Skip to main content
SpringerLink
Log in

Genetic relationships and structure among open-pollinated maize varieties adapted to eastern and southern Africa using microsatellite markers

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Molecular characterization of open-pollinated maize varieties (OPVs) is fundamentally important in maize germplasm improvement. We investigated the extent of genetic differences, patterns of relationships, and population structure among 218 diverse OPVs widely used in southern and eastern Africa using the model-based population structure, analysis of molecular variance, cluster analysis, principal component analysis, and discriminant analysis. The OPVs were genotyped with 51 microsatellite markers and the fluorescent detection system of the Applied Biosystems 3730 Capillary Sequencer. The number of alleles detected in each OPV varied from 72 to 155, with an overall mean of 127.6. Genetic distance among the OPVs varied from 0.051 to 0.434, with a mean of 0.227. The different multivariate methods suggest the presence of 2–4 possible groups, primarily by maturity groups but also with overlapping variation between breeding programs, mega-environments, and specific agronomic traits. Nearly all OPVs in group 1 and group 2 belong to the intermediate-late and early maturity groups, respectively. Group 3 consisted of mainly intermediate maturing OPVs, while group 4 contained OPVs of different maturity groups. The OPVs widely used in eastern Africa either originated from the southern African maize breeding programs, or the majority of inbred lines used as parents by the two breeding programs in developing the OPVs might be genetically related. Some of the OPVs are much older than others, but they still did not show a clear pattern of genetic differentiation as compared with the recently developed ones, which is most likely due to recycling of the best parental lines in forming new OPVs.

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

Similar content being viewed by others

References

  • Bänziger M, Meyer J (2002) Collaborative maize variety development for stress-prone environments in southern Africa. In: Cleveland DA, Soleri D (eds) Farmers, scientists, and plant breeding: integrating knowledge and practice. CABI, Oxon, pp 269–296

    Chapter  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  PubMed  CAS  Google Scholar 

  • Dubreuil P, Warburton M, Chastanet M, Hoisington D, Charcosset A (2006) More on the introduction of temperate maize into Europe: large-scale bulk SSR genotyping and new historical elements. Maydica 51:281–291

    Google Scholar 

  • Dvornyk V, Long JR, Xiong DH, Liu PY, Zhao LJ, Shen H, Zhang YY, Liu YJ, Rocha-Sanchez S, Xiao P, Recker RR, Deng HW (2004) Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. BMC Genet 5:25

    Article  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Eschholz TW, Peter R, Stamp P, Hund A (2008) Genetic diversity of Swiss maize (Zea mays L. ssp. mays) assessed with individuals and bulks on agarose gels. Genet Resour Crop Evol 55:971–983

    Article  Google Scholar 

  • Etten JV, Lopez MRF, Monterroso LGM, Samayoa KMP (2008) Genetic diversity of maize (Zea mays L. ssp. mays) in communities of the western highlands of Guatemala: geographical patterns and processes. Genet Resour Crop Evol 55:303–317

    Article  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  CAS  PubMed Central  Google Scholar 

  • Gupta P, Balyan H, Edwards K, Isaac P, Korzun V, Roder M, Gautier MF, Joudrier P, Schlatter A, Dubcovsky J, De la Pena R, Khairallah M, Penner G, Hayden M, Sharp P, Keller B, Wang R, Hardouin J, Jack P, Leroy P (2002) Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor Appl Genet 105:413–422

    Article  PubMed  CAS  Google Scholar 

  • Hamblin MT, Warburton ML, Buckler ES (2007) Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS ONE 2:e1367

    Article  PubMed  PubMed Central  Google Scholar 

  • Hamrick JL, Godt MJW (1997) Allozyme diversity in cultivated crops. Crop Sci 37:26–30

    Article  CAS  Google Scholar 

  • Idury RM, Cardon LR (1997) A simple method for automated allele binning in microsatellite markers. Genome Res 7:1104–1109

