Skip to main content

Advertisement

Springer Nature Link
Log in

Genetic Diversity and Selection of Suitable Molecular Markers for Characterization of Indigenous Zizyphus Germplasm

Genetische Diversität und Auswahl geeigneter Molekularmarker für die Bestimmung des genetischen Materials einheimischer Jujube-Genotypen

  • Original Article
  • Published:
Erwerbs-Obstbau Aims and scope Submit manuscript

Abstract

Indian jujube (Zizyphus mauritiana Lamk), belonging to family Rhamnaceae, is an underutilized fruit crop which can grow under harsh environments. It is becoming an important fruit crop due to its wide adaptation, early age bearing, easy management, rich nutrition and numerous uses. Evaluation of genetic diversity through molecular markers is very poor in this fruit crop. DNA finger printing of various genotypes through molecular markers is very essential for crop improvement programs and genetic studies. In the present study, genetic relationship among 17 genotypes of Z. mauritiana Lamk and one accession of Z. rotundifolia Lamk was studied using ISSR markers. A total of 191 scorable bands were identified with 20 ISSRs and out of these 162 fragments were polymorphic (84.82%) and remaining 29 as monomorphic (15.18%). Genetic similarity ranged from 37 to 76% and suggested that 18 Zizyphus genotypes used in this study had broad genetic base and were considered as divergent. Cluster investigation based on UPGMA method grouped these 18 genotypes into 3 different clusters (cluster 1, 2 and 3). Cluster 3 was the largest cluster with 3 subclusters (3a, 3b, 3c) and comprised of 13 genotypes. The cultivar ‘Suffon’ remained independent during cluster formation, indicating maximum genetic diversity. The primer UBC-847 gave the maximum PIC (0.433) and Dj (0.755). Therefore, it is considered more efficient primer for estimation of genetic diversity in Zizyphus genotypes. In the present study, phenotypically similar genotypes were successfully distinguished with ISSRs, indicating that these have potential to differentiate the genotypes on basis of their genetic make-up.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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
Fig. 4

Similar content being viewed by others

Explore related subjects

Discover the latest articles and news from researchers in related subjects, suggested using machine learning.

References

  • Ahmed M, Anjum MA, Rabbani MA, Hassan L (2009) Characterization of indigenous Pyrus germplasm of Azad Jammu and Kashmir revealed by SDS-PAGE analysis. Afr J Biotechnol 8:6442–6452

    Article  CAS  Google Scholar 

  • Akinnifesi FK, Kwesiga FK, Mhango J, Chilanga T, Mkonda A, Kadu CAC, Kadzere I, Mithofer D, Saka JDK, Sileshi G, Ramadhani T, Dhliwayo P (2006) Towards the development of miombo fruit trees as commercial tree crops in Southern Africa. For Trees Live 16:103–121

    Article  Google Scholar 

  • Alcaraz ML, Hormaza JI (2007) Molecular characterization and genetic diversity in an avocado collection of cultivars and local Spanish genotypes using SSRs. Hereditas 144:244–253

    Article  CAS  Google Scholar 

  • Ali SA, Bonkoungou E, Bowe C, Dekok C, Godara A, Williams JT (2006) Ber and other jujubes. In: Williams JT, Smith RW, Haq N, Dunsigaer Z (eds) Fruits for the future. Southampton Centre for Underutilized Crops, Southampton, pp 119–129

    Google Scholar 

  • Anderson JT, Wilson SM, Datar KV, Swanson MS (1993) A yeast nuclear polyadenylated RNA-binding protein essential for cell viability. Mol Cell Biol 13:2730–2741

    Article  CAS  Google Scholar 

  • Anonymous (2015) Fruit, vegetables and condiments statistics of Pakistan. Government of Pakistan 2014–2015. Ministry of National Food Security and Research, Economic Wing, Islamabad, pp 1–6

