Skip to main content
SpringerLink
Log in

Morphological characterization and analysis of genetic diversity and population structure in Citrus × jambhiri Lush. using SSR markers

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

Abstract

Rough lemon (Citrus × jambhiri Lush.) is one of the important species largely used as a rootstock for commercial plantations of Citrus across the world. In the present study, thirty-eight accessions of C. jambhiri were characterized using morphological and SSR markers for diversity analysis and population structure studies. Morphological characterization of 27 qualitative and 14 quantitative characters indicated the existence of moderate to sufficiently high amount of variability as revealed from the pair-wise similarity analysis value of 0.36. Molecular diversity analysis using 17 SSR primers detected 85.29% polymorphism indicating existence of moderately high amount of variability between the accessions in terms of studied loci. A total of 60 bands were generated, of which all the 60 were polymorphic (100%). The total number of alleles produced varied from 1 to 5 alleles with an average of 3.52 alleles per locus. Although the correlation between the morphological and molecular data was low in the analysed accessions of C. jambhiri, both methods allowed the clustering of accessions based on the analysed traits. Population genetic analysis by SSR markers revealed that accessions collected from North Eastern India were most diverse in terms of genetic diversity parameters and genetic distance analysis of populations showed that the accessions from North East and Himachal Pradesh were most similar genetically while population collected from Himachal Pradesh and Karnataka were the most distinct genetically. Structure analysis of different populations revealed that there is no genetic differentiation happening between the populations.

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
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Akhter S, Ferdous MJ, Hossain MR, Rabbani G (2009) Molecular characterization of Jamir (Citrus jambhiri) accessions of Bangladesh through PCR based RAPD markers. J Agrfor Environ 3(1):21–24

    Google Scholar 

  • Barbhuiya AR, Khan ML, Dayanandan S (2016) Genetic structure and diversity of natural and domesticated populations of Citrus medica L. in the Eastern Himalayan region of Northeast India. Ecol Evol 6(12):3898–3911

    Article  PubMed  PubMed Central  Google Scholar 

  • Barkley NA, Roose ML, Krueger RR, Federici CT (2006) Assessing genetic diversity and population structure in a Citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112:1519–1531

    Article  CAS  PubMed  Google Scholar 

  • Chen H, Hong C, Liangliang H, Lixia W, Suhua W, Ming LW, Cheng X (2017) Genetic diversity and a population structure analysis of accessions in the Chinese cowpea [Vigna unguiculata (L.) Walp.] germplasm collection. Crop J 5(5):363–372

    Article  Google Scholar 

  • Doyle JJ, Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12:13–15

    Google Scholar 

  • Gaikwad KA, Patil SR, Nagre PK, Potdukhe NR (2018) Morphological characterization of citrus rootstock genotypes. Int J Chem Sci 6(2):516–529

    Google Scholar 

  • Jena SS, Kumar S, Nair NK (2009) Molecular phylogeny in Indian Citrus L. (Rutaceae) inferred through PCR-RFLP and trnL-trnF sequence data of chloroplast DNA. Sci Hortic 119:403–416

    Article  CAS  Google Scholar 

  • Lamine M, Mliki A (2015) Elucidating genetic diversity among sour orange rootstocks: a comparative study of the efficiency of RAPD and SSR markers. Appl Biochem Biotechnol 175(6):2996–3013

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Maya MA, Rabbani MG, Mahboob MG, Matsubara Y (2012) Assessment of genetic relationship among 15 citrus fruits using RAPD. Asian J Biotechnol 4(1):30–37

    Article  CAS  Google Scholar 

  • Mouei RE, Choumane W, Dway F (2011) Characterization and estimation of genetic diversity in citrus rootstocks. Int J Agric Biol 13(4):571–575

    Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106(949):283–292

    Article  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    CAS  PubMed  PubMed Central  Google Scholar 

  • NHB (2017–18) Fruit production database. National Horticulture Board. New Delhi, India. http://www.nhb.in

