Microsatellite Marker for Genetic Variation Analysis in Local Chili Pepper (Capsicum frutescens L.) Induced by Ethyl Methane Sulfonate (EMS)


  • Ria Reinnata Juliandari Brawijaya University
  • Retno Mastuti
  • Estri Laras Arumningtyas
  • Estri Laras Arumningtyas




Chili (C. frutescens L.), EMS, Microsatellite Marker, Genetic Variation


Mutation using Ethyl Methane Sulfonate (EMS) is a simple and quick method to produce genetic variation in chili pepper. In this study, a total of 3 genotypes of local chili pepper (Capsicum frutescens L.), i.e. Genotype 2 (G2), Genotype 7 (G7), and Genotype 11 (G11) were induced by EMS with concentrations of 0% (K0), 0.01% (K1), 0.02% (K2), and 0.04% (K3). Genetic variation analysis in mutant was performed based on 3 microsatellite markers CA 19, CA 27, CA 62. Those molecular markers successfully detected the genetic variation in chili pepper mutant based on the number and size of microsatellite alleles variation. The 3 genotypes of chili pepper mutant produced a total of 15 alleles with the average Polymorphism Information Content (PIC) value of 0.82. Compared to the control plant, genetic variations in genome level were observed in local chili pepper. Furthermore, the treatment of EMS with concentration of 0.04% produced the most notable genetic variation in 3 genotypes of local chili pepper.


Author Biography

Ria Reinnata Juliandari, Brawijaya University

Postgraduated student in Biology Department, Brawijaya University, Malang, Indonesia


Carvalho SLC, Ragassi CF, Oliveira LB et al. (2015) Transferability of microsatellite markers of Capsicum annuum L. to C. frutestescens L. and C. chinense Jacq. Genetics and Molecular Research 14 (3): 7937 – 7946. doi: 10.4238/2015.july.17.1.

Musfiroh I, Mutakin T, Angelina, Muchtaridi M (2013) Capsaicin level of various capsicum fruits. International Journal of Pharmacy and Pharmaceutical Sciences 5 (1): 248 – 251.

Keyhaninejad N, Curry J, Romero J, O’Connell MA (2014) Fruit specific variability in capsaicinoid accumulation and transcription of structural and regulatory genes in capsicum fruit. Plant Science 215 – 216: 59 – 68. doi: 10.1016/j.plantsci.2013.10.013.

Djarwaningsih T (2005) Capsicum spp. (Chilli): origin, distribution, and its economical value. Biodiversitas 6 (4): 292 – 296. doi: 10.13057/biodiv/d060417.

Wahyuni Y, Ballester AR, Sudarnowati E et al. (2011) Metabolite biodiversity in Pepper (Capsicum) fruits of thirty-two diverse accessions: Variation in health-related compounds and amplifications for breeding. Phytochem-istry 72 (11 – 12): 1358 – 1370. doi: 10.1016/j.phytochem.2011.03.016.

Materska M, Perucka I (2005) Antioxidant activity of the main phenolic compounds isolated from hot pepper fruit (Capsicum annuum L.). Journal Agriculture Food Chemistry 53 (5): 1750 – 1756. doi: 10.1021/jf035331k.

Mori A, Lehman S, O’Kelly J et al. (2006) Capsaicin, a component of red peppers, inhibits the growth of androgen-independent, p53 mutant prostate cancer cells. Cancer Research 66 (6): 3222 – 3229. doi: 10.1158/0008-5472.can-05-0087.

Aza-Gonzales C, Nunez-Palenius HG, Ochoa-Alejo N (2011) Molecular biology of capsaicinoid biosynthesis in chili pepper (Capsicum spp.). Plant Cell Reports 30 (5): 695 – 706. doi: 10.1007/s00299-010-0968-8.

Dima C, Coman G, Cotarlet M, Alexe P, Dim S (2013) Antioxidant and antibacterial properties of capsaicin microemulsions. Food Technology 37 (1): 39 – 49.

Gudeva LK, Mitrev S, Maksimova V, Spasov D (2013) Content of capsaicin extracted from hot pepper (Capsicum annuum spp. microcarpum L.) and its use as an ecopesticide. Hemijska Industrija 67 (4): 671-675. doi: 10.2298/hemind120921110k.

