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Molecular characterization and assessment of genetic diversity of inbred lines showing variability for drought tolerance in maize

Abstract

A set of 24 genotypes bred at different centres in India as well as in CIMMYT showing variability for drought tolerance were selected for molecular and morpho-physiological characterization. A set of 35 SSR markers, having genome-wide coverage, was chosen for genotyping the inbreds. These markers generated a total of 111 polymorphic alleles with an average of 3.17 alleles per locus. The minimum and maximum PIC value was 0.27 and 0.77 with a mean of 0.5. A total of 13 unique alleles were found in the 24 inbred lines. The coefficient of genetic dissimilarity ranged from 0.192 to 0.803. NJ-based tree suggested the presence of three major clusters of which, two of them had subgroups. Phenotyping of inbreds by morpho-physiological traits revealed that there was a positive relationship among root length, chlorophyll content, relative water content while anthesis-silking interval was negative relationship with all these traits. Genotyping data complemented by morpho-physiological parameters were used to identify a number of pair-wise combinations for the development of mapping population segregating for drought tolerance and potential heterotic pairs for the development of drought tolerant hybrids.

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Abbreviations

RWC:

Relative water content

ASI:

Anthesis-silking interval

RL:

Root length

CC:

Chlorophyll content

LAI:

Leaf area index

QTL:

Quantitative trait locus

References

  • Ajmone-Marsan P, Castiglioni P, Fusari F, Kuiper M, Motto M (1998) Genetic diversity and its relationship to hybrid performance in maize as revealed by RFLP and AFLP markers. Theor Appl Genet 96:219–227

    Article  Google Scholar 

  • Barata C, Carena MJ (2006) Classification of North Dakota maize inbred lines into heterotic groups based on molecular and testcross data. Euphytica 151:339–349

    Article  CAS  Google Scholar 

  • Beck DL, Vasal SK, Crossa J (1991) Heterosis and combining ability among subtropical and temperate intermediate-maturity maize germplasm. Crop Sci 31:68–73

    Article  Google Scholar 

  • Chin ECL, Senior ML, Shu H, Smith JSC (1996) Maize simple repetitive DNA sequences: abundance and allele variation. Genome 39:866–873

    PubMed  Article  CAS  Google Scholar 

  • Dickson Ng’uni, Mulatu Geleta, Tomas Bryngelsson (2011) Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR) 148:52–62.

    Google Scholar 

  • Dubreuil P, Charcosset A (1999) Relationships among maize inbred lines and populations from European and North-American origins as estimated using RFLP markers. Theor Appl Genet 99:473–480

    PubMed  Article  CAS  Google Scholar 

  • Dubreuil P, Dufour P, Krejci E, Causse M, de Vienne D, Gallais A, Charcosset A (1996) Organization of RFLP diversity among inbred lines of maize representing the most significant heterotic groups. Crop Sci 36:790–799

    Article  Google Scholar 

  • Enoki H, Sato H, Koinuma K (2002) SSR analysis of genetic diversity among maize inbred lines adapted to cold regions of Japan. Theor Appl Genet 104:1270–1277

    PubMed  Article  CAS  Google Scholar 

  • GENSTAT 14 Committee. 2011. GENSTAT 6 reference manual. Clarendon Press, Oxford, UK.

  • Chenyang H, Wang L, Ge H, Dong Y, Zhang X (2011) Genetic diversity and linkage disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) revealed by SSR markers. PLoS ONE 6(2):e17279

    Article  Google Scholar 

  • Gethi JG, Labate JA, Lamkey KR, Smith ME, Kresovich S (2002) SSR variation in important US maize inbred lines. Crop Sci 42:951–957

    Article  CAS  Google Scholar 

  • Goodman MM, Bird RM (1977) The races of maize IV: tentative grouping of 219 Latin American races. Econ Bot 31:204–221

    Article  Google Scholar 

  • Heckenberger M, Melchinger AE, Ziegle JS, Joe LK, Hauser JD, Hutton M, Bohn M (2002) Variation of DNA fingerprints among accessions within maize inbred lines with regard to the identification of essentially derived varieties. I. Genetic and technical sources of variation in SSR data. Mol Breed 10:181–191

    Article  CAS  Google Scholar 

  • Jiang H-F, Ren X-P, Zhang X-J, Huang J-Q, Lei Y, Yan L-Y, Liao B-S, Upadhyaya HD, Holbrook CC (2010) Comparison of genetic diversity based on SSR markers between peanut mini core collections from China and ICRISAT. Acta Agron Sin 36:1084–1091

    Article  CAS  Google Scholar 

  • Le Clerc V, Bazante F, Baril C, Guiard J, Zhang D (2005) Assessing temporal changes in genetic diversity of maize varieties using microsatellite markers. Theor Appl Genet 110:294–302

    PubMed  Article  Google Scholar 

  • Legesse BW, Myburg AA, Pixley KV, Botha AM (2007) Genetic diversity of African maize inbred lines revealed by SSR markers. Hereditas 144:10–7

    PubMed  Article  CAS  Google Scholar 

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

    PubMed  Article  CAS  Google Scholar 

  • Liu ZW, Biyashev R, Saghai-Maroof M (1996) Development of simple sequence repeats DNA markers and their integration into a barley linkage map. Theor Appl Genet 93:869–876

