Optimization of the genotyping-by-sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa

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

The plants of the genus Physalis L. have been extensively utilized in traditional and indigenous Chinese medicinal practices for treating a variety of ailments, including dermatitis, malaria, asthma, hepatitis, and liver disorders. The present review aims to achieve a comprehensive and up-to-date investigation of the genus Physalis, a new model crop, to understand plant diversity and fruit development. Several chloroplast DNA-, nuclear ribosomal DNA-, and genomic DNA-based markers, such as psbA-trnH, internal-transcribed spacer (ITS), simple sequence repeat (SSR), random amplified microsatellites (RAMS), sequence-characterized amplified region (SCAR), and single nucleotide polymorphism (SNP), were developed for molecular identification, genetic diversity, and phylogenetic studies of Physalis species. A large number of functional genes involved in inflated calyx syndrome development (AP2-L, MPF2, MPF3, and MAGO), organ growth (AG1, AG2, POS1, and CNR1), and active ingredient metabolism (24ISO, DHCRT, P450-CPL, SR, DUF538, TAS14, and 3β-HSB) were identified contributing to the breeding of novel Physalis varieties. Various omic studies revealed and functionally identified a series of reproductive organ development-related factors, environmental stress-responsive genes, and active component biosynthesis-related enzymes. The chromosome-level genomes of Physalis floridana Rydb., Physalis grisea (Waterf.) M. Martínez, and Physalis pruinosa L. have been recently published providing a valuable resource for genome editing in Physalis crops. Our review summarizes the recent progress in genetic diversity, molecular identification, phylogenetics, functional genes, and the application of omics in the genus Physalis and accelerates efficient utilization of this traditional herb.

Population-tailored mock genome enables genomic studies in species without a reference genome

Based on molecular markers, genomic prediction enables us to speed up breeding schemes and increase the response to selection. There are several high-throughput genotyping platforms able to deliver thousands of molecular markers for genomic study purposes. However, even though its widely applied in plant breeding, species without a reference genome cannot fully benefit from genomic tools and modern breeding schemes. We used a method to assemble a population-tailored mock genome to call single-nucleotide polymorphism (SNP) markers without an available reference genome, and for the first time, we compared the results with standard genotyping platforms (array and genotyping-by-sequencing (GBS) using a reference genome) for performance in genomic prediction models. Our results indicate that using a population-tailored mock genome to call SNP delivers reliable estimates for the genomic relationship between genotypes. Furthermore, genomic prediction estimates were comparable to standard approaches, especially when considering only additive effects. However, mock genomes were slightly worse than arrays at predicting traits influenced by dominance effects, but still performed as well as standard GBS methods that use a reference genome. Nevertheless, the array-based SNP markers methods achieved the best predictive ability and reliability to estimate variance components. Overall, the mock genomes can be a worthy alternative for genomic selection studies, especially for those species where the reference genome is not available.