Construction, Characterization, and Expressed Sequence Tag (EST) Analysis of Normalized cDNA Library of Thermo-Photoperiod-Sensitive Genic Male Sterile (TPGMS) Wheat from Spike Developmental Stages

Abstract

Thermo-photoperiod-sensitive genic male sterile (TPGMS) wheat is important in utilization of heterosis. To facilitate the use of such wheat line in agriculture, more knowledge about molecular mechanisms of TPGMS genes is required. In this study, we set up a normalized complementary DNA (cDNA) library based on the strategy of saturation hybridization with genomic DNA using TPGMS wheat line. This normalized cDNA library consists of cDNA from six directionally cloned cDNA libraries constructed with spike and anther tissues from spike developmental stages. From the normalized cDNA library, 3,264 single-pass expressed sequence tag (EST) were obtained. Exclusion of sequences shorter than 100 bp resulted in 3,223 vector-trimmed ESTs with a mean length of 926 bp. Clustering and assembly analysis resulted in 2,175 unique ESTs from 423 contigs and 1,752 singletons. Taking advantage of various tools and database, gene function classification showed that 60% of the ESTs were predicted to have putative gene function. Of the 2,175 unique ESTs, 264 (12%) displayed significant homology (BlastX E values <10 −5 ) to genes previously reported to be involved in cold-response related processes. Among these, sequences encoding activities related to primary metabolism, signal transduction, and transcriptional regulation were observed. Finally, in the total EST sequences, 108 potential SSRs were found. The unigene dataset will now be used to fabricate biochips carrying all identified genes for TPGMS wheat functional genomic research.

Uncovering Small RNA-Mediated Responses to Cold Stress in a Wheat Thermosensitive Genic Male-Sterile Line by Deep Sequencing

“…cshl.edu/fastx_toolkit/index.html). The ESTs from the NCBI public and private wheat EST databases were assembled by CAP3 into wheat unigenes for bioinformatic analysis (Huang and Madan, 1999;Yang et al, 2009). For the smRNA libraries, smRNAs ranging from 18 to 28 nucleotides were collected and mapped to the wheat unigene data set using SOAP2 .…”

Preparing and Analyzing Expressed Sequence Tags (ESTs) Library for the Mammary Tissue of Local Turkish Kivircik Sheep

“…EST projects are powerful tools for analyzing gene expression patterns in a given tissue and/or at a certain stage and the identification of genes [22–24]. These technologies are very important for obtaining genomic sequence information of organisms [25].…”

Construction of a Full-Length cDNA Library and Analysis of Expressed Sequence Tags from Inflorescence of Apomictic Sabaigrass (Eulaliopsis binata)

“…MADS-box transcription factor 13 1,253 Table 1 List of important predicted transcription factor and other regulation genes a The length of genes are not equated to inserts gene expression patterns in a given tissue and/or at specific developmental stages and in the identification of novel biochemical pathway-related genes (Chen et al 2009;Thanh et al 2011;Wang et al 2011;Yang et al 2009). These technologies are particularly important for organisms lacking genomic sequence information (Gueguen et al 2003).…”

“…Large-scale EST databases are valuable source for gene discovery and have played an important role in functional genomics research in a wide range of organisms (Singh et al 2007;Wang et al 2009;Yang et al 2009); they provide an overview of transcriptional activities within tissues and can be exploited for marker discovery (Zhang et al 2010). Besides, by use of expression sequence analysis, exploitation of EST-based simple sequence repeat (SSR) is a powerful tool to further detection of genetic diversity among close related species or varieties (Nicot et al 2004).…”