Skip to main content
SpringerLink
Log in

Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs

  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

In order to get an overview on the genetic relatedness of sorghum (Sorghum bicolor) landraces and cultivars grown in low-input conditions of small-scale farming systems, 46 sorghum accessions derived from Southern Africa were evaluated on the basis of amplified fragment length polymorphism (AFLPs), random amplified polymorphic DNAs (RAPDs) and simple sequence repeats (SSRs). By this approach all sorghum accessions were uniquely fingerprinted by all marker systems. Mean genetic similarity was estimated at 0.88 based on RAPDs, 0.85 using AFLPs and 0.31 based on SSRs. In addition to this, genetic distance based on SSR data was estimated at 57 according to a stepwise mutation model (Δμ-SSR). All UPGMA-clusters showed a good fit to the similarity estimates (AFLPs: r = 0.92; RAPDs: r = 0.88; SSRs: r = 0.87; Δμ-SSRs: r = 0.85). By UPGMA-clustering two main clusters were built on all marker systems comprising landraces on the one hand and newly developed varieties on the other hand. Further sub-groupings were not unequivocal. Genetic diversity (H, DI) was estimated on a similar level within landraces and breeding varieties. Comparing the three approaches to each other, RAPD and AFLP similarity indices were highly correlated (r = 0.81), while the Spearman's rank correlation coefficient between SSRs and AFLPs was r = 0.57 and r = 0.51 between RAPDs and SSRs. Applying a stepwise mutation model on the SSR data resulted in an intermediate correlation coefficient between Δμ-SSRs and AFLPs (r = 0.66) and RAPDs (r = 0.67), respectively, while SSRs and Δμ-SSRs showed a lower correlation coefficient (r = 0.52). The highest bootstrap probabilities were found using AFLPs (56% on average) while SSR, Δμ-SSR and RAPD-based similarity estimates had low mean bootstrap probabilities (24%, 27%, 30%, respectively). The coefficient of variation (CV) of the estimated genetic similarity decreased with an increasing number of bands and was lowest using AFLPs.

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

  • Ahmed MM, JH Sanders JH, Nell WT (2000) New sorghum and millet cultivar introduction in Sub-Saharan Africa: impacts and research agenda. Agric Systems 64:55–65

    Article  Google Scholar 

  • Ayana A, Bryngelsson T, Bekele E (2000) Genetic variation of Ethiopian and Eritrean sorghum (Sorghum bicolor (L.) Moench) germplasm assessed by random amplified polymorphic DNA (RAPD). Genet Res Crop Evol 47:471–428

    Article  Google Scholar 

  • Bohn M, Utz FH, Melchinger AE (1999) Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs and SSRs and their use for predicting progeny variance. Crop Sci 39:228–237

    CAS  Google Scholar 

  • Brown SM, Hopkins MS, Mitchell CV, Senior ML, Wang TY, Duncan RR, Gonzalez-Candelas F, Kresovich S (1996) Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum (Sorghum bicolor (L.) Moench). Theor Appl Genet 93:190–198

    Article  CAS  Google Scholar 

  • Dean RE, Dahlberg JA, Hopkins MS, Mitchell CV, Kresovich S (1999) Genetic redundancy and diversity among 'orange' accessions in the U.S. national sorghum collection as assessed with simple sequence repeat (SSR) markers. Crop Sci 39:1215–1221

    Google Scholar 

  • Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci USA 91:3166–3170

    PubMed  Google Scholar 

  • Djè Y, Forcioli D, Ater M, Lefèbvre C, Vekemans X (1999) Assessing population genetic structure of sorghum landraces from North-Western Morocco using allozyme and microsatellite markers. Theor Appl Genet 99:157–163

    Article  Google Scholar 

  • Djè Y, Heurtz M, Lefèbre C, Vekemans X (2000) Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers. Theor Appl Genet 100:918–925

    Article  Google Scholar 

  • Doyle JF, Doyle JL (1990) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Focus 12:13–15

    Google Scholar 

  • Efron B, Tibshirani T (1986) Bootstrap coefficient of variation, confidence limits and other methods for statistical accuracy measurements. Theor Popul Biol 53:256–271

