Location: Genomics and Gene Discovery
2009 Annual Report
The omega gliadins, which comprise about 5-10% of wheat flour protein, have been implicated in wheat flour quality and wheat-related allergies. To further understand the biology of omega gliadins, we analyzed all available omega gliadin sequence information and investigated the details of the omega gliadin coding regions. Sequences derived from the orthologous Gli-3 loci in chromosome 1A, 1B and 1D were compared. The transcriptional activities of the omega gliadin genes were examined and the evidence of cysteine-containing omega gliadins in wheat was assessed.
To further analyze genes coding for major seed storage proteins in wheat, five BAC clones containing LMW-glutenin genes derived from a large contig spanning the protein storage protein regions have been sequenced and annotated. Comparative analysis with the orthologous regions from other cereal genomes has been performed.
Several marker systems based upon TE sequences have been developed, mostly based upon polymorphism at their sites of insertion. We exploited this property to develop molecular markers for genetic analysis in wheat. We utilized the retrotransposon-based insertion polymorphism to generate repeat DNA junction markers (RJM) to map four randomly chosen BAC clones to wheat chromosome arms. Our work allowed the rapid development of genome-specific PCR-based RJM using BES and random shotgun sequences from the D genome donor Ae. tauschii for use in hexaploid wheat.
In a study together with ARS and non-ARS collaborators, the effect of polyploidy in allohexaploid wheat was investigated. Large-scale analysis of nonadditive gene expression using DNA microarrays showed that approximately 16% of genes displayed nonadditive expression in synthetic T. aestivum. A certain fraction of the genes (2.9%) showed overdominance or underdominance. The data demonstrated that allopolyploidization, per se, results in rapid initiation of differential expression of homoeologous loci and nonadditive gene expression in T. aestivum.
The on-going project to develop and utilize Brachypodium as a model system for Triticeae research for grain quality and other traits has progressed significantly. We completed the construction of Brachypodium genome physical map and performed genome-wide comparison with wheat and rice. A comprehensive study of syntenic relationship between Brachypodium and wheat was carried out. Seven wheat BAC contigs each spanning a ~ 1Mb region has been sequenced and annotated and detailed comparative analysis with Brachypodium orthologous regions has been performed. Furthermore, the identity of the major seed storage proteins in Brachypodium was determined for further dissection of storage protein biology in grasses.
Stamova, B., Roessner, U., Suren, S., Chingcuanco, D.L., Bacic, A., Beckles, D. 2008. Metabolic profiling of transgenic wheat over-expressing the high-molecular weight Dx5 glutenin subunit. Metabolomics. 5(2):239-252.
Wanjugi, H., Coleman-Derr, D., Huo, N., Kianian, S.F., Luo, M., Wu, J., Anderson, O.D., Gu, Y.Q. 2009. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome. 52:576-587.
Yu, G., Cai, X., Harris, M., Gu, Y.Q., Luo, M., Xu, S.S. 2009. Saturation and comparative mapping of genomic region harboring Hessian fly resistance gene H26 in wheat. Theoretical and Applied Genetics. 118(8):1589-1599.
Kalavachrla, V., Hossia, K., Gu, Y.Q., Maan, S., Kianian, S. 2009. Radiation hybrid mapping in crop plants. Advances in Agronomy. 102:199-219.
Bai, W., Cai, A., Rz, Z., Li, A., Huo, N., Li, S., Gu, Y.Q., Yabut, L., Jia, J., Qi, Y. 2009. Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Functional and Integrative Genomics. 9:532-541.
Anderson, O.D. 2009. EST mining for structure and expression of genes in the region of the wheat high-molecular-weight glutenin loci . Genome. 52:1-15.
Ma, W., Anderson, O.D., Kuchen, H., Bonnardeaux, Y., Collins, H., Morell, M., Langridge, P., Appels, R. 2009. Genomics of Quality Traits. Genetics and Genomics of the Triticeae. 7:611-651.
Pumphrey, M.O., Bai, J., Chingcuanco, D.L., Anderson, O.D., Gill, B. 2009. Non-Additive Expression of Homoeologous Genes is Established Upon Polyploidization in Hexaploid Wheat. Genetics. 181(3):1147-1157.