Population structure of wild wheat D-genome progenitor Aegilops tauschii Coss.: implications for intraspecific lineage diversification and evolution of common wheat NOBUYUKI MIZUNO,* MASANORI YAMASAKI,† YOSHIHIRO MATSUOKA,‡ TAIHACHI KAWAHARA§ and SHIGEO TAKUMI* *Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan, †Food Resources Education and Research Centre, Kobe University, Kasai, Hyogo 675-2103, Japan, ‡Fukui Prefectural University, Matsuoka, Eiheiji, Yoshida, Fukui 910-1195, Japan, §Graduate School of Agriculture, Kyoto University, Muko 617-0001, Japan Abstract Aegilops tauschii Coss. is the D-genome progenitor of hexaploid wheat. Aegilops tauschii, a wild diploid species, has a wide natural species range in central Eurasia, spreading from Turkey to western China. Amplified fragment length polymorphism (AFLP) analysis using a total of 122 accessions of Ae. tauschii was conducted to clarify the population structure of this widespread wild wheat species. Phylogenetic and principal component analyses revealed two major lineages in Ae. tauschii. Bayesian population structure analyses based on the AFLP data showed that lineages one (L1) and two (L2) were respectively significantly divided into six and three sublineages. Only four out of the six L1 sublineages were diverged from those of western habitats in the Transcaucasia and northern Iran region to eastern habitats such as Pakistan and Afghanistan. Other sublineages including L2 were distributed to a limited extent in the western region. Subspecies strangulata seemed to be differentiated in one sublineage of L2. Among three major haplogroups (HG7, HG9 and HG16) previously identified in the Ae. tauschii population based on chloroplast variation, HG7 accessions were widely distributed to both L1 and L2, HG9 accessions were restricted to L2, and HG16 accessions belonged to L1, suggesting that HG9 and HG16 were formed from HG7 after divergence of the first two lineages of the nuclear genome. These results on the population structure of Ae. tauschii and the genealogical relationship among Ae. tauschii accessions should provide important agricultural and evolutionary knowledge on genetic resources and conservation of natural genetic diversity. Keywords: genetic resource, intraspecific variation, local adaptation, nuclear and cytoplasmic differentiation, population structure, wild wheat Received 29 September 2009; revision received 13 December 2009; accepted 28 December 2009 Introduction Domestication is the process of genetic selection that, by altering key traits, transforms wild forms into domesticated varieties of crops (Salamini et al. 2002). Molecular evolutionary studies have made the origin of crops much clearer than before (Doebley et al. 2006; Pu- rugganan & Fuller 2009). This is particularly the case for the major crops that were domesticated from the wild ancestors without undergoing changes in ploidy. For example, phylogeographic analyses based on nuclear and chloroplast DNA sequences showed multi- ple evolutionary origins for cultivated rice in eastern Asia (Londo et al. 2006) and barley in the Fertile Cres- cent and Central Asia (Morrell & Clegg 2007; Saisho & Purugganan 2007), whereas phylogenetic analyses based on multilocus microsatellite genotyping showed a single domestication event for maize ca. 9000 years ago (Matsuoka et al. 2002). Correspondence: Shigeo Takumi, Fax: +81 78 803 5859; E-mail: takumi@kobe-u.ac.jp Ó 2010 Blackwell Publishing Ltd Molecular Ecology (2010) 19, 999–1013 doi: 10.1111/j.1365-294X.2010.04537.x