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Analysis of genetic diversity and relationships of Perilla frutescens using novel EST-SSR markers derived from transcriptome between wild-type and mutant Perilla

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Abstract

Background

Perilla frutescens (Lamiaceae) is distributed in East Asia and is classified into var. frutescens and crispa. P. frutescens is multipurpose crop for human health because of a variety of secondary metabolites such as phenolic compound and essential oil. However, a lack of genetic information has hindered the development and utilization of Perilla genotypes.

Methods and results

This study was performed to develop expressed sequence tag—simple sequence repeat (EST-SSR) markers from P. frutescens var. crispa (wild type) and Antisperill (a mutant cultivar) and used them to assess the genetic diversity of, and relationships among, 94 P. frutescens genotypes. We obtained 65 Gb of sequence data comprising 632,970 transcripts by de novo RNA-sequencing. Of the 14,780 common SSRs, 102 polymorphic EST-SSRs were selected using in silico polymerase chain reaction (PCR). Overall, successful amplification from 58 EST-SSRs markers revealed remarkable genetic diversity and relationships among 94 P. frutescens genotypes. In total, 268 alleles were identified, with an average of 4.62 alleles per locus (range 2–11 alleles/locus). The average polymorphism information content (PIC) value was 0.50 (range 0.04–0.86). In phylogenetic and population structure analyses, the genotypes formed two major groups: Group I (var. crispa) and Group II (var. frutescens).

Conclusion

This results suggest that 58 novel EST-SSR markers derived from wild-type cultivar (var. crispa) and its mutant cultivar (Antisperill) have potential uses for population genetics and recombinant inbred line mapping analyses, which will provide comprehensive insights into the genetic diversity and relationship of P. frutescens.

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References

  1. Nitta M, Lee JK, Ohnishi O (2003) Asianperilla crops and their weedy forms: their cultivation, utilization and genetic relationships. Econ Bot 57(2):245–253

    Article  Google Scholar 

  2. Lee JH, Park KH, Lee M-H, Kim H-T, Seo WD, Kim JY, Baek I-Y, Jang DS, Ha TJ (2013) Identification, characterisation, and quantification of phenolic compounds in the antioxidant activity-containing fraction from the seeds of Korean perilla (Perilla frutescens) cultivars. Food Chem 136(2):843–852

    Article  CAS  PubMed  Google Scholar 

  3. Izumi Y, Matsumura A, Wakita S, Akagi K-i, Fukuda H, Kume T, Irie K, Takada-Takatori Y, Sugimoto H, Hashimoto T (2012) Isolation, identification, and biological evaluation of Nrf2-ARE activator from the leaves of green perilla (Perilla frutescens var. crispa f. viridis). Free Radic Biol Med 53(4):669–679

    Article  CAS  PubMed  Google Scholar 

  4. Osakabe N, Yasuda A, Natsume M, Yoshikawa T (2004) Rosmarinic acid inhibits epidermal inflammatory responses: anticarcinogenic effect of Perilla frutescens extract in the murine two-stage skin model. Carcinogenesis 25(4):549–557

    Article  CAS  PubMed  Google Scholar 

  5. Lee JK, Ohnishi O (2001) Geographic differentiation of morphological characters among Perilla crops and their weedy types in East Asia. Breed Sci 51(4):247–255

    Article  Google Scholar 

  6. Ito M (1996) A taxonomic study of Japanese wild Perilla (Labiatae). J Phytogeogr Taxon 44:43–52

    Google Scholar 

  7. Honda G, Kubo A, Kojima T, Tabata M (1994) Chemotaxonomic and cytogenetic studies on Perilla frutescens var. citriodora ('Lemon Egoma’). Nat Med 48(3):185–190

    CAS  Google Scholar 

  8. Honda G, Koezuka Y, Tanata M (1990) Genetic studies of fruit color and hardness in Perilla frutescens. Jpn J Breed 40(4):469–474

    Article  Google Scholar 

  9. Sa KJ, Choi I-Y, Park K-C, Lee JK (2018) Genetic diversity and population structure among accessions of Perilla frutescens (L.) Britton in East Asia using new developed microsatellite markers. Genes Genom 40(12):1319–1329

