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Genetic diversity among barley cultivars assessed by sequence-specific amplification polymorphism

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Abstract

We analyzed the genetic structure and relationships among barley cultivars (Hordeum vulgare L.) with sequence-specific amplification polymorphisms (S-SAPs). Polymorphisms were identified in 824 individual barley plants representing 103 cultivars (eight plants per cultivar) widely grown in Canada and the United States, using PCR primers designed from the long terminal repeat of the barley retrotransposon BARE-1 and a subset of four selective MseI primers. From the 404 bands scored, 150 were polymorphic either within or between cultivars. Genetic structure assessed with analysis of molecular variance attributed the largest component of variation to the within groups of cultivars (69–86%). Within-cultivar genetic variation was estimated as average gene diversity over loci and ranged from 0 (completely homogenous) to 0.076 (most heterogeneous cultivar). Only 17 out of 103 cultivars (16%) were judged to be homogenous by this criterion. Relationships among cultivars were analyzed by cluster analysis using unweighted pair-groups using arithmetic averages and found groups similar to those determined by agriculturally significant phenotypic traits such as spike morphology (two-rowed or six-rowed), cultivar type (malting or feed), seed characteristic (hull-less or hulled), and growth habit (winter or spring), with minor overlaps. Discriminant analysis of groups determined by these phenotypic traits fully supported the different groups with minor overlaps between the malting/feed. S-SAP markers generated from retrotransposons such as BARE-1 are invaluable tools for the study of genetic diversity in organisms with a narrow genetic base such as barley. In this study, S-SAP analysis revealed significant amounts of cryptic variation in closely related cultivars including somaclonal variation, which could not be inferred by the pedigree analysis.

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References

  • Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphism of simple sequence repeat DNA in soybean. Genetics 132:1131–1139

    CAS  PubMed  Google Scholar 

  • Anderson TW (1984) An introduction to multivariate statistical analysis, 2nd edn. Wiley, New York

    Google Scholar 

  • Barrett BA, Kidwell KK, Fox PN (1998) Comparison of AFLP and pedigree based genetic diversity assessment methods using wheat cultivars from the Pacific Northwest. Crop Sci 38:1271–1278

    Google Scholar 

  • Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR (2000) The MITE family Heartbreaker (Hbr): molecular markers in maize. Proc Natl Acad Sci USA 97:10083–10089

    Google Scholar 

  • Cochrane WG, Hopkins CE (1961) Some classification problems with multivariate qualitative data. Biometrics 17:10–32

    Google Scholar 

  • Dice LR (1945) Measure of the amount of ecological association between species. Ecology 26:297–302

    Google Scholar 

  • Ellis THN, Poyer SJ, Knox MR, Vershinin AV, Ambrose MJ (1998) Tyl-copia class retrotransposon insertion site polymorphism for linkage and diversity analysis in pea. Mol Gen Genet 260:9–19

    CAS  PubMed  Google Scholar 

  • Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992) Ty1- copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res 20:3639–3644

    Google Scholar 

  • Gilbert E S (1968) On discrimination using qualitative variables. J Am Stat Assoc 63:1399–1412

    Google Scholar 

  • Gribbon BM, Pearce SR, Kalendar R, Schulman AH, Pauline L, Jack P, Kumar A, Flavell AJ (1999) Phylogeny and transcriptional activity of Ty1-copia group retrotransposons in cereal genomes. Mol Gen Genet 261:883–891

    CAS  PubMed  Google Scholar 

  • Hirochika H, Fukuchi A, Kikuchi F (1992) Retrotransposon families in rice. Mol Gen Genet 233:209–216

    CAS  PubMed  Google Scholar 

  • Hirochika H, Sugimoto K, Otsuki Y, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93: 7783–7788

    Article  CAS  PubMed  Google Scholar 

  • Horsely RD, Schwarz PB, Hammond JJ (1995) Genetic diversity in malt quality of North American six-rowed spring barley. Crop Sci 35:113–118

    Google Scholar 

  • Jaaskelainen M, Mykkanen AH, Arna T, Vicient C, Souniemi A, Kalendar A, Savilahti H, Schulman AH (1999) Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells. Plant J 20: 413–422

