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ARS Home » Pacific West Area » Kimberly, Idaho » Northwest Irrigation and Soils Research » Research » Publications at this Location » Publication #227464
Title: Identification of differentially expressed UniGenes in developing wheat seed using digital differential display

Author
item Eujayl, Imad
item Morris, Craig

Submitted to: Journal of Cereal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/11/2008
Publication Date: 3/7/2009
Citation: Eujayl, I.A., Morris, C.F. 2009. Identification of differentially expressed UniGenes in developing wheat seed using digital differential display. Journal of Cereal Science. 49:316-318.

Interpretive Summary: Wheat kernel texture is the most single important trait of wheat postharvest processing. Kernel texture (hard or soft) is a complicated trait and deciphering the genes controlling this trait of paramount importance to producing cultivars with desired kernel texture for wheat industry. Modern molecular tools for gene analysis created a wealth of DNA sequences that are publically available. This research utilized Expressed Sequence Tags (ESTs) which deposited in the GenBank. A bioinformatics tool called Digital Differential Display (DDD) was used to analyze these ESTs, which revealed differentially expressed seed-specific and developmentally-specific genes. Some of these genes were found to be expressed at higher levels in hard varieties than soft varieties. This study created a short list of deciphered differentially expressed genes that can be used in molecular breeding of wheat.

Technical Abstract: The wheat Expressed Sequence Tags (ESTs) in the GenBank totaled 1,051,465 ESTs offer a platform for deciphering differentially expressed genes in wheat. These ESTs are clustered into 41,256 UniGene sets that are non-redundant gene-oriented clusters. This study presented means to efficiently utilize this public database for gene expression profiling of wheat developing-seed. Using a data mining tool called Digital Differential Display (DDD), thirteen pair-wise comparisons were performed on seven cDNA libraries from five cultivars at various developing stages. DDD revealed 46 seed-specific UniGene sets, excluding the well characterized seed storage proteins. Additionally, developmentally-specific UniGenes were identified. Some of these genes encode for proteins such as purothionins, serpins, alpha amylase-inhibitor enzymes, lipid transfer proteins in addition to novel gene sequences. Specifically, the wheat serpin and ß -purothionin precursor were found to be expressed at higher levels in hard varieties than soft varieties. This study supports the starting premise that by implementing in-silico analysis of the wheat UniGene database, it is possible to rapidly create transcriptional profiles of known and novel genes in specific tissues.