Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice

Abstract

BackgroundIn flowering plants, the anther is the site of male gametophyte development. Two major events in the development of the male germline are meiosis and the asymmetric division in the male gametophyte that gives rise to the vegetative and generative cells, and the following mitotic division in the generative cell that produces two sperm cells. Anther transcriptomes have been analyzed in many plant species at progressive stages of development by using microarray and sequence-by synthesis-technologies to identify genes that regulate anther development. Here we report a comprehensive analysis of rice anther transcriptomes at four distinct stages, focusing on identifying regulatory components that contribute to male meiosis and germline development. Further, these transcriptomes have been compared with the transcriptomes of 10 stages of rice vegetative and seed development to identify genes that express specifically during anther development.ResultsTranscriptome profiling of four stages of anther development in rice including pre-meiotic (PMA), meiotic (MA), anthers at single-celled (SCP) and tri-nucleate pollen (TPA) revealed about 22,000 genes expressing in at least one of the anther developmental stages, with the highest number in MA (18,090) and the lowest (15,465) in TPA. Comparison of these transcriptome profiles to an in-house generated microarray-based transcriptomics database comprising of 10 stages/tissues of vegetative as well as reproductive development in rice resulted in the identification of 1,000 genes specifically expressed in anther stages. From this sub-set, 453 genes were specific to TPA, while 78 and 184 genes were expressed specifically in MA and SCP, respectively. The expression pattern of selected genes has been validated using real time PCR and in situ hybridizations. Gene ontology and pathway analysis of stage-specific genes revealed that those encoding transcription factors and components of protein folding, sorting and degradation pathway genes dominated in MA, whereas in TPA, those coding for cell structure and signal transduction components were in abundance. Interestingly, about 50% of the genes with anther-specific expression have not been annotated so far.ConclusionsNot only have we provided the transcriptome constituents of four landmark stages of anther development in rice but we have also identified genes that express exclusively in these stages. It is likely that many of these candidates may therefore contribute to specific aspects of anther and/or male gametophyte development in rice. In addition, the gene sets that have been produced will assist the plant reproductive community in building a deeper understanding of underlying regulatory networks and in selecting gene candidates for functional validation.

Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks

“…Transcriptomic studies have been conducted in pollen, sperm, and anthers in diverse plant species, including Arabidopsis, rice, B. rapa, maize, and cotton (Gossypium hirsutum; Honys and Twell, 2004;Ma et al, 2007Ma et al, , 2008Ma et al, , 2012Chen et al, 2010;Fujita et al, 2010;Deveshwar et al, 2011;Yang et al, 2011;Dong et al, 2013;Wuest et al, 2013). While some studies were focused on tapetum and male gametophytes, others compared anthers of male sterile mutants with anthers of the wild type.…”

Gene-Sharing Networks Reveal Organizing Principles of Transcriptomes in Arabidopsis and Other Multicellular Organisms

“…A tissue-specific gene expresses in one particular tissue or cell type, whereas a housekeeping gene expresses in all tissues. Tissue-specific genes are believed to contribute mainly to the structural and functional diversification of different tissue types; thus, the functions of tissue-specific genes are often experimentally tested in the tissue in which the gene is expressed (Endo et al, 2008;Deveshwar et al, 2011;Xie et al, 2011).…”

Development of male sterile transgenic lines in rice by tapetum specific expression of barnase gene

“…Comparison of the DNA sequence of the RTS promoter isolated from the rice cultivar IR54 (Luo et al 2006) and IR64 (Deveshwar et al 2011) showed the insertion of a 44 bp stretch (at -1005 to -962 position) apart from 3 substitutions and 3 single base insertions. The promoter also carried an additional 264 bp at its 5' end.…”

“…These differences may have led to the loss of tight regulation at the RTS promoter making the promoter leaky. Further, in the study by Deveshwar et al (2011), the activity of the gene was mainly studied by comparative analysis of the transcriptome and in situ hybridization studies. Strategies like comparative analysis of transcriptome and in situ hybridization, analyses activity of the promoter at its original genomic location, whereas studies done by developing transgenics, analyses activity of promoters at ectopic genomic locations.…”

“…OsC6 (Tsuchiya et al 1994;Yokoi et al 1997), OsRA8 (Jeon et al 1999), OsRA39 (Ding et al 2002), OsYY2 (Kuriakose et al 2009), OsRTS (Luo et al 2006;Deveshwar et al 2011), OsIPP3, OsbHLH, OsIPK, OsFbox, OsIPA, (Swapna et al 2011;Khurana et al 2012;Khurana et al 2013), OsSCP1, OsSCP2, and OsSCP3 (Park et al 2006). Of these, the OsRTS promoter from rice cultivar IR54 has been used to demonstrate the development of male sterile line by expression of the barnase gene under the control of this promoter (Luo et al 2006).…”