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Genetic structure and diversity of Triticum monococcum ssp. aegilopoides and T. urartu in Iran

Published online by Cambridge University Press:  08 April 2014

Fatemeh Nasernakhaei ,
Mohammad Reza Rahiminejad ,
Hojjatollah Saeidi  and
Manoochehr Tavassoli
Fatemeh Nasernakhaei
Affiliation:
Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
Mohammad Reza Rahiminejad*
Affiliation:
Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
Hojjatollah Saeidi
Affiliation:
Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
Manoochehr Tavassoli
Affiliation:
Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
*
*Corresponding author. E-mail: [email protected]
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Abstract

To preliminarily evaluate the genetic diversity of the Iranian diploid Triticum L. gene pool, in this study, a total of 176 individuals belonging to T. monococcum L. ssp. aegilopoides (Link) Thell. and T. urartu Thum. ex Gandil. were pre-screened using single-strand conformation polymorphism (SSCP) analysis of the Acc-1 and Pgk-1 loci. A selected set of 76 DNA samples corresponding to the observed SSCP variants were sequenced for both loci and evaluated for nucleotide diversity associated with the taxonomic groups and geographical regions. We found three haplotypes, including one that was new for Iran, at each locus. Population structure and analysis of molecular variation results proved that the collection evaluated could be genetically divided into two distinct groups, which to a great extent was in accordance with the taxonomic classification. A genetic leakage from T. monococcum ssp. aegilopoides into T. urartu was observed during structure analysis, which was inferred on the basis of occasional outcrossing, despite their inbreeding nature. The results revealed that there was no variation within the populations belonging to T. urartu, while a meaningful variation was found between the geographical regions for T. monococcum ssp. aegilopoides. The median-joining networks revealed a conflict between morphology and haplotype variation, which was interpreted on the basis of introgressive hybridization, recombination signature and rapid speciation. In conclusion, we suggest that SSCP analysis is a useful tool in regions where thorough sequencing of an enormous number of DNA samples is time consuming and not affordable.

Keywords

Acc-1diploidgenetic diversityPgk-1population structureTriticum
Type
Research Article
Information
Plant Genetic Resources , Volume 13 , Issue 1 , April 2015 , pp. 1 - 8
Copyright
Copyright © NIAB 2014 

