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Genetic diversity analysis of maize lines using AFLP and TE-based molecular marker systems

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Abstract

Maize has been domesticated in diverse environments ranging from low latitudes in tropical countries to high latitudes in Canada. Because maize breeding programs primarily focus on hybrid vigor by selectively crossing inbred lines to maximize recombination, we collected a diverse array of commercial hybrid and inbred lines from southern Asia, China, and Canada and analyzed them by amplified length fragment polymorphism (AFLP), sequence-specific amplified polymorphism (SSAP), and CACTA-transposon display (TD) analyses. Cluster analyses using these molecular marker systems clearly differentiated these maize lines into three groups: southern Asian lines, northern Asian lines, and Canadian lines. However, principal coordinate analysis (PCoA) based on Nei’s distances grouped them into two groups: Asian and Canadian lines. Thus, groupings by cluster dendrograms and PCoA showed that geographic origin was a more dominant factor than growing seasonal differences resulting from different latitudes. The overall genetic diversity (Ht) was found to be high (more than 80 % molecular variations) among the maize lines by all three of the marker systems.

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References

  • 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 

  • Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon JM, Westerman RP, Sanmiguel PJ, Bennetzen JL (2009) Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet 5:e1000732

    Article  PubMed  PubMed Central  Google Scholar 

  • Buckler ES, Stevens NM (2006) Maize origins, domestication, and selection. Darwin’s Harvest. Columbian University Press, New York

    Google Scholar 

  • Dao A, Sanou J, Mitchell SE, Gracen V, Danquah EY (2014) Genetic diversity among INERA maize inbred lines with single nuculeotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines. BMC Genet 15:127

    Article  PubMed  PubMed Central  Google Scholar 

  • Fedoroff N, Bennetzen JL (2013) Transposons, genomic shock, and genome evolution. In: Fedorff N (ed) Plant transposons and genome dynamics in evolution, 1st edn. Wiley, pp 181–201

  • Finnegen DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5:103–107

    Article  Google Scholar 

  • Hirano R, Naito K, Fukunaga K, Watanabe KN, Ohsawa R, Kawase M (2011) Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet. Genome 54:498–506

    Article  CAS  PubMed  Google Scholar 

  • Il Lee S, Park KC, Ha MW, Kim KS, Jang YS, Kim NS (2012) CACTA transposon-derived Ti-SCARs for cultivar fingerprinting in rapeseed. Genes Genomics 34:575–579

    Article  Google Scholar 

  • Kalendar R, Flavell AJ, Ellis T, Sjakste T, Moisy C, Schulman A (2011) Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106:520–530

    Article  CAS  PubMed  Google Scholar 

  • Kwon SJ, Park KC, Kim JH, Lee JK, Kim NS (2005) Rim 2/Hipa CACTA transposon display: a new genetic marker technique in Oryza species. BMC Genet 6:15

    Article  PubMed  PubMed Central  Google Scholar 

  • Loarce Y, Gallego R, Ferrer E (1996) A comparative analysis of the genetic relationships between rye cultivars using RFLP and RAPD markers. Euphytica 88:107–115

    Article  Google Scholar 

  • Lou Q, Chen J (2007) Ty1-copia retrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits. Genome 50:802–810

    Article  CAS  PubMed  Google Scholar 

  • Mardi M, Naghavi MR, Pirseyedi SM, Alamooti MK, Monfared SR, Ahkami AH, Omidbakhsh MA, Alavi NS, Shanjani PS, Katsiotis A (2011) Comparative assessment of SSAP, AFLP and SSR markers for evaluation of genetic diversity of durum wheat (Triticum turgidum L. var. durum). J Agric Sci Technol 13:905–920

    Google Scholar 

  • Matsuoka Y, Vigouroux Y, Gooman MM, Sanchez GJJ, Buckler E, Doebley J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99:6080–6084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McClintock B (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA 36:344–355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nagaraju J, Reddy KD, Nagaraja GM, Sethuraman BN (2001) Comparison of multilocus RFLPs and PCR-based marker systems for genetic analysis of the silkworm, Bombyx mori. Heredity 86:588–597

    Article  CAS  PubMed  Google Scholar 

  • Peakall R, Smouse P (2005) Appendix 1—methods and statistics in GenAlEx 6 by Rod Peakall and Peter Smouse. Statistics (Ber) 5:1–23

    Google Scholar 

  • Phumichai C, Dougchan W, Puddlanon P, Jampatong S, Gruloyma P, Kirdsri C, Chungwonse J, Pulam Y (2008) SSR-based and grain yield-based diversity of hybrid maize in Thailand. Field Crop Res 108:157–162

