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Evolution of tetraploid wheat based on variations in 5′ UTR regions of Ppd-A1: evidence of gene flow between emmer and timopheevi wheat

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Abstract

Previous study showed that tetraploid wheat was divided into two groups (Type AI and Type AII) based on sequences around Ppd-A1 gene (Takenaka and Kawahara in Theor Appl Genet 125(5):999–1014, 2012). That study focused on domesticated emmer wheat and used only 19 wild emmer wheats, so could not be clear the evolutional relationship between Type AI and Type AII. Here, a total of 669 accessions comprising 65 einkorn wheats, 185 wild emmer wheats, 107 hulled emmer wheats, 204 free-threshing (FT) emmer wheats, and 108 timopheevii wheats were studied by PCR assay and DNA sequencing for Type AI/AII. Type AII was an older type than Type AI because all einkorn accessions had Type AII. In wild emmer, Type AI was distributed in the northeast regions of its distribution and Type AII was found to be centered on Israel. A total of 37.4 % of hulled emmer accessions were Type AI, while 92.2 % of FT emmer accessions were Type AI. Differences in the proportion of Type AI/AII in domesticated emmer suggested a strong bottle-neck effect. We also found two MITE-like sequence deletion patterns from a part of Type AII accessions (dic-del and ara-del). Dic-del was found from only Israeli wild emmer accessions and ara-del was found from almost all timopheevii wheat accessions. Only three timopheevii accessions did not have ara-del, and one wild emmer accession and ten hulled emmer accessions had ara-del. These accessions suggested gene flow between emmer and timopheevii wheat.

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References

  • Asakura N, Mori N, Ishido T, Ohtsuka I, Nakamura C (2001) Single nucleotide polymorphisms in an STS region linked to the ncc-tmp1A locus are informative for characterizing the differentiation of chromosome 1A in wheat. Genes & Genetic Systems 76(5):295–304

    Article  CAS  Google Scholar 

  • Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48

    Article  PubMed  CAS  Google Scholar 

  • Bellwood PS (2005) First farmers: the origins of agricultural societies. Wiley-Blackwell, Oxford

    Google Scholar 

  • Brown-Guedira G, Badaeva E, Gill B, Cox T (1996) Chromosome substitutions of Triticum timopheevii in common wheat and some observations on the evolution of polyploid wheat species. Theor Appl Genet 93(8):1291–1298

    Article  Google Scholar 

  • Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316(5833):1862

    Article  PubMed  CAS  Google Scholar 

  • Dvořák J, di Terlizzi P, Zhang HB, Resta P (1993) The evolution of polyploid wheats: identification of the A genome donor species. Genome 36(1):21–31

    Article  PubMed  Google Scholar 

  • Escaravage N, Questiau S, Pornon A, Doche B, Taberlet P (1998) Clonal diversity in a Rhododendron ferrugineum L. (Ericaceae) population inferred from AFLP markers. Mol Ecol 7(8):975–982

    Article  CAS  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hammer K, Filatenko AA, Pistrick K (2011) Taxonomic remarks on Triticum L. and × Triticosecale Wittm. Genet Resour Crop Evol 58:3–10

    Article  Google Scholar 

  • Harlan JR (1975) Our vanishing genetic resources. Science 188(4188):618–621

    Google Scholar 

  • Hirosawa S, Takumi S, Ishii T, Kawahara T, Nakamura C, Mori N (2004) Chloroplast and nuclear DNA variation in common wheat: insight into the origin and evolution of common wheat. Genes & Genetic Systems 79(5):271–282

    Article  CAS  Google Scholar 

  • Hori T, Tsunewaki K (1967) Study on substitution lines of several emmer wheats having the cytoplasm of Triticum boeoticum. Seiken Ziho 19:55–59

    Google Scholar 

  • Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R et al (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 99(12):8133

    Article  PubMed  CAS  Google Scholar 

  • Ishii T, Mori N, Ogihara Y (2001) Evaluation of allelic diversity at chloroplast microsatellite loci among common wheat and its ancestral species. Theor Appl Genet 103(6):896–904

    Article  CAS  Google Scholar 

  • Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9(4):286–298

    Article  PubMed  CAS  Google Scholar 

  • Kilian B, Özkan H, Deusch O, Effgen S, Brandolini A, Kohl J et al (2007) Independent wheat B and G genome origins in outcrossing Aegilops progenitor haplotypes. Mole. Bio. Evol. 24(1):217

    Article  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mole. Evol. 16(2):111–120

    Article  CAS  Google Scholar 

  • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451

    Article  PubMed  CAS  Google Scholar 

  • Lilienfeld F (1951) H. Kihara: genome-analysis in Triticum and Aegilops. Cytologia 16(2):101–123

    Article  Google Scholar 

  • Luo MC, Yang ZL, You FM, Kawahara T, Waines JG, Dvorak J (2007) The structure of wild and domesticated emmer wheat populations, gene flow between them, and the site of emmer domestication. Theor Appl Genet 114(6):947–959

    Article  PubMed  Google Scholar 

  • Maan S (1973) Cytoplasmic and cytogenetic relationships among tetraploid Triticum species. Euphytica 22(2):287–300

    Article  Google Scholar 

  • Maan S, Lucken KA (1971) Nucleo-cytoplasmic interactions involving Aegilops cytoplasms and Triticum genomes. J Hered 62(3):149–152

