Submitted to: Functional and Integrative Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 1/7/2008
Publication Date: 1/2/2008
Citation: Faris, J.D., Zhang, Z., Fellers, J.P., Gill, B.S. 2008. Micro-colinearity between rice, Brachypodium, and Triticum monococcum at the wheat domestication locus Q. Functional and Integrative Genomics. 8:149-164 Interpretive Summary: Wheat is a cereal crop with a very large genome, which makes it difficult to conduct genome analysis and gene-discovery experiments. Rice is a distant relative of wheat with a small genome that has been extensively characterized. Therefore, many studies to determine the utility of the rice genome information for understanding the wheat genome have been conducted, but most have concluded that rice is not suitable for this purpose. Therefore, it has recently been proposed to use Brachypodium as a model for grass genomics, because it also has a small genome size and is more closely related to wheat than rice is. This study was conducted to compare the level of conservation at the DNA level (micro-colinearity) between wheat, rice and Brachypodium within a genomic region harboring the wheat domestication gene Q. We found that the micro-colinearity of genes was more conserved between wheat and rice than between wheat and Brachypodium. However, comparisons of the DNA sequences between colinear genes among the three species indicated that, evolutionarily, Brachypodium is more closely related to wheat than rice is. We conclude that, similar to rice, Brachypodium will be helpful for the genomic analysis of wheat, but will not preclude the need to conduct large-scale genomics experiments in wheat.
Technical Abstract: Brachypodium, a wild temperate grass with a small genome, was recently proposed as a new model organism for the large-genome grasses. However, few studies have been conducted to determine the level of conservation at the DNA level (micro-colinearity) between Brachypodium and wheat. In this study, we evaluated gene content and micro-colinearity between diploid wheat (Triticum monococcum), Brachypodium sylvaticum, and rice at a local genomic region harboring the major wheat domestication gene Q. Gene density was much lower in T. monococcum (one per 41 kb) due to gene duplication and an abundance of transposable elements within intergenic regions as compared to B. sylvaticum (one per 14 kb) and rice (one per 10 kb). For the Q gene region, micro-colinearity was more conserved between wheat and rice than between wheat and Brachpodium. B. sylvaticum contained two genes not present within the orthologous regions of T. monococcum and rice. Also, a 40S ribosomal-like gene present in T. monococcum and rice was highly degenerate in B. sylvaticum. However, an F-box-like gene present as a single copy in B. sylvaticum and four copies in T. monococcum was absent in rice. Phylogenetic analysis of Q and leukotriene A-4 hydrolase-like gene orthologs, which were colinear among the three species, showed that Brachypodium is more closely related to wheat than rice, which agrees with previous studies. We conclude that, similar to rice, Brachypodium will be a useful tool for gene discovery, comparative genomics, gene annotation, and the study of evolutionary relationships among the grasses, but will not preclude the need to conduct large-scale genomics experiments in the Triticeae.