Analysis of the Female Gametophyte Transcriptome of Arabidopsis by Comparative Expression Profiling

Abstract

The extensive data on the transcription of the plant genome are derived primarily from the sporophytic generation. There currently is little information on genes that are expressed during female gametophyte development in angiosperms, and it is not known whether the female gametophyte transcriptome contains a major set of genes that are not expressed in the sporophyte or whether it is primarily a subset of the sporophytic transcriptome. Because the embryo sac is embedded within the maternal ovule tissue, we have utilized the Arabidopsis (Arabidopsis thaliana) mutant sporocyteless that produces ovules without embryo sacs, together with the ATH1 Arabidopsis whole-genome oligonucleotide array, to identify genes that are preferentially or specifically expressed in female gametophyte development. From analysis of the datasets, 225 genes are identified as female gametophyte genes, likely a lower limit as stringent criteria were used for the analysis, eliminating many low expressed genes. Nearly 45% of the identified genes were not previously detected by sporophytic expression profiling, suggesting that the embryo sac transcriptome may contain a significant fraction of transcripts restricted to the gametophyte. Validation of six candidate genes was performed using promoter::b-glucuronidase fusions, and all of these showed embryo sac-specific expression in the ovule. The unfiltered expression data from this study can be used to evaluate the possibility of female gametophytic expression for any gene in the ATH1 array, and contribute to identification of the functions of the component of the Arabidopsis genome not represented in studies of sporophytic expression and function.

Whole Genome Analysis of Gene Expression Reveals Coordinated Activation of Signaling and Metabolic Pathways during Pollen-Pistil Interactions in Arabidopsis

“…A primary transcriptomic comparison of UP, ovules, and siliques enriched the UP and ovule data sets for stage-specific transcripts by excluding common sporophyte-expressed genes potentially involved in carpel and ovule determination, such as SEEDSTICK (STK; Rounsley et al, 1995) and SHATTERPROOF1 (SHP1; Flanagan et al, 1996), a phosphogluconolactonase (At5g24420) that is expressed in ovule integuments and in the ovary wall (Scutt et al, 2003), as well as genes involved in later stages of seed development, such as MEDEA (MEA; Vielle-Calzada et al, 1999), FERTILIZATION INDE-PENDENT SEED2 (Luo et al, 1999), and FLOWERING WAGENINGEN (Kinoshita et al, 2004). Using the parameters outlined in "Materials and Methods" and further comparison with publicly available data sets (Zimmermann et al, 2004;Tung et al, 2005;Yu et al, 2005;Steffen et al, 2007;Borges et al, 2008;Wang et al, 2008;Qin et al, 2009;Wuest et al, 2010), a total of 42 genes were considered enriched or preferentially expressed in ovules (Supplemental File S1). As anticipated, 27 out of 42 transcripts preferentially expressed in ovules and 96 out of 1,275 ovule-enriched transcripts were previously reported to be expressed specifically in the embryo sac or enriched in female gametophytic cells (Supplemental File S1; Yu et al, 2005;Johnston et al, 2007;Punwani et al, 2007;Steffen et al, 2007;Wuest et al, 2010).…”

“…Using the parameters outlined in "Materials and Methods" and further comparison with publicly available data sets (Zimmermann et al, 2004;Tung et al, 2005;Yu et al, 2005;Steffen et al, 2007;Borges et al, 2008;Wang et al, 2008;Qin et al, 2009;Wuest et al, 2010), a total of 42 genes were considered enriched or preferentially expressed in ovules (Supplemental File S1). As anticipated, 27 out of 42 transcripts preferentially expressed in ovules and 96 out of 1,275 ovule-enriched transcripts were previously reported to be expressed specifically in the embryo sac or enriched in female gametophytic cells (Supplemental File S1; Yu et al, 2005;Johnston et al, 2007;Punwani et al, 2007;Steffen et al, 2007;Wuest et al, 2010). Ovule-expressed transcripts likely include plausible candidates for shortrange pollen tube attractants expressed in the embryo sac (Higashiyama et al, 2001(Higashiyama et al, , 2003Chen et al, 2007;Okuda et al, 2009) but also of other modulators expressed in the surrounding sporophytic tissues that could function as long-range pollen tube attractants.…”

“…The transcriptional profiles of pollen (Becker et al, 2003;Twell, 2003, 2004;Pina et al, 2005; for review, see Becker and Feijó , 2007), embryo sac (Yu et al, 2005;Johnston et al, 2007;Jones-Rhoades et al, 2007;Steffen et al, 2007), pistil (Scutt et al, 2003;Tung et al, 2005), and embryo or seed developmental stages (Chen et al, 2001;Hennig et al, 2004;Yoshida et al, 2005, Le et al, 2010 were recently analyzed. More notably, recent progress in the isolation of Arabidopsis (Arabidopsis thaliana) gametes allowed genomewide expression profiling of purified sperm cells (Borges et al, 2008) as well as of isolated egg and central cells (Wuest et al, 2010).…”

The COMATOSE ATP-Binding Cassette Transporter Is Required for Full Fertility in Arabidopsis

“…Whereas CTS is expressed ubiquitously, it should be noted that transcripts are not expressed preferentially in either male or female gametophytic tissues or in specific sporophytic tissues (Becker et al, 2003;Twell, 2003, 2004;Wellmer et al, 2004;Yu et al, 2005). Thus, CTS could play a role in either or both sporophytic or gametophytic tissues.…”

Analysis of stunter1, a Maize Mutant with Reduced Gametophyte Size and Maternal Effects on Seed Development

“…Additionally, many studies have been done in an attempt to elucidate the genetic makeup of the female haploid plant in maize and Arabidopsis (Patterson 1978;Cordts et al 2001;Le et al 2005;Pagnussat et al 2005;Sprunck et al 2005;Yu et al 2005;Yang et al 2006;Jones-Rhoades et al 2007;Steffen et al 2007;Wuest et al 2010). Many of these mutant and gene expression studies helped determine that early seed development is largely under the control of the maternal genome (Vielle-Calzada et al 2000).…”