    Article  Google Scholar 

  • Mori N, Liu YG, Tsunewaki K (1995) Wheat phylogeny determined by RFLP analysis of nuclear DNA. 2. wild tetraploid wheats. Theor Appl Genet 90(1):129–134

    Article  CAS  Google Scholar 

  • Mori N, Moriguchi T, Nakamura C (1997) RFLP analysis of nuclear DNA for study of phylogeny and domestication of tetraploid wheat. Genes & Genetic Systems 72(3):153–161

    Article  CAS  Google Scholar 

  • Mori N, Ishii T, Ishido T, Hirosawa S, Watatani H, Kawahara T, et al (2003). Origin of domesticated emmer and common wheat inferred from chloroplast DNA fingerprinting. In: Paper presented at the 10th international wheat genetics symposium, pp 1–6

  • Mori N, Kondo Y, Ishii T, Kawahara T, Valkoun J, Nakamura C (2009) Genetic diversity and origin of timopheevii wheat inferred by chloroplast DNA fingerprinting. Breed. Sci. 59(5):571–578

    Article  CAS  Google Scholar 

  • Nesbitt M, Samuel D (1996) From staple crop to extinction? The archaeology and history of the hulled wheats. In: Padulosi S, Hammer K, Heller J (eds) Hulled wheats. Proceedings of the 1st international workshop on hulled wheats. Castelvecchio Pascoli. Italy, pp 41–100

  • Nesbitt M, Samuel D (1998) Wheat domestication: archaeobotanical evidence. Science 279(5356):1431

    Article  Google Scholar 

  • Ogihara Y, Tsunewaki K (1982) Molecular basis of the genetic diversity of the cytoplasm in Triticum and Aegilops, 1: diversity of the chloroplast genome and its lineage revealed by the restriction pattern of ct-DNAs. Jpn J Genet 57:371–396

    Article  Google Scholar 

  • Özkan H, Brandolini A, Schäfer-Pregl R, Salamini F (2002) AFLP analysis of a collection of tetraploid wheats indicates the origin of emmer and hard wheat domestication in southeast Turkey. Mole. Bio. Evol. 19(10):1797–1801

    Article  Google Scholar 

  • Özkan H, Brandolini A, Pozzi C, Effgen S, Wunder J, Salamini F (2005) A reconsideration of the domestication geography of tetraploid wheats. Theor Appl Genet 110(6):1052–1060

    Article  PubMed  Google Scholar 

  • Özkan H, Willcox G, Graner A, Salamini F, Kilian B (2011) Geographic distribution and domestication of wild emmer wheat (Triticum dicoccoides). Genet Resour Crop Evol 58(1):11–53

    Article  Google Scholar 

  • Rawal K, Harlan J (1975) Cytogenetic analysis of wild emmer populations from Turkey and Israel. Euphytica 24(2):407–411

    Article  Google Scholar 

  • Rodriguez S, Perera E, Maestra B, Diez M, Naranjo T (2000) Chromosome structure of Triticum timopheevii relative to T. turgidum. Genome 43(6):923–930

    PubMed  CAS  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132(3):365–386

    PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mole. Bio. Evol. 4(4):406

    CAS  Google Scholar 

  • Salamini F, Özkan H, Brandolini A, Schafer-Pregl R, Martin W (2002) Genetics and geography of wild cereal domestication in the near east. Nat Rev Genet 3(6):429–441

    PubMed  CAS  Google Scholar 

  • Takenaka S, Kawahara T (2012) Evolution and dispersal of emmer wheat (Triticum sp.) from novel haplotypes of Ppd-1 (photoperiod response) genes and their surrounding DNA sequences. Theor Appl Genet 125(5):999–1014

    Article  PubMed  CAS  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Bio. Evol. 28(10):2731–2739

    Article  CAS  Google Scholar 

  • Tanaka M, Kawahara T, Sano J (1978) The origin and the evolution of tetraploid wheats. Wheat Inf. Serv. 47–48:7–11

    Google Scholar 

  • Tanno K, Willcox G (2006) How fast was wild wheat domesticated? Science 311(5769):1886

    Article  PubMed  CAS  Google Scholar 

  • Tsunewaki K (2009) Plasmon analysis in the Triticum–Aegilops complex. Breed. Sci. 59(5):455–470

    Article  CAS  Google Scholar 

  • Wilhelm EP, Turner AS, Laurie DA (2009) Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.). Theor Appl Genet 118(2):285–294

    Article  PubMed  CAS  Google Scholar 

  • Zohary D, Hopf M (2000) Domestication of plants in the old world: the origin and spread of cultivated plants in west Asia, Europe, and the Nile valley. Oxford University Press, USA

    Google Scholar 

Download references

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Authors and Affiliations

  1. Laboratory of Crop Evolution, Plant Germ-plasm Institute, Graduate School of Agriculture, Kyoto University, Muko, Kyoto, 617-0001, Japan

    Shotaro Takenaka & Taihachi Kawahara

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  1. Shotaro Takenaka
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  2. Taihachi Kawahara
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Correspondence to Shotaro Takenaka.

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Takenaka, S., Kawahara, T. Evolution of tetraploid wheat based on variations in 5′ UTR regions of Ppd-A1: evidence of gene flow between emmer and timopheevi wheat. Genet Resour Crop Evol 60, 2143–2155 (2013). https://doi.org/10.1007/s10722-013-9983-2

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