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The introns in FLOWERING LOCUS T-LIKE (FTL) genes are useful markers for tracking paternity in tetraploid Chenopodium quinoa Willd.

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Abstract

Quinoa (Chenopodium quinoa) is an important crop of the Andean region of South America. It is an allotetraploid closely related to Chenopodium berlandieri Moq. with largely unknown genomic structure. We used the third introns of two FLOWERING LOCUS T-LIKE genes, CrFTL1 and CrFTL2 as markers in an attempt to identify ancestral origins of the two diploid subgenomes of quinoa. The introns underwent rapid evolution with frequent indel losses and gains, including a recent insertion of mitochondrial DNA in C. quinoa. However, they could be unambiguously aligned and used for the construction of phylogenetic trees. We distinguished two parental subgenomes participating in the origin of quinoa. One parent was related to North American C. standleyanum Aellen, C. incanum (S. Wats.) Heller, or another closely related diploid. The other parent was close to Eurasian C. suecicum J. Murr, C. ficifolium Sm. or another related diploid species. Quinoa is a promising grain crop owing to its salt and drought tolerance. Its importance grows as the change of world climate deepens. Understanding its ancestry will help to facilitate future breeding efforts to improve quinoa’s poor heat and biotic stress resistances.

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References

  • Aellen P, Just T (1943) Key and synopsis of American species of the genus Chenopodium L. Am Midl Nat 30:47–76

    Article  Google Scholar 

  • Alvarez I, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29:417–434. doi:10.1016/S1055-7903(03)00208-2

    Article  CAS  PubMed  Google Scholar 

  • Borsch T, Quandt D (2009) Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Syst Evol 282:169–199. doi:10.1007/s00606-009-0210-8

    Article  CAS  Google Scholar 

  • Cháb D, Kolář J, Olson MS, Štorchová H (2008) Two Flowering Locus T (FT) homologs in Chenopodium rubrum differ in expression patterns. Planta 228:929–940. doi:10.1007/s00425-008-0792-3

  • Christensen SA, Pratt DB, Pratt C, Nelson PT, Stevens MR, Jellen EN, Coleman CE et al (2007) Assessment of genetic diversity in the USDA and CIP-FAO international nursery collections of quinoa (Chenopodium quinoa Willd.) using microsatellite markers. Plant Genet Resour Charact Util 5:82–95. doi:10.1017/S1479262107672293

    Article  CAS  Google Scholar 

  • Clemants SE, Mosyakin SL (2003) Flora of North America, vol 4. http://www.efloras.org. Accessed 1 Aug 2014

  • Crepet WL, Niklas KJ (2009) Darwin second “abominable mystery”: Why are there so many angiosperm species? Am J Bot 96:366–381. doi:10.3732/ajb.0800126

    Article  PubMed  Google Scholar 

  • Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772

    Article  CAS  PubMed  Google Scholar 

  • Duarte JM, Wall PK, Edger PP, Landherr LL, Ma H, Pires JC, Leebens-Mack J, dePamphilis CW (2010) Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol Biol 10:61. doi:10.1186/1471-2148-10-61

    Article  PubMed Central  PubMed  Google Scholar 

  • Fuentes-Bazan S, Mansion G, Borsch T (2012a) Towards a species level tree of the globally diverse genus Chenopodium (Chenopodiaceae). Mol Phylogenet Evol 62:359–374. doi:10.1016/j.ympev.2011.10.006

    Article  PubMed  Google Scholar 

  • Fuentes-Bazan S, Uotila P, Borsch T (2012b) A novel phylogeny-based generic classification for Chenopodium sensu lato, and a tribal rearrangement of Chenopodioideae (Chenopodiaceae). Willdenowia 42:5–24. doi:10.3372/wi42.42101

  • Hughes CE, Eastwood RJ, Bailey CD (2006) From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Philos Trans R Soc B Biol Sci 361:211–225. doi:10.1098/rstb.2005.1735

    Article  Google Scholar 

  • Iehisa JCM, Shimizu A, Sato K, Nishijima R, Sakaguchi K, Matsuda R, Nasuda S, Takumi S (2014) Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii. Theor Appl Genet 127:261–271. doi:10.1007/s00122-013-2215-5

    Article  CAS  PubMed  Google Scholar 

  • Kardailsky I, Shukla VK, Ahn JH, Dagenais N, Christensen SK, Nguyen JT, Chory J et al (1999) Activation tagging of the floral inducer FT. Science 286:1962–1965. doi:10.1126/science.286.5446.1962

    Article  CAS  PubMed  Google Scholar 

  • Kolano B, Gardunia BW, Michalska M, Bonifacio A, Fairbanks D, Maughan PJ, Coleman CE et al (2011) Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome. Genome 54:710–717. doi:10.1139/G11-035

    Article  CAS  PubMed  Google Scholar 

  • Lee JH, Hong SM, Yoo SJ, Park OK, Lee JS, Ahn JH (2006) Integration of floral inductive signals by flowering locus T and suppressor of overexpression of Constans 1. Physiol Plant 126:475–483. doi:10.1111/j.1399-3054.2005.00619.x

    CAS  Google Scholar 

  • Leister D (2005) Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet 21:655–663. doi:10.1016/j.tig.2005.09.004

    Article  CAS  PubMed  Google Scholar 

  • Maughan PJ, Kolano BA, Maluszynska J, Coles ND, Bonifacio A, Rojas J, Coleman CE et al (2006) Molecular and cytological characterization of ribosomal RNA genes in Chenopodium quinoa and Chenopodium berlandieri. Genome 49:825–839. doi:10.1139/G06-033

