Genetic diversity and structure in husk tomato (Physalis philadelphica Lam.) based on SNPs: a case of diffuse domestication

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 (HE = 0.082–0.147) and lower to moderate pairwise genetic differentiation (FST =  − 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 (Ht = 0.322 vs. Ht = 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.