|L Chingcuanco, Debbie|
Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/28/2005
Publication Date: 6/8/2006
Citation: Chao, S., Lazo, G.R., You, F., Crossman, C.C., Hummel, D.D., Lui, N., Laudencia-Chingcuanco, D., Anderson, J.A., Close, T.J., Dubcovsky, J., Gill, B.S., Gill, K.S., Gustafson, J.P., Kianian, S.F., Lapitan, N.L.V., Nguyen, H.T., Sorrells, M.E., McGuire, P.E., Qualset, C.O., Anderson, O.D. 2006. Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivum L.). Genome. 49:531-544 (2006). Interpretive Summary: Expressed sequence tags (ESTs) are partial sequences of randomly cloned DNAs derived from expressed gene segments on chromosomes. Due to the recent advancement of high throughput automated sequencing technology, large-scale EST sequencing has become a cost-effective method of producing large amounts of sequence information from the expressed portion of the genomes. Bread wheat (Triticum aestivum L.) is one of the world's most important food crops. Because of its large genome size, whole genome sequencing of wheat genomes will not be feasible in the near future, thus, the large amount of sequence information derived from expressed genes will provide a valuable resource to allow the functional portion of the wheat genomes to be studied systematically. In this paper, results from a generation of over 100,000 ESTs from wheat genomes were presented. These ESTs were derived from tissues collected from various stages of plant growth and development and under a diverse regimen of stress treatments. Analysis of these ESTs was performed using statistical methods. The results reported in this paper provide an overview on changes of wheat gene expression patterns among different tissue types, during different stages of tissue development, and under various stress growth conditions in wheat. Also, genes were identified that showed elevated expression under different stress treatments, thus providing insight into genes responsible for stress tolerance in wheat.
Technical Abstract: Large-scale EST sequencing projects have been carried out in many higher plants and have proven critically important for plants where whole genome sequences are known; i.e., in Arabidopsis and rice (Oryza sativa L.) EST data have assisted in locating gene regions and splice junctions. Hexaploid bread wheat (Triticum aestivum L.), even though it is one of the world’s foundation food plants, will not be completely sequenced in the near future because of its large genome size (16,000 Mbp). Thus, ESTs are more important for wheat, particularly as markers, sources of candidate genes, and a valuable resource for systematic study of the functional portion of the wheat genome. From hexaploid wheat and its close relatives including diploid wheat (T. monococcum L. and Aegilops speltoides L.), tetraploid wheat (T. turgidum L.), and rye (Secale cereale L.), 42 cDNA libraries were created using tissues collected from various stages of plant growth and development and under a diverse regiment of abiotic and biotic stress treatments. Presented here are details of the production of 116,272 ESTs, including 100,674 5' ESTs and 15,598 3' ESTs from these libraries. ESTs were assembled into 18,876 contigs and 23,034 singletons, or 41,910 wheat unigenes. Over 90% of the contigs were found to contain less than 10 EST members, implying that the ESTs represented a diverse selection of genes, and that genes expressed at low and moderate to high levels were well sampled. To reveal gene expression profiling in hexaploid wheat, statistical methods were employed to study the correlation of gene expression pattern for the 1,536 contigs containing at least 10 EST members - representing the most abundant genes expressed in wheat. Analysis further identified genes in wheat that were significantly up-regulated (p < 0.05) in tissues under various abiotic stresses when compared with control tissues. Though the function annotation cannot be assigned for many of these genes, their possible role in stress response can be predicted. This study has uncovered functionality for 4% of total wheat unigenes, which leaves the remaining 96% with their functional role and expression pattern largely unknown. Nonetheless, the EST data generated in this project provide a diverse and rich source for gene discovery in wheat.