    Google Scholar 

  • Ashraf J, Malik W, Iqbal MZ, Khan AA, Qayyum A, Noor E, Abid MA, Cheema HMN, Ahmad MQ (2016) Comparative analysis of genetic diversity among Bt cotton genotypes using EST-SSR, ISSR and morphological markers. J Agr Sci Tech 18:517–531

    Google Scholar 

  • Ballox F, Moulin LN (2002) The estimate of population differentiation with microsatellite markers. Mol Ecol 11:155–165

    Article  Google Scholar 

  • Belaj A, Satovic Z, Rallo L, Trujillo I (2002) Genetic diversity and relationships in olive (Olea europaea L.) germplasm collections as determined by randomly amplified polymorphic DNA. Theor Appl Genet 105:638–644

    Article  CAS  Google Scholar 

  • Biswas MK, Xu Q, Deng X (2010) Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus species. Sci Hortic 124:254–261

    Article  CAS  Google Scholar 

  • Chakravarthi BK, Naravaneni R (2006) SSR markers based DNA fingerprinting and diversity study in rice (Oryza sativa L.). Afr J Biotechnol 5:684–688

    CAS  Google Scholar 

  • Devanshi SAK, Sharma P, Singh B, Singh R, Singh NK (2007) Molecular profiling and genetic relationship among ber (Zizyphus sp.) genotypes using RAPD markers. Ind J Genet Plant Breed 67:121–127

    CAS  Google Scholar 

  • Dongre A, Parkhi V, Gahukar S (2004) Characterization of cotton (G. hirsutum) germplasm by ISSR, RAPD markers and agronomic value. Ind J Biotechnol 3:388–393

    CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus (Madison) 12:13–15

    Google Scholar 

  • Galvan MZ, Bornet B, Balatti PA, Branchard M (2003) Inter simple sequence repeat (ISSR) markers as a tool for the assessment of both genetic diversity and gene pool origin in common bean (Phaseolus vulgaris L.). Euphytica 132(3):297–301

    Article  CAS  Google Scholar 

  • Ivanova AS (1982) Comparative characteristics of the quality composition of some stone fruits and subtropical fruit crops [In Russian]. Bull Gosudarst Nikitsk Bot Sada 47:93–98

    Google Scholar 

  • Joshi SP, Ranjekar PK, Gupta VS (1999) Molecular markers in plant genome analysis. Curr Sci 77:230–240

    CAS  Google Scholar 

  • Kaundun S, Park Y (2002) Genetic structure of six Korean tea populations as revealed by RAPD-PCR Markers. Plant Genet Resour 42:594–601

    CAS  Google Scholar 

  • Khorshidi S, Davarynejad G, Samiei L, Moghaddam M (2017) Study of genetic diversity of pear genotypes and cultivars (Pyrus communis L.) using inter-simple sequence repeat markers (ISSR). Erwerbs-Obstbau 59:301–308

    Article  Google Scholar 

  • Mitra C, Kharb P, Uppal S, Jain S (2011) Genetic diversity analysis in date palm (Phoenix dactylifera L): a comparative assessment using ISSR and RAPD marker assays. J Hortic Sci Biotechnol 86:398–402

    Article  CAS  Google Scholar 

  • Nagaraju J, Kathirvel M, Kumar R, Siddiq EA, Hasnain SE (2002) Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proc Nat Acad Sci USA 99:5836–5841

    Article  CAS  Google Scholar 

  • Ngwa AT, Mafeni JM (2000) Feed selection and dietary preferences of forage by small ruminants grazing natural pastures in the Sahelian zone of Cameroon. Anim Feed Sci Technol 88:253–266

    Article  Google Scholar 

  • Obeed RS, Harhash MM, Mawgood AL (2008) Fruit properties and genetic diversity of five ber (Ziziphus mauritiana Lamk) cultivars. Pak J Biol Sci 11:888–893

    Article  CAS  Google Scholar 

  • Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112

    Article  CAS  Google Scholar 

  • Riek JD, Calsyn E, Everaert I, Bockstaele EV, Loose MD (2001) AFLP based alternatives for the assessment of distinctness, uniformity and stability of sugar beet varieties. Theor Appl Genet 103:1254–1265

