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A haplotype specific to North European wheat (Triticum aestivum L.)

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Abstract

A previous study indicated decreased DNA content of chromosome 4A in the wheat (Triticum aestivum L. cv. Tähti) compared to cvs. Chinese Spring and Rennan. Here we show that the lower 4A DNA content is associated with a specific haplotype in the distal part of 4AL. In 41 cultivars of bread wheat (T. aestivum L.), including cv. Tähti, a common haplotype was identified in the linkage disequilibrium region on the long arm of chromosome 4A (4AL). The haplotype (haplotype A) is characterized by 7 SSR and 5 EST marker alleles, including five zero-alleles. Haplotype A was found in 46 % of the Swedish/Finnish/Estonian spring wheat genotypes, while only one of the modern wheat accessions from Germany carried the same haplotype. Fluorescent cytometry analysis linked haplotype A to diminished DNA content of chromosome 4A. The haplotype was introduced into the Canadian and US breeding programs at the beginning of the twentieth century (cvs. Marquis, Thatcher, Ruby) from the common progenitor, the Polish landrace Fife, and it is still found in modern wheat germplasm in these countries. Zero-alleles characteristic for haplotype A were also detected in several accessions of European spelt (Triticum spelta L.), and in two accessions of tetraploid Triticum timopheevii Zhuk. The presence of haplotype A in European spelt indicates the considerable antiquity of the haplotype, as it must have been inherited from the hexaploid or tetraploid parent of spelt in at least one hybridization event.

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References

  • Abrouk M, Klocová B, Šimková H, Kominkova E, Pingault L, Martis MM, Jakobson I, Järve K, PauxE International Wheat Genome Sequencing Consortium. In: Kilian A, Doležel J, Valárik M (eds) In-silico identification and characterization of wheat 4AL - Triticum militinae introgression (under review)

  • Akpinar BA, Yuce M, Lucas S, Vrána J, Burešová V, Doležel J, Budak H (2015) Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides. Sci Rep 5:10763

    Article  PubMed  Google Scholar 

  • Badaeva ED, Budashkina EB, Bilinskaya EN, Pukhalskiy VA (2010) Intergenomic chromosome substitutions in wheat interspecific hybrids and their use in the development of genetic nomenclature of Triticum timopheevii chromosomes. Russ J Genet 46(7):769–785

    Article  CAS  Google Scholar 

  • Bedbrook JR, Jones J, O’Dell M, Thompson RD, Flavell RB (1980) A molecular description of telomeric heterochromatin in secale species. Cell 19(2):545–560

    Article  CAS  PubMed  Google Scholar 

  • Bertin P, Gregoire D, Massart S, de Froidmont D (2001) Genetic diversity among European cultivated spelt revealed by microsatellites. Theor Appl Genet 102:148–156

    Article  CAS  Google Scholar 

  • Blatter RHE, Jacomet S, Schlumbaum A (2002) Spelt-specific alleles in HMW glutenin genes from modern and historical European spelt (Triticum spelta L.). Theor Appl Genet 104:329–337

    Article  CAS  PubMed  Google Scholar 

  • Blatter RHE, Jacomet S, Schlumbaum A (2004) About the origin of European spelt (Triticum spelta L.): allelic differentiation of the HMW Glutenin B1-1 and A1-2 subunit genes. Theor Appl Genet 108:360–367

    Article  CAS  PubMed  Google Scholar 

  • Bonjean AP, Angus WJ, van Ginkel M (eds) (2011) The world wheat book: a history of wheat breeding, vol 2. Lavoisier Publishing, Paris

  • Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier M-F, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B (2005) Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 17:1033–1045

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chao S, Zhang W, Dubcovsky J, Sorrels M (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among U.S. wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci 47:1018–1030

    Article  CAS  Google Scholar 

  • Crossa J, Burgueno J, Dreisigacker S, Vargas M, Herrera-Foessel SA, Lillemo M, Singh RP, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch JH, Ortiz R (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dorofeyev VF, Jakubtsiner MM, Rudenko MI, Migushova EF, Udachin RA, Merezhko AF, Semenova LV, Novikova MV, Gradchaninova OD, Shitova IP (1976) The wheats of the world. In: Brezhnev DD, Dorofeyev VF (eds). Kolos Publ., Leningrad (in Russian)

  • Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316:1862–1866

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dvorák J, Luo M-C, Yang Z-L (1998) Restriction fragment length polymorphism and divergence in the genomic regions of high and low recombination in self-fertilizing and cross-fertilizing Aegilops species. Genetics 148:423–434

    PubMed  PubMed Central  Google Scholar 

  • Dvorák J, Yang Z-L, You FM, Luo M-C (2004) Deletion polymorphism in wheat chromosome regions with contrasting recombination rates. Genetics 168(3):1665–1675

