Skip to main content
SpringerLink
Log in

DNA fingerprinting and genetic diversity analysis with SCoT markers of Persian walnut populations (Juglans regia L.) in Iran

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Juglans regia L. is the most widely cultivated and economically important species of edible nuts. Iran is known as a center of origin of genetically rich walnut germplasm and expected to be found a large diversity within Iranian walnut populations. A detailed population genetic of local populations is useful for developing an optimal strategy for in situ conservation and can assist the breeders in crop improvement programmes. The main aim of the present study was genetic fingerprinting of 20 Persian walnut populations, including 3 wild and 17 cultivated populations by using SCoT markers. We also aimed to evaluate the discriminating power of SCoT markers in these populations. The correlation between genetic distance and geographical distance has also investigated. The results showed that SCoT marker has a good discrimination power and can differentiate the studied populations. This marker can be used to evaluate genetic diversity, identify genotypes and DNA finger printing of Persian walnut populations. The present study also revealed that there are at least two genetic groups in the studied Persian walnut populations and the geographical features of cultivated populations can be influenced grouping of them. The studied populations differed genetically and showed isolation by distance.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Agarwal A, Gupta V, Haq S, Jatav P, Kothari SL, Kachhwaha S (2018) Assessment of genetic diversity in 29 Rose germplasms using SCoT marker. J King Saud Univ Sci. https://doi.org/10.1016/j.jksus.2018.04.022

    Article  Google Scholar 

  • Anderson KJ, Teuber SS, Gobeille A, Cremin P, Waterhouse AL, Steinberg FM (2001) Walnut polyphenolics inhibit in vitro human plasma and LDL oxidation. J Nutr 131:2837–2842

    CAS  PubMed  Google Scholar 

  • Arab MM, Marrano A, Abdollahi-Arpanahi R, Leslie CA, Askari H, Neale DB, Vahdati K (2019) Genome-wide patterns of population structure and association mapping of nut-related traits in Persian walnut populations from Iran using the Axiom J. regia 700 K SNP array. Sci Rep 9:1–14

    CAS  Google Scholar 

  • Aradhya M, Velasco D, Ibrahimov Z, Toktoraliev B, Maghradze D, Musayev M, Bobokashvili Z, Preece JE (2017) Genetic and ecological insights into glacial refugia of walnut (Juglans regia L.). PLoS ONE 2(10):e0185974

    Google Scholar 

  • Arzani K, Mansouri-Ardakan H, Vezvaei A, Roozban MR (2008) Morphological variation among Persian walnut (Juglans regia) genotypes from central Iran. N Z J Crop Hortic 36(3):159–168

    Google Scholar 

  • Aslantas R (2006) Identification of superior walnut (Juglans regia) genotypes in north-eastern Anatolia, Turkey. N Z J Crop Hortic Sci 34:231–237

    Google Scholar 

  • Atefi J (1997) Study on phenological and pomological characters on walnut promising clones in Iran. Acta Hortic 442:101–108

    Google Scholar 

  • Baghizadeh A, Dehghan E (2018) Efficacy of SCoT and ISSR markers in assessment of genetic diversity in some Iranian pistachio (Pistacia vera L.) cultivars. PHJ 1(1):37–43

    Google Scholar 

  • Bayazit S, Kazan K, Gülbitti S, Cevik V, Ayanoglu H, Ergül A (2007) AFLP analysis of genetic diversity in low chill requiring walnut (Juglans regia L.) genotypes from Hatay, Turkey. Sci Hortic 111:394–398

    CAS  Google Scholar 

  • Bernard A, Barreneche T, Lheureux F, Drilewanger E (2018) Analysis of genetic diversity and structure in a worldwide walnut (Juglans regia L.) germplasm using SSR markers. PLoS ONE 13(11):1–19

    Google Scholar 

  • Chai XT, Dong R, Liu WX, Wang YR, Liu ZP (2017) Optimizing sample size to assess the genetic dsiversity in common vetch (Vicia sativa L.) populations using Start Codon Targeted (SCoT) markers. Molecules 22:2–10

    Google Scholar 

  • Collard BC, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plan Mol Biol Rep 27:86–93

    CAS  Google Scholar 

  • Cosmulescu S (2013) Phenotypic diversity of walnut (Juglans regia L.) in Romania-opportunity for genetic improvement. South Western J Hortic Biol Env 4(2): 117-126