    Article  Google Scholar 

  10. Nitta M, Ohnishi O (1999) Genetic relationships among two Perilla crops, shiso and egoma, and the weedy type revealed by RAPD markers. Genes Genet Syst 74(2):43–48

    Article  CAS  Google Scholar 

  11. Nitta M, Lee JK, Kang CW, Katsuta M, Yasumoto S, Liu D, Nagamine T, Ohnishi O (2005) The distribution of Perilla species. Genet Resour Crop Evol 52(7):797–804

    Article  Google Scholar 

  12. Lee JK, Ohnishi O (2003) Genetic relationships among cultivated types of Perilla frutescens and their weedy types in East Asia revealed by AFLP markers. Genet Resour Crop Evol 50(1):65–74

    Article  CAS  Google Scholar 

  13. Booy G, Hendriks R, Smulders M, Van Groenendael J, Vosman B (2000) Genetic diversity and the survival of populations. Plant Biol 2(4):379–395

    Article  Google Scholar 

  14. Jeong N, Kim K-S, Jeong S, Kim J-Y, Park S-K, Lee JS, Jeong S-C, Kang S-T, Ha B-K, Kim D-Y (2019) Korean soybean core collection: Genotypic and phenotypic diversity population structure and genome-wide association study. PLoS ONE 14(10):e0224074

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Seo E, Kim K, Jun T-H, Choi J, Kim S-H, Muñoz-Amatriaín M, Sun H, Ha B-K (2020) Population structure and genetic diversity in Korean cowpea germplasm based on SNP markers. Plants 9(9):1190

    Article  CAS  PubMed Central  Google Scholar 

  16. Ma SJ, Sa KJ, Hong TK, Lee JK (2017) Genetic diversity and population structure analysis in Perilla frutescens from Northern areas of China based on simple sequence repeats. Genet Mol Res 16(3):16039746

    Article  Google Scholar 

  17. Jeong SW, Kwon S-J, Ryu J, Kim J-B, Ahn J-W, Kim SH, Jo YD, Choi H-I, Im SB, Kang S-Y (2017) Development of EST-SSR markers through de novo RNA sequencing and application for biomass productivity in kenaf (Hibiscus cannabinus L.). Genes Genom 39(10):1139–1156

    Article  CAS  Google Scholar 

  18. Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genom 12(1):451

    Article  CAS  Google Scholar 

  19. Gong W, Ma L, Gong P, Liu X, Wang Z, Zhao G (2019) Development and application of EST–SSRs markers for analysis of genetic diversity in erect milkvetch (Astragalus adsurgens Pall.). Mol Biol Rep 46(1):1323–1326

    Article  CAS  PubMed  Google Scholar 

  20. Yu J-K, La Rota M, Kantety R, Sorrells M (2004) EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genom 271(6):742–751

    Article  CAS  Google Scholar 

  21. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23(1):48–55

    Article  CAS  PubMed  Google Scholar 

  22. Ellis J, Burke J (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99(2):125–132

    Article  CAS  PubMed  Google Scholar 

  23. Kim JM, Lyu JI, Lee M-K, Kim D-G, Kim J-B, Ha B-K, Ahn J-W, Kwon S-J (2019) Cross-species transferability of EST-SSR markers derived from the transcriptome of kenaf (Hibiscus cannabinus L.) and their application to genus Hibiscus. Genet Resour Crop Evol 66(7):1543–1556

    Article  CAS  Google Scholar 

  24. Seong ES, Yoo JH, Choi JH, Kim CH, Jeon MR, Kang BJ, Lee JG, Choi SK, Ghimire BK, Yu CY (2015) Expressed sequence tags analysis and design of simple sequence repeats markers from a full-length cDNA library in Perilla frutescens (L.). Int J Genom. https://doi.org/10.1155/2015/679548

    Article  Google Scholar 

  25. Shen Q, Wen H, Zhang T, Xu J (2019) Large scale identification of SSR markers in perilla by next generation sequencing. Oil Crop Sci 4(2):100–109

