Skip to main content

Advertisement

SpringerLink
Log in

Groupwise sampling: a strategy to sample core entries from RAPD marker data with application to mulberry

  • Original Paper
  • Published:
Trees Aims and scope Submit manuscript

Abstract

Key message

A strategy for effective utilization of RAPD marker data for sampling diverse entries was suggested and utilized for the development of mulberry core collection.

Abstract

Mulberry (Morus spp.) is a perennial tree cultivated mainly for its foliage in sericulture industry and also known for its edible fruits, fodder, and valued timber. In recent years, mulberry cultivation is confronted with several abiotic and biotic stresses due to inimical climatic factors and this has necessitated the genetic improvement of the crop. Core collection is an efficient way of harnessing the trait variation and novel genes available in a natural gene pool for the development of improved elite lines. In this study, we analyzed 850 mulberry accessions assembled from 23 countries with separate sets of polymorphic RAPD markers along with a limited number of ISSR, SSR, and phenotypic markers. A total of 75 accessions were duplicated in 20 clusters among five natural groups. The limitations of the RAPD marker system like problem in cross gel comparison were tackled by adopting a novel “Groupwise sampling” approach. A mulberry core collection with 100 diverse entries was selected using maximization method implemented in MSTRAT software. The mean Dice dissimilarity coefficient computed from marker data was 0.308 among core entries. Indigenous and exotic entries were not discriminated in cluster and principal component analysis supporting the spread of mulberry far from the place of origin. Accessions belonging to two wild mulberry species from Andaman Islands and Himalayan region formed separate clusters indicating the geographical, reproductive, and taxonomic distinction. The identified core collection will be available for researchers for intensive mining of desirable alleles in mulberry improvement as well as in genome resequencing program.

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

Similar content being viewed by others

References

  • Balakrishna R, Sarakar A, Kumar JS (2002) Plasticity of some important traits in mulberry grown under shade and open condition. In: Dandin SB, Gupta VP (eds) Advances in Indian Sericulture Research, Proceedings of the national conference on strategies for sericulture research and development, Central Sericultural Research and Training Institute, Mysore, India, pp 4–7, Nov 16–18, 2000

  • Bouchez A, Causse M, Gallais A, Charcosset A (2002) Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines. Genetics 162(4):1945–1959

    CAS  PubMed Central  PubMed  Google Scholar 

  • Concibido V, la Vallee B, Mclaird P, Pineda N, Meyer J, Hummel L, Yang J, Wu K, Delannay X (2003) Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars. Theor Appl Genet 106(4):575–582

    CAS  PubMed  Google Scholar 

  • Das BC, Krishnaswami S (1965) Some observations on interspecific hybridization in mulberry. Indian J Sericult 4:1–8

    Google Scholar 

  • Dulloo ME, Thormann I, Fiorino E, de Felice S, Rao VR, Snook L (2013) Trends in research using plant genetic resources from germplasm collections: from 1996 to 2006. Crop Sci 53(4):1217–1227

    Article  Google Scholar 

  • Franco J, Crossa J, Warburton ML, Taba S (2006) Sampling strategies for conserving maize diversity when forming core subsets using genetic markers. Crop Sci 42(2):854–864

    Article  Google Scholar 

  • Frankel OH (1984) Genetic perspectives of germplasm conservation. In: Arber W, Llimensee K, Peacock WJ, Starlinger P (eds) Genetic manipulation: impact on man and society. Cambridge University Press, Cambridge, pp 170–191

    Google Scholar 

  • Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M, Heuer S (2012) The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488(7412):535–539

    Article  CAS  PubMed  Google Scholar 

  • Gouesnard B, Bataillon TM, Decoux G, Rozale C, Schoen DJ, David JL (2001) MSTRAT: an algorithm for building germplasm core collections by maximizing allelic or phenotypic richness. J Hered 92:93–94

    Article  CAS  PubMed  Google Scholar 

  • Guruprasad (2011) Development of core collection of mulberry (Morus spp.) germplasm by molecular marker aided analysis. Ph.D. Thesis. University of Mysore

  • He N, Zhang C, Qi X, Zhao S, Tao Y, Yang G et al. (2013) Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun doi:10.1038/ncomms3445

  • Hu J, Zhu J, Xu HM (2000) Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor Appl Genet 101:264–268

    Article  CAS  Google Scholar 

  • Krishnan RR, Naik VG, Ramesh SR, Qadri SMH (2013) Microsatellite marker analysis reveals the events of the introduction and spread of cultivated mulberry in the Indian subcontinent. Plant Genet Resour. doi:10.1017/S1479262113000415

    Google Scholar 

  • Le S, Josse J, Husson F (2008) FactoMineR: an R package for multivariate analysis. J Stat Softw 25(1):1–18

    Google Scholar 

  • Meunier JR, Grimont PAD (1993) Factors affecting reproducibility of random amplified polymorphic DNA fingerprinting. Res Microbiol 144(5):373–379

