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Modern hexaploid bread wheat has been derived by human selection from at least 3 diploid ancestors. We sought to understand the effects of this domestication on the rhizosphere microbiome by recapitulating the hybridization event, which occurred over the last ten thousand years with the formation of synthetic hexaploid wheat (SHW) by introducing the DD genome of Aegilops tauschii into tetraploid Triticum durum. The rhizosphere communities of 22 wheat accessions (wild: T. dicoccoides, Ae. tauschii, modern: T. aestivum, T. durum, and synthetic: Synthetic Hybrid Wheat lines (SHW) and back-cross lines (BC)) were then analyzed. Major differences occurred in the prokaryotic community between bulk soil and the rhizosphere of different plants, with subtler differences in the eukaryotic community. AM fungi (Glomeromycota) were present in all wheat lines, but especially abundant in the diploid Ae. tauschii. The fungal communities of the synthetic hexaploid lines were more similar to the parental species Ae. tauschii than to the other hexaploid lines, indicating the DD genome plays a major role in selection of several fungal genera and Nematoda. Furthermore, domestication has influenced the contribution of the DD genome on the selection of the wheat microbiome indicating it is at least partly under plant genetic control. Understanding this is an important first step in incorporating the soil microbiome into plant breeding. |