    Google Scholar 

  26. Zheng K, Huang N, Bennett J, Khush GS (1995) PCR-based marker-assisted selection in rice breeding. IRRI Discussion Paper Series (Philippines)

  27. Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinform 11(1):1–6

    Article  Google Scholar 

  28. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28(8):1086–1092

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3):411–422

    Article  CAS  PubMed  Google Scholar 

  31. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucleic Acids Res 40(15):e115–e115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129

    Article  CAS  PubMed  Google Scholar 

  33. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599

    Article  CAS  PubMed  Google Scholar 

  34. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620

    Article  CAS  PubMed  Google Scholar 

  35. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14):1801–1806

    Article  CAS  PubMed  Google Scholar 

  36. Mondini L, Noorani A, Pagnotta MA (2009) Assessing plant genetic diversity by molecular tools. Diversity 1(1):19–35

    Article  CAS  Google Scholar 

  37. Huang Z, Peng G, Liu X, Deora A, Falk KC, Gossen BD, McDonald MR, Yu F (2017) Fine mapping of a clubroot resistance gene in Chinese cabbage using SNP markers identified from bulked segregant RNA sequencing. Front Plant Sci 8:1448

    Article  PubMed  PubMed Central  Google Scholar 

  38. Fukushima A, Nakamura M, Suzuki H, Saito K, Yamazaki M (2015) High-throughput sequencing and de novo assembly of red and green forms of the Perilla frutescens var crispa transcriptome. PLoS ONE 10(6):e0129154

    Article  PubMed  PubMed Central  Google Scholar 

  39. Tong W, Kwon S-J, Lee J, Choi I-Y, Park Y-J, Choi SH, Sa KJ, Kim BW, Lee JK (2015) Gene set by de novo assembly of Perilla species and expression profiling between P. frutescens (L.) var. frutescens and var. crispa. Gene 559(2):155–163

    Article  CAS  PubMed  Google Scholar 

  40. Wang Q, Fang L, Chen J, Hu Y, Si Z, Wang S, Chang L, Guo W, Zhang T (2015) Genome-wide mining, characterization, and development of microsatellite markers in Gossypium species. Sci Rep 5:10638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Sa KJ, Choi SH, Ueno M, Lee JK (2015) Genetic diversity and population structure in cultivated and weedy types of Perilla in East Asia and other countries as revealed by SSR markers. Hortic Environ Biotechnol 56(4):524–534

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the Nuclear R&D program of KAERI and Radiation Technology R&D Program (NRF-2017M2A2A6A05018538) through the National Research Foundation of Korea funded by the Ministry of Science and ICT.

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Author notes

  1. Jung Min Kim and Jae Il Lyu have contributed equally to this work.

Authors and Affiliations

  1. Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Korea

    Jung Min Kim, Jae Il Lyu, Dong-Gun Kim, Nguyen Ngoc Hung, Jaihyunk Ryu, Jin-Baek Kim, Joon-Woo Ahn & Soon-Jae Kwon

  2. Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea

    Jung Min Kim, Nguyen Ngoc Hung & Bo-Keun Ha

  3. Department of Life-Resources, Graduate School, Sunchon National University, Suncheon, 57922, Korea

    Dong-Gun Kim

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Contributions

Conceptualization, BKH and SJK; methodology, JMK and JIL; software, JMK and JIL; validation, JR; formal analysis, JMK and JIL; investigation, JMK and DGK; resources, JBK; data curation, JMK and NNH; writing—original draft preparation, JMK; writing—review and editing, JIL and SJK; visualization, JMK and JIL; supervision, BKH and SJK; project administration, JWA; funding acquisition, JBK. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Bo-Keun Ha or Soon-Jae Kwon.

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Kim, J.M., Lyu, J.I., Kim, DG. et al. Analysis of genetic diversity and relationships of Perilla frutescens using novel EST-SSR markers derived from transcriptome between wild-type and mutant Perilla. Mol Biol Rep 48, 6387–6400 (2021). https://doi.org/10.1007/s11033-021-06639-9

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