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Location: Genomics and Gene Discovery
Title: Exploring the diploid wheat ancestral A genome through sequence comparison at the High-Molecular-Weight glutenin locus region
Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 13, 2012
Publication Date: September 28, 2012
Citation: Dong, L., Huo, N., Wang, Y., Deal, K., Luo, M., Wang, D., Anderson, O.D., Gu, Y.Q. 2012. Exploring the diploid wheat ancestral A genome through sequence comparison at the High-Molecular-Weight glutenin locus region. Molecular Genetics and Genomics. 287:855-866.
Wheat is one of the most important food crop worldwide. However, due to its large and complex genome with polyploidy nature, map-based cloning of genes controlling important agronomical traits still represent a great challenge for wheat improvement. In this work, we explore the utility of diploid ancestor species of the modern hexaploid wheat to see if the sequence information in the ancestor genome can be directly used for genetic mapping in hexaploid wheat. We selected the T. urartu, the A genome donor of hexaploid wheat and sequenced a 277-kb genomic region carrying the gene controlling the baking quality of wheat flour. By comparing the sequences from the diploid species and bread wheat, we found that besides the conservation of gene contents and order, the sequences between these genes are also conserved. The primers designed based on sequence information from the diploid species can be directly applied for mapping in hexaploid wheat. Our result demonstrated that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat.
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 accurate assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (AuAu) 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 (AmAm), and polyploid T. turgidum (AtAtBB) and T. aestivum (AaAaBBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the Au, At and Aa genomes, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats was originated from the diploid Au genome. The difference in the compared region between Au and Aa 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 Aa to Au than to Am. The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the Au 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.