Comparative transcript analyses of the ovule, microspore, and mature pollen in Brassica napus Carrie A. Whittle • Meghna R. Malik • Rong Li • Joan E. Krochko Received: 29 March 2009 / Accepted: 26 October 2009 / Published online: 1 December 2009 Ó Her Majesty the Queen in Right of Canada 2009 Abstract Transcriptome data for plant reproductive organs/cells currently is very limited as compared to spo- rophytic tissues. Here, we constructed cDNA libraries and obtained ESTs for Brassica napus pollen (4,864 ESTs), microspores (i.e., early stage pollen development; 6,539 ESTs) and ovules (10,468 ESTs). Clustering and assembly of the 21,871 ESTs yielded a total of 10,782 unigenes, with 3,362 contigs and 7,420 singletons. The pollen transcrip- tome contained high levels of polygalacturonases and pectinesterases, which are involved in cell wall synthesis and expansion, and very few transcription factors or tran- scripts related to protein synthesis. The set of genes expressed in mature pollen showed little overlap with genes expressed in ovules or in microspores, suggesting in the latter case that a marked differentiation had occurred from the early microspore stages through to pollen devel- opment. Remarkably, the microspores and ovules exhibited a high number of co-expressed genes (N = 1,283) and very similar EST functional profiles, including high transcript numbers for transcriptional and translational processing genes, protein modification genes and unannotated genes. In addition, examination of expression values for genes co- expressed among microspores and ovules revealed a highly statistically significant correlation among these two tissues (R = 0.360, P = 1.2 9 10 -40 ) as well as a lack of dif- ferentially expressed genes. Overall, the results provide new insights into the transcriptional profile of rarely stud- ied ovules, the transcript changes during pollen develop- ment, transcriptional regulation of pollen tube growth and germination, and describe the parallels in the transcript populations of microspore and ovules which could have implications for understanding the molecular foundation of microspore totipotency in B. napus. Keywords Pollen Á Microspores Á Ovules Á Transcriptome Á Brassica napus Introduction Transcript data for plant reproductive organs/cells are important for gene discovery and for understanding gene expression patterns, developmental regulation and molec- ular pathways in these tissues (Honys and Twell 2004; Schmid et al. 2005; Yang et al. 2006). In addition, gene specificity and gene expression levels in reproductive tis- sues are known to largely influence the rigor of gameto- phytic selection, which acts to ensure the survival of the most adaptive genotypes into successive generations (Mulcahy et al. 1996; Bernasconi et al. 2004; Hedhly et al. 2005), and thereby plays an essential role in plant popu- lation genetics and evolution (Kondrashov 1998). How- ever, the transcriptional profiles of reproductive organs/ cells are vastly underrepresented in the current literature as compared to sporophytic tissues (including leaves, stems, guard cells, roots and seeds) for most plant species (Schmid et al. 2005; Yang et al. 2006), and particularly for Brassica napus. Electronic supplementary material The online version of this article (doi:10.1007/s11103-009-9567-x) contains supplementary material, which is available to authorized users. C. A. Whittle Á M. R. Malik Á R. Li Á J. E. Krochko (&) Plant Biotechnology Institute, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada e-mail: Joan.Krochko@nrc-cnrc.gc.ca M. R. Malik Agrisoma Biosciences Inc., 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada 123 Plant Mol Biol (2010) 72:279–299 DOI 10.1007/s11103-009-9567-x