Development of Chloroplast Microsatellite Markers and Evaluation of Genetic Diversity and Population Structure of Cutleaf Groundcherry (Physalis angulata L.) in China

Abstract

Cutleaf groundcherry (Physalis angulata L.), an annual plant containing a variety of active ingredients, has great medicinal value. However, studies on the genetic diversity and population structure of P. angulata are limited. In this study, we developed chloroplast microsatellite (cpSSR) markers and applied them to evaluate the genetic diversity and population structure of P. angulata. A total of 57 cpSSRs were identified from the chloroplast genome of P. angulata. Among all cpSSR loci, mononucleotide markers were the most abundant (68.24%), followed by tetranucleotide (12.28%), dinucleotide (10.53%), and trinucleotide (8.77%) markers. In total, 30 newly developed cpSSR markers with rich polymorphism and good stability were selected for further genetic diversity and population structure analyses. These cpSSRs amplified a total of 156 alleles, 132 (84.62%) of which were polymorphic. The percentage of polymorphic alleles and the average polymorphic information content (PIC) value of the cpSSRs were 81.29% and 0.830, respectively. Population genetic diversity analysis indicated that the average observed number of alleles (Na), number of effective alleles (He), Nei’s gene diversity (h), and Shannon information indices (I) of 16 P. angulata populations were 1.3161, 1.1754, 0.1023, and 0.1538, respectively. Moreover, unweighted group arithmetic mean, neighbor-joining, principal coordinate, and STRUCTURE analyses indicated that 203 P. angulata individuals from 16 populations were grouped into four clusters. A molecular variance analysis (AMOVA) illustrated the considerable genetic variation among populations, while the gene flow (Nm) value (0.2324) indicated a low level of gene flow among populations. Our study not only provided a batch of efficient genetic markers for research on P. angulata but also laid an important foundation for the protection and genetic breeding of P. angulata resources.

Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan

“…SSRs are widespread throughout plastid genomes across different species and are extensively employed in plant population studies [58][59][60]. In this study, the identified SSRs varied in number, with counts ranging from 198 in C. nitrarium to 208 in C. dzhungaricum plastomes, resulting in a total of 814 SSRs (Table 4).…”

UPLC-Q-Orbitrap-MS/MS-Guided Isolation of Bioactive Withanolides from the Fruits of Physalis angulata

“…P. angulata is applied as a traditional folk medicine to cure sore throats, coughs, rheumatism, and hepatitis in many countries, including China, Mexico, Indonesia, and Brazil . The fruits, a sweet or tasteless berry-type climacteric fruit, are known as wild tomato, winter cherry, and gooseberry. − A previous study on its whole plant generated a variety of withanolide derivatives, which exhibited cytotoxic and good anti-inflammatory activities. ,, UPLC-Q-Orbitrap-MS/MS was used for the first time to study bioactive withanolides from the fruits of P.…”

Advances in Physalis molecular research: applications in authentication, genetic diversity, phylogenetics, functional genes, and omics

“…SSRs are co-dominant, multi-allelic, highly polymorphic, and have been widely used in various fields, including genetic diversity, phylogenetic studies, molecular identification, and genetic mapping ( Poczai et al., 2013 ). Several SSR markers have been developed and extensively utilized in the investigation of genetic diversity within Physalis species ( Simbaqueba et al., 2011 ; Wei et al., 2012 ; Delgado-Bastidas et al., 2019 ; Feng et al., 2023 ). In a study by Delgado-Bastidas et al.…”