  • Paudyal KP, Haq N (2008) Variation of pomelo (Citrus grandis (L.) Osbeck) in Nepal and participatory selection of strains for further improvement. Agrofor Syst 72:195–204

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28(19):2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perrier X, Jacquemoud-Collet J (2006) DARwin software; [cited November 15, 2010]. http://darwin.cirad.fr/

  • Rohlf FJ (2000) NTSYS-pc: numerical taxonomy and multivariate analysis system, ver.2.10e. Exter Ltd, Setauket

    Google Scholar 

  • Scora RW (1975) On the history and Origin of Citrus. Bull Torrey Bot Club 102:369–375

    Article  Google Scholar 

  • Singh IP, Singh S (2006) Citrus monograph. National Research Centre for Citrus, Nagpur, pp 1–96

    Google Scholar 

  • Singh J, Dhaliwal HS, Thakur A, Chhuneja P, Sidhu G, Singh R (2017) Morphological and genetic diversity in citrus genotypes to substantiate rootstock breeding for root rot resistance. Ind J Hortic 74(3):326

    Article  Google Scholar 

  • Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Mitchel SE, Kresorich S, Tiegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theor Appl Genet 95:163–173

    Article  CAS  Google Scholar 

  • Tanaka T (1954) Species problem in Citrus (RevisioAurantiacearum IX). Jpn Soc Promot Sci, Tokyo

    Google Scholar 

  • Uchoi A, Malik SK, Chaudhary R, Kumar S, Rohini MR, Pal D, Ercisli S, Chaudhury R (2016) Inferring phylogenetic relationships of Indian citron (Citrus medica L.) based on rbcL and matK sequences of chloroplast DNA. Biochem Genet 54(3):249–269

    Article  CAS  PubMed  Google Scholar 

  • Webber HJ, Reuther W, Lawton HW (1967) History and development of the citrus industry. In: Reuther W, Webber HJ, Batchelor LD (eds) The citrus industry, history, world distribution, botany, and varieties, vol I. University of California, Division of Agricultural Sciences, Berkeley, pp 1–39

    Google Scholar 

  • Yao D, Myriam H, Mohamed A, Claude L, Xavier V (2007) Evaluation de la diversité morphologique des variétés traditionnelles de sorgho du Nord- ouest du Maroc. Biotechnol Agron Soc Environ 11(1):39–46

    Google Scholar 

  • Zerihun DU, Vashist U, Boora KS (2009) Molecular characterization of citrus cultivars using DNA markers. Int J Biotechnol Biochem 5(3):271–280

    Google Scholar 

  • Zhu YF, Qin GC, Hu J, Wang J, Wang JC, Zhu S (2012) Fingerprinting and variety identification of rice (Oryza sativa L.) based on simple sequence repeat markers. Plant Omics J 5:421–426

    CAS  Google Scholar 

Download references

Acknowledgements

Authors are thankful to Indian Council of Agricultural Research, New Delhi, Director, ICAR-National Bureau of Plant Genetic Resources, New Delhi, Director, ICAR-Indian Institute of Horticultural Research, Banglore for providing the fund and facilities for this research work.

Author information

Authors and Affiliations

  1. Division of Floriculture and Medicinal Crops, ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India

    M. R. Rohini

  2. Division of Fruit Crops, ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India

    M. Sankaran

  3. Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India

    S. Rajkumar & A. Gaikwad

  4. Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute, Kasargode, Kerala, 671124, India

    K. Prakash

  5. Tissue Culture and Cryopreservation Unit, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India

    R. Chaudhury

  6. Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India

    S. K. Malik

Authors
  1. M. R. Rohini
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Sankaran
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. Rajkumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K. Prakash
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. Gaikwad
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. R. Chaudhury
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. S. K. Malik
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to M. R. Rohini.

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

Rohini, M.R., Sankaran, M., Rajkumar, S. et al. Morphological characterization and analysis of genetic diversity and population structure in Citrus × jambhiri Lush. using SSR markers. Genet Resour Crop Evol 67, 1259–1275 (2020). https://doi.org/10.1007/s10722-020-00909-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-020-00909-4

Keywords

Search

Navigation