Skip to main content
SpringerLink
Log in

Genomic-derived microsatellite markers for diversity analysis in Jatropha curcas

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

Abstract

Key message

New set of 1,122 novel genomic-derived microsatellite markers developed, validated and a set of 447 polymorphic SSR identified for Jatropha curcas. The AMOVA showed that 6 % of the total genetic variation exists among the population and 94 % within the populations.

Abstract

Jatropha curcas L., a non-edible, oil-rich crop has attracted global attention as a promising renewable resource for biodiesel production. Limited numbers of validated and characterized markers such as SSRs are available that could be utilized for molecular breeding in Jatropha. To enrich the marker resources, we have employed next-generation 454 sequencing to develop a large number of microsatellite markers from trinucleotide-enriched genomic libraries. A total of 124,279 raw reads were assembled into 2,845 contigs and 22,650 singletons. We designed 1,122 SSR flanking primer pairs and validated them with a panel of seven accessions of J. curcas and one J. integerrima to identify polymorphic SSRs. Out of these 1,122 SSRs, 447 (39.83 %) were found to be polymorphic among J. curcas accessions. A higher transferability of SSRs (76 %) to J. integerrima was noticed. A subset of randomly selected SSRs (41 SSRs) was amplified across 96 accessions of J. curcas, which detected a total of 152 alleles ranging from 2 to 9 with an average of 4.0 ± 1.9 alleles/SSR. The analysis of molecular variance (AMOVA) showed that 6 % of the total genetic variation exists among the population and 94 % within the populations indicated high genetic variation within population. The neighbor-joining (NJ) tree based on Jaccard’s coefficient grouped the 96 accessions into three major clusters. The non-toxic accessions form a separate cluster and rest of the accessions intermixed irrespective of geographical distribution. STRUCTURE-based clustering also resulted in a similar pattern of grouping.

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

Similar content being viewed by others

References

  • Basha SD, Sujatha M (2007) Inter and intra-population variability of Jatropha curcas (L.) characterized by RAPD and ISSR markers and development of population-specific SCAR markers. Euph 156:375–386

    Article  CAS  Google Scholar 

  • Basha SD, Francis G, Makkar HPS, Becker K, Sujatha M (2009) A comparative study of biochemical traits and molecular markers for assessment of genetic relationships between Jatropha curcas L. germplasm from different countries. Plant Sci 176:812–823

    Article  CAS  Google Scholar 

  • Becker K, Makkar HPS (2008) Jatropha curcas: a potential source for tomorrow’s oil and biodiesel. Lipid Technol 20:104–107

    Article  CAS  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    PubMed Central  CAS  PubMed  Google Scholar 

  • Camellia NA, Thohirah LA, Abdullah NAP (2012) Genetic relationships and diversity of Jatropha curcas accessions in Malaysia. Afr J Biotechnol 11:3048–3054

    Google Scholar 

  • Carvalho CR, Clarindo WR, Prac MM, Araujo FS, Carels N (2008) Genome size, base composition and karyotype of Jatropha curcas L. an important biofuel plant. Plant Sci 174:613–617

    Article  CAS  Google Scholar 

  • Castillo A, Budak H, Martin AC, Dorado G, Borner A, Roder M, Hernandez P (2010) Interspecies and intergenus transferability of barley and wheat D-genome microsatellite markers. Ann Appl Biol 156:347–356

    Article  CAS  Google Scholar 

  • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  • Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analysis. Heredity 99:125–132

    Article  CAS  PubMed  Google Scholar 

  • Ellstrand NC, Roose ML (1987) Patterns of genotypic diversity in clonal plant species. Am J Bot 74:123–131

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred From metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    PubMed Central  CAS  PubMed  Google Scholar 

  • Fairless D (2007) Biofuel: the little shrub that could—maybe. Nature 449:652–655

    Article  PubMed  Google Scholar 

  • Grativol C, Fonseca D, Lira MC, Hemerly AS, Ferreira PC (2011) High efficiency and reliability of inter-simple sequence repeats (ISSR) markers for evaluation of genetic diversity in Brazilian cultivated Jatropha curcas L. accessions. Mol Biol Rep 38:245–256