    Google Scholar 

  • Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new fingerprinting techniques. Theor Appl Genet 98:704–711

    Article  CAS  Google Scholar 

  • Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman A (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603–6607

    Article  CAS  PubMed  Google Scholar 

  • Kidwell MG, Lisch D (1997) Transposable elements are sources of variation in animals and plants. Proc Natl Acad Sci USA 94:7704–7711

    Google Scholar 

  • Krzanowski WJ (1975) Discrimination and classification using both binary and continuous variables. J Am Stat Assoc 70:782–790

    Google Scholar 

  • Kshirsagar AM (1972) Multivariate analysis. Marcel Dekker, New York

    Google Scholar 

  • Kumar A, Bennetzen JL (1999) Plant retrotransposons. Ann Rev Genet 33:479–532

    Google Scholar 

  • Labra M, Imazio S, Grassi F, Rossoni M, Sala F (2004) vine-1 retrotransposon-based sequence-specific amplified polymorphism for Vitis vinifera L. genotyping. Plant Breed 123:180–185

    Google Scholar 

  • Lachenbruch PA, Mickey MA (1968) Estimation of error rates in discriminant analysis. Technometrics 10:1–10

    Google Scholar 

  • Leigh F, Kalendar R, Lea V, Lee D, Donini P, Schulman AH (2003) Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Mol Genet Genomics 269:464–474

    CAS  PubMed  Google Scholar 

  • Liu B, Wendel JF (2000) Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome 43:874–880

    Google Scholar 

  • Manninen I, Schulman AH (1993) BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol Biol 22:829–846

    CAS  PubMed  Google Scholar 

  • Martin JM, Blake TK, Hockett EA (1991) Diversity among North American spring barley based on coefficient of parentage. Crop Sci 31:1131–1137

    Google Scholar 

  • Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H (2003) Target site specificity of Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771–1780

    Google Scholar 

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Nevo E (1992) Origin, evolution, population genetics and resources for breeding of wild barley, Hordeum spontaneum, in the Fertile Crescent. In: Shewry PR (ed) Barley: genetics, biochemistry, molecular biology and biotechnology. CAB International, Oxford, pp 19–43

    Google Scholar 

  • Noma K, Ohtsubo E, Ohtsubo H (1999) Non-LTR retrotransposon LINEs are ubiquitous components of plant genomes. Mol Gen Genet 261:71–79

    Article  Google Scholar 

  • Olufowote JO, Xu Y, Chen X, Park WD, Beachell HM, Dilday RH, Goto M, McCouch SR (1997) Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellites and RFLP markers. Genome 40:370–378

    CAS  PubMed  Google Scholar 

  • Perry DJ (2004) Identification of Canadian durum wheat varieties using a single PCR. Theor Appl Genet 109:55–61

    Google Scholar 

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

    Google Scholar 

  • Qi X, Lindhout P (1997) Development of AFLP markers in barley. Mol Gen Genet 254:330–336

    Article  CAS  PubMed  Google Scholar 

  • Queen RA, Gribbon BM, James C, Jack P, Flavell AJ (2004) Retrotransposon-based molecular markers for linkage and genetic diversity analysis in wheat. Mol Gen Genomics 271:91–97

    Google Scholar 

  • Rao CR (1952) Advanced statistical methods in biometric research. Wiley, New York

    Google Scholar 

  • Reamon-Buttner SM, Jung C (2000) AFLP-derived STS markers for the identification of sex in Asparagus officinalis L. Theor Appl Genet 100:432–438

    Article  Google Scholar 

  • Rohlf FJ (2000) NTSYS-pc. Numerical taxonomy and multivariate analysis system. Ver. 2.1 Exeter software, Setauket, New York

  • SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765–764

    Google Scholar 

  • SAS Institute (2002) SAS/STAT user’s guide, version 8.2 [computer program] SAS Institute, Cary

  • Schneider S, Kueffer JM, Roessli D, Excoffier L (1997) Arlequin, a software for population genetic data analysis. Ver. 1.1. Available via http://anthropologie.unige.ch/arlequin.