    PubMed  CAS  PubMed Central  Google Scholar 

  • Le Hellard SP, Ballereau SPJ, Visscher PM, Torrance HS, Pinson J, Morris SW, Thomson ML, Semple CAM, Muir WJ, Blackwood DHR, Porteous DJ, Evans KL (2002) SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res 30:e74–e74

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Lu H, Bernardo R (2001) Molecular marker diversity among current and historical maize inbreds. Theor Appl Genet 103:613–617

    Article  CAS  Google Scholar 

  • Lu Y, Yan J, Guimaraes C, Taba S, Hao Z, Gao S, Chen S, Li J, Zhang S, Vivek B, Magorokosho C, Mugo S, Makumbi D, Parentoni S, Shah T, Rong T, Crouch J, Xu Y (2009) Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet 120:93–115

    Article  PubMed  CAS  Google Scholar 

  • Narro LA, Duran JF, George MLC, Lucia Arcos A, Viviana Osorio K, Warburton ML (2012) Comparison of the performance of synthetic maize varieties created based on either genetic distance or general combining ability of the parents. Maydica 57:83–91

    Google Scholar 

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

    PubMed  CAS  PubMed Central  Google Scholar 

  • Prasanna B, Pixley K, Warburton M, Xie CX (2010) Molecular marker-assisted breeding options for maize improvement in Asia. Mol Breed 26:339–356

    Article  CAS  Google Scholar 

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

    PubMed  CAS  PubMed Central  Google Scholar 

  • Reif JC, Xia XC, Melchinger AE, Warburton ML, Hoisington DA, Beck D, Bohn M, Frisch M (2004) Genetic diversity determined within and among CIMMYT maize populations of tropical, subtropical, and temperate germplasm by SSR markers. Crop Sci 44:326–334

    Article  CAS  Google Scholar 

  • Reif JC, Hamrit S, Heckenberger M, Schipprack W, Peter MH, Bohn M, Melchinger AE (2005) Genetic structure and diversity of European flint maize populations determined with SSR analyses of individuals and bulks. Theor Appl Genet 111:906–913

    Article  PubMed  CAS  Google Scholar 

  • Rholf FJ (1993) NTSYS-pc, numerical taxonomy and multivariate analysis system. Exeter software, New York

    Google Scholar 

  • Rogers JS (1972) Measures of genetic similarity and genetic distance. Stud Genet VII Univ Tex Publ 7213:145–153

    Google Scholar 

  • Semagn K, Beyene Y, Makumbi D, Mugo S, Prasanna BM, Magorokosho C, Atlin G (2012a) Quality control genotyping for assessment of genetic identity and purity in diverse tropical maize inbred lines. Theor Appl Genet 125:1487–1501

    Article  PubMed  Google Scholar 

  • Semagn K, Magorokosho C, Vivek BS, Makumbi D, Beyene Y, Mugo S, Prasanna BM, Warburton ML (2012b) Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers. BMC Genomics 13:113. doi:10.1186/1471-2164-13-113

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14

    Article  CAS  Google Scholar 

  • Setimela PS, Vivek B, Banziger M, Crossa J, Maideni F (2007) Evaluation of early to medium maturing open pollinated maize varieties in SADC region using GGE biplot based on the SREG model. Field Crop Res 103:161–169

    Article  Google Scholar 

  • Shelton CA (2006) Quantitative PCR approach to SNP detection and linkage mapping in Caenorhabditis elegans. Biotechniques 41:583–588

    Article  PubMed  CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  • Van Inghelandt D, Melchinger A, Lebreton C, Stich B (2010) Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theor Appl Genet 120:1289–1299

    Article  PubMed  PubMed Central  Google Scholar 

  • Warburton ML, Xia X, Crossa J, Franco J, Melchinger AE, Frisch M, Bohn M, Hoisington D (2002) Genetic characterization of CIMMYT inbred maize lines and open pollinated populations using large scale fingerprinting methods. Crop Sci 42:1832–1840

