii) compare the genetic diversity of the cultivated and wild pools. We identified 270 single nucleotide polymorphisms from 40 samples using multiplex ISSR genotyping by sequencing (MIG-seq). The results showed lower to moderate diversity in each cultivar (H_E = 0.082–0.147) and lower to moderate pairwise genetic differentiation (F_ST = − 0.011 to 0.195) between cultivars. The Bayesian clustering analysis identified three genetic groups (K = 3) with ancestry coefficients (Q = 0.6–0.89) that suggest gene flow among cultivars. Ordination and classification analysis based on genetic distances revealed two main genetic clusters related to fruit traits and geographic regions where cultivars are commercialized, while a third group included the Wild and Milpero. Analysis of molecular variance revealed higher variation within cultivars (80%) than among cultivars (18%). The cultivated pool harbors 96% of the diversity present in the wild (H_t = 0.322 vs. H_t = 0.311) and does not show severe genetic bottlenecks related to the domestication process. Our results suggest that husk tomato domestication, like other Mesoamerican crops, might be diffuse rather than from a single geographic origin.

壳番茄是一种一年生蔬菜作物，在墨西哥种植其果实，在那里杂草和野生。根据形态和生态特征，从野生（Wild 和 Milpero）和栽培（Arandas、Manzano、Puebla、Rendidora、Salamanca 和 Tamazula）条件中识别出八个种族。然而，很少有研究涉及所有种族的遗传多样性和差异。我们的目的是 (i) 评估代表公认的壳番茄品种的 10 个栽培品种的遗传多样性和结构，以及 (ii) 比较栽培和野生池的遗传多样性。我们使用多重 ISSR 基因分型（MIG-seq）从 40 个样本中鉴定了 270 个单核苷酸多态性。结果显示每个品种的多样性较低到中等（H _E = 0.082–0.147) 和 栽培品种之间的低到中等成对遗传分化（F _ST = - 0.011 到 0.195）。贝叶斯聚类分析确定了三个遗传组 (K = 3)，其祖先系数 (Q = 0.6-0.89) 表明栽培品种之间存在基因流动。基于遗传距离的排序和分类分析揭示了与果实性状和栽培品种商业化的地理区域相关的两个主要遗传簇，而第三组包括 Wild 和 Milpero。分子方差分析显示，品种内（80%）的变异高于品种之间（18%）。栽培池包含 96% 的野生多样性（H _t  = 0.322 vs. H _t = 0.311）并且没有表现出与驯化过程相关的严重遗传瓶颈。我们的结果表明，与其他中美洲作物一样，番茄壳驯化可能是分散的，而不是来自单一的地理起源。