  • Ebrahimi A, Fatahi R, Zamani Z (2011) Analysis of genetic diversity among some Persian walnut genotypes (Juglans regia L.) using morphological traits and SSRs markers. Sci Hortic 130:146–151

    CAS  Google Scholar 

  • Ebrahimi A, Khadivi-Khub A, Nosrati Z, Karimi R (2015) Identification of superior walnut (Juglans regia) genotypes with lateleafing and high kernel quality in Iran. Sci Hortic 193:195–201

    Google Scholar 

  • Etminan A, Pour-Aboughadareh AR, Mohammadi R, Ahmadi-Rad A, Noori A, Mahdavian Z, Moradi Z (2016) Applicability of start codon targeted (SCoT) and inter-simple sequence repeat (ISSR) markers for genetic diversity analysis in durum wheat genotypes. Biotechnol Biotec Eq 30(6):1075–1081

    Google Scholar 

  • FAO (2009) Production Yearbook. Food and Agriculture Organization, Rome, Italy

    Google Scholar 

  • FAO (2012) Food and Agriculture Organization of the United Nations. FAOSTAT. http://faostat.fao.org

  • Fjellstrom RG, Parfitt DE, Mcgranahan GH (1994) Genetic relationship and characterization of Persian walnut (Juglans regia L.) cultivars using restriction fragment length polymorphisms (RFLPs). J Am Soc Hortic Sci 119:833–839

    CAS  Google Scholar 

  • Germain E (1997) Genetic improvement of the Persian walnut (Juglans regia L.). Acta Hort 442:21–31

    Google Scholar 

  • Germain E, Prunet JP, Garcin A (1999) Le noyer monographie. CTIFL, Paris

    Google Scholar 

  • Ghanbari A, Faraji M, Shokouhian A, Pyrayesh A (2018) Evaluation of quantitative and qualitative characteristics of Persian walnut (Juglans regia L.) genotypes in the west of Meshkin–shahr. J Nuts 9(1):57–65

    Google Scholar 

  • Guo DL, Zhang JY, Liu CH (2012) Genetic diversity in some grape varieties revealed by SCoT analyses. Mol Biol Rep 39:5307–5313

    CAS  PubMed  Google Scholar 

  • Hamidi H, Talebi R, Keshavarzi F (2014) Comparative efficiency of functional gene-based markers, start codon targeted polymorphism (SCoT) and conserved DNA-derived polymorphism (CDDP) with ISSR markers for diagnostic fingerprinting in wheat (Triticum aestivum L.). Cereal Res Commun 42(4):558–567

    CAS  Google Scholar 

  • Hammer Ø, Harper DAT, Ryan PD (2012) PAST: paleontological Statistics software package for education and data analysis. Palaeontol Electron 4:9

    Google Scholar 

  • Hao J, Jiao K, Yu C, Guo H, Zhu Y, Yang X, Zhang S, Zhang L, Feng S, Song Y, Dong M, Wang H, Shen C (2018) Development of SCoT-based SCAR marker for rapid authentication of Taxus media. Biochem Genet 56:1–12

    Google Scholar 

  • Hassani D (2017a) Chaldoran, a productive and precocious new walnut cultivar with lateral fruiting habit.Temperate Fruits Research Center, Research Achievements. http://tfri.areeo.ac.ir

  • Hassani D (2017b) Caspian, a late-leafing new walnut cultivar with lateral fruiting habit and high quality fruit and Kernal. Temperate Fruits Research Center, Research Achievements. http://tfri.areeo.ac.ir

  • Hassani D (2017c) Alvand, a productive and precocious new walnut cultivar with lateral fruiting habit. Fruits Research Center, Research Achievements. http://tfri.areeo.ac.ir

  • Hassani D (2017d) Persia, a late-leafing new walnut cultivar with lateral fruiting habit and high quality fruit and Kernal. Temperate Fruits Research Center, Research Achievements. http://tfri.areeo.ac.ir

  • Hassani D, Atefi J, Haghjooyan R, Dastjerdi R, Keshavarzi M, Mozaffari MR, Soleimani A, Rahmanian AR, Nematzadeh F, Malmir A (2012a) Jamal, a new Persian walnut cultivar for moderate-cold areas of Iran. Seed Palnt Improve J 28(1):523–525

    Google Scholar 

  • Hassani D, Atefi J, Haghjooyan R, Dastjerdi R, Keshavarzi M, Mozaffari MR, Soleimani A, Rahmanian AR, Nematzadeh F, Malmir A (2012b) Damavand, a new walnut cultivar as a pollinizer for Iranian walnut cultivars and genotypes. Seed Palnt Improve J 28(1):529–531

