Genetic Diversity of Iranian Cumin (Cuminum cyminum L.) Accessions, using Inter-Simple Sequence Repeat (ISSR) and Start Codon Targeted (SCoT) Markers

Document Type : Research Paper

Authors

1 Department of Horticulture Sciences and Agronomy, Agriculture and Food Science college, Science and Research Branch, Islamic Azad University, Tehran, Iran

2 Research Center of Agricultural and Natural Resources, Education and Extension Organization (AREEO), Semnan, Iran

3 Department of Horticulture, College of Agriculture, Saveh Branch, Islamic Azad University, Saveh, Iran

4 Seed and Plant Certification and Registration Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran

Abstract

Cuminum cyminum L. (cumin) is an aromatic plant, commonly used in food industries and traditional medicine, especially in tropical Asia. Various accessions of C. cyminum with different aromatic properties could be found in Iran, as a main region of cumin production. This study was conducted to evaluate genetic diversity of 22 accessions of C. cyminum from different parts of Iran. The seeds were cultivated in a randomized complete block design (RCBD), with 22 accessions and three replicates, and their agro-morphological traits were measured. Genetic variations of the studied accessions were evaluated using inter simple sequence repeat (ISSR) and start codon targeted (SCoT) markers. Estimate of molecular variance showed a significant genetic difference between the studied accessions, whereby 57% of total variance was occurred between the populations. Based on the Mantel test for association of genetic diversities and geographical distances, increase of geographical distance did not influence the genetic differentiation. Significant differences were observed between the studied agro-morphological traits, other than the number of branches. Canonical correspondence analysis of genetic features and environmental factors, including five geographic and climatic factors of the seed’s origin, showed significant influences of altitude and latitude on genetic variation of the studied accessions. However, despite the observed genetic variations, the studied cumin accessions, are not totally isolated and hence some amount of gene flow has been occurred between them. Therefore, no isolation by distance exists between the studied accessions. Generally, the results confirmed that both ISSR and SCoT markers were reliable and useful tools for analyzing the genetic diversity of cumin in Iran.

