Genetic Variation and Association Mapping in the F2 Population of the Perilla Crop (Perilla Frutescens L.) using new Developed Perilla SSR Markers

Abstract

The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of SSR markers for nonmodel crop. 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. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. A total of 130 alleles were detected segregating in nine Perilla accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of Perilla crop, a total of 40 individuals from the F2 population of Perilla were selected for association analysis based on their leaf- and plant-related characteristics. In an association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F2 population, we identified 12 and 11 SSR markers associated with leaf-related traits and plant-related traits, respectively. Therefore, the new Perilla SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for Perilla crop breeding programs, and allowing Perilla breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs.

Genetic Variation of Native <em>Perilla</em> Germplasms Collected from South Korea Using SSR Markers and Morphological Characteristics

“…As explained in the Introduction, SSR markers have many advantages over the other molecular marker systems: simple experimental methods, high reproducibility, polymorphic genetic information contents, the codominant nature of SSR polymorphisms, and their abundance and distribution in genomes [19,21,22]. These advantages make them a suitable tool for studying genetic diversity, genetic relationships, and population structure in Perilla crop [9,14,20,23,33,34]. In our study, we detected a total of 137 alleles with 20 SSRs segregating in the 200 accessions of cultivated P. frutescens var.…”

“…For SSR analysis, the total DNA of 200 Perilla accessions was extracted from young leaf tissue of individual representative plants of each accession according to Plant DNAzol Reagent protocols (GibcoBRL Inc., Grand Island, NY, USA). In a preliminary test with over 100 SSR primer sets developed by many researchers [18,19,23,39,40], we selected 20 SSR primer sets that showed high allele band amplification and a clear banding pattern in Perilla accessions (Supplement Table 3). The SSR amplification method for the Perilla crop has been described in a previous study by Kim et al (2021) [23].…”

“…In a preliminary test with over 100 SSR primer sets developed by many researchers [18,19,23,39,40], we selected 20 SSR primer sets that showed high allele band amplification and a clear banding pattern in Perilla accessions (Supplement Table 3). The SSR amplification method for the Perilla crop has been described in a previous study by Kim et al (2021) [23]. After polymerase chain reaction (PCR) amplification using Perilla SSR primer sets, DNA electrophoresis analysis was performed with a QIAxcel advanced system (QIAGEN Co., Hilden, Germany) according to the protocol described in the QIAxcel DNA Handbook.…”

“…In Perilla crop, many researchers have been used to analyze genetic diversity, genetic relationships, and population structure of accessions of cultivated and weedy types of Perilla crop using several DNA molecular marker systems including random amplification of polymorphic DNAs (RAPD) [17], amplified fragment length polymorphisms (AFLP) [3], and simple sequence repeats (SSRs) [9, 13, 14, 18, 19; 20]. Among these DNA molecular markers, particularly SSR markers have provided useful information for the analysis of genetic diversity, genetic relationships, population structure, and association mapping in the germplasm of Perilla crop because they are highly polymorphic, generally codominant, reproducible, and abundant in plant genomes [19][20][21][22][23]. Therefore, SSR markers are expected to be useful for analysis of the genetic diversity, genetic relationships, and population structure of the germplasm of cultivated P. frutescens var.…”

Identifying SSR Markers Related to Seed Fatty Acid Content in Perilla Crop (Perilla frutescens L.)

“…Among the many molecular marker systems, in particular, the SSR marker system has provided useful information for the analysis of genetic diversity and relationships, population structure, genetic mapping (construct linkage maps), and association mapping in many crop species because of high reproducibility, allelic variation, codominant nature, and abundant crop genomes [ 22 , 24 , 27 , 30 , 31 ]. Recently, in the Perilla crop, SSR primer sets have been developed by many researchers [ 32 , 33 , 34 , 35 , 36 ]. They have successfully analyzed genetic diversity and relationships, population structure, and association mapping among the accessions of cultivated and weedy types of Perilla crop [ 4 , 5 , 26 , 34 , 36 , 37 , 38 , 39 ].…”