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Genetic diversity and population structure of Perilla frutescens collected from Korea and China based on simple sequence repeats (SSRs)

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Abstract

Background

Perilla frutescens (L.) Britt. is divided into two varieties based on morphology and use. One is P. frutescens var. frutescens, which is used both as a leafy vegetable and as an oil obtained from the seeds. The other variety is P. frutescens var. crispa, a Chinese medicine or spice vegetable crop. In addition, weedy types of var. frutescens and var. crispa are occasionally grown as relict forms and are easy to find on roadsides, in waste areas and around farmers’ fields or farmhouses. SSR markers have been successfully used to examine the genetic diversity and relationships of cultivated and weedy types of Perilla in many regions.

Objectives

In this study, we used 25 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 90 Perilla accessions from Korea and China.

Methods

A total of 90 accessions of Perilla were collected in Korea and China included 45 accessions from each of Korea and China. We selected 25 SSR markers representing the polymorphism of and adequately amplifying all the Perilla accessions.

Results

A total of 153 alleles were identified, with an average of 6.12 alleles per locus. The GD level and PIC value for cultivated and weedy types of P. frutescens from China were higher than those for accessions from Korea. Weedy accessions had higher GD and PIC values than cultivated accessions. In the population structure analysis using the model-based method, the 90 Perilla accessions were divided into two main group and an admixed group based on a membership probability threshold of 0.8. Based on the distance-based unweighted pair group method with the arithmetic mean (UPGMA), all accessions were classified into four major groups with a genetic similarity of 32.8%.

Conclusion

Finally, the findings of this study will provide useful theoretical knowledge for further study of the population structure and genetic diversity of Perilla species and benefit Perilla crop breeding and germplasm conservation in Korea and China.

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References

  • Brown WL (1983) Genetic diversity and genetic vulnerability-an appraisal. Econ Bot 37:4–12

    Article  Google Scholar 

  • Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26:297–302

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Hamza S, Hamida WB, Rebai A, Harrabi M (2004) SSR-based genetic diversity assessment among Tunisian winter barley and relationship with morphological traits. Euphytica 135:107–118

    Article  CAS  Google Scholar 

  • Kwon SJ, Lee JK, Kim NS, Yu JW, Dixit A, Cho EG, Park YJ (2005) Isolation and characterization of SSR markers in Perilla frutescens Britt. Mol Ecol Notes 5:454–456

    Article  Google Scholar 

  • Lee JK, Kim NS (2007) Genetic diversity and relationships of cultivated and weedy types of Perilla frutescens collected from East Asia revealed by SSR markers. Korean J Breed Sci 39:491–499

    Google Scholar 

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

    Article  Google Scholar 

  • 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 50:65–74

    Article  CAS  Google Scholar 

  • Lee JK, Nitta M, Kim NS, Park CH et al (2002) Genetic diversity of Perilla and related weedy types in Korea determined by AFLP analyses. Crop Sci 42:2161–2166. https://doi.org/10.2135/cropsci2002.2161

    Article  CAS  Google Scholar 

  • Lee JK, Kwon SJ, Park BJ, Kim MJ, Park YJ, Ma KH, Lee SY, Kim JH (2007) Analysis of genetic diversity and Relationships of cultivated and weedy types of Perilla frutescens collected from Korea by using microsatellite markers. Korean J Genet 29:81–89

    CAS  Google Scholar 

  • Li HL (1969) The vegetables of ancient China. Econ Bot 23:235–260

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Liu YX, Zhang WM (1998) Classification and resources distribution of Perilla. Chin Wild Plant Resour 17:1–4

    CAS  Google Scholar 

  • Liu YX, Zhang WM, Qian XS (1996) Research and utilization of Perilla. Chin Wild Plant Resour 3:24–27

    Google Scholar 

  • Ma SJ, Lee JK (2017) Morphological variation of two cultivated types of Perilla crop from different areas of China. Korean J Hortic Sci Biotechnol 35:510–522

    Google Scholar 

  • Ma SJ, Sa KJ, Hong TK, Lee JK (2019) Genetic diversity and population structure analysis in Perilla crop and their weedy types from northern and southern areas of China based on simple sequence repeat (SSRs). Genes Genom 41:267–281

    Article  CAS  Google Scholar 

  • Makino T, Hara H, Tuyama T, Fumio M (1961) Makino’s new illustrated flora of Japan. Hokuryukan, Tokyo, p 1060

    Google Scholar 

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

    Article  Google Scholar 

  • Palmer JD, Jansen RK, Michaels HJ, Chase MW, Manhart JR (1988) Chloroplast DNA variation and plant phylogeny. Ann Mo Bot Gard 75:1180–1206

    Article  Google Scholar 

  • Park YJ, Dixit A, Ma KH, Lee JK et al (2008) Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens (L.) Britt. using microsatellite markers. Genet Resour Crop Evol 55:523–535

    Article  CAS  Google Scholar 

  • Park YJ, Lee JK, Kim NS (2009) Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. Molecules 14:4546–4569