    Article  Google Scholar 

  • Warburton ML, Ribaut JM, Franco J, Crossa J, Dubreuil P, Betran FJ (2005) Genetic characterization of 218 elite CIMMYT maize inbred lines using RFLP markers. Euphytica 142:97–106

    Article  CAS  Google Scholar 

  • Warburton ML, Reif JC, Frisch M, Bohn M, Bedoya C, Xia XC, Crossa J, Franco J, Hoisington D, Pixley K, Taba S, Melchinger AE (2008) Genetic diversity in CIMMYT nontemperate maize germplasm: landraces, open pollinated varieties, and inbred lines. Crop Sci 48:617–624

    Article  Google Scholar 

  • Warburton ML, Setimela P, Franco J, Cordova H, Pixley K, Banziger M, Dreisigacker S, Bedoya C, MacRobert J (2010) Toward a cost-effective fingerprinting methodology to distinguish maize open-pollinated varieties. Crop Sci 50:467–477

    Article  Google Scholar 

  • Wen W, Araus JL, Trushar S, Cairns J, Mahuku G, Banziger M, Torres JL, Sanchez C, Yan J (2011) Molecular characterization of a diverse maize inbred line collection and its potential utilization for stress tolerance improvement. Crop Sci 51:2569–2581

    Article  Google Scholar 

  • Wen W, Franco J, Chavez-Tovar VH, Yan J, Taba S (2012) Genetic characterization of a core set of a tropical maize race Tuxpeño for further use in maize improvement. PLoS ONE 7:e32626

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Xia XC, Reif JC, Hoisington DA, Melchinger AE, Frisch M, Warburton ML (2004) Genetic diversity among CIMMYT maize inbred lines investigated with SSR markers: I. Lowland tropical maize. Crop Sci 44:2230–2237

    Article  Google Scholar 

  • Xia XC, Reif JC, Melchinger AE, Frisch M, Hoisington DA, Beck D, Pixley K, Warburton ML (2005) Genetic diversity among CIMMYT maize inbred lines investigated with SSR markers: II. Subtropical, tropical midlatitude, and highland maize inbred lines and their relationships with elite U.S. and European maize. Crop Sci 45:2573–2582

    Article  CAS  Google Scholar 

  • Yan J, Shah T, Warburton ML, Buckler ES, McMullen MD, Crouch J (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. PLoSOne 4:e8451

    Article  Google Scholar 

  • Zhou Gh, Kamahori M, Okano K, Chuan G, Harada K, Kambara H (2001) Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER). Nucleic Acids Res 29:e93–e93

    Article  PubMed  CAS  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was part of the “Drought Tolerant Maize for Africa” projects and is financially supported by Bill and Melinda Gates Foundation.

Author information

Authors and Affiliations

  1. International Maize and Wheat Improvement Center (CIMMYT), P. O. Box 1041, Village Market 00621, Nairobi, Kenya

    Kassa Semagn, Veronica Ogugo & Dan Makumbi

  2. CIMMYT, 12.5 Km peg Mazowe Road, Mount Pleasant, P.O. Box MP163, Harare, Zimbabwe

    Cosmos Magorokosho

  3. Corn Host Plant Resistance Research Unit, United States Department of Agriculture-Agricultural Research Service, Box 9555, Mississippi State, MS, 39762, USA

    Marilyn L. Warburton

Authors
  1. Kassa Semagn
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Cosmos Magorokosho
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Veronica Ogugo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Dan Makumbi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Marilyn L. Warburton
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kassa Semagn.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Semagn, K., Magorokosho, C., Ogugo, V. et al. Genetic relationships and structure among open-pollinated maize varieties adapted to eastern and southern Africa using microsatellite markers. Mol Breeding 34, 1423–1435 (2014). https://doi.org/10.1007/s11032-014-0126-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-014-0126-z

Keywords

Search

Navigation