Utilization of Novel Perilla SSR Markers to Assess the Genetic Diversity of Native Perilla Germplasm Accessions Collected from South Korea

Abstract

The Perilla crop is highly regarded in South Korea, both as a health food and traditional food. However, there is still a lack of Perilla SSR primer sets (PSPSs) for studying genetic variation among accessions of cultivated and weedy types of Perilla crop (CWTPC) from South Korea. In this study, 30 PSPSs were newly developed based on transcriptome contigs in P. frutescens, and 17 of these PSPSs were used to study the genetic diversity, phylogenetic relationships and structure population among 90 accessions of the CWTPC collected from South Korea. A total of 100 alleles were detected from selected 17 PSPSs, with an average of 5.9 alleles per locus. The gene diversity (GD) ranged from 0.164 to 0.831, with an average of 0.549. The average GD values from the cultivated var. frutescens, weedy var. frutescens, and weedy var. crispa, were 0.331, 0.588, and 0.389 respectively. In addition, most variance shown by Perilla SSR markers was within a population (73%). An analysis of the population structure and phylogenetic relationships showed that the genetic relationship among accessions of the weedy var. frutescens and weedy var. crispa is closer than that for the accessions of the cultivated var. frutescens. Based on association analysis between 17 PSPSs and three seed traits in 90 Perilla accessions, we detected 11 PSPSs that together were associated with the seed size and seed hardness traits. Therefore, the newly developed PSPSs will be useful for analyzing genetic variation among accessions of the CWTPC, association mapping, and selection of important morphological traits in Perilla crop breeding programs.

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

“…SSR molecular markers are among the most commonly used molecular marker technologies, with the advantages of co-dominant inheritance, high stability and polymorphism, and high reproducibility. It is widely used in genetic diversity analysis, kinship determination, variety identification, core germplasm screening, molecular identification, and the construction of various plants [ 13 , 14 ].…”

Association mapping analysis for cultivated and weedy types of Perilla crop collected from South Korea using morphological characteristics and SSR markers

“…frutescens (WF) and weedy var. crispa (WC), are frequently encountered in South Korea, often being observed in areas like wastelands, around farmers' houses, and within farmers’ fields [ 4 , 9 , [12] , [13] , [14] ]. In addition, many plant taxonomists have conducted research to differentiate between and within accessions of the TCWTPC.…”

“…In particular, in Perilla crop, Perilla SSRs or microsatellite markers are recognized as the preferred molecular markers for GD and genetic relationship studies between and within accessions of the TCWTPC. This preference is attributed to their codominance, high reproducibility, DNA polymorphism, and ease of use with polymerase chain reaction (PCR)-marker technology [ 13 , [23] , [24] , [25] ]. However, the amount of developed Perilla SSR primer sets in the TCWTPC remains insufficient for comprehensive genetic diversity and relationships studies between and within accessions of the TCWTPC.…”

“…Recently, Fu et al (2022) developed 30 new Perilla SSR primer sets (mainly dinucleotide SSR type) from Perilla crop using RNA sequencing and used 17 of these Perilla SSR primer sets for GD analysis and phylogenetic relationship studies among accessions of the TCWTPC collected in South Korea. Furthermore, many researchers in our laboratory team recently reported that they had developed new SSR primer sets in Perilla crop [ 13 , 22 , 26 ], and they have used these successfully for studies on GD, phylogenetic relationships, and association mapping analysis (AMA) among TCWTPC accessions.…”

“…Hence, the objective of this study is to develop molecular markers related to morphological traits that show differences between and within accessions of the TCWTPC using new Perilla SSR primer sets recently developed by Fu et al [ 13 ]. Expected outcomes from this study include valuable markers for future differentiation of TCWTPC accessions and the identification of molecular markers for advantageous morphological traits in breeding programs for Perilla crop, including applications like marker-assisted selection (MAS).…”