Screening and Identification of Differentially Expressed Genes in Reproductive Stage of Rice (Oryza sativa) Using Digital Differential Display Tools

Research Article

J Plant Chem and Ecophysiol. 2016; 1(2): 1011.

Screening and Identification of Differentially Expressed Genes in Reproductive Stage of Rice (Oryza sativa) Using Digital Differential Display Tools

Ebadi H, Ahmadi DN and Sorkheh K*

Department of Agronomy and Plant Breeding, Shahid Chamran University of Ahvaz, Iran

*Corresponding author: Karim Sorkheh, Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box 61355/144, Iran

Received: October 31, 2016; Accepted: December 07, 2016; Published: December 09, 2016

Abstract

Growth and development of any plant tissue due to variation in genes expression level related to each tissue, indicates the specific pattern of genes expression. The whole of Expressed Sequence Tags (ESTs) of rice clustered in unigene sets in NCBI UniGene database that offer a platform for identifying differentially expressed genes in rice reproductive stage. This report illustrates a means to efficiency utilize this public database for gene expression (transcriptome) profiling reproductive stage. Using a data mining tool known as Digital Differential Display (DDD), comparisons were performed between 52 libraries of reproductive stage and 110 libraries of vegetative stage. DDD identiï¬ed 812 specific unigene set in reproductive stage. Some of these genes encode for proteins such as prolamin, lipid transfer proteins, glutelin proteins and other unknown but novel gene sequences that’s coded expression proteins without reveal functional. Also, part of genes screened was related to housekeeping genes. This study proves that the use of in silico analysis of the rice UniGene database led to the acceleration in create transcriptional proï¬les of known and novel genes in developing reproductive stage.

Keywords: Rice; Reproductive stage; Digital Differential Display (DDD)

Introduction

Rice (Oryza sativa L.) is one of the most important cereal crops worldwide, and the major source of human nutrition and livestock feed in many countries [1]. Considering the importance of reproductive phase of plants, identification of specific genes of a reproductive stage can be effective in improving the quality and quantity of cereals. In order to screen these genes, use of expression patterns is resultful [2]. Two analysis approaches, analog and digital used for the estimate of expression level. The analog approach based on oligonucleotide probe hybridizations such as microarray while the digital approach is based on the high-throughput generation of gene transcripts as in the case of Expressed Sequence Tags (ESTs) [2,3]. ESTs are a fast; inexpensive way to determine which genes are being actively transcribed in a tissue or organ at a given stage of development [4,5]. The one of high-throughput generation is Digital Differential Display (DDD) [2]. The goal of this study was to screen and identify genes specifically expressed in the reproductive stage of rice with DDD tool.

Methods and Materials

Extraction of rice cDNA library

In order to determine the level of genes expression was use a total of 623800 rice Expressed Sequence Tags (ESTs) (December 2015) that are available from the National Center for Biotechnology Information (NCBI) database. The ESTs sequences have been divided into162 library. The ESTs were computationally clustered into unigene set. Each unigene set is defined as hypothetical genes that based on sequence homology, originate from the same gene or expressed pseudogene in this study, the UniGene database was analyzed by an in silico tool known as Digital Differential Display (DDD).

Digital differential displays analysis

DDD is an online bioinformatics tool for identification of differentially expressed genes. The general framework of DDD is based on the comparison between the relative abundance of ESTs from various libraries [2,6]. To eliminate the difference caused by the unequal number of ESTs in each selected libraries, DDD uses the Fisher Exact Test. The output provided a numerical value in each pool denoting the fraction of sequences within the pool that mapped to the unigene cluster [2,7]. In the current work Comparisons between libraries related to reproductive phase and other libraries (Vegetative tissue) was used to identify unigene sets that were reproductive stage specific. Libraries chosen for DDD comparison are listed in Table 1. For those libraries that have sequences in UniGene, DDD lists the title and tissue source and provides a general description of each UniGene.