Habibi M, Manggabarani AM, Sulasmi ES, Listyorini D (2013) AT3 gene (Acyltransferase) isolation from Capsicum frutescens L. cv. Cakra Hijau. Journal of Tropical Life Science 3 (2): 83-86. doi: 10.11594/jtls.03.02.02.

Arisha MH, Shah AYM, Gong Z et al. (2015) Ethyl methane sulfonate induced mutations in M2 generation and physiological variations in M1 generation of peppers (Capsicum annuum L.). Frontiers in Plant Science 6: 399. doi: 10.3389/fpls.2015.00399.

Laskar RA, Chaudhary C, Khan S, Chandra A (2016) Induction of mutagenized tomato populations for investigation on agronomic traits and mutant phenotyping. Journal of The Saudi Society of Agricultural Sciences 17 (1): 51 – 60. doi: 10.1016/j.jssas.2016.01.002.

Devi AS, Mullainathan L (2011) Physical and chemical mutagenesis for improvement of chili (Capsicum annuum L.). World Applied Sciences Journal 15 (1): 108 – 113.

Dhakshanamoorthy D, Selvaraj R, Chidambaram A (2014) Utility RAPD marker for genetic diversity analysis in gamma rays and Ethyl Methane Sulphonate (EMS) treated Jatropha curcas plants. Comptes Rendus Biologies 388 (2): 75 – 82. doi: 10.1016/j.crvi.2014.12.002.

Sega GA (1984) A review of the genetic effects of Ethyl Methane Sulfonate. Mutation Research 134: 113 – 142.

Mullainathan TAL (2015) Effect of gamma rays and EMS on phytochemical constituents in Chili (Capsicum annuum L.var-K1 in M2 generation). International Journal of Pharmacy and Pharmaceutical Research 4 (3): 92 – 101.

Efendi R, Sunarti S, Musa Y et al. (2015) Selection of homozygosity and genetic diversity of Maize Inbred using Simple Sequence Repeats (SSRs) marker. International Journal of Current Research in Biosciences and Plant Bi-ology 2 (3): 19 – 28.

Zhang XM, Zhang ZH, Gu XZ et al. (2016) Genetic diversity of pepper (Capsicum spp.) germpalsm resources in China reflects selection for cultivar types and spatial distribution. Journal of Integrative Agriculture 15 (9): 1991 – 2001. doi: 10.1016/S2095-3119(16)61364-3.

Kwon YS, Lee JM, Yi GB et al. (2005) Use of SSR markers to complement tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Molecules and Cells 3 (19): 428 – 435.

Talebi AB, Talebi AB, Shahrokhifar B (2012) Ethyl Methane Sulphonate (EMS) induced mutagenesis in Malaysian rice (cv.MR219) for lethal dose determination. American Journal of Plant Sciences 3 (12): 1661 – 1665. doi: 10.4236/ajps.2012.312202.

Rocha EA, Paiva LV, Carvalho HH, Guimaraes CT (2010) Molecular characterization and genetic diversity of potato cultivars using SSR and RAPD markers. Crop Breeding and Applied Biotechnology 10 (3): 204 – 210. doi: 10.1590/S1984-70332010000300004.

Smith JSC, Chin ECL, Shu H et al. (1997) An evaluation of the utility of SSR loci as molecular markers in Maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics 95 (1 – 2): 163-173. doi: 10.1007/s001220050544.

Carvalho N, Canela FM, Leitie PHS et al. (2017) Analysis of genetic variability of commercial melon cultivars using SSR molecular markers. Genetic and Molecular Research 16 (3): 1 – 8. doi: 10.4238/gmr16039739.

Britt AB (1996) DNA damage and repair in plants. Annual Review of Plant Physiology and Plant Molecular Biology 47: 75-100. doi: 10.1146/annurev.arplant.47.1.75.

Shahriar MH, Robin AHK, Begum SN, Haque A (2014) Diversity analysis of some selected rice genotypes through SSR based molecular markers. Journal Bangladesh Agri-cultural University 12 (2): 307 – 311. doi: 10.3329/jbau.v12i2.28689.

Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19 (1): 11 – 15.