    Article  CAS  Google Scholar 

  • Liu K, Goodman M, Muse S et al (2003) Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117–2128

    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 

  • Matsuoka Y, Mitchell SE, Kresovich S (2002) Microsatellites in Zea -variability, patterns of mutations and use for evolutionary studies. Theor Appl Genet 104:436–450

    PubMed  Article  CAS  Google Scholar 

  • Melchinger AE, Gumber RK (1998) Overview of heterosis and heterotic groups in agronomic crops. In: Lamkey KR, Staub JE (eds) Concepts and breeding of heterosis in crop plants. CSSA, Madison, pp 29–44

    Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325

    PubMed  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. Science Publishers Montpellier, Enfield, pp 43–76

    Google Scholar 

  • Pinto LR, Vieira MLC, de Souza CL et al (2003) Genetic diversity assessed by microsatellites in tropical maize population submitted to high-density reciprocal recurrent selection. Euphytica 134:277–286

    Article  Google Scholar 

  • Reif JC, Melchinger AE, Xia XC, Warburton ML et al (2003) Use of SSRs for establishing heterotic groups in subtropical maize. Theor Appl Genet 107:947–957

    PubMed  Article  CAS  Google Scholar 

  • Ron Parra J, Hallauer AR (1997) Utilization of exotic maize germplasm. Plant Breed Rev 14:165–187

    Google Scholar 

  • Saker MM, Youssef SS, Abdallah NA, Bashandy HS et al (2005) Genetic analysis of some Egyptian rice genotypes using RAPD, SSR and AFLP. Afr J Biotechnol 4:882–890

    CAS  Google Scholar 

  • Schug MD, Hutter CM, Wetterstr KA et al (1998) The mutation rate of di, tri and tetra-nucleotide repeats in Drosophila melanogaster. Mol Biol Evol 15:1751–1760

    PubMed  Article  CAS  Google Scholar 

  • Semagn K, Bjørnstad A, Ndjiondjop MN (2006) Principles, requirements and prospects of genetic mapping in plants. African J Biotech 5:2569–2587

    CAS  Google Scholar 

  • Senior ML, Chin ECL, Lee M et al (1996) Simple sequences repeat markers developed from maize sequences found in the GENEBANK database: map construction. Crop Sci 36:1676–1683

    Article  CAS  Google Scholar 

  • Senior ML, Murphy JP, Goodman MM et al (1998) Utility of SSRs for determining genetic similarities and relationships in maize using agarose gel system. Crop Sci 38:1088–1098

    Article  Google Scholar 

  • Sharon EM, Kresovich S, Jester CA, Hernandez CJ, Szewc-McFadden AK (1997) Application of multiplex PCR and fluorescence-based, semi-automated allele sizing technology for genotyping plant genetic resources. Crop Sci 37:617–624

    Article  Google Scholar 

  • Singh NN, Venkatesh S, Sekhar JC, Zaidi PH (2005) Stresses on maize in the tropics - progress and challenges. In: Stresses on maize in tropics. Directorate of Maize Research, New Delhi, India

  • Smart RE, Bingham GE (1974) Rapid estimates of relative water content. Plant Physiol 53:258–260

    PubMed  Article  CAS  Google Scholar 

  • Smith JSC, Smith OS (1992) Fingerprinting crop varieties. Adv Agron 47:85–140

    Article  CAS  Google Scholar 

  • 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 95:163–173

    Article  CAS  Google Scholar 

  • Souza SGH, Carpentieri-Pípolo V, Ruas CF, Carvalho VP et al (2008) Comparative analysis of genetic diversity among the maize inbred lines (Zea mays L.) obtained by RAPD and SSR markers. Braz Arch Biol Technol 51:183–192

    Google Scholar 

  • Tautz D (1989) Hypervariablity of simple sequences as a general source of polymorphic DNA markers. Nucleic Acids Res 17:6463–6471

    PubMed  Article  CAS  Google Scholar 

  • Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981

    PubMed  Article  Google Scholar 

  • 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 120:1289–1299

    PubMed  Article  Google Scholar 

  • Vaz Patto MC, Satovic Z, Pego S et al (2004) Assessing the genetic diversity of Portuguese maize germplasm using microsatellite markers. Euphytica 137:63–72

    Article  Google Scholar 

  • Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci 99:9650–9655

    PubMed  Article  CAS  Google Scholar 

  • Warburton ML, Xianchun X, Crossa J et al (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, 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 non-temperate maize germplasm: landraces, open pollinated varieties, and inbred lines. Crop Sci 48:617–624

    Article  Google Scholar 

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Acknowledgement

The authors sincerely acknowledge the National Agricultural Innovation Project (NAIP) for their financial support to carry out this research.

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Correspondence to T. Nepolean.

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Nepolean, T., Singh, I., Hossain, F. et al. Molecular characterization and assessment of genetic diversity of inbred lines showing variability for drought tolerance in maize. J. Plant Biochem. Biotechnol. 22, 71–79 (2013). https://doi.org/10.1007/s13562-012-0112-7

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  • DOI: https://doi.org/10.1007/s13562-012-0112-7

Keywords

  • Genetic diversity
  • SSRs
  • Drought
  • Mapping population
  • Heterotic grouping
  • Maize