    Article  Google Scholar 

  • Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323

    Article  CAS  PubMed  Google Scholar 

  • Gupta P, Idris A, Mantri S, Asif MH, Yadav HK, Roy JK, Tuli R, Mohanty CS, Sawant SV (2012) Discovery and use of single nucleotide polymorphic (SNP) markers in Jatropha curcas L. Mol Breed 30:1325–1335

    Article  CAS  Google Scholar 

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ince AG, Karaca M, Onus AN (2010) Polymorphic microsatellite markers transferable across Capsicum species. Plant Mol Biol Rep 28:285–291

    Article  CAS  Google Scholar 

  • Johnson TS, Eswaran N, Sujatha M (2011) Molecular approaches to improvement of Jatropha curcas L. as a sustainable energy crop. Plant Cell Rep 30:1573–1591

    Article  Google Scholar 

  • King K, He W, Cuevas JA, Freudenberger M, Ramiaramanana D, Graham IA (2009) Potential of Jatropha curcas as a source of renewable oil and animal feed. J Exp Bot 60:2897–2905

    Article  CAS  PubMed  Google Scholar 

  • King AJ, Montes LR, Clarke JG, Affleck J, Li Y, Witsenboer H, van der Vossen E, van der Linde P, Tripathi Y, Tavares E, Shukla P, Rajasekaran T, van Loo EN, Graham IA (2013) Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity. Plant Biotech J 11:989–996

    Article  Google Scholar 

  • Kumar S, Kumaria S, Sharma SK, Rao SR, Tandon P (2011) Genetic diversity assessment of Jatropha curcas L. germplasm from northeast India. Biomass Bioenergy 35:3063–3070

    Article  CAS  Google Scholar 

  • Kumar S, Kumaria S, Tandon P (2013) SPAR methods coupled with seed-oil content revealed intra-specific natural variation in Jatropha curcas L. from northeast India. Biomass Bioenergy 54:100–106

    Article  CAS  Google Scholar 

  • Kumari M, Grover A, Yadav PV, Arif M, Ahmed Z (2013) Development of EST-SSR markers through data mining and their use for genetic diversity study in Indian accessions of Jatropha curcas L.: a potential energy crop. Genes Genom 35:661–670

    Article  CAS  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 

  • Machua J, Muturi G, Omondi SF, Gicheru J (2011) Genetic diversity of Jatropha curcas L. populations in Kenya using RAPD molecular markers: implication to plantation establishment. Afr J Biotechnol 10:3062–3069

    CAS  Google Scholar 

  • Makkar HPS, Aderibigbe AO, Becker K (1998) Comparative evaluation of non-toxic and toxic varieties of Jatropha curcas for chemical composition, digestibility, protein degradability and toxic factors. Food Chem 62:207–215

    Article  CAS  Google Scholar 

  • Mastan SG, Pamidimarri DVNS, Rahman H, Ghosh A, Rathore MS, Prakash CR, Chikara J (2012) Molecular characterization of intra-population variability of Jatropha curcas L. using DNA based molecular markers. Mol Biol Rep 39:4383–4390

    Article  CAS  PubMed  Google Scholar 

  • Maurya R, Gupta A, Singh SK, Rai KM, Chandrawati, Sawant SV, Yadav HK (2013) Microsatellite polymorphism in Jatropha curcas L.—a biodiesel plant. Ind Crops Prod 49:136–142

    Article  CAS  Google Scholar 

  • Openshaw K (2000) A review of Jatropha curcas an oil plant of unfulfilled promise. Biomass Bioenerg 19:1–15

    Article  Google Scholar 

  • Osorio LRM, Salvador AFT, Jongschaap REE, Perez CAA, Sandoval JEB, Trindade LM, Visser RGF, van Loo EN (2014) High level of molecular and phenotypic biodiversity in Jatropha curcas from Central America compared to Africa, Asia and South America. BMC Plant Biol 14:77

    Article  Google Scholar 

  • Ouattara B, Ndir KN, Gueye MC, Diedhiou I, Barnaud A, Fonceka D, Cisse N, Akpo EL, Diouf D (2014) Genetic diversity of Jatropha curcas L in Senegal compared with exotic accessions based on microsatellite markers. Genet Resour Crop Evol. doi:10.1007/s10722-014-0106-5

