, Volume 204, Issue 1, pp 49–61 | Cite as

Genetic purity and patterns of relationships among tropical highland adapted quality protein and normal maize inbred lines using microsatellite markers

  • Demissew Abakemal
  • Shimelis Hussein
  • John Derera
  • Kassa Semagn


Conversion of normal maize (Zea mays L.) into quality protein maize (QPM) significantly improves its nutritional value for humans and animals. Highland adapted normal maize inbred lines were backcrossed with selected QPM donor lines to incorporate the opaque-2 gene. The objectives of this study were to verify the genetic purity, determine the effect of conversion of normal maize lines to QPM and understand patterns of relationships among 36 white maize inbred lines (30 QPM and 6 non-QPM) using 25 simple sequence repeat (SSR) markers. The proportion of observed heterozygosity within an inbred line varied from 4 to 16.7 % and the average was 7.9 %. Twenty of the 36 inbred lines (55.6 %) showed higher than the expected 6.25 % mean residual heterozygosity for inbred lines developed after four generations of selfing. The genetic distances between pair-wise comparisons of the 36 inbred lines ranged from 0.077 to 0.780 and the average was 0.52. Nearly 98 % of the pair-wise comparisons had a distance between 0.30 and 0.78, which indicates large genetic differences among most lines. The model-based population structure, principal coordinate and neighbor-joining cluster analyses revealed the presence of two to three groups, which is generally consistent with pedigree information and partly with heterotic grouping. Analysis of molecular variance indicated that difference among heterotic groups explained 8.6 to 15.4 % of the total SSR variance, indicating the presence of moderate to great genetic differentiation among heterotic groups.


Genetic diversity Heterotic group Highland maize Microsatellite marker Quality protein maize 



The first author would like to thank the Alliance for a Green Revolution in Africa (AGRA) for providing PhD scholarship and also the Ethiopian Institute of Agricultural Research for granting the study leave and research support. The genotyping component of this project was funded by the Generation Challenge Program (GCP) as part of the molecular breeding platform. Advice provided by the late Dr. Twumasi-Afriyie and Dr Jedidah Danson is also acknowledged. CIMMYT is thanked for protein quality analysis of the inbred lines.


