Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/30/2008
Publication Date: 7/15/2008
Citation: Chalupska, D., Lee, H.Y., Faris, J.D., Evrard, A., Chalhoub, B., Haselkorn, R., Gornicki, P. 2008. Acc homoeoloci and the evolution of wheat genomes. Proceedings of the National Academy of Sciences. 105:9691-9696 Interpretive Summary: Common bread wheat is one of the world's most important crops, and it has a relatively complex genome compared to other crop species. Wheat evolved through the convergence of three ancestral grass species with relatively simple genomes.In recent decades, wheat's progenitor species have been identified through various studies. We examined the DNA sequences of 100 kilobase pairs spanning acetyl-CoA carboxylase (Acc) genes in wheat and its relatives to study wheat genome evolution. The homoeologous chromosomes of the wheat ancestors diverged about 2.3 million years ago (MYA). Wheat and barley diverged 11.6 MYA and wheat and rice diverged 50 MYA. Regions of DNA flanking the Acc genes were not conserved between the homoeologous genomes, and regions between genes consisted primarily of repetitive sequences and had higher substitution rates than regions within genes. This research indicates that tetraploid wheat formation occurred less than 0.5 MYA.
Technical Abstract: We analyzed the DNA sequences of BACs from many wheat libraries containing the Acc-1 and Acc-2 loci, encoding the plastid and cytosolic forms of the enzyme acetyl-CoA carboxylase, to gain understanding of the evolution of these genes and the origin of the three genomes in modern hexaploid wheat. More than 100 kb of DNA containing the Acc-1 and Acc-2 loci from each of the wheats Ttriticum urartu (A genome), Aegilops tauschii (D genome), T. turgidum (AB genome) and T. aestivum (ABD genome), as well as two Acc-2-related pseudogenes from T. urartu, were analyzed. The 2.3-2.4 million years ago (MYA) divergence time calculated here for the three homoeologous chromosomes, based on coding and intron sequences of the Acc-1 genes, is at the low end of previous estimates. Our clock was calibrated using 60 MYA for the divergence between wheat and maize. Using this scale, wheat and barley diverged 11.6 MYA based on sequences of Acc and other genes. The regions flanking the Acc genes are not conserved between the A, B and D genomes, but they are conserved among them.Substitution rates in intergenic regions consisting primarily of repetitive sequences vary substantially along the loci and on average are 3.5-fold higher than the Acc intron substitution rates. The composition of the Acc homoeoloci suggests haplotype divergence exceeding in some cases 0.5 MYA. Such variation might result in a significant overestimate of the time since tetraploid wheat formation, which occurred no more than 0.5 MYA.