    Article  Google Scholar 

  • Rohlf FJ (2002) NTSYS-pc numerical taxonomy and multivariate analysis system (Version 2.0). Exterer Software, Setauket, New York

    Google Scholar 

  • Saini M, Singh S, Hussain Z, Sikka VK (2010) RAPD analysis in mung bean [Vigna radiate (L.)Wilczek.] II: A comparison of efficiency parameters of RAPD primers. Ind J Biotechnol 9:276–282

    CAS  Google Scholar 

  • Sharma SN, Kumar V, Mathur S (2009) Comparative analysis of RAPD and ISSR markers for characterization of sesame (Sesamum indicum L.) genotypes. J Plant Biochem Biotechnol 18:37–43

    Article  CAS  Google Scholar 

  • Singh AK, Sharma RK, Singh NK, Bansal KC, Koundal KR (2006) Genetic diversity in ber (Ziziphus spp.) revealed by AFLP markers. J Hortic Sci Biotechnol 81:205–210

    Article  CAS  Google Scholar 

  • Singh AK, Singh R, Singh NK (2009) Comparative evaluation of genetic relationships among ber (Ziziphus sp.) genotypes using RAPD and ISSR markers. Ind J Genet 69:50–57

    CAS  Google Scholar 

  • Teng Y, Tanabe K, Tamura F, Itai A (2002) Genetic relationships of Pyrus species and cultivars native to East Asia revealed by randomly amplified polymorphic DNA markers. J Am Soc Hortic Sci 127:262–270

    Article  CAS  Google Scholar 

  • Tessier C, David J, This P, Boursiquot JM, Charrier A (1999) Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theor Appl Genet 98:171–177

    Article  CAS  Google Scholar 

  • Thottappilly G, Magonouna HD, Omitogun OG (2000) The use of DNA markers for rapid improvement of crops in Africa. Afr Crop Sci 8:99–108

    Google Scholar 

  • Wang SY, Tian CY, Ye YZ, Yeng QS, Wang YZ, Zhang QL, Fan LM (1992) The wild fruit germplasm resources of Hanan Province. J Fruit Sci 19:239–242

    Google Scholar 

  • Wunsch A, Hormaza JI (2007) Characterization of variability and genetic similarity of European pear using microsatellite loci developed in apple. Sci Hortic 173:37–43

    Article  Google Scholar 

  • Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183

    Article  CAS  Google Scholar 

Download references

Funding

Funding

The authors are highly grateful to the Horticulturist, Horticulture Research Station, Bahawalpur for providing the plant material, and Bahauddin Zakariya University, Multan for financial support to conduct the study.

Author information

Authors and Affiliations

  1. Department of Horticulture, Bahauddin Zakariya University, 60800, Multan, Pakistan

    Riaz Ahmad & Muhammad Akbar Anjum

  2. Genomics Lab., Department of Plant Breeding & Genetics, Bahauddin Zakariya University, 60800, Multan, Pakistan

    Waqas Malik

Authors
  1. Riaz Ahmad
    View author publications

    Search author on:PubMed Google Scholar

  2. Waqas Malik
    View author publications

    Search author on:PubMed Google Scholar

  3. Muhammad Akbar Anjum
    View author publications

    Search author on:PubMed Google Scholar

Corresponding author

Correspondence to Muhammad Akbar Anjum.

Ethics declarations

Conflict of interest

R. Ahmad, W. Malik and M.A. Anjum declare that they have no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ahmad, R., Malik, W. & Anjum, M.A. Genetic Diversity and Selection of Suitable Molecular Markers for Characterization of Indigenous Zizyphus Germplasm. Erwerbs-Obstbau 61, 345–353 (2019). https://doi.org/10.1007/s10341-019-00438-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10341-019-00438-0

Keywords

Schlüsselwörter