    Article  PubMed  PubMed Central  Google Scholar 

  • Dvorák J, Deal KR, Luo M-C, You FM, Von Borstel K, Dehghani H (2012) The origin of spelt and free-threshing hexaploid wheat. J Hered 103(3):426–441

    Article  PubMed  Google Scholar 

  • Feuillet C, Langridge P, Waugh R (2008) Cereal breeding takes a walk on the wild side. Trends Genet 24:24–32

    Article  CAS  PubMed  Google Scholar 

  • Flavell RB, Bennett MD, Smith JB, Smith DB (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12:257

    Article  CAS  PubMed  Google Scholar 

  • Gill BS, Friebe BR, White FF (2011) Alien introgressions represent a rich source of genes for crop improvement. Proc Nat Acad Sci USA 108:7657–7658

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Giorgi D, Farina A, Grosso V, Gennaro A, Ceoloni C et al (2013) FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy. PLoS One 8(2):e57994. doi:10.1371/journal.pone.0057994

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gordeeva EI, Leonova IN, Kalinina NP, Salina EA, Budashkina EB (2009) Comparative cytological and molecular analysis of common wheat introgression lines containing genetic material of Triticum timopheevii Zhuk. Russ J Genet 45:1428–1437

    Article  CAS  Google Scholar 

  • Griffin WB (1987) Outcrossing in New Zealand wheats measured by occurrence of purple grain. N Z J Agricu Res 30(3):287–290

    Article  Google Scholar 

  • Harberd NP, Flavell RB, Thompson RD (1987) Identification of a transposon-like insertion in a Glu-1 allele of wheat. Mol Gen Genet 209:326

    Article  CAS  PubMed  Google Scholar 

  • Hernandez P, Martis M, Dorado G, Pfeifer M, Gálvez S, Schaaf S, Jouve N, Šimková H, Valárik M, Doležel J, Mayer KFX (2012) Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J 69:377–386

    Article  CAS  PubMed  Google Scholar 

  • Huang X-Q, Brûlé-Babel A (2012) Sequence diversity, haplotype analysis, association mapping and functional marker development in the waxy and starch synthase IIa genes for grain-yield-related traits in hexaploid wheat (Triticum aestivum L.). Mol Breed 30(2):627–645

    Article  CAS  Google Scholar 

  • Jakobson I, Peusha H, Timofejeva L, Järve K (2006) Adult plant and seedling resistance to powdery mildew in a Triticum aestivum × Triticum militinae hybrid line. Theor Appl Genet 112:760–769

    Article  PubMed  Google Scholar 

  • Jakobson I, Reis D, Tiidema A, Peusha H, Timofejeva L, Valárik M, Klavdivová M, Šimkova H, Doležel J (2012) Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat–Triticum militinae introgression line. Theor Appl Gen 125(3):609–623

    Article  Google Scholar 

  • Jiang J, Friebe B, Gill BS (1994) Recent advances in alien gene transfer in wheat. Euphytica 73:199–212

    Article  Google Scholar 

  • Khlestkina EK, Kumar U, Röder MS (2010) Ent-kaurenoic acid oxidase genes in wheat. Mol Breed 25(2):251–258

    Article  CAS  Google Scholar 

  • Kidwell MG, Lisch D (1997) Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci USA 94(15):7704–7711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kubaláková M, Macas J, Doležel J (1997) Mapping of repeated DNA sequences in plant chromosomes by PRINS and C-PRINS. Theor Appl Genet 94:758–763

    Article  Google Scholar 

  • Kubaláková M, Vrána J, Číhalíková J, Šimková H, Doležel J (2002) Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). Theor Appl Genet 104:1362–1372

    Article  PubMed  Google Scholar 

  • Kubaláková M, Valárik M, Bartoš J, Vrána J, Číhalíková J, Molnár-Láng M, Doležel J (2003) Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. Genome 46:893–905

    Article  PubMed  Google Scholar 

  • Kubaláková M, Kovářová P, Suchánková P, Číhalíková J, Bartoš J, Lucretti S, Watanabe N, Kianian SF, Doležel J (2005) Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics 170(2):823–829

    Article  PubMed  PubMed Central  Google Scholar 

  • Leonova IN, Röder MS, Budashkina EB, Kalinina NP, Salina EA (2002) Molecular analysis of leaf rust-resistant introgression lines obtained by crossing of hexaploid wheat Triticum aestivum with tetraploid wheat Triticum timopheevii. Russ J Genet 38(12):1397–1403

    Article  CAS  Google Scholar 

  • Liu L, Wang L, Yao J, Zheng Y, Zhao C (2010) Association mapping of six agronomic traits on chromosome 4A of wheat (Triticum aestivum L.). Mol Plant Breed 1(5):27–36

