United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA.
Mol Genet Genomics. 2012 Dec;287(11-12):855-66. doi: 10.1007/s00438-012-0721-9. Epub 2012 Sep 28.
The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurately assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (A(u)A(u)) was analyzed by comparing its 277-kb large genomic region carrying the important Glu-1 locus with the homologous regions from the A genomes of the diploid T. monococcum (A(m)A(m)), tetraploid T. turgidum (AABB), and hexaploid T. aestivum (AABBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the A(u) genome and the A genomes in polyploid wheats, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats originated from the diploid A(u) genome. The difference in the compared region between A(u) and A is mainly caused by four differential TE insertion and two deletion events between these genomes. The estimated divergence time of A genomes calculated on nucleotide substitution rate in both shared TEs and collinear genes further supports the closer evolutionary relationship of A to A(u) than to A(m). The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the A(u) sequence for mapping the A genome in hexaploid wheat. Eighty percent of these repeat junction markers were successfully mapped to the corresponding region in hexaploid wheat, suggesting that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat.
六倍体小麦（T. aestivum，AABBDD）的多倍体性质在遗传图谱、重要基因的图谱定位克隆以及测序和基因组精确组装等各个方面都带来了巨大的挑战。为了探索多倍体小麦祖先二倍体物种的应用价值，我们通过比较携带重要Glu-1 基因座的 277kb 大片段基因组区域，分析了 T. urartu（A(u)A(u)）的序列变异，该区域与二倍体 T. monococcum（A(m)A(m)）、四倍体 T. turgidum（AABB）和六倍体 T. aestivum（AABBDD）的同源区域进行了比较。结果表明，除了高度的基因共线性外，A(u)基因组和多倍体小麦 A 基因组中的嵌套反转录元件结构也得到了很好的保守，这表明多倍体小麦 A 基因组中的大多数重复序列来源于二倍体 A(u)基因组。A(u)和 A 之间比较区域的差异主要是由于这两个基因组之间的四个差异 TE 插入和两个缺失事件造成的。基于共享转座子和共线性基因的核苷酸替代率计算的 A 基因组的估计分歧时间进一步支持了 A 与 A(u)的进化关系比与 A(m)的更密切。重复区的结构保守性促使我们根据 A(u)序列开发了用于在六倍体小麦中定位 A 基因组的重复接头标记。这些重复接头标记中有 80%成功地映射到六倍体小麦的相应区域，这表明 T. urartu 可以作为一个有用的资源，用于开发六倍体小麦遗传和育种研究的分子标记。
