Abstract
BackgroundTo provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. Our aims were to: 1) identify genes expressed in a tissue-specific and temporal-specific manner; 2) define clusters of genes showing similar patterns of spatial and temporal expression; and 3) identify stage-specific or transition-specific candidate genes for further functional genomic analyses.ResultsWe analyzed gene expression during S. chacoense embryogenesis in a series of experiments with probes derived from ovules isolated before and after fertilization (from 0 to 22 days after pollination), and from leaves, anthers, and styles. From the 6374 unigenes present in our array, 1024 genes were differentially expressed (≥ ± 2 fold change, p value ≤ 0.01) in fertilized ovules compared to unfertilized ovules and only limited expression overlap was observed between these genes and the genes expressed in the other tissues tested, with the vast majority of the fertilization-regulated genes specifically or predominantly expressed in ovules (955 genes). During embryogenesis three major expression profiles corresponding to early, middle and late stages of embryo development were identified. From the early and middle stages, a large number of genes corresponding to cell cycle, DNA processing, signal transduction, and transcriptional regulation were found. Defense and stress response-related genes were found in all stages of embryo development. Protein biosynthesis genes, genes coding for ribosomal proteins and other components of the translation machinery were highly expressed in embryos during the early stage. Genes for protein degradation were overrepresented later in the middle and late stages of embryo development. As expected, storage protein transcripts accumulated predominantly in the late stage of embryo development.ConclusionOur analysis provides the first study in a solanaceous species of the transcriptional program that takes place during the early phases of plant reproductive development, including all embryogenesis steps during a comprehensive time-course. Our comparative expression profiling strategy between fertilized and unfertilized ovules identified a subset of genes specifically or predominantly expressed in ovules while a closer analysis between each consecutive time point allowed the identification of a subset of stage-specific and transition-specific genes.
Highlights
To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 expressed sequence tags (ESTs) isolated from Solanum chacoense ovules bearing embryos from all developmental stages
Based on the global trend from the three major clusters specifying early, middle and late stages of embryogenesis, we found that the transcriptional pattern of some functional categories could specify embryo developmental stages
The TOPLESSRELATED 1 (TPR1) gene is involved in maintenance of shoot fates during A. thaliana embryogenesis defining the apical pole of embryo [103]. Transcriptional activation of this protein in our study suggests that the S. chacoense TPR1 ortholog is developmentally regulated during embryogenesis and might act as a determinant of embryo polarity in solanaceous species
Summary
To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. Embryogenesis patterning starts with an asymmetric cell division that produces a small apical cell, that becomes the embryo, and a large basal cell (leading to the suspensor) that functions to provide nutrients from the endosperm to the growing embryo [6]. The first phase involves morphogenesis and pattern formation, during which the polar axis of the plant body is defined by specification of the shoot and root apices, and the embryonic tissue and organ systems are formed (pattern formation/cell proliferation/cell division). In Arabidopsis embryogenesis is rapid, requiring only 14 days after pollination to produce the desiccated mature seed [10]. In Solanum phureja, embryo maturation, excluding desiccation, is only completed 27 days after pollination [11]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