    Google Scholar 

  • Pamidimarri DVNS, Reddy MP (2014) Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis. Mol Biol Rep 41:3225–3234

    Article  Google Scholar 

  • Pamidimarri DVNS, Singh S, Mastan SG, Patel J, Reddy MP (2009) Molecular characterization and identification of markers for toxic and non-toxic varieties of Jatropha curcas L. using RAPD, AFLP and SSR markers. Mol Biol Rep 36:1357–1364

    Article  CAS  Google Scholar 

  • Pecina-Quintero V, Anaya-Lopez JL, Colmenero AZ, Garcia NM, Colin CAN, Bonilla JLS, Agilar-Rangel MR, Langarica JLS, Bustamante DJM (2011) Molecular characterization of Jatropha curcas L. genetic resources from Chiapas, Mexico through AFLP markers. Biomass Bioenerg 35:1897–1905

    Article  CAS  Google Scholar 

  • Pecina-Quintero V, Anaya-Lopez JL, Zamarripa-Colmenero A, Nunez-Colın CA, Montes-Garcıa N, Solıs-Bonilla JL, Jimenez-Becerril MF (2014) Genetic structure of Jatropha curcas L. in Mexico and probable centre of origin. Biomass Bioenerg 60:147–155

    Article  CAS  Google Scholar 

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield Science Publishers, Montpellier, pp 43–76

    Google Scholar 

  • Powell W, Machray G, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed Central  CAS  PubMed  Google Scholar 

  • Rafii MY, Shabanimofrad M, Edaroyati PMW, Latif MA (2012) Analysis of the genetic diversity of physic nut Jatropha curcas L. accessions using RAPD markers. Mol Biol Rep 39:6505–6511

    Article  CAS  PubMed  Google Scholar 

  • Ricci A, Chekhovskiy K, Azhaguvel P, Albertini E, Falcinelli M, Saha M (2012) Molecular characterization of Jatropha curcas resources and identification of population-specific markers. Bioenerg Res 5:215–224

    Article  Google Scholar 

  • Rosado TB, Laviola BG, Faria DA, Pappas MR, Bhering LL, Quirino B, Grattapaglia D (2010) Molecular marker reveal limited genetic diversity in large germplasm collection of the biofuel crop Jatropha curcas L. in Brazil. Crop Sci 50:2372–2382

    Article  CAS  Google Scholar 

  • Salvador-Figueroa M, Magana-Ramos J, Vazquez-Ovando JA, Adriano-Anaya ML, Ovando-Medina I (2014) Genetic diversity and structure of Jatropha curcas L. in its centre of origin. Plant Genet Resour Charact Util. doi:10.1017/S1479262114000550

    Google Scholar 

  • Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A (2011) Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res 18:65–76

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    Article  CAS  PubMed  Google Scholar 

  • Shen J, Khongsak P, David B, Xiaoyang C (2012) AFLP-based molecular characterization of 63 populations of Jatropha curcas L. grown in provenance trials in China and Vietnam. Biomass Bioenerg 37:265–274

    Article  CAS  Google Scholar 

  • Sudheer PDVN, Rahman H, Mastan SG, Reddy MP (2010) Isolation of novel microsatellites using FIASCO by dual probe enrichment from Jatropha curcas L. and study on genetic equilibrium and diversity of Indian population revealed by isolated microsatellites. Mol Biol Rep 37:3785–3793

    Article  CAS  PubMed  Google Scholar 

  • Sujatha M, Prabakaran AJ (2003) New ornamental Jatropha hybrids through interspecific hybridization. Genet Resour Crop Evol 50:75–82

    Article  CAS  Google Scholar 

  • Sun F, Liu P, Ye J, Lo L, Cao S, Li L, Yue G, Wang C (2012) An approach for Jatropha improvement using pleiotropic QTLs regulating plant growth and seed yield. Biotechnol Biofuels 5:12

    Article  CAS  Google Scholar 

  • Tanya P, Dachapak S, Tar MM, Srinives P (2011) New microsatellite markers classifying nontoxic and toxic Jatropha curcas. J Genet 90:e76–e78

    PubMed  Google Scholar 

  • Wang CM, Liu P, Yi C, Gu K, Sun F, Li L, Lo LC, Liu X, Feng F, Lin G, Cao S, Hong Y, Yin Z, Yue GH (2011) A first generation microsatellite and SNP based linkage map of Jatropha. PLoS One 6:e23632

