Analysis of the wheat endosperm transcriptome

Debbie L. Laudencia-Chingcuanco, Boryana Stamova, Gerard R. Lazo, Xiangqin Cui, Olin D. Anderson

Research output: Contribution to journalArticle

22 Scopus citations

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 genes that are expressed in the wheat endosperm. We analyzed the 17 949 publicly available wheat endosperm EST sequences to identify genes involved in the biological processes that occur within this tissue. Clustering and assembly of the ESTs resulted in the identification of 6 187 tentative unique genes, 2 358 of which formed contigs and 3 829 remained as singletons. A BLAST similarity search against the NCBI non-redundant sequence database revealed abundant messages for storage proteins, putative defense proteins, and proteins involved in starch and sucrose 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 61% of the endosperm ESTs has been tentatively 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.

Original languageEnglish (US)
Pages (from-to)287-302
Number of pages16
JournalJournal of Applied Genetics
Volume47
Issue number4
DOIs
StatePublished - Jan 1 2006

Keywords

  • Endosperm
  • EST
  • Mapping
  • Micro-array
  • Transposon
  • Wheat

ASJC Scopus subject areas

  • Genetics

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    Laudencia-Chingcuanco, D. L., Stamova, B., Lazo, G. R., Cui, X., & Anderson, O. D. (2006). Analysis of the wheat endosperm transcriptome. Journal of Applied Genetics, 47(4), 287-302. https://doi.org/10.1007/BF03194638