Abstract
The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of simple sequence repeat (SSR) markers for nonmodel crop. In the Perilla crop, analysis of the distribution of different repeat motifs showed that the most abundant type was dinucleotide repeats (62.0%), 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. In total, 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, 40 individuals from an F2 population of Perilla were selected for association analysis based on their leaf- and plant-related characteristics. An association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F2 population was conducted. From the analysis, we identified 12 SSR markers associated with leaf-related traits and 11 SSR markers associated with plant-related traits. 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.
Highlights
Perilla frutescens Britt. is a self-fertilizing species of Labiatae
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
SSR markers in particular have many advantages compared with other marker systems as follows: the first 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 F2 populations or pedigree analysis in hybrids (Park et al 2009; Pejic et al 1998; Sa et al 2018)
Summary
Perilla frutescens Britt. is a self-fertilizing species of Labiatae. Perilla species is widely distributed and cultivated in East Asia, especially in South Korea, Japan, and China. Crispa is used as a vegetable crop or herbal medicine crop (jaso in Korean, shiso in Japanese, and zisu in Chinese) (Lee and Ohnishi 2001, 2003; Lee et al 2002; Nitta and Ohnishi 1999; Nitta et al 2003). These two cultivated types of Perilla crop have a long history of cultivation and are very important as oil crop and vegetable or medicine crop in East Asia (Lee and Ohnishi 2001, 2003; Nitta et al 2003). Perilla frutescens var. crispa is smaller in plant height and seed size (below 2 mm), has only hard seeds, has red or green coloration in the leaves and stem, and has wrinkly or non-wrinkly leaves and a fragrance specific to the var. crispa (Lee and Ohnishi 2001, 2003; Lee et al 2002; Nitta et al 2003)
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