    Article  CAS  Google Scholar 

  • Park YJ, Ramekar RV, Sa KJ, Lee JK (2015) Genetic diversity, population structure, and association mapping of biomass traits in maize with simple sequence repeat markers. Genes Genom 37:725–735

    Article  CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M et al (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Pritchard JK, Wen W (2003) Documentation for STRUCTURE software: version 2. Available from http://www.pritch.bsd.uchicago.edu

  • Rao NK (2004) Plant genetic resources: advancing conservation and use through biotechnology. Afr J Biotechnol 3:136–145

    Google Scholar 

  • Rao VR, Hodgkin T (2002) Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Organ Cult 68:1–19

    Article  Google Scholar 

  • Rohlf FJ (1998) NTSYS-pc: numerical taxonomy and multivariate analysis system version. Version: 2.02. Exter Software, Setauket

    Google Scholar 

  • Sa KJ, Choi SH, Ueno M, Park KC et al (2013) Identification of genetic variations of cultivated and weedy types of Perilla species in Korea and Japan using morphological and SSR markers. Genes Genom 35:649–659

    Article  CAS  Google Scholar 

  • 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 56:524–534

    Article  Google Scholar 

  • Sa KJ, Choi IK, Park KC, 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 40:1319–1329

    Article  Google Scholar 

  • Tan M, Yan M, Wang L, Wang L, Yan X (2012) Research progress on Perilla frutescens. Chin J Oil Crop Sci 34:225–231

    CAS  Google Scholar 

  • Vaiman D, Mercier D, Moazai G (1994) A set of 99 cattle microsatellite, characterization, synteny mapping and polymorphism. Mamm Genome 5:288–297

    Article  CAS  Google Scholar 

  • Villa TCC, Maxted N, Scholten M, Ford-Lloyd B (2006) Defining and identifying crop landraces. Plant Genet Resour 3:373–384

    Article  Google Scholar 

  • Wang S, Guo F (2012) Genetic diversity of Perilla frutescens from Yunnan based on ISSR. Chin J Oil Crop Sci 34:372–376

    CAS  Google Scholar 

  • Wang R, Yu Y, Zhao J, Shi Y et al (2008) Population structure and linkage disequilibrium of a mini core set of maize inbred lines in China. Theor Appl Genet 117:1141–1153

    Article  CAS  Google Scholar 

  • Wei Z, Li H, Feng B, Lin T, Lin W (2015) Studies on the germplasm resource investigation and utilization of Perilla frutescens (L.) in Guizhou. Seed 34:58–60

    Google Scholar 

  • Xia XC, Reif JC, Melchinger AE, Frisch M et al (2005) Genetic diversity among CIMMYT maize inbred lines investigated with SSR markers: II. Subtropical, tropical midaltitude, and highland maize inbred lines and their relationships with elite U.S. and European maize. Crop Sci 45:2573–2582

    Article  CAS  Google Scholar 

  • Xie CX, Warburton M, Li MS, Li XH, Xiao MJ, Hao ZF, Zhao Q, Zhang SH (2008) An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines. Mol Breed 21:407–418

    Article  Google Scholar 

  • Xie W, Zhang X, Cai H, Liu W et al (2010) Genetic diversity analysis and transferability of cereal EST-SSR markers to orchardgrass (Dactylis glomerata L.). Biochem Syst Ecol 38:740–749

    Article  CAS  Google Scholar 

  • Zeven AC (1998) Landraces: a review of definitions and classifications. Euphytica 104:127–139

    Article  Google Scholar 

  • Zeven AC, de-Wet JMJ (1982) Dictionary of cultivated plants and their regions of diversity. Centre for Agricultural Publishing and Documentation, Wageningen, p 34

    Google Scholar 

  • Zhang X, Wu W, Zheng YL, Chen L, Cai Q (2009) Essential oil variations in different Perilla L. accessions: chemotaxonomic implications. Plant Syst Evol 281:1–10

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This study was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (#2016R1D1A1B01006461), and the Cooperative Research Program for Agriculture Science and Technology Development (Project nos. PJ014227032019 and PJ0142272019), Rural Development Administration, Republic of Korea.

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Author notes

  1. Dae Hyun Park and Kyu Jin Sa contributed equally to this work.

Authors and Affiliations

  1. Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, 24341, Korea

    Dae Hyun Park, Kyu Jin Sa, Su Eun Lim, Shi Jun Ma & Ju Kyong Lee

  2. School of Life Sciences, Shandong University, No. 72 Binhai Road, Jimo District, Qingdao, 266237, People’s Republic of China

    Shi Jun Ma

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  1. Dae Hyun Park
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Correspondence to Ju Kyong Lee.

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Dae Hyun Park declares that he has no conflict of interest. Kyu Jin Sa declares that he has no conflict of interest. Su Eun Lim declares that she has no conflict of interest. Shi Jun Ma declares that she has no conflict of interest. Ju Kyong Lee declares that he has no conflict of interest.

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Park, D.H., Sa, K.J., Lim, S.E. et al. Genetic diversity and population structure of Perilla frutescens collected from Korea and China based on simple sequence repeats (SSRs). Genes Genom 41, 1329–1340 (2019). https://doi.org/10.1007/s13258-019-00860-4

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