Genetic diversity and population structure among accessions of Perilla frutescens (L.) Britton in East Asia using new developed microsatellite markers

Abstract

SSRs were successfully isolated from the Perilla crop in our current study, and used to analyze Perilla accessions from East Asia. Analyses of the clear genetic diversity and relationship for Perilla crop still remain insufficient. In this study, 40 new simple sequence repeat (SSR) primer sets were developed from RNA sequences using transcriptome analysis. These new SSR markers were applied to analyze the diversity, relationships, and population structure among 35 accessions of the two cultivated types of Perilla crop and their weedy types. A total of 220 alleles were identified at all loci, with an average of 5.5 alleles per locus and a range between 2 and 10 alleles per locus. The MAF (major allele frequency) per locus varied from 0.229 to 0.943, with an average of 0.466. The average polymorphic information content (PIC) value was 0.603, ranging from 0.102 to 0.837. The genetic diversity (GD) ranged from 0.108 to 0.854, with an average of 0.654. Based on population structure analysis, all accessions were divided into three groups: Group I, Group II and the admixed group. This study demonstrated the utility of new SSR analysis for the study of genetic diversity and population structure among 35 Perilla accessions. The GD of each locus for accessions of cultivated var. frutescens, weedy var. frutescens, cultivated var. crispa, and weedy var. crispa were 0.415, 0.606, 0.308, and 0.480, respectively. Both weedy accessions exhibited higher GD and PIC values than their cultivated types in East Asia. The new SSR primers of Perilla species reported in this study may provide potential genetic markers for population genetics to enhance our understanding of the genetic diversity, genetic relationship and population structure of the cultivated and weedy types of P. frutescens in East Asia. In addition, new Perilla SSR primers developed from RNA-seq can be used in the future for cultivar identification, conservation of Perilla germplasm resources, genome mapping and tagging of important genes/QTLs for Perilla breeding programs.

Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers

“…Among various molecular markers, SSR markers in particular have many advantages compared with other marker systems as follows: the rst advantage is high reproducibility, which is most important in genetic analysis; the second advantage of the SSR marker system is the polymorphic genetic information contents, and the hypervariable nature of SSRs produces very high allelic variations even among very closely related varieties; and the third advantage relates to the codominant nature of SSR polymorphisms, as the codominant nature of SSRs is suitable for genetic analysis in segregation of F 2 populations or pedigree analysis in hybrids (Park et al 2009;Pejic et al 1998;Sa et al 2018).…”

“…This information will help develop SSR primers for Perilla crop. As explained in the Introduction, Sa et al (2018) detected a total of 15,991 SSR loci based on the SSR anking sequences via de novo assembly of the PF98095 RNA-seq data (Tong et al 2015), which were classi ed based on the number of repeating units. Dinucleotide SSRs had the highest number of SSRs (9,910), followed by trinucleotide SSRs (5,652) and tetranucleotide SSRs (429) (Sa et al 2018).…”

“…As explained in the Introduction, Sa et al (2018) detected a total of 15,991 SSR loci based on the SSR anking sequences via de novo assembly of the PF98095 RNA-seq data (Tong et al 2015), which were classi ed based on the number of repeating units. Dinucleotide SSRs had the highest number of SSRs (9,910), followed by trinucleotide SSRs (5,652) and tetranucleotide SSRs (429) (Sa et al 2018). In the Perilla crop, analysis of the distribution of different repeat motifs showed that dinucleotide repeats were the most abundant (62.0%) type, followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats.…”

“…frutescens (PF98095). In a previous study, Sa et al (2018) detected a total of 15,991 SSR loci. All SSRs can be classi ed according to the number of repeating units: dinucleotide SSRs had the highest number of SSRs (9,910), followed by trinucleotide SSRs (5,652) and tetranucleotide SSRs (429).…”

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“…Compared to those SSRs derived from the neutral parts of a plant genome, these transcriptome derived SSRs are potentially more useful, in particular for constructing crop core collections in which selection in relation to focused phenotypic traits is the primary purpose. Currently, transcriptome derived SSR markers have been widely applied in population genetic analyses of medicinal plants, such as Picria felterrae (Yan et al, 2019), Gynostemma pentaphyllum (Zhang et al, 2019), and Perilla frutescens (Sa et al, 2018). Researches on constructing core collections of medicinal plants using transcriptome derived SSRs are also quickly increased in recent years.…”