Keywords


  1. Kafie M, Rashed-Mohasel MH, Koocheki A, Nassiri M. Cumin (Cuminum cyminum) production and processing, Ferdowsi University Press, Iran. 2002.
  2. Lodha S, Mawar R. Cumin Wilt Management: A Review. J Spice Aroma Crop. 2014;23:145-155.
  3. Hashemian N, Pirbalouti AG, Hashemi M, Golparvar A, Hamedi B. Diversity in Chemical Composition and Antibacterial Activity of Essential Oils of Cumin (Cuminum cyminum L.) Diverse from Northeast of Iran. Aust J Crop Sci. 2013;7:1752-1760.
  4. Parashar M, Jakhar ML, Malik C.P. A review on biotechnology, genetic diversity in cumin (Cuminum cyminum). A Review. Int J Life Sci Pharm Re. 2014;4:17-34.
  5. Kazemi N, Kahrizi D, Mansouri M. Effects of Plant Growth Regulators and Explant on Callus Induction in Cuminum cymium L. J Gen Res. 2016;2:23-28.
  6. Soorni J, Kahrizi D. Effect of genotype, explant type and 2,4-D on cell dedifferentiation and callus induction in cumin (Cuminum cyminum L.) medicinal plant. J App Biotechnol Rep. 2015;2:265-270.
  7. Weising K, Atkinson RG, Gardner R.C. Genomic fingerprinting by microsatellite-primed PCR: A critical evaluation. PCR Meth Appl. 1995;4:249-255.
  8. Shahlaei A, Torabi S, Khosroshahli M. Efficacy of SCoT and ISSR markers in assessment of tomato (Lycopersicum esculentum Mill.) genetic diversity. Int J Biosci. 2014;5:14-22.
  9. Afshar F, Sheidai M, Talebi S.M, Keshavari M. Bayesian and Multivariate Analyses of combined molecular and morphological data in Linum austriacum (Linaceae) populations: Evidence for infra specific taxonomic groups. Biodiversity. 2015;16:179-187.
  10. Xiong F.Q, Zhong R.C, Han Z.Q. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol Biol Rep. 2011;38:3487-3494.
  11. Amirmoradi B, Talebi R, Karami E. Comparison of genetic variation and differentiation among annual Cicer species using start codon targeted (SCoT) polymorphism, DAMD-PCR, and ISSR markers. Plant Syst Evol. 2012;298:1679-1688.
  12. Mulpuri S, Muddanuru T, Francis G. Start codon targeted (SCoT) polymorphism in toxic and nontoxic accessions of Jatropha curcas L. and development of a codominant SCAR marker. Plan Sci. 2013;207:117-127.
  13. Marsjan P, Oldenbroek J. Molecular markers, a tool for exploring genetic diversity. In: Rischkowsky, B., Pilling, D. (Eds.), The State of the World's Animal Genetic Resources for Food and Agriculture. FAO, Rome. 2007;359:379.
  14. Samantaray S, Dhagat U.M, Maiti S. Evaluation of genetic relationships in Plantago species using Random Amplified Polymorphic DNA (RAPD) markers. Plant Biotechnol. 2010;27:297-303.
  15. Rahimi M, Nazari L, Kordrostami M, Safari P. SCoT marker diversity among Iranian Plantago ecotypes and their possible association with agronomic traits. Sci Hort. 2018;233:302-309.
  16. Pradeep Reddy MN, Sarla Siddiq EA. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica. 2002;128:9-17.
  17. Xu JY, Zhu Y,Yi Z, Wu G, Xie GY,Qin MJ. Molecular diversity analysis of Tetradium ruticarpum (WuZhuYu) in China based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Chin J Nat Med. 2018;16:1-9.
  18. Collard BC, Mackill DJ. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep. 2009;27:86-93.
  19. Bahraminejad A, Mohammadi-Nejad G,Abdul Khadir M. Study of genetic diversity of cumin (Cumin cyminum L.) based on phenotypic characteristics. Aust J Cop Sci. 2011;5:301-307.
  20. Bahraminejad A, Mohammadi-Nejad G, Abdul Khadir M, Bin Yusop M. Molecular diversity of cumin (Cuminum cyminum L.) using RAPD markers. Aust J Cop Sci. 2012;6:194-199.
  21. Bahraminejad A, Mohammadinejad G. Use of microsatellite markers for molecular characterization of cumin (Cuminum cyminum L.) ecotypes. IranJ Genet Plant Breed. 2013;2:35-41.
  22. Rostami-Ahmadvandi H, Cheghamirza D, Kahrizi S, Bahraminejad M. Comparison of morphoagronomic traits versus RAPD and ISSR markers in order to evaluate genetic diversity among Cuminum cyminum L. Accessions. Aust J Crop Sci. 2013;7:361-367.
  23. Doyle J.J, Doyle J.L. Isolation of plant DNA from fresh tissue. Focus. 1990;12:13-15.
  24. Ghasemzadeh Baraki S, Nikzat Siahkolaee S, Mousavi A. Optimization of the genomic DNA extraction in some mosses. Rostaniha. 2018;19:165-175.
  25. Freeland J.R, Kirk H. Peterson, S.D. Molecular Ecology, 2nd ed. Wiley-Blackwell, UK. 2011.
  26. Podani J. Introduction to the Exploration of Multivariate Data. Backhuys Publ., Leiden. 2000.
  27. Hamer Ø, Harper D.A.T, Ryan P.D. PAST: Paleontological statistics software package for education and data analysis. Palaeontol. Electronica. 2001;4:1-9.
  28. Lou Y, Hu L, Chen L, Sun X, Yang Y, Liu H, Xu Q. Association analysis of simple sequence repeat (SSR) markers with agronomic traits in tall fescue (Festuca arundinacea Schreb.). PLoS One. 2015;10:e0133054.
  29. Aminpoor R, Mousavi S. The Effects of number of Irrigations on development stages, yield and yield components of cumin. Water Soil Sci. 1997;1:1-8.
  30. Luo C, He XH, Chen H, Ou SJ, Gao MP. Analysis of diversity and relationships among mango cultivars using Start Codon Targeted (SCoT) markers. Biochem Syst Ecol. 2010;38:1176-1184.
  31. Rahimi M, Kordrostami M. Genetic Diversity Evaluation of Lemon balm (Melissa officinalis L.) Ecotypes Using Morphological Traits and Molecular Markers. J Med Plant Res. 2017;1:97-104.
  32. Sheidai M, Zanganeh S, Haji-Ramezanali R, Nouroozi M, Noormohammadi Z, Ghsemzadeh-Baraki S. Genetic diversity and population structure in four Cirsium (Asteraceae) species. Biologia. 2013;68:384-397.
  33. Jolivet C, Bernasconi G. Molecular and quantitative genetic differentiation in European populations of Silene latifolia (Caryophyllaceae). J Hum Genet. 2007;177:1239-1247.
  34. Qiu Y.X, Hong D.Y, Fu C.X, Kenneth M.C. Genetic variation in the endangered and endemic species Changium smyrnioides (Apiaceae). Biochem Sys. Ecol. 2004;32:583-596.
  35. Ding G, Zhang D.Z, Yu Y.Q, Zhao L.L, Zhang B.B. Analysis of genetic variability and population structure of the endemic medicinal Limonium sinense using molecular markers. Gene. 2013;520:189-193.
  36. Liu F, Guo QS, Shi HZ, Wang T, Zhu ZB. Genetic diversity and phylogenetic relationships among and within populations of Whitmania pigra and Hirudo nipponica based on ISSR and SRAP markers. Biochem Syst Ecol. 2013;51:215-223.
  37. Mosca E, Eckert A.J, Di PE, Rocchini D, La P.N, Belletti P, Neale D.B. The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps. Mol Ecol. 2012;21:5530-5545.
  38. Avolio M.L, Beaulieu J.M, Smith M.D. Genetic diversity of a dominant C4 grass is altered with increased precipitation variability. Oecologia. 2013;171:571-581.
  39. Wang M.L, Zhu C, Barkley N.A, Chen Z, Erpelding J.E, Murray S.C, Tuinstra M.R, Tesso T, Pederson G.A, Yu J. Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection. Theor Appl Genet. 2009;120:13-23.
  40. Zhao N.X, Gao Y.B, Wang J.L, Ren A.Z, Xu H. RAPD diversity of Stipa grandis populations and its relationship with some ecological factors. Acta Ecol Sin. 2006;26:1312-1319.
  41. Huang WD, Zhao XY, Zhao X, Li YL, Lian J, Pan CC. Environmental determinants of genetic diversity in Caragana microphylla (Fabaceae) in northern China. Ecol Evol. 2016;6:8256-8266.
  42. Huang WD, Zhao XY, Zhao X, Li YQ, Lian J, Yun JY. Relationship between the genetic diversity of Artemisia halodendron and climatic factors. Acta Oecolog. 2014;55:97-103.