Genetic variability in Rubus ellipticus collections assessed by morphological traits and EST-SSR markers


Rubus ellipticus Smith. commonly known as ‘Yellow Himalayan raspberry’ is an important member of Rosaceae family with high medicinal importance having antioxidant and antibacterial properties. This study was done with the objective of characterizing 21 R. ellipticus collections from different regions of India, based on morphological descriptors and expressed sequence tags-simple sequence repeat (EST-SSR) markers. Broad phenotypic variability among the R. ellipticus collections was detected by using morphological descriptors. The Euclidian distance matrix discriminated two groups, based on morphological characters. A set of 68 EST-SSR markers were developed based on 7777 unigenes generated by us from ‘Kumarhatti-1’ collection of R. ellipticus using assembled pair—end sequences from Illumina NextSeq 500. The ESTs containing simple sequence repeat motifs were extracted using Microsatellite identification tool and primers were designed. Out of 68 EST-SSRs polymorphism was detected using 61 (89.7%) primer pairs, indicating high genetic variability in the R. ellipticus collections. Effective multiplex ratio, marker index and polymorphism information content were 0.43, 0.24 and 0.50, respectively. The unweighted pair group method with arithmetic mean coincided with the bootstrap analysis and two groups were formed, separating the collections Uttrakhand from the other. Morphological descriptors along with EST-SSR markers proved efficient in detecting the levels of genetic variability among the collections maintained in the field. These results can be used as an additional source of exploitation in R. ellipticus breeding programs.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7



Expressed sequence tags-simple sequence repeat


Unweighted pair group method with arithmetic mean


Total soluble solid


Cetyl tri-methyl ammonium bromide


Ethylene diamine tetra acetic acid


Poly vinyl pyrrolidone


Deoxyribonucleic acid


Ribonucleic acid


Sequential agglomerative hierarchical nesting


Polymorphism information content


Effective multiplex ratio


Marker index


  1. Arbeiter AB, Hladnik M, Jakse J, Bandelj D (2017) Identification and validation of novel EST-SSR marker in olives. Sci Agric 74(3):215–225

    CAS  Article  Google Scholar 

  2. Chomczynski P, Mackey K (1995) Short technical report. Modification of the TRIZOL reagent procedure for isolation of RNA from polysaccharide-and proteoglycan-rich sources. Biotechniques 19(6):942–5

    CAS  PubMed  Google Scholar 

  3. Doyle JJ, Doyle JJ (1987) A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem Bull 19:11–15

    Google Scholar 

  4. Hoque M, Rahman L (2007) Estimation of Euclidian distance for different morpho-physilogical characters in some wild and cultivated rice genotypes (Oryza sativa L.). J Biol Sci 1:77–79

    Google Scholar 

  5. Jaccard P (1908) Nouvelles Recherches sur la distribution florale. Bulletin de la Societe Vaudoise des Sciences Naturelles 44:223–270

    Google Scholar 

  6. Jaliseh SA, Mehregan I, Tarang A, Nejadsattari T (2015) Genetic diversity of Rubus L. (Rosaceae) in the Northern Iran. Bull Georgian Natl Acad Sci 9:387–394

    Google Scholar 

  7. Jenning DL (1988) Raspberry and blackberries: their breeding, disease and growth. Academic Press, London

    Google Scholar 

  8. Jian ZH, Liu XS, Hu JB, Chen YH, Feng JC (2012) Mining microsatellite markers from public expressed sequence tag sequences for genetic diversity analysis in pomegranate. J Genet 9:353–358

    Article  Google Scholar 

  9. Jung S, Abbott A, Jesudurai C, Tomkins J, Main D (2005) Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Funct Integr Genom 5:136–143

    CAS  Article  Google Scholar 

  10. Kim SH, Chung HG, Han J (2008) Breeding of Korean black raspberry (Rubus coreanus Miq.) for high productivity in Korea. Acta Hortic 777:141–146

    Article  Google Scholar 

  11. Lee KJ, Lee GA, Kang HK, Lee JR, Raveendar S, Shin MJ et al (2016) Genetic diversity and population structure of Rubus accessions using simple sequence repeat markers. Plant Breed Biotechnol 4:345–351

    Article  Google Scholar 

  12. Liu SR, Li WY, Long D, Hu CG, Zhang JZ (2013) Development and characterization of genomic and expressed SSRs in citrus by genome-wide analysis. PLoS ONE 8:e75149

    CAS  Article  Google Scholar 

  13. Long W, Hu M, Gao J, Sun L, Zhang J, Pu H (2019) Identification and application of markers closely linked to the restorer gene (Rfm) in rapeseed (Brassica napus L.). Breed Sci 69:316–322

    CAS  Article  Google Scholar 

  14. Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants salient statistical tools and considerations. Crop Sci 43:1235–1248

    Article  Google Scholar 

  15. Moore PP, Veazie PP, Weber CA, Howard L (2008) Environmental effect on antioxidant content of ten raspberry cultivars. Acta Hortic 777:493–504