    Google Scholar 

  • Hassani D, Dastjerdi R, Haghjooyan R, Soleimani A, Keshavarzi M, Atefi J, Mozaffari M, Rezaee R, Fahadan A, Rahmanian A (2014) Genetic Improvement of Persian walnut (Juglans regia L.) in Iran. In: Acta Horticulturae VIIth International Walnut Symposium, pp. 95–102

  • Iv APG (2016) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants. Bot J Linn Soc 181:1–20

    Google Scholar 

  • Karimi R, Ershadi A, Vahdati K, Woeste K (2010) Molecular characterization of persian walnut populations in Iran with microsatellite markers. Hortic Sci 45(9):1403–1406

    Google Scholar 

  • Karimi R, Ershadi A, Nia AE, Sharifani M, Ebrahimi A, Vahdati K (2014) Morphological and molecular evaluation of persian walnut populations in northern and western regions of Iran. J Nuts 5(2):21–31

    Google Scholar 

  • Križman M, Jakše J, Baričevič D, Javornik B, Prošek M (2006) Robust CTAB-activated charcoal protocol for plant DNA extraction. Agric Slov 87:427–433

    Google Scholar 

  • Kumar LS (1999) DNA markers in plant improvement. Biotechnol Adv 17:143–183

    CAS  PubMed  Google Scholar 

  • Lu AM (1982) The geographical dispersal of Juglandaceae. Acta Phytotaxa Sin 20:257–271

    Google Scholar 

  • Luo C, He X, Chen H, Ou S, Gao M (2010) Analysis of diversity and relationships among mango cultivars using Start Codon Targeted (SCoT) markers. Biochem Syst Ecol 38(6):1176–1184

    CAS  Google Scholar 

  • Maghsoodi M, Sheidai M, Koohdar F (2018) Population genetic study in Juglans regia L. (Persian walnut) and its taxonomic status within the genus Juglans L. Phytotaxa 376(4):154–166

    Google Scholar 

  • Mahmoodi R, Rahmani F, Rezaee R (2013) Genetic diversity among Juglans regia L. genotypes assessed by morphological traits and microsatellite markers. Span J Agric Res 11(2):431–437

    Google Scholar 

  • Mantel N (1967) The detection of disease clustering and a generalizes regression approach. Cancer Res 27:209–220

    CAS  PubMed  Google Scholar 

  • McGranahan GH, Leslie C (1990) Walnuts (Juglans). Acta Hortic 290:905–951

    Google Scholar 

  • McGranahan GH, Charles A, Leslie CA, Philips HA, Dandaker A (1998) Walnut propagation. In: Romos D (ed) Walnut production manual. Univ of California, DANR Publ, Davis, pp 71–83

    Google Scholar 

  • Mulpuri S, Muddanuru T, Francis G (2013) Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker. Plant Sci 207:117–127

    CAS  PubMed  Google Scholar 

  • Nicese FP, Hormaza JI, Mcgranahan GH (1998) Molecular characterization and genetic relatedness among walnut (Juglans regia L.) genotypes based on RAPD markers. Euphytica 101:199–206

    CAS  Google Scholar 

  • Ninot A, Aletà N (2003) Identification and genetic relationship of Persian walnut genotypes using isozyme markers. J Am Pomol Soc 57:106–114

    Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Google Scholar 

  • Pereira JA, Oliveira I, Sousa A, Ferreira IC, Bento A, Estevinho L (2008) Bioactive properties and chemical composition of six walnut (Juglans regia L.) cultivars. Food Chem Toxicol 46:2103–2111

    CAS  PubMed  Google Scholar 

  • Poczai P, Varga I, Laos M, Cseh A, Bell N, Valkonen HP, Hyvönen J (2013) Advances in plant gene-targeted and functional markers: a review. Plant Methods 9(1):6

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pollegioni P, Woeste KE, Olimpieri I, Marandola D, Cannata F, Malvolti ME (2010) Long-term human impacts on genetic structure of Italian walnut inferred by SSR markers. Tree Genet Genomes 7(4):707–723

    Google Scholar 

  • Pollegioni P, Woeste KE, Chiocchini F, Olimpieri I, Tortolano V, Clark J, Hemery GH, Mapelli S, Malvolti ME (2014) Landscape genetics of Persian walnut (Juglans regia L.) across its Asian range. Tree Genet Genomes 10:1027–1043

