Analysis of Transcriptome of Rice Anther

Important phenomena related to rice, such as Cytoplasmic male sterility (CMS), self-incompatibility and sex determination, are involved in sexual reproduction. For rice, the development process of male gametophyte and pollen contains several stages, including pre-meiotic anther (PMA), meiosis (MEI), tetrad (TET), uninuclear (UN) microspore, bicellular (BC) pollen, tricellular (TC) pollen, MEI, TET, and UN tapetum. With the 44K rice microarray chip and RNAs derived from LM-separated microspore/pollen and tapetum cells, in this paper, we identified the expression patterns involved in different stages. Furthermore, we also detected the enriched promoter motifs and enriched functions for each cluster, which are expected to provide biological insights into developmental procedure of male gametophyte and pollen. Abbreviations CMS, Cytoplasmic male sterility; PMA, pre-meiotic anther; MEI, meiosis; TET, tetrad; UN, uninuclear; BC, bicellular; TC, tricellular; LM, Laser microdissection; MCL , Markov Cluster; std, standard deviation; GO, Gene Ontology; BiNGO, Biological Networks Gene Ontology tool. 1 Background Rice is one of the most important crops in the world. Important phenomena related to rice, such as Cytoplasmic male sterility (CMS), self-incompatibility and sex determination, are observed in sexual reproduction, which includes a key phase for producing male and female gametes[1]. The male gametophyte, i.e. the pollen, develops in the anther of flowering plants [2]. The microspore/pollen, endothecium and outer tapetum are differentiated from L2 layer in the anther tissues, which consist of three layers, i.e. L1, L2 and L3. However, gene functions in pollen and tapetum are distinct [3]. Pollen mother cells undergo meiosis to release microspores in the anther locule. These microspores then mature into pollen grains through cell division and * Corresponding author: Xing-Ming Zhao, [email protected] The Third International Symposium on Optimization and Systems Biology (OSB’09) Zhangjiajie, China, September 20–22, 2009 Copyright © 2009 ORSC & APORC, pp. 371–378 formation of complex pollen wall. Through an asymmetric mitosis, the uninuclear microspore divides into a larger vegetative cell and a smaller generative cell that consist of bicellular pollen. Sequentially, the generative cell undergoes a second mitosis to form two sperm cells in rice. Tapetum cells function as nurse cells during pollen maturation, where the tapetum makes contribution to pollen development by secreting nutrients and other secondary metabolites. The tapetum provides materials for pollen wall formation, and then degrades in the later stages of pollen development [2,3]. The important biological events described above involve complex gene regulation in both gametophytic and sporophytic tissues during anther development. Therefore, it is necessary to analyze the transcriptomes of microspore/pollen and tapetum, which can help to understand the development process of anther [2]. Laser microdissection (LM) is a powerful tool for isolating specific cells from complicated tissues, and can be applied to extract purified transcriptomes. In this study, with the 44K rice microarray chip and RNAs derived from LM-separated microspore/pollen and tapetum cells, the expression patterns involved in different stages were identified by utilizing transcriptomes of microspore/pollen and tapetum. Furthermore, enriched promoter motifs were predicted and enriched functions were detected, which can provide biological insights into developmental mechanisms of the male gametophyte and pollen.