  • Shapiro JA (1999) Transposable elements are the key to the 21st century view of evolution. Genetica 107:171–179

    Google Scholar 

  • Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10:908–915

    Google Scholar 

  • Soleimani VD, Baum BR, Johnson DA (2002) AFLP and Pedigree-based genetic diversity estimates in modern cultivars of durum wheat [Triticum turgidum L. subsp. durum (Desf.) Husn.]. Theor Appl Genet 104:350–357

    Google Scholar 

  • Soleimani VD, Baum BR, Johnson DA (2003) Efficient validation of single nucleotide polymorphisms in plants by allele-specific PCR, with an example from barley. Plant Mol Biol Rep 21:281–288

    Google Scholar 

  • Suoniemi A, Narvanto A, Schulman A (1996) The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol Biol 31:295–306

    CAS  PubMed  Google Scholar 

  • Suoniemi A, Tanskanen J, Schulman AH (1998) Gypsy-like retrotransposons are widespread in the plant kingdom. Plant J 13:699–705

    Article  Google Scholar 

  • Suoniemi A, Schmidt D, Schulman AH (1999) BARE-1 insertion site preferences and evolutionary conservation of RNA and cDNA processing sites. Genetica 100:219–230

    Google Scholar 

  • Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138

    CAS  PubMed  Google Scholar 

  • Thormann CE, Osborn TC (1993) Use of RAPD and RFLP markers for germplasm evaluation. In: Neff M (ed) Application of RAPD technology to plant breeding. ASHS, St. Paul

    Google Scholar 

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

    Google Scholar 

  • Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11:1769–1784

    Google Scholar 

  • Vignols F, Rigau J, Torres MA, Capellades M, Puigdomenech P (1995) The brown midrib3 (bm3) mutation in maize occurs in the gene encoding caffeic acid O-methyltransferase. Plant Cell 7:407–416

    Article  CAS  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

    CAS  PubMed  Google Scholar 

  • Voytas DF, Cummings MP, Konieczny A, Ausubel FM, Rodermel SR (1992) Copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89:7124–7128

    CAS  PubMed  Google Scholar 

  • Waugh R, Mclean K, Flavell AJ, Pearce SR, Kumar A (1997) Genetic distribution of BARE-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplified polymorphism (S-SAP). Mol Gen Genet 253:687–694

    Article  CAS  PubMed  Google Scholar 

  • White SE, Habers L, Wessler SR (1994) Retrotransposons in the flanking regions of normal plant genes. A role for copia-like elements in the evolution of gene structure and expression. Proc Natl Acad Sci USA 91:11792–11796

    Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6231–6235

    Google Scholar 

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Acknowledgements

The authors would like to thank Ajit Singh Sahota from the Canadian Food Inspection Agency (CFIA) and Jean Mellish from the Canadian Grain Commission (CGC) for providing plant material. We would also like to thank Dr. Thin-Meiw (Alek) Choo of Agriculture and Agri-Food Canada for providing cultivar description of barley material. We are indebted to him for his advice and discussions. This study was partially funded by the Automated Quality Testing (AQT). This paper benefited from comments by Dr. Steve Molnar and Dr. Nick Tinker of Agriculture and Agri-Food Canada, and we thank them for their valuable comments and advice on an earlier draft of the manuscript.

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  1. Agriculture and Agri-Food Canada, K. W. Neatby Building, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada

    V. D. Soleimani & B. R. Baum

  2. Ottawa-Carleton Institute of Biology, University of Ottawa, 150 Louis Pasteur, P.O. Box 450, Station A, Ottawa, ON, K1N 6N5, Canada

    V. D. Soleimani & D. A. Johnson

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  1. V. D. Soleimani
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Correspondence to B. R. Baum.

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Communicated by H.C. Becker

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Soleimani, V.D., Baum, B.R. & Johnson, D.A. Genetic diversity among barley cultivars assessed by sequence-specific amplification polymorphism. Theor Appl Genet 110, 1290–1300 (2005). https://doi.org/10.1007/s00122-005-1966-z

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