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References

Adderley, S and Sun, G (2014) Molecular evolution and nucleotide diversity of nuclear plastid phosphoglycerate kinase (PGK) gene in Triticeae (Poaceae). Gene 533: 142–148.CrossRefGoogle ScholarPubMed
Avise, JC (2000) Phylogeography: The History and Formation of Species. Cambridge: Harvard University Press.CrossRefGoogle Scholar
Bandelt, HJ, Forster, P and Rohl, A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37–48.Google Scholar
Chantret, N, Salse, J, Sabot, F, Rahman, S, Bellec, A, Laubin, B, Dubois, I, Dossat, C, Sourdille, P, Joudrier, P, Gautier, MF, Cattolico, L, Beckert, M, Aubourg, S, Weissenbach, J, Caboche, M, Bernard, M, Leroy, P and Chalhoub, B (2005) Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). The Plant Cell 17: 1033–1045.Google Scholar
Doyle, JJ (1992) Gene trees and species trees: molecular systematic as one-character taxonomy. Systematic Botany 17: 144–163.CrossRefGoogle Scholar
Dvorak, J, Luo, MC and Akhunov, ED (2011) N.I. Vavilov's theory of centers of diversity in light of current understanding of wheat diversity, domestication and evolution. Czech Journal of Genetics and Plant Breeding 47: S20–S27.Google Scholar
Earl, DA and vonHoldt, BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Excoffier, L, Smouse, P and Quattro, J (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479–491.CrossRefGoogle ScholarPubMed
Excoffier, L, Laval, G and Schneider, S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics 1: 47–50.Google Scholar
Fan, X, Zhang, HQ, Sha, LN, Zhang, L, Yang, RW, Ding, CB and Zhou, YH (2007) Phylogenetic analysis among Hystrix, Leymus and its affinitive genera (Poaceae: Triticeae) based on the sequences of gene encoding plastid acetyl-CoA carboxylase. Plant Science 174: 701–707.CrossRefGoogle Scholar
Gawel, NJ and Jarret, RL (1991) A modified CTAB DNA extraction procedure for Musa and Ipomoea . Plant Molecular Biology Reporter 9: 262–266.CrossRefGoogle Scholar
Golovnina, KA, Kondratenko, EY, Blinov, AG and Goncharov, NP (2009) Phylogeny of the A genome of wild and cultivated wheat species. Russian Journal of Genetics 43: 1360–1367.CrossRefGoogle Scholar
Goncharov, NP, Golovnina, KA, Kilian, B, Glushkov, S, Blinov, A and Shummy, K (2008) Evolutionary history of wheats – the main cereal of mankind. In: Dobretsov, N, Kolchanov, N, Rozanov, A and Zavarzin, G (eds) Biosphere Origin and Evolution. Berlin: Springer-Verlag, pp. 407–419.CrossRefGoogle Scholar
Hall, TA (1999) BioEdit: a user-friendly biological sequence alignment editor analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.Google Scholar
Haudry, A, Cenci, A, Ravel, C, Bataillon, T, Brunel, D, Poncet, C, Hochu, I, Poirier, S, Santoni, S, Glémin, S and David, J (2007) Grinding up wheat: a massive loss of nucleotide diversity since domestication. Molecular Biology and Evolution 24: 1506–1517.CrossRefGoogle Scholar
Heun, M, Schafer-Pregl, R, Klawan, D, Castagana, R, Accerbi, M, Borghi, B and Salamini, F (1997) Site of einkorn wheat domestication identified by DNA fingerprinting. Science 278: 1312–1314.CrossRefGoogle Scholar
Huang, S, Sirikhachornkit, A, Su, X, Faris, J, Gill, B, Haselkorn, R and Gornicki, P (2002 a) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proceedings of the National Academy of Sciences of the United States of America 99: 8133–8138.Google Scholar
Huang, S, Sirikhachornkit, A, Faris, JD, Su, X, Gill, BS, Haselkorn, R and Gornicki, P (2002 b) Phylogenetic analysis of the acetyl-CoA carboxylase and 3-phosphoglycerate kinase loci in wheat and other grasses. Plant Molecular Biology 48: 805–820.Google Scholar
Jakobsson, M and Rosenberg, NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801–1806.Google Scholar
Kang, HY, Fan, X, Zhang, HQ, Sha, LN, Sun, GL and Zhou, YH (2010) The origin of Triticum petropavlovskyi Udacz. et Migusch.: demonstration of the utility of the genes encoding plastid acetyl-CoA carboxylase sequence. Molecular Breeding 25: 381–395.Google Scholar
Kilian, B, Ozkan, H, Deusch, O, Effgen, S, Brandolini, A, Kohl, J, Martin, W and Salamini, F (2007 a) Independent wheat B and G genome origins in out-crossing Aegilops progenitor haplotypes. Molecular Biology and Evolution 24: 217–227.CrossRefGoogle Scholar
Kilian, B, Özkan, H, Walther, A, Kohl, J, Dagan, T, Salamini, F and Martin, W (2007 b) Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (Einkorn) domestication: implication for the origin of agriculture. Molecular Biology and Evolution 24: 2657–2668.CrossRefGoogle ScholarPubMed