    Google Scholar 

  • Ma L, Vu GTH, Schubert V, Watanabe K, Stein N, Houben A, Schubert I (2010) Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res 18:841–850

    Article  CAS  PubMed  Google Scholar 

  • MacKey J (1966) Species relationship in Triticum. Hereditas 2:237–276

    Google Scholar 

  • Martin TJ (1990) Outcrossing in twelve hard red winter wheat cultivars. Crop Sci 30(1):59–62

    Article  Google Scholar 

  • Nakamura T, Vrinten P, Saito M, Konda M (2002) Rapid classification of partial waxy wheats using PCR-based markers. Genome 45:1150–1156

    Article  CAS  PubMed  Google Scholar 

  • Paillard S, Schnurbusch T, Winzeler M, Messmer M, Sourdille P, Abderhalden O, Keller B, Schachenmayr G (2003) An integrative genetic linkage map of winter wheat (Triticum aestivum L.). Theor Appl Genet 107(7):1235–1242

    Article  CAS  PubMed  Google Scholar 

  • Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma XF, Miftahudin Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NL, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS (2004) A chromosome bin map of 16,000 EST loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168:701–712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plasche J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  PubMed Central  Google Scholar 

  • Šafář J, Šimková H, Kubaláková M, Číhalíková J, Suchánková P, Bartoš J, Doležel J (2010) Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res 129:211–223

    Article  PubMed  Google Scholar 

  • Schiemann E (1931) Pfahlbauweizen. Historiches und Phylogenetisches. Z Pflanzenzücht 17:36–53

    Google Scholar 

  • Shinde D, Lai Y, Sun F, Arnheim N (2003) Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites. Nucl Acids Res 31(3):974–980

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Siedler H, Messmer MM, Schachermayr GM, Winzeler H, Keller B (1994) Genetic diversity in European wheat and spelt breeding materials based on RFLP data. Theor Appl Genet 88:994–1003

    Article  CAS  PubMed  Google Scholar 

  • Somers DJ, Isaac P, Edwards K (2004) A high-density wheat microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114

    Article  CAS  PubMed  Google Scholar 

  • Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, Gill BS, Ward R, Cregan PB (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110(3):550–560

    Article  CAS  PubMed  Google Scholar 

  • Vrána J, Kubaláková M, Šimková H, Číhalíková J, Lysák MA, Doležel J (2000) Flow-sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156:2033–2041

    PubMed  PubMed Central  Google Scholar 

  • Vrána J, Kubaláková M, Číhalíková J, Valárik M, Doležel J (2015) Preparation of sub-genomic fractions enriched for particular chromosomes in polyploid wheat. Biol Plant 59(3):445–455

    Article  Google Scholar 

  • Webster MT, Hurst LD (2012) Direct and indirect consequences of meiotic recombination: implications for genome evolution. Trends Genet 28(3):101–109

    Article  CAS  PubMed  Google Scholar 

  • Xue SL, Zhang ZZ, Lin F et al (2008) A high-density intervarietal map of the wheat genome enriched with markers derived from expressed sequence tags. Theor Appl Genet 117(2):181–189

    Article  CAS  PubMed  Google Scholar 

  • Zeven AC, Zeven-Hissink NCh (1976) Genealogies of 14000 wheat varieties. Netherlands Cereal Center and International Maize and Wheat Improvement Center, Wageningen, Mexico

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Acknowledgments

We would like to thank Zdenka Dubská and Romana Šperková for excellent technical support in the preparation of chromosome suspensions. This work has been supported by the program “Collection and Conservation of Plant Genetic Resources for Food and Agriculture in 2014–2020” (Estonian Ministry of Agriculture), by institutional research funding IUT 193 of the Estonian Ministry of Education and Research, by the award LO1204 from the National Program of Sustainability I, and by the Czech Science Foundation (award 14-07164S).

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Authors and Affiliations

  1. Department of Gene Technology, Tallinn University of Technology, 12618, Tallinn, Estonia

    Jelena Tsõmbalova, Hilma Peuša, Irena Jakobson & Kadri Järve

  2. Institute of Experimental Botany, Centre of the Region Haná for Biotechnical and Agricultural Research, Olomouc, Czech Republic

    Miroslava Karafiátová, Jan Vrána, Marie Kubaláková, Miroslav Valárik & Jaroslav Doležel

  3. Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, 51010, Tartu, Estonia

    Mari Järve

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  1. Jelena Tsõmbalova
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  2. Miroslava Karafiátová
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Correspondence to Kadri Järve.

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Tsõmbalova, J., Karafiátová, M., Vrána, J. et al. A haplotype specific to North European wheat (Triticum aestivum L.). Genet Resour Crop Evol 64, 653–664 (2017). https://doi.org/10.1007/s10722-016-0389-9

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