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Open Access Highly Accessed Methodology article

Screening and identification of seed-specific genes using digital differential display tools combined with microarray data from common wheat

Xinglu Yang1, Hongliang Xu1, Wenhui Li1, Le Li1, Jinyue Sun2, Yaxuan Li1, Yueming Yan1 and Yingkao Hu1*

Author Affiliations

1 College of Life Sciences, Capital Normal University, Beijing, 100048, China

2 Plant Biotechnology Institute, National Research Council Canada, Saskatoon, S7N 0W9, Canada

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BMC Genomics 2011, 12:513  doi:10.1186/1471-2164-12-513

Published: 17 October 2011



Wheat is one of the most important cereal crops for human beings, with seeds being the tissue of highly economic value. Various morphogenetic and metabolic processes are exclusively associated with seed maturation. The goal of this study was to screen and identify genes specifically expressed in the developing seed of wheat with an integrative utilization of digital differential display (DDD) and available online microarray databases.


A total of 201 unigenes were identified as the results of DDD screening and microarray database searching. The expressions of 6 of these were shown to be seed-specific by qRT-PCR analysis. Further GO enrichment analysis indicated that seed-specific genes were mainly associated with defense response, response to stress, multi-organism process, pathogenesis, extracellular region, nutrient reservoir activity, enzyme inhibitor activity, antioxidant activity and oxidoreductase activity. A comparison of this set of genes with the rice (Oryza sativa) genome was also performed and approximately three-fifths of them have rice counterparts. Between the counterparts, around 63% showed similar expression patterns according to the microarray data.


In conclusion, the DDD screening combined with microarray data analysis is an effective strategy for the identification of seed-specific expressed genes in wheat. These seed-specific genes screened during this study will provide valuable information for further studies about the functions of these genes in wheat.