Liberado, P and Rozas, J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452.CrossRefGoogle Scholar
Lischer, HEL and Excoffier, L (2012) PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28: 298–299.CrossRefGoogle ScholarPubMed
Longstaff, M, Raines, CA, McMorrow, EM, Bradbeer, JW and Dyer, TA (1989) Wheat phosphoglycerate kinase: evidence for recombination between the genes for the chloroplastic and cytosolic enzymes. Nucleic Acids Research 17: 6569–6580.Google Scholar
Maleki, M, Naghavi, MR, Alizadeh, H, Potki, P, Kazemi, M, Pirseyedi, SM, Mardi, M and Fakhr Tabatabaei, M (2006) Study of genetic variation in wild diploid wheat (Triticum boeoticum) from Iran using AFLP markers. Iranian Journal of Biotechnology 4: 269–274.Google Scholar
Maxted, N, Kell, S and Ford-Lloyd, B (2008) Crop wild relative conservation and use: establishing the context. In: Maxted, N, Ford-Lloyd, B, Kell, S, Iriondo, JM, Dulloo, E and Turok, J (eds) Crop Wild Relative Conservation and Use. Wallingford: CABI Publishing, pp. 3–30.Google Scholar
Naghavi, MR, Malaki, M, Alizadeh, H, Pirseiedi, M and Mardi, M (2009) An assessment of genetic diversity in wild diploid wheat Triticum boeoticum from West of Iran using RAPD, AFLP and SSR markers. Journal of Agricultural Science and Technology 11: 585–598.Google Scholar
Nasernakhaei, F, Rahiminejad, MR, Saeidi, H and Tavassoli, M (2013) Taxonomic identity of the Iranian diploid Triticum as evidenced by nrDNA ITS analysis. Phytotaxa 143: 43–53.Google Scholar
Nei, M (1987) Molecular Evolutionary Genetics. New York: Columbia University Press.Google Scholar
Nejat-Boshehri, AA and Fakhr Tabatabaei, M (2001) Protein fingerprinting of Triticum thaoudar Reut. population in Iran. Iranian Journal of Agriculture Science 3: 567–573 (in Persian).Google Scholar
Nesbitt, M (2001) Wheat evolution: integrating archaeological and biological evidence. In: Caligari, PDS and Brandham, PE (eds) Wheat Taxonomy: The Legacy of John Percival. London: The Linnean Society of London, pp. 37–59.Google Scholar
Peng, J, Sun, D and Nevo, E (2011) Domestication evolution, genetics and genomics in wheat. Molecular Breeding 28: 281–301.Google Scholar
Pritchard, JK, Stephens, P and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Puchta, H (2005) The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. Journal of Experimental Botany 56: 1–14.Google Scholar
Riehl, S, Benz, M, Conard, NJ, Darabi, H, Deckers, K, Fazeli Nashli, H and Zeidi-Kulehparcheh, M (2012) Plant use in three Pre-Pottery Neolithic sites of the northern and eastern Fertile Crescent: a preliminary report. Vegetation History and Archaeobotany 21: 95–106.Google Scholar
Riehl, S, Zeidi, M and Conard, NJ (2013) Emergence of agriculture in the foothills of the Zagros Mountains of Iran. Science 341: 65–67.Google Scholar
Rodriguez, F, Cai, D, Teng, Y and Spooner, D (2011) Asymmetric single-strand conformation polymorphism: an accurate and cost-effective method to amplify and sequence allelic variants. American Journal of Botany 98: 1061–1067.CrossRefGoogle ScholarPubMed
Rosenberg, NA (2004) DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes 4: 137–138.Google Scholar
Sanguinetti, CJ, Dias Neto, E and Simpson, AJG (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17: 915–919.Google Scholar
Sasaki, Y and Nagano, Y (2004) Plant acetyl-CoA carboxylase: structure, biosynthesis, regulation, and gene manipulation for plant breeding. Bioscience, Biotechnology, and Biochemistry 68: 1175–1184.CrossRefGoogle ScholarPubMed
Takenaka, SH, Mori, N and Kawahara, T (2010) Genetic variation in domesticated emmer wheat (Triticum turgidum L.) in and around Abyssinian highlands. Breeding Science 60: 212–227.Google Scholar
van Slageren, MW (1994) Wild Wheats: A Monograph of Aegilops L. and Amblyopyrum (Jaub. & Spach) Eig. (Poaceae). Wageningen: Wageningen Agricultural University.Google Scholar
Wicker, T, Krattinger, SG, Lagudah, ES, Komatsuda, T, Pourkheirandish, M, Matsumoto, T, Cloutier, S, Reiser, L, Kanamori, H, Sato, K, Perovic, D, Stein, N and Keller, B (2009) Analysis of intraspecies diversity in wheat and barley genomes identifies breakpoints of ancient haplotypes and provides insight into the structure of diploid and hexaploid Triticeae gene pools. Plant Physiology 149: 258–270.Google Scholar
Zohary, D and Hopf, M (2000) Domestication of Plants in the Old World. Oxford: Oxford University Press.Google Scholar
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