    Google Scholar 

  16. Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EH, Allan AC, Beuning LL et al (2006) Analysis of expressed sequence tags from apple. Plant Physiol 141(1):147–166

    Article  Google Scholar 

  17. Palmieri DA, Novelli VM, Bastianel M, Cristofani YM, Astua MG, Carlos EF et al (2007) Frequency and distribution of microsatellites from ESTs of citrus. Genet Mol Biol 30(3):1009–1018

    CAS  Article  Google Scholar 

  18. Ranganna S (1986) Handbook of analysis and quality control for fruit and vegetable products, 2nd edn. Tata McGraw Hill, New Delhi

    Google Scholar 

  19. Rohlf FJ (2000) NTSYSpc numerical taxonomy and multivariate analysis version 2.0.h. Applied Biostatics Inc, New York

    Google Scholar 

  20. Saklani S, Chandra S, Badoni PP, Dogra S (2012) Antimicrobial activity, nutritional profile and phytochemical screening of wild edible fruit of Rubus ellipticus. Int J Med Aromat Plants 2(2):269–274

    Google Scholar 

  21. Samriti, Kaur R, Shilpa, Malhotra EV, Poonam, Thakur D, Kumar K (2017) Assessment of genetic diversity in Rubus ellipticus (Smith) using molecular markers. Proc Indian Natl Sci Acad 83(3):669–679

    Google Scholar 

  22. Seco DG, Zhang Y, Manero FJG, Martin C, Solano BR (2015) RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit. BMC Genom.

    Article  Google Scholar 

  23. Shabir G, Aslam K, Khan AR, Shahid M, Manzoor H, Noreen S, Khan MA, Baber M, Sabar M, Shah SM, Arif M (2017) Rice molecular markers and genetic mapping: current status and prospects. J Integr Agric 16(9):1879–1891

    CAS  Article  Google Scholar 

  24. Sharma S, Sharma A (2018) Molecular markers based plant breeding. Adv Res 16(1):1–15

    Article  Google Scholar 

  25. Sharma S, Dobhal S, Thakur S (2018) Analysis of genetic diversity in parents and hybrids of Populus deltoides Bartr. using microsatellite markers. Appl Biol Res 20(3):262–270

    Article  Google Scholar 

  26. Sharma S, Kaur R, Solanke AKU, Dubey H, Tiwari S, Kumar K (2019) Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers. 3 Biotech.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Sharma S, Dobbal S, Kumar R, Thakur S (2019) Morphological, physiological and molecular analysis of Line×Tester in Populus deltoides Bartr. Indian J Plant Physiol.

    Article  Google Scholar 

  28. Singh D, Kumar K, Sharma VK, Singh M (2009) Expression of genetic variability and character association in raspberry (Rubus ellipticus Smith) growing wild in North-Western Himalayas. J Hortic Sci 4(1):28–31

    Google Scholar 

  29. Singh TJ, Gupta T, Sharma S (2019) Development and purity identification of hybrids by using molecular marker in wild pomegranate (Punica granatum L.). Sci Hortic 247:436–448

    CAS  Article  Google Scholar 

  30. Smith JS, Chin EC, Shu H, Smith OS, Wall SJ, Senior ML et al (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisions with data from RFLPs and pedigree. Theor Appl Genet 95:163–173

    CAS  Article  Google Scholar 

  31. Sneath PHA, Sokal RR (1973) Numerical taxonomy. W H Freeman and Company, San Francisco, CA

    Google Scholar 

  32. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    CAS  Article  Google Scholar 

  33. Trivedi AK, Verma SK, Tyagi RK (2016) Variability in morpho-physiological traits and antioxidant potential of Rubus species in Central Himalayan Region. Ind Crops Prod 82:1–8

    CAS  Article  Google Scholar 

  34. Vaidya E (2014) Studies on QTL analysis for growth characteristics in apple Malus x domestica Borkh. Ph.D. thesis, Dr Y S Parmar University of Horticulture and Forestry, Nauni, Solan, India

  35. Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A (2007) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173:638–649

    CAS  Article  Google Scholar 

  36. You FM, Wanjugi H, Huo N, Lazo GR, Luo MC, Anderson OD, Dvorak J, Gu YQ (2010) RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development. Nucleic Acids Res 38:313–320

    Article  Google Scholar 

  37. Zhao Y, Williams R, Prakash CS, He G (2012) Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.). BMC Plant Biol.

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information




All authors have participated in (a) conception and design, or analysis and interpretation of the data; (b) drafting the article or revising it critically for important intellectual content; and (c) approval of the final version.

Corresponding author

Correspondence to Samriti Sharma.

Ethics declarations

Conflict of interest

I certify that there is no actual or potential conflict of interest in relation to this article.

Additional information

Publisher's Note

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

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 189 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Sharma, S., Kaur, R., Kumar, K. et al. Genetic variability in Rubus ellipticus collections assessed by morphological traits and EST-SSR markers. J. Plant Biochem. Biotechnol. 30, 37–55 (2021).

Download citation


  • Rubus ellipticus
  • Molecular markers
  • EST-SSRs
  • Morphological traits
  • Genetic diversity