    Google Scholar 

  • Feldmann MW, Bergmann A, Pollock DD, Goldstein DB (1997) Microsatellite genetic distances with range constraints: analytical description and problems of estimation. Genetics 145:207–216

    CAS  PubMed  Google Scholar 

  • Goldstein DB, Ruíz-Linares A, Cavalli-Sforza LL, Feldmann MW (1995a) An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463–471

    CAS  PubMed  Google Scholar 

  • Goldstein DB, Ruíz-Linares A, Feldman M, Cavalli-Sforza LL (1995b) Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci USA 92:6720–6727

    PubMed  Google Scholar 

  • Graner A, Ludwig WF, Melchinger AE (1994) Relationships among European barley germplasm. Crop Sci 34:1199–1205

    Google Scholar 

  • Grenier C, Deu M, Kresovich S, Bramel-Cox PJ, Hamon P (2000) Assessment of genetic diversity in three subsets constituted from the ICRISAT sorghum collection using random vs non-random sampling procedures B. Using molecular markers. Theor Appl Genet 101:197–202

    Article  CAS  Google Scholar 

  • Haussmann BIG, Obilana AB, Ayiecho PO, Blum A, Schipprack W, Geiger HH (2000) Yield and yield stability of four population types of grain sorghum in a semi arid area of Kenya. Crop Sci 40:319–329

    Google Scholar 

  • Karp A, Isaac PG, Ingram DS (1998) Molecular tools for screening biodiversity. Chapman & Hall, London

  • Kong L, Dong J, Hart GE (2000) Characteristics, linkage-map position, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple sequence repeats (SSRs). Theor Appl Genet 101:438–448

    Article  CAS  Google Scholar 

  • Le Thierry d'Ennequin M, Pannaud O, Toupance B, Sarr A (2000) Assessment of genetic relationships between Setaria italica and its wild relative S. viridis using AFLP markers. Theor Appl Genet 100:1061–1066

    Article  Google Scholar 

  • Lima MLA, Garcia AAF, Oliveira KM, Matsuoko S, Arizono H, de Souza Jr CL, de Souza AP (2002) Analysis of genetic similarity detected by AFLP and coefficient of parentage among genotypes of sugar cane (Saccarum spp). Theor Appl Genet 104:30–38

    CAS  Google Scholar 

  • Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Mol Ecol 3:91–99

    CAS  PubMed  Google Scholar 

  • Mantel M (1967) The detection of disease clustering and generalized regression approach. Cancer Res 27:209–220

    CAS  PubMed  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323

    CAS  PubMed  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleasis. Proc Natl Acad Sci USA 76:5269–5273

    CAS  PubMed  Google Scholar 

  • Ordon F, Bauer E, Friedt W, Graner A (1995) Marker-based selection for the ym4 BaMMV-resistance gene in barley using RAPDs. Agronomie 15:481–485

    Google Scholar 

  • Ordon F, Schimann A, Friedt W (1997) Assessment of the genetic relatedness of barley accessions (Hordeum vulgare s.l.) resistant to soil-borne mosaic-inducing viruses (BaMMV, BaYMV, BaYMV-2) using RAPDs. Theor Appl Genet 94:325–330

    Article  CAS  Google Scholar 

  • Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs and AFLPs. Theor Appl Genet 97:1248–1255

    Article  CAS  Google Scholar 

  • Pollock DD, Bergmann A, Feldmann MW, Goldstein DB (1998) Microsatellite behaviour with range constraints: Parameter estimation and improved distances for use in phylogenetic reconstruction. Theor Pop Biol 53:256–271

    Article  CAS  Google Scholar 

  • Ribaut JM, Hoisington D (1998) Marker-assisted selection: new tools and strategies. Trends Plant Sci 3:236–239

    Article  Google Scholar 

  • Rohlf FJ (2000) NTSYS-pc numerical taxonomy and multivariate analysis system, version 2.1. Exeter Publ, New York

  • Russel JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R (1997) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714–722

    Article  CAS  Google Scholar 

  • Scheurer KS, Friedt W, Huth W, Waugh R, Ordon F (2001) QTL analysis of tolerance to a German strain of BYDV-PAV in barley (Hordeum vulgare L.). Theor Appl Genet 103:1074–1083