    Article  CAS  PubMed  Google Scholar 

  • Maughan PJ, Yourstone SM, Jellen EN, Udall JA (2009) SNP discovery via genomic reduction, barcoding, and 454-pyrosequencing in Amaranth. Plant Genome 2:260–270. doi:10.3835/plantgenome2009.08.0022

    Article  CAS  Google Scholar 

  • Maughan PJ, Smith SM, Rojas-Beltrán JA, Elzinga D, Raney JA, Jellen EN, Bonifacio A et al (2012) Single nucleotide polymorphism identification, characterization, and linkage mapping in quinoa. Plant Genome 5:114–125. doi:10.3835/plantgenome2012.06.0011

    Article  CAS  Google Scholar 

  • Mosyakin SL, Clemants SE (1996) New infrageneric taxa and combinations in Chenopodium L. (Chenopodiaceae). Novon 6:398–403

    Article  Google Scholar 

  • Muller K (2005) SeqState—primer design and sequence statistics for phylogenetic DNA data sets. Appl Bioinform 4:65–69

    Article  Google Scholar 

  • Noutsos C, Richly E, Leister D (2005) Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants. Genome Res 15:616–628. doi:10.1101/gr.9788705

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581–583. doi:10.1093/bioinformatics/btm388

    Article  CAS  PubMed  Google Scholar 

  • Partap T, Joshi BD, Galway NW (1998) Chenopods. Chenopodium spp. (Promoting the conservation and use of underutilized and neglected crops). 22. Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany, & the International Plant Genetic Resources Institute, Rome, Italy

  • Pin PA, Benlloch R, Bonnet D, Wremerth-Weich E, Kraft T, Gielen JJL, Nilsson O (2010) An antagonistic pair of FT homologs mediates the control of flowering time in sugar beet. Science 330:397–1400. doi:10.1126/science.1197004

    Article  Google Scholar 

  • Rambaut A (2012) FigTree, version v1.4. for Windows. Computer program and documentation distributed by the author, website: http://tree.bio.ed.ac.uk/software/figtree/. Accessed 1 Aug 2014

  • Rana TS, Narzary D, Ohri D (2010) Genetic diversity and relationships among some wild and cultivated species of Chenopodium L. (Amaranthaceae) using RAPD and DAMD methods. Curr Sci India 98:840–846

    CAS  Google Scholar 

  • Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B et al (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542. doi:10.1093/sysbio/sys029

    Article  PubMed Central  PubMed  Google Scholar 

  • Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49:369–381

    Article  CAS  PubMed  Google Scholar 

  • Soltis DE, Soltis PS (2009) The role of hybridization in plant speciation. Annu Rev Plant Biol 60:561–588. doi:10.1146/annurev.arplant.043008.092039

    Article  CAS  PubMed  Google Scholar 

  • Štorchová H, Hrdličková R, Chrtek J Jr, Tetera M, Fitze D, Fehrer J (2000) An improved method of DNA isolation from plants collected in the field and conserved in saturated NaCl/CTAB solution. Taxon 49:79–84. doi:10.2307/1223934

    Article  Google Scholar 

  • Swofford DL (2003) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts

  • Udall JA, Wendel JF (2006) Polyploidy and crop improvement. Crop Sci 46:S3–S14. doi:10.2135/cropsci2006.07.0489tpg

    Article  Google Scholar 

  • Wilson HD (1980) Artificial hybridization among species of Chenopodium sect. Chenopodium. Syst Bot 5:253–263. doi:10.2307/2418372

    Article  Google Scholar 

  • Yamaguchi A, Kobayashi Y, Goto K, Abe M, Araki T (2005) TWIN SISTER OF FT (TSF) acts as a floral pathway integrator redundantly with FT. Plant Cell Physiol 46:1175–1189. doi:10.1093/pcp/pci151

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors thank C. E. Coleman and two anonymous reviewers for helpful comments, P. Kominek and J. Dostálek for Chenopodium seeds, and L. Pollicino for help with sequencing. Some useful advice from K. Krák on phylogenetic analysis and the excellent technical assistance of K. Haškovcová are highly appreciated. Financial support was provided through the Grant Agency of the Czech Republic P506/12/1359 to H.S.

Conflict of interest

The authors declare that they have no conflicts of interest.

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Authors and Affiliations

  1. Plant Reproduction Laboratory, Institute of Experimental Botany v.v.i., Academy of Sciences of the Czech Republic, 16500, Prague, Lysolaje, Czech Republic

    Helena Štorchová, Jana Drabešová, David Cháb & Jan Kolář

  2. Department of Plant and Wildlife Science, Brigham Young University, Provo, UT, 84602, USA

    Eric N. Jellen

Authors
  1. Helena Štorchová
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  2. Jana Drabešová
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  3. David Cháb
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  4. Jan Kolář
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  5. Eric N. Jellen
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Corresponding author

Correspondence to Helena Štorchová.

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Štorchová, H., Drabešová, J., Cháb, D. et al. The introns in FLOWERING LOCUS T-LIKE (FTL) genes are useful markers for tracking paternity in tetraploid Chenopodium quinoa Willd.. Genet Resour Crop Evol 62, 913–925 (2015). https://doi.org/10.1007/s10722-014-0200-8

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