  1. Babu BK, Agrawal PK, Mahajan V, Gupta HS (2009) Molecular and biochemical characterization of short duration quality protein maize. J Plant Biochem Biotechnol 18:93–96CrossRefGoogle Scholar
  2. Babu BK, Pooja P, Bhatt JC, Agrawal PK (2012) Characterization of Indian and exotic quality protein maize (QPM) and normal maize (Zea mays L.) inbreds using simple sequence repeat (SSR) markers. Afr J Biotechnol 11:9691–9700CrossRefGoogle Scholar
  3. Bantte K, Prasanna BM (2003) Simple sequence repeat polymorphism in quality protein maize (QPM) lines. Euphytica 129:337–344CrossRefGoogle Scholar
  4. Benchimol LL, Souza-Junior CL, Garcia AAF, Kono PMS, Mangolin CA, Barbosa AMM, Coelho ASG, Souza APD (2000) Genetic diversity in tropical maize inbred lines: heterotic group assignment and hybrid performance determined by RFLP markers. Plant Breed 119:491–496CrossRefGoogle Scholar
  5. Bertan I, Carvalho FIF, Oliveira AC (2007) Parental selection strategies in plant breeding programs. J Crop Sci Biotechnol 10:211–222Google Scholar
  6. Beyene Y, Botha AM, Myburg AA (2006) Genetic diversity among traditional Ethiopian highland maize accessions assessed by simple sequence repeat (SSR) markers. Genet Resour Crop Evol 53:1579–1588CrossRefGoogle Scholar
  7. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedCentralPubMedGoogle Scholar
  8. Demissew A, Hussein S, Derera J, Laing M (2013) Farmers’ perceptions of maize production systems and breeding priorities, and their implications for the adoption of new varieties in selected areas of the highland agro-ecology of Ethiopia. J Agric Sci 5:159–172Google Scholar
  9. Dhliwayo T, Pixley K, Menkir A, Warburton M (2009) Combining ability, genetic distances, and heterosis among elite CIMMYT and IITA tropical maize inbred lines. Crop Sci 49:1201–1210CrossRefGoogle Scholar
  10. Duvick DN (2001) Biotechnology in the 1930s: the development of hybrid maize. Nat Rev Genet 2:69–74PubMedCrossRefGoogle Scholar
  11. 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 131:479–491PubMedCentralPubMedGoogle Scholar
  12. Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E, Springer NM (2009) Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS One 4:e7433PubMedCentralPubMedCrossRefGoogle Scholar
  13. Gupta HS, Agrawal PK, Mahajan V, Bisht GS, Kumar A, Verma P, Srivastava A, Saha S, Babu R, Pant MC, Mani VP (2009) Quality protein maize for nutritional security: rapid development of short duration hybrids through molecular marker assisted breeding. Curr Sci 96:230–237Google Scholar
  14. 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:e1367PubMedCentralPubMedCrossRefGoogle Scholar
  15. Hamrick JL, Godt MJW (1997) Allozyme diversity in cultivated crops. Crop Sci 37:26–30CrossRefGoogle Scholar
  16. Han GC, Vasal SK, Beck DL, Elias E (1991) Combining ability of inbred lines derived from CIMMYT maize (Zea mays L.) germplasm. Maydica 36:57–64Google Scholar
  17. Heckenberger M, Bohn M, Ziegle JS, Joe LK, Hauser JD, Hutton M, Melchinger AE (2002) Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties. I. Genetic and technical sources of variation in SSR data. Mol Breed 10:181–191CrossRefGoogle Scholar
  18. Huff DR, Peakall R, Smouse PE (1993) RAPD variation within and among natural populations of out crossing buffalo grass [(Buchloe dactyloides (Nutt.) Engelm]. Theor Appl Genet 86:927–934PubMedCrossRefGoogle Scholar
  19. Idury RM, Cardon LR (1997) A simple method for automated allele binning in microsatellite markers. Genome Res 7:1104–1109PubMedCentralPubMedGoogle Scholar
  20. Krishna MSR, Reddy SS, Naik VCB (2012) Assessment of genetic diversity in quality protein maize (QPM) lines using simple sequence repeat (SSR) markers. Afr J Biotechnol 11:16427–16433Google Scholar
  21. Krivanek AF, Groote HD, Gunaratna NS, Diallo AO, Friesen DK (2007) Breeding and disseminating quality protein maize (QPM) for Africa. Afr J Biotechnol 6:312–324Google Scholar
  22. Lee M (1995) DNA markers and plant breeding programs. Adv Agron 55:265–344Google Scholar
  23. Legesse BW, Myburg AA, Pixley KV, Botha AM (2007) Genetic diversity of African maize inbred lines revealed by SSR markers. Hereditas 144:10–17PubMedCrossRefGoogle Scholar
  24. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129PubMedCrossRefGoogle Scholar
  25. 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 120:93–115PubMedCrossRefGoogle Scholar
  26. Mahar K, Agrawal PK, Babu BK, Gupta HS (2009) Assessment of genetic diversity among the elite maize (Zea mays L.) genotypes adapted to North-Western Himalayan region of India using microsatellite markers. J Plant Biochem Biotechnol 18:217–220CrossRefGoogle Scholar
  27. Makumbi D, Betrán JF, Bänziger M, Ribaut JM (2011) Combining ability, heterosis and genetic diversity in tropical maize (Zea mays L.) under stress and non-stress conditions. Euphytica 180:143–162CrossRefGoogle Scholar
  28. Melchinger AE, Lee M, Lamkey KR, Hallauer AR, Woodman ML (1990) Genetic diversity for restriction fragment length polymorphisms and heterosis for two diallel sets of maize inbreds. Theor Appl Genet 80:488–496PubMedCrossRefGoogle Scholar
  29. Mertz ET, Bates LS, Nelson OE (1964) Mutant gene that changes protein composition and increases lysine content of maize endosperm. Science 145:279–280PubMedCrossRefGoogle Scholar