    Article  CAS  Google Scholar 

  • Schiemann A, Dauck V, Friedt W, Streng S, Graner A, Ordon F (1999) Establishment of a flourescence-based AFLP technique and rapid marker detection for the resistance locus rym5. Barley Genet Newslett 29:http://wheat.pw.usda.gov/ggpages/bgn/29/a29-01.html

  • Simioniuc D, Uptmoor R, Friedt W, Ordon W (2002) Genetic diversity and relationships among pea cultivars (Pisum sativum L.) revealed by RAPDs and AFLPs. Plant Breed 121:429–435

    Google Scholar 

  • Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462

    CAS  PubMed  Google Scholar 

  • Tanksley SD, McCouch R (1997) Seed banks and molecular maps: Unlocking genetic potential from the wild. Science 277:1063–1066

    CAS  PubMed  Google Scholar 

  • Taramino G, Tarchini R, Ferrario S, Lee M, Pe ME (1997) Characterization and mapping of simple sequence repeats (SSRs) of Sorghum bicolor. Theor Appl Genet 95:66–72

    CAS  Google Scholar 

  • Tinker NA, Fortin MG, Mather DE (1993) Random amplified polymorphic DNA and pedigree relationships in spring barley. Theor Appl Genet 85:976–984

    CAS  Google Scholar 

  • Tivang JG, Nienhuis J, Smith OS (1994) Estimation of sampling variance of molecular marker data using the bootstrap procedure. Theor Appl Genet 89:259–264

    Google Scholar 

  • Udupa SM, Robertson LD, Weigand F, Baum M, Kahl G (1999) Allelic variation at (TAA)n microsatellite loci in a world chickpea collection (Cicer arietinum L.) germplasm. Mol Gen Genet 261:354–363

    Google Scholar 

  • Vekemans X, Beauvens T, Lemaire M, Roldan-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 11:139–151

    CAS  PubMed  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA Fingerprinting. Nucleic Acids Res 23:4407–4414

    CAS  PubMed  Google Scholar 

  • Wenzel WG, van Loggerenberg M, Ordon F (2001a) Quick screening methods for sorghum quality traits. J Appl Bot 75:43–45

    Google Scholar 

  • Wenzel WG, Ayisi KK, Mogashoa A, Donaldson G, Mohammed R, Uptmoor R, Ordon F, Friedt W (2001b) Improved sorghum varieties for smallholder farmers. J Appl Bot 75:207–209

    Google Scholar 

Download references

Acknowledgements

The author would like to thank Natalia Lest, Franziska Müller and Roland Kürschner for their excellent technical assistance. Financial support of the Bundesministerium für Wirtschaftliche Zusammenarbeit (BMZ) and the Deutsche Forschungsgemeinschaft (DFG), Project No. FR 682/9-2 is gratefully acknowledged.

Author information

Author notes

  1. F. Ordon

    Present address: Institute of Epidemiology and Resistance, Federal Centre for Breeding Research on Cultivated Plants, Theodor-Roemer-Weg 4, 06449 Aschersleben, Germany,

Authors and Affiliations

  1. Institute for Crop Science and Plant Breeding I, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany

    R. Uptmoor, W. Wenzel, W. Friedt & F. Ordon

  2. Agricultural Research Council (ARC), Grain Crops Institute (GCI), Private Bag X1251 Potchefstroom 2520, South Africa

    W. Wenzel

  3. Northern Province Department of Agriculture, Land and Environment, Potgietersrus, South Africa

    G. Donaldson

  4. Department of Plant Production, University of the North, Private Bag X1106, Sovenga 0727, South Africa

    K. Ayisi

Authors
  1. R. Uptmoor
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. W. Wenzel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. W. Friedt
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. G. Donaldson
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. K. Ayisi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. F. Ordon
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to F. Ordon.

Additional information

Communicated by H.C. Becker

Rights and permissions

Reprints and permissions

About this article

Cite this article

Uptmoor, R., Wenzel, W., Friedt, W. et al. Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs, AFLPs and SSRs. Theor Appl Genet 106, 1316–1325 (2003). https://doi.org/10.1007/s00122-003-1202-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-003-1202-7

Keywords

Search

Navigation