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Title: Dynamic evolution of Rht-1 homologous regions in grass genomes

Author
item WU, JING - Chinese Academy Of Agricultural Sciences
item KONG, XIUYING - Chinese Academy Of Agricultural Sciences
item SHI, CHAO - Chinese Academy Of Agricultural Sciences
item Gu, Yong
item JIN, CUIYUN - Chinese Academy Of Agricultural Sciences
item GAO, LIZHI - Chinese Academy Of Agricultural Sciences
item JIA, JIZENG - Chinese Academy Of Agricultural Sciences

Submitted to: PLoS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/18/2013
Publication Date: 9/24/2013
Citation: Wu, J., Kong, X., Shi, C., Gu, Y.Q., Jin, C., Gao, L., Jia, J. 2013. Evolutionary dynamics of Rht-1, a "green revolution" gene homologous regions across the subgenomes, ploids and related grass genomes. PLoS One. 8(9):e75544.

Interpretive Summary: The reduced height genes (Rht-1) in wheat play a major role in modern agriculture due to their dwarfing trait which provides plants with increased resistance to lodging often caused by heavy rains and strong winds. In this study, we identified, sequenced Rht-1 regions from the diploid, tetraploid and hexaploid wheat species, and then investigated the molecular basis of genomic rearrangements that occurred at the Rht-1 locus by comparing corresponding sequences of diploid, tetraploid, and hexaploid wheat species (Triticum and Aegilops), which diverged relatively recently. We also focused on the characterization of sequence variation to investigate molecular evolution of the wheat Rht-1 homologous genomic regions during the process of polyploidization. To gain a broad insight into the patterns and evolutionary mechanisms of the Rht-1 homologous regions along diverse grass lineages, we also included and compared with the corresponding genomic regions from O. sativa, B. distachyon, S. bicolor, Z. mays and S. italic. The comparative analyses of these regions provided the first view of sequence divergence on a large scale in the wheat A, B, and D genomes, and enhanced our understanding of molecular evolution of Rht-1 genomic regions across diverse lineages of grasses.

Technical Abstract: Bread wheat contains A, B, and D subgenomes with its well characterized ancestral genomes that exist at the diploid and tetraploid levels. Therefore, the wheat genome system acts as a model specie for studying genome evolutionary dynamics. Here, we performed intra- and inter-species comparative analysis of wheat and related grass genomes to examine the dynamics of homologous regions surrounding Rht-1, a well-known “green revolution” gene. Our results showed that the divergence of the two A genomes in the Rht-1 region from the diploid and tetraploid species is greater than that from the tetraploid and hexaploid wheats. The divergence of D genome between diploid and hexaploid is less than those of A genome, suggesting that D genome divergence is latter than the A and B genomes. The divergences among the subgenome of wheat were greater than those among homologous genomes from different ploids. However, several conserved non-coding sequences were identified to be shared among three subgenomes of wheat, suggesting that they may play important role to keep the homoeologous of three subgenomes. This is a pilot study on wheat evolutional dynamics across ploids, subgenomes and different grasses. These results provided new insights into our understanding of evolutional dynamics at the genomic sequence level as well as offered a useful resource for research including selective sweep analysis and haplotype detection in crops.