  30. Nesbitt KA, Potts BM, Vaillancourt RE, West AK (1995) Partitioning and distribution of RAPD variation in a forest tree species, Eucalyptus globulus (Myrtaceae). Heredity 74:628–637CrossRefGoogle Scholar
  31. Nurit E, Tiessen A, Pixley KV, Palacios-Rojas N (2009) Reliable and inexpensive colorimetric method for determining protein bound tryptophan in maize kernels. J Agric Food Chem 57:7233–7238PubMedCrossRefGoogle Scholar
  32. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedCentralPubMedGoogle Scholar
  33. Pswarayi A, Vivek BS (2008) Combining ability amongst CIMMYT’s early maturing maize (Zea mays L.) germplasm under stress and non-stress conditions and identification of testers. Euphytica 162:353–362CrossRefGoogle Scholar
  34. Rajab C, Abdolahadi H, Ghannadha MR, Warburton ML, Talei AR, Mohammadi SA (2006) Use of SSR data to determine relationships and potential heterotic groupings within medium to late maturing Iranian maize inbred lines. Field Crop Res 95:212–222CrossRefGoogle Scholar
  35. Reif JC, Melchinger AE, Xia XC, Warburton ML, Hoisington DA, Vasal SK, Beck D, Bohn M, Frisch M (2003a) Use of SSRs for establishing heterotic groups in subtropical maize. Theor Appl Genet 107:947–957PubMedCrossRefGoogle Scholar
  36. Reif JC, Melchinger AE, Xia XC, Warburton ML, Hoisington DA, Vasal SK, Beck D, Bohn M, Frisch M (2003b) Genetic distance based on simple sequence repeats and heterosis in tropical maize populations. Crop Sci 43:1275–1282CrossRefGoogle Scholar
  37. Rogers JS (1972) Measures of genetic similarity and genetic distance. Stud Genet VII 7213:145–153Google Scholar
  38. 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 125:1487–1501PubMedCrossRefGoogle Scholar
  39. 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 PubMedCentralPubMedCrossRefGoogle Scholar
  40. Shiferaw B, Prasanna BM, Hellin J, Bänziger M (2011) Crops that feed the world 6. Past successes and future challenges to the role played by maize in global food security. Food Secur 3:307–327CrossRefGoogle Scholar
  41. Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Mitchell SE, Kresovich S, Ziegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theor Appl Genet 95:163–173CrossRefGoogle Scholar
  42. Twumasi-Afriyie S, Zelleke H, Yihun K, Assefa B, Tariku S (2002) Development and improvement of highland maize in Ethiopia. In: Nigusse M, Tanner D (eds.) Proceedings of the second national maize workshop of Ethiopia, EARO (Ethiopian Agricultural Research Organization) and CIMMYT, 12–16 November 2001, Addis Ababa, Ethiopia, p 31–38Google Scholar
  43. Twumasi-Afriyie S, Demissew A, Gezahegn B, Wende A, Gudeta N, Demoz N, Friesen D, Kassa Y, Bayisa A, Girum A, Wondimu F (2012) A decade of quality protein maize research progress in Ethiopia (2001–2011). In: Worku M et al. (ed.) Meeting the challenges of global climate change and food security through innovative maize research. Proceedings of the third national maize workshop of Ethiopia, Ethiopian Institute of Agricultural Research (EIAR) and CIMMYT, 18–20 April 2011, Addis Ababa, Ethiopia, p 47–57Google Scholar
  44. Van Inghelandt D, Melchinger AE, 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 120:1289–1299PubMedCentralPubMedCrossRefGoogle Scholar
  45. Vivek BS, Krivanek AF, Palacios-Rojas N, Twumasi-Afriyie S, Diallo AO (2008) Breeding quality protein maize (QPM): protocols for developing QPM cultivars. International Maize and Wheat Improvement Center (CIMMYT), Mexico D.FGoogle Scholar
  46. 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 42:1832–1840CrossRefGoogle Scholar
  47. 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 142:97–106CrossRefGoogle Scholar
  48. 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 50:467–477CrossRefGoogle Scholar
  49. 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 51:2569–2581CrossRefGoogle Scholar
  50. Wright S (1978) Evolution and the genetics of populations: variability within and among natural populations. University of Chicago Press, ChicagoGoogle Scholar
  51. Wu Y, Zheng Y, Sun R, Wu S, Gu H, Bi Y (2004) Genetic diversity of waxy corn and popcorn landraces in Yunnan by SSR markers. Acta Agron Sin 30:36–42Google Scholar
  52. 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 mid-altitude, and highland maize inbred lines and their relationships with elite U.S. and European maize. Crop Sci 45:2573–2582CrossRefGoogle Scholar
  53. Yang X, Gao S, Xu S, Zhang Z, Prasanna B, Li L, Li J, Yan J (2011) Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Mol Breed 28:511–526CrossRefGoogle Scholar
  54. Yao Q, Fang P, Kang K, Pan G (2008) Genetic diversity based on SSR markers in maize (Zea mays L.) landraces from Wuling mountain region in China. J Genet 87:287–291CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Demissew Abakemal
    • 1
    • 2
  • Shimelis Hussein
    • 1
  • John Derera
    • 1
  • Kassa Semagn
    • 3
  1. 1.African Center for Crop ImprovementUniversity of KwaZulu-NatalPietermaritzburgSouth Africa
  2. 2.Ethiopian Institute of Agricultural ResearchAmbo-Plant Protection Research CenterAmboEthiopia
  3. 3.International Maize and Wheat Improvement Center (CIMMYT)NairobiKenya

Personalised recommendations