    Article  Google Scholar 

  • Porceddu A, Albertini E, Barcaccia G, Bertoli F, Vereonesi F (2002) Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L. Mol Genet Genomics 267:107–114

    Article  CAS  PubMed  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Prasanna BM (2012) Diversity in global maize germplasm: characterization and utilization. J Biosci 37:1–13

    Article  Google Scholar 

  • Prigge V, Melchinger AE (2012) Production of haploids and doubled haploids in maize. Methods Mol Biol 877:161–172

    Article  CAS  PubMed  Google Scholar 

  • Ranum P, Peña-Rosas JP, Garcia-Casal MN (2014) Global maize production, utilization, and consumption. Ann N Y Acad Sci 1312:105–112

    Article  PubMed  Google Scholar 

  • Reid LM, Xiang K, Zhu X, Baum BR, Molnar SJ (2011) Genetic diversity analysis of 119 Candian maize inbred lines based on pedigree and simple sequence repeat markers. Can J Plant Sci 91:651–661

    Article  Google Scholar 

  • Roy N, Choi JY, Lee SI, Kim NS (2015a) Marker utility of transposable elements for plant genetics, breeding, and ecology: a review. Genes Genomics 37:141–151

    Article  CAS  Google Scholar 

  • Roy N, Choi JY, Lim MJ, Lee SI, Choi HJ, Kim NS (2015b) Genetic and epigenetic diversity among dent, waxy, and sweet corns. Genes Genomics 37:865–874

    Article  Google Scholar 

  • Sánchez GJJ, Stuber CW, Goodman M (2000) Isozymatic diversity in the races of maize in Americas. Maydica 45:185–203

    Google Scholar 

  • Sánchez GJJ, Goodman M, Stuber CW (2007) Racial diversity of mazie in Brazil and adjacenty areas. Maydica 52:13–30

    Google Scholar 

  • Sanmiguel P, Vitte C (2009) The LTR-retrotransposons of maize. Maize handbook, vol 2. Springer, Berlin, pp 307–327

    Book  Google Scholar 

  • Sanz AM, Gonzalez SG, Syed NH, Suso MJ, Saldana CC, Flavell AJ (2007) Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers. Mol Genet Genomics 278:433–441

    Article  CAS  PubMed  Google Scholar 

  • Schnable PS, Warer D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al (2009) The B73 maize genome: compexity, diversity, and dinamics. Science 326:1112–1115

    Article  CAS  PubMed  Google Scholar 

  • Syed NH, Flavell AJ (2006) Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions. Nat Protoc 1:2746–2752

    Article  CAS  PubMed  Google Scholar 

  • Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce SR, Grandbastien (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet 110:819–831

    Article  CAS  PubMed  Google Scholar 

  • Tenallion MI, Sawkins MC, Long AD, Gaut RL, Doebly JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. Mays L.). Proc Natl Acad Sci USA 98:9161–9166

    Article  Google Scholar 

  • Vigouroux Y, Glaubitz JC, Matusoka Y, Goodman MM, Sanchez H, Doebley J (2008) Population structure and genetic diversity of new world maize races assessed by DNA microsatellites. Am J Bot 95:1240–1253

    Article  PubMed  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van der 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Q, Dooner HK (2006) Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc Natl Acad Sci USA 21:17644–17649

    Article  Google Scholar 

  • Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982

    Article  CAS  PubMed  Google Scholar 

  • Yeh FC, Yang RC, Boyle T, Freeware MW (1999) Popgene version 1.31. University of Alberta and Tim Boyle Center for International Forestry Research, Alberta, pp 1–29

    Google Scholar 

Download references

Acknowledgments

This work was funded by a grant from the Golden Seed Project, Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development of Korea (RDA), and the Korea Forest Service (Project Number: ATIS-PJ00994003, FRIS-213001-04-3-SBA20), as well as a 2015 research grant from Kangwon National University (Grant No. 520159395).

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  1. Department of Molecular Bioscience, Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 200-701, South Korea

    Neha Samir Roy & Nam-Soo Kim

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  1. Neha Samir Roy
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  2. Nam-Soo Kim
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Correspondence to Nam-Soo Kim.

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Neha Roy declares that she does not have conflict of interest. Nam-Soo Kim declares that he does not have conflict of interest.

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Roy, N.S., Kim, NS. Genetic diversity analysis of maize lines using AFLP and TE-based molecular marker systems. Genes Genom 38, 1005–1012 (2016). https://doi.org/10.1007/s13258-016-0461-z

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