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yadav HK, Ranjan A, Asif MH, Mantri S, Sawant SV, Tuli R (2011) EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera. Tree Genet Genomes 7:207–219

    Article  Google Scholar 

  • Yu J, Zhao H, Zhu Y, Chen L, Peng J (2013) Transferability of rice SSR markers to Miscanthus sinensis, a potential biofuel crop. Euphytica 191:455–468

    Article  CAS  Google Scholar 

  • Zalapa EJ, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, Mccown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99:193–208

    Article  CAS  PubMed  Google Scholar 

  • Zhang S, Tang C, Zhao Q, Li J, Yang L, Qie L, Fan X, Li L, Zhang N, Zhao M, Liu X, Chai Y, Zhang X, Wang H, Li Y, Li W, Zhi H, Jia G, Diao X (2014) Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.]. BMC Genom 15:78

    Article  CAS  Google Scholar 

Download references

Author contribution statement

HKY and SVS conceived the idea and planned work. RM, AG and CW performed the genotyping and data analysis. SKS and KMR performed sequencing and data analysis. HKY and RM prepared the manuscript. SVS and RK helped in data interpretation and manuscript preparation.

Acknowledgments

This work is financially supported by the Department of Biotechnology, Ministry of Science and Technology, Government of India (Grant No. BT/PR012559/PBD/26/26/04/2009). The authors also thank Dr. SA Ranade, Chief Scientist and Dr. KN Nair, Senior Principal Scientist, NBRI for critically examining the manuscript and helpful suggestions.

Conflict of interest

The authors declare no conflict of interest.

Author information

Author notes

    Authors and Affiliations

    1. CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India

      Ramanuj Maurya, Astha Gupta, Sunil Kumar Singh, Krishan Mohan Rai,  Chandrawati, Samir V. Sawant & Hemant Kumar Yadav

    2. Academy of Scientific and Innovative Research (AcSIR), New Delhi, India

      Astha Gupta,  Chandrawati, Samir V. Sawant & Hemant Kumar Yadav

    3. Department of Botany, Lucknow University, Lucknow, India

      Ratna Katiyar

    Authors
    1. Ramanuj Maurya
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Astha Gupta
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Sunil Kumar Singh
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Krishan Mohan Rai
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Chandrawati
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. Ratna Katiyar
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. Samir V. Sawant
      View author publications

      You can also search for this author in PubMed Google Scholar

    8. Hemant Kumar Yadav
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding author

    Correspondence to Hemant Kumar Yadav.

    Additional information

    Communicated by J. Carlson.

    R. Maurya and A. Gupta contributed equally.

    The raw data have been submitted to the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) with SRA accession SRR1055943.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary material 1 Distribution of various classes of simple repeat units in J. curcas (PPTX 45 kb)

    468_2015_1166_MOESM2_ESM.pptx

    Supplementary material 2 UPGMA dendrogram of 7 accessions of Jatropha curcas and 1 Jatropha integerrima showing genetic relatedness (PPTX 48 kb)

    468_2015_1166_MOESM3_ESM.ppt

    Supplementary material 3 Annotation of genomic SSRs developed from enriched libraries of J. curcas. Each pie indicates the proportion of BLAST matches showing highest identity to one of eight different plant species. (PPT 296 kb)

    468_2015_1166_MOESM4_ESM.pptx

    Supplementary material 4 PIC distribution of 41 polymorphic SSR loci calculated across 96 J. curcas accessions. (PPTX 46 kb)

    468_2015_1166_MOESM5_ESM.docx

    Supplementary material 5 Details of accessions of J. curcas used in microsatellite characterization and diversity analysis (DOCX 22 kb)

    Supplementary material 6 Polymorphism features of 41 SSR markers surveyed over 96 J. curcas accessions (DOCX 15 kb)

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Maurya, R., Gupta, A., Singh, S.K. et al. Genomic-derived microsatellite markers for diversity analysis in Jatropha curcas . Trees 29, 849–858 (2015). https://doi.org/10.1007/s00468-015-1166-7

    Download citation

    • Received:

    • Revised:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s00468-015-1166-7

    Keywords

    Search

    Navigation