    Google Scholar 

  • Rahimi M, Nazari L, Kordrostami M, Safari P (2018) SCoT marker diversity among Iranian Plantago ecotypes and their possible association with agronomic traits. Sci Hortic 233:302–309

    CAS  Google Scholar 

  • Rezaei RGH, Hassani GH, Hassani D, Vahdati K (2008) Morphobiological characteristics of some newly selected walnut genotypes from seedling collection of Kahriz–Orumia. J Hortic Sci 9(3):205–214

    Google Scholar 

  • Roor W, Konard H, Mamadjanov D, Geburek T (2017) Population differentiation in common walnut (Juglans regia L.) across major parts of Its native range—insights from molecular and morphometric data. Heredity 108:391–404

    Google Scholar 

  • Ros E, Mataix J (2006) Fatty acid composition of nuts–implications for cardiovascular health. Br J Nutr 96:S29–S35

    CAS  PubMed  Google Scholar 

  • Ruiz-Garcia L, Lopez-Ortega G, Denia AF, Frutos Tomas D (2011) Identification of a walnut (Juglans regia L.) germplasm collection and evaluation of their genetic variability by microsatellite markers. Span J Agric Res 9:179–192

    Google Scholar 

  • Saboori S, Noormohammadi Z, Sheidai M, Marashi SS (2019) SCoT molecular marker and genetic fingerprinting of data palm (Phoenix dactylifera L.) cultivars. Genet Resour Crop Evel 1:1–10

    Google Scholar 

  • Solar A, Smole J, Stampar F, Virscekmarn M (1994) Characterization of isozyme variation in walnut (Juglans regia L.). Euphytica 77:105–112

    CAS  Google Scholar 

  • Tiwari G, Singh R, Singh N, Choudhury DR, Paliwal R, Kumar A, Gupta V (2016) Study of arbitrarily amplified (RAPD and ISSR) and gene targeted (SCoT and CBDP) markers for genetic diversity and population structure in Kalmegh [Andrographis paniculata (Burm. f.) Nees]. Ind Crops Prod 86:1–11

    CAS  Google Scholar 

  • Weising K, Nybom H, Wolff K, Kahl G (2005) DNA fingerprinting in plants. Principles, methods, and applications. CRC Press, Boca Rayton, p 472

    Google Scholar 

  • Woodworth RH (1930) Meiosis of micro-sporogenesis in the Juglandaceae. Am J Bot 17:863–869

    Google Scholar 

  • Yeh FC, Yang RC, Boyle T (1999) POPGENE. Microsoft windows-based freeware for population genetic analysis. Release 1.31. Edmonton, University of Alberta

  • Ebrahimi A, Zarei, A, Lawson S, Woeste KE (2016) Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African and Asian countries using SSR markers.Tree Gent Genomes 12: 114

  • Zeneli G, Kola H, Dida M (2005) Phenotypic variation innative walnut populations of Northern Albania. Sci Hortic 105(1):91–100

    Google Scholar 

  • Zeng B, Zhang Y, Huang L, Jiang X, Luo D, Yin G (2014) Genetic diversity of orchardgrass (Dactylis glomerata L.) germplasms with resistance to rust diseases revealed by Start Codon Targeted (SCoT) markers. Biochem Syst Ecol 54:96–102

    CAS  Google Scholar 

Download references

Acknowledgements

We would like to thank Mr. Fahimi from Shahmirzad Agro-Industry Company, Dr. Mahmoodi from Department of Horticulture, Seed and Plant Improvement Institute in Karaj for assistance in collection of the Persian walnut populations.

Author information

Authors and Affiliations

  1. Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran

    Melika Tabasi, Masoud Sheidai & Fahimeh Koohdar

  2. Temperate Fruits Research Center, Horticultural Science Research Institute, Agricultural Research, Education and Extension Organizations, Karaj, Iran

    Darab Hassani

Authors
  1. Melika Tabasi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Masoud Sheidai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Darab Hassani
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Fahimeh Koohdar
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Masoud Sheidai.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tabasi, M., Sheidai, M., Hassani, D. et al. DNA fingerprinting and genetic diversity analysis with SCoT markers of Persian walnut populations (Juglans regia L.) in Iran. Genet Resour Crop Evol 67, 1437–1447 (2020). https://doi.org/10.1007/s10722-020-00914-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-020-00914-7

Keywords

Search

Navigation