    Article  CAS  PubMed  Google Scholar 

  • Naik VG, Dandin SB (2005) Molecular characterization of some improved and promising mulberry varieties (Morus spp.) of India by RAPD and ISSR markers. Indian J Sericult 44(1):59–68

    Google Scholar 

  • Naik VG, Dandin SB (2006) Identification of duplicate collections in the mulberry (Morus spp.) germplasm using RAPD analysis. Indian J Genet 66(4):287–292

    CAS  Google Scholar 

  • Oakey HJ, Gibson LF, George AM (1998) Co-migration of RAPD-PCR amplicons from Aeromonas hydrophila. FEMS Microbiol Lett 164(1):35–38

    Article  CAS  PubMed  Google Scholar 

  • Odong TL, Jansen J, van Eeuwijk FA, van Hintum TJL (2013) Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation. Theor Appl Genet 126(2):289–305

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Paraguison RC, Faylon MPP, Flores EB, Cruz LC (2012) Improved RAPD-PCR for discriminating breeds of water buffalo. Biochem Genet 50(7):579–584

    Article  CAS  PubMed  Google Scholar 

  • Penner GA, Bush A, Wise R, Kim W, Domier L, Kasha K et al (1993) Reproducibility of random amplified polymorphic DNA (RAPD) analysis among laboratories. Genome Res 2(4):341–345

    Article  CAS  Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin.cirad.fr/darwin. Accessed 14 March 2013

  • Ravindran S, Tikader A, Naik VG, Rao AA, Mukherjee P (1998) Distribution of mulberry species in India and its utilization. Indian J Plant Genet Resour 12(2):163–168

    Google Scholar 

  • Sarkar A, Kumar JS, Datta RK (2000) Gradual improvement of mulberry varieties under irrigated condition in South India and optimal programme for varietal selection in the tropics. Sericologia 40:449–461

    Google Scholar 

  • Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327(5967):818–822

    Article  CAS  PubMed  Google Scholar 

  • Thangavelu K, Mukherjee P, Tikader A, Ravindran S, Goel AK, Ananda Rao A, Naik VG, Shekar S (1997) Catalogue on mulberry (Morus spp.) germplasm, vol I. Central Sericultural Germplasm Resources Centre, Hosur

    Google Scholar 

  • Upadhyaya HD, Ravishankar CR, Narasimhudu Y, Sarma NDRK, Singh SK, Varshney RK et al (2011) Identification of trait-specific germplasm and developing a mini core collection for efficient use of foxtail millet genetic resources in crop improvement. Field Crops Res 124(3):459–467

    Article  Google Scholar 

  • Vijayan K, Srivatsava PP, Nair CV, Awasthi AK, Tikader A, Sreenivasa B, Urs SR (2006) Molecular characterization and identification of markers associated with yield traits in mulberry using ISSR markers. Plant Breeding 125(3):298–301

    Article  CAS  Google Scholar 

  • Wickham H (2009) ggplot2: elegant graphics for data analysis. Springer, New York

    Book  Google Scholar 

  • Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18(22):6531–6535

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhang DP, Ghislain M, Huaman Z, Rodrguez F, Cervantes JC (1996) Identifying duplicates in sweetpotato germplasm using RAPD. International potato center program report 1995–1996. International Potato Center, Lima, pp 90–96

    Google Scholar 

Download references

Acknowledgments

Authors thank the two anonymous reviewers for their critical comments and suggestions, which has helped us to improve the quality of the manuscript. VGN acknowledges the financial support received from the Central Silk Board, Ministry of Textiles, Government of India, Bangalore, India to undertake this research work in the project (Code #PIB-3370; Sanction Order No. CSB/RTI/PMCE/245(3)/2006-07 dated 24.07.2006). Guruprasad received Senior Research Fellowship under the project grant. The authors are grateful to the Director, Central Sericultural Germplasm Resource Center, Hosur, Tamil Nadu, India for providing mulberry germplasm leaf samples to carry out this work.

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Host Plant Improvement (Molecular Biology Laboratory), Central Sericultural Research and Training Institute, Srirampura, Manandavadi Road, Mysore, 570008, Karnataka, India

    Guruprasad, R. Ramesh Krishnan & V. Girish Naik

  2. University of Horticultural Sciences, Sector No. 60, Bagalkot, 587102, Navanagar, India

    S. B. Dandin

Authors
  1. Guruprasad
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. Ramesh Krishnan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. B. Dandin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. V. Girish Naik
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to V. Girish Naik.

Additional information

Communicated by R. Alia.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Guruprasad, Ramesh Krishnan, R., Dandin, S.B. et al. Groupwise sampling: a strategy to sample core entries from RAPD marker data with application to mulberry. Trees 28, 723–731 (2014). https://doi.org/10.1007/s00468-014-0984-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00468-014-0984-3

Keywords

Search

Navigation