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Genomic Expression Profiling of Mature Soybean (Glycine max) Pollen

ABSTRACT: Background: Pollen, the male partner in the reproduction of flowering plants, comprises either two or three cells at maturity. The current knowledge of the pollen transcriptome is limited to the model plant Arabidopsis thaliana, which has tri-cellular pollen grains at maturity. Comparative studies on pollen of other genera, particularly crop plants, are needed to understand the pollen gene networks that are subject to functional and evolutionary conservation. In this study, we used the Affymetrix Soybean GeneChip® to perform transcriptional profiling on mature bi-cellular soybean pollen. Results: Compared to the sporophyte transcriptome, the soybean pollen transcriptome revealed a restricted and unique repertoire of genes, with a significantly greater proportion of specifically expressed genes than is found in the sporophyte tissue. Comparative analysis shows that, among the 37,500 soybean unique transcripts addressed in this study, 10,299 genes (27.46%) are expressed in pollen. Of the pollen-expressed genes, about 9,489 (92.13%) are also expressed in sporophytic tissues, and 810 (7.87%) are selectively expressed in pollen. Overall, the soybean pollen transcriptome shows an enrichment of transcription factors (mostly zinc finger family proteins), cell cycle-related transcripts, signal recognition receptors, ethylene responsive factors, chromatin remodeling factors, and members of the ubiquitin proteasome proteolytic pathway. Moreover, we identify several new pollen-specific candidate genes that might play a significant role in pollen biology. Conclusion: This is the first report of a soybean pollen transcriptional profile. These data extend our current knowledge regarding regulatory pathways that govern the gene regulation and development of pollen. We also demonstrate that pollen is a rich store of regulatory proteins that are essential and sufficient for de novo gene expression. A comparison between transcription factors up-regulated in soybean and those upregulated in Arabidopsis revealed some divergence in the numbers and kinds of regulatory proteins expressed in both species.

ORGANISM(S): Glycine max

PROVIDER: GSE12286 | GEO | 2009/03/26

SECONDARY ACCESSION(S): PRJNA113571

REPOSITORIES: GEO

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Project description:Pollen development is central for plant reproduction and is assisted by changes of the transcriptome and the proteome. At the same time, pollen is largely heat sensitive, particularly at early developmental stages. To define the changes during development and the response of different stages to elevated temperatures we investigated the transcriptome and proteome of pollen at tetrad, post-meiotic and mature stage before and after application of elevated temperatures. We used Solanum lycopersicum as an economically important crop. We demonstrate that the number of transcripts declines from tetrad to mature stage, while the protein content shows the opposite trend. Comparison of the transcriptome and proteome led to the discovery of two translational modes assigned as direct translation – transcripts increased in a specific pollen stage lead to increased translation in the same stage – and delayed translation – transcripts are produced for translation in later stages. The response to elevated temperatures is with ~5% of all genes being upregulated comparable to general plant behavior. The alteration at proteome level marked the mature pollen as least responsive and the post-meiotic stages as most responsive with altered levels of 40% of the identified proteins. For a subset of the genes with direct translation we observed a downregulation of protein levels after heat stress, whereas some of the genes with delayed translation showed a shift from delayed to direct translation when heat stress is applied. Further, Hsps, proteasome subunits, ribosomal proteins as well as eukaryotic initiation factors are the most drastically affected groups. On the example of Hsps we document that the response at transcriptome and proteome levels in e.g. the post-meiotic and mature stage does not correlate. Moreover, while all stages respond to heat stress with regulation of transcript abundance of Hsps in a comparable manner, changes at proteome level are distinct. Thus, we demonstrate that the difference in heat stress response in different stages of pollen development is rather manifested by significant changes of protein than transcript abundance.

Project description:Soybean is one of the main sources of oil worldwide, and the cotton bollworm [Helicoverpa armigera (Hübner)] is one of the common herbivores seriously affecting soybean production. After being attacked by herbivores, multiple signaling patheways will be triggered in plants, which induces the production of toxic, repellent, or anti-digestive compounds. Genetic engineering and breeding of resistant plant lines are the most effective and environmentally friendly approaches to control herbivores and improve the performance of plants. This study focuses on founding changes genes and proteins in soybean defense response induced by H. armigera. Illumina Solexa sequencing platform and iTRAQ were used for the comparative analysis of transcriptome and proteome profiles in the leaves of Tianlong 2 (a cultivated soybean susceptible to herbivores) and ED059 (a wild soybean resistant to herbivores) in response to infestation by H. armigera. Transcriptome data show that 2073 differentially expressed genes (DEGs) were uniquely expressed in ED059 compared with those in Tianlong 2 after 24 h of H. armigera treatment. Based on gene ontology classification of these 2073 DEGs, we identified 233 DEGs corresponded to various signaling pathways, including protein kinases, transcriptional factors, hormone biosynthesis and signal transduction pathways. In addition, a large number of genes related to antinutritive or toxic proteins were special induced in ED059. By combining the gene expression at the transcriptomic and proteomic levels, results reveal that no significantly high correlation was detected between the expression of mRNAs and proteins. Functional analysis of three candidate genes was accomplished by Agrobacterium-mediated transformation in Arabidopsis thaliana, and a MYB transcription factor 109 (MYB109) was identified with herbivore defense function in ED059. This study provides insights into the identification of the potential genes and proteins involved in herbivore defense, and a possible understanding of the herbivore defense mechanism in a wild soybean by combining analysis of transcriptome and proteome data. Moreover, a novel gene associated with herbivore resistance function was identified and validated.

Project description:Pollen germination, along with pollen tube growth, is an essential process for the reproduction of flowering plants. The germinating pollen with tip-growth characteristics provides an ideal model system for the study of cell growth and morphogenesis. As an essential step towards a detailed understanding of this important process, the objective of this study was to comprehensively analyze the transcriptome changes during pollen germination and pollen tube growth. Using Affymetrix Arabidopsis ATH1 Genome Arrays, this study is the first to show the changes in the transcriptome from desiccated mature pollen grains to hydrated pollen grains and then to pollen tubes of Arabidopsis thaliana. The number of expressed genes, either for total expressed genes or for specifically expressed genes, increased significantly from desiccated mature pollen to hydrated pollen and again to growing pollen tubes, which is consistent with the finding that pollen germination and tube growth was significantly inhibited in vitro by a transcriptional inhibitor. The results of GO analyses showed that expression of genes related to cell rescue, transcription, signal transduction and cellular transport were significantly changed, especially for up-regulation, during pollen germination and tube growth, respectively. In particular, genes of the CaM/CML, CHX and Hsp families showed the most significant changes during pollen germination and tube growth. These results demonstrate that the overall transcription of genes, both in the number of expressed genes and in the levels of transcription, was increased. Furthermore, the appearance of many novel transcripts during pollen germination as well as tube growth indicates that these newly expressed genes may function in this complex process. SUBMITTER_CITATION: Yi Wang, Wen-Zheng Zhang, Lian-Fen Song, Jun-Jie Zou, Zhen Su, and Wei-Hua Wu. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol. September 5, 2008; 10.1104/pp.108.126375 Experiment Overall Design: Three samples are analyzed in this experiment. They are desiccated mature pollen grains (MP), hydrated pollen grains (HP) and growing pollen tubes (PT) of Arabidopsis thaliana, respectively. Each sample has two biological replicates, so that there are 6 data sets of ATH1 array in this experiment.

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Genomic Expression Profiling of Mature Soybean (Glycine max) Pollen

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