Submitted to: Journal of Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/26/2006
Publication Date: 12/1/2006
Citation: Chingcuanco, D., Stamova, B., Lazo, G., Cui, X., Anderson, O. 2006. Analysis of the wheat endosperm transcriptome. Journal of Applied Genetics. 47:287-302.
Interpretive Summary: In this study we used a genomics approach to identify the genes that are expressed in the endosperm by mining the ESTs sequenced from endosperm-specific cDNA libraries. Our results identified 6,187 genes, half of which still have unknown function. Advances in molecular techniques have made it possible for us to identify and monitor the expression of genes preferentially expressed in the endosperm relative to the vegetative tissues. The information from the EST sequencing and expression profiling using microarrays will allow researchers to prioritize which genes to study further. We identified the endosperm genes with genetic map information, which could provide links to quantitative trait loci known to affect grain qualities. The results from this research will provide the knowledge to establish relationships between mechanisms that control key molecular events in the endosperm that could facilitate the improvement of grain qualities that are focused on end-users' needs.
Technical Abstract: Among the cereals, wheat is the most widely grown geographically and is part of the staple diet in much of the world. Understanding how the cereal endosperm develops and functions will help generate better tools to manipulate grain qualities important to end-users. We used a genomics approach to identify and characterize the genes that are expressed in wheat endosperm. We analyzed the 17,949 publicly available wheat endosperm EST sequences to identify genes involved in the biological processes that occur in this tissue. Clustering and assembly of the ESTs resulted in the identification of 6,187 tentative unique genes, 2,358 of which clustered into contigs and 3,829 remained as singletons. BLAST similarity search against the NCBI non-redundant sequence database revealed abundant messages for storage proteins, defense, and proteins involved in starch metabolism. The level of abundance of the putatively identified genes reflects the physiology of the developing endosperm. Half of the identified genes have unknown functions. Approximately 25% of the identified genes expressed in the endosperm have been mapped in the hexaploid wheat genome. Using microarrays for global RNA profiling, we identified endosperm genes that are specifically up regulated in the developing grain.