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A cross-species transcriptomics approach to identify genes involved in leaf development.

ABSTRACT: BACKGROUND: We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments. RESULTS: Transcription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL. CONCLUSION: This work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.

SUBMITTER: Street NR

PROVIDER: S-EPMC2621207 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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A cross-species transcriptomics approach to identify genes involved in leaf development.

Street Nathaniel Robert NR Sjödin Andreas A Bylesjö Max M Gustafsson Petter P Trygg Johan J Jansson Stefan S

BMC genomics 20081205

<h4>Background</h4>We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in Populus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgen ...[more]

PMID: 19061504

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Project description:BackgroundField observations and a few physiological studies have demonstrated that peach embryogenesis and fruit development are tightly coupled. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools have failed. Moreover, physiological disturbances during early embryo development lead to seed abortion and fruitlet abscission. Later in embryo development, the interactions between seed and fruit development become less strict. As there is limited genetic and molecular information about seed-pericarp cross-talk and development in peach, a massive gene approach based on the use of the μPEACH 1.0 array platform and quantitative real time RT-PCR (qRT-PCR) was used to study this process.ResultsA comparative analysis of the transcription profiles conducted in seed and mesocarp (cv Fantasia) throughout different developmental stages (S1, S2, S3 and S4) evidenced that 455 genes are differentially expressed in seed and fruit. Among differentially expressed genes some were validated as markers in two subsequent years and in three different genotypes. Seed markers were a LTP1 (lipid transfer protein), a PR (pathogenesis-related) protein, a prunin and LEA (Late Embryogenesis Abundant) protein, for S1, S2, S3 and S4, respectively. Mesocarp markers were a RD22-like protein, a serin-carboxypeptidase, a senescence related protein and an Aux/IAA, for S1, S2, S3 and S4, respectively.The microarray data, analyzed by using the HORMONOMETER platform, allowed the identification of hormone-responsive genes, some of them putatively involved in seed-pericarp crosstalk. Results indicated that auxin, cytokinins, and gibberellins are good candidates, acting either directly (auxin) or indirectly as signals during early development, when the cross-talk is more active and vital for fruit set, whereas abscisic acid and ethylene may be involved later on.ConclusionsIn this research, genes were identified marking different phases of seed and mesocarp development. The selected genes behaved as good seed markers, while for mesocarp their reliability appeared to be dependent upon developmental and ripening traits. Regarding the cross-talk between seed and pericarp, possible candidate signals were identified among hormones.Further investigations relying upon the availability of whole genome platforms will allow the enrichment of a marker genes repertoire and the elucidation of players other than hormones that are involved in seed-pericarp cross-talk (i.e. hormone peptides and microRNAs).

Project description:BackgroundMany reptiles exhibit temperature-dependent sex determination (TSD). The initial cue in TSD is incubation temperature, unlike genotypic sex determination (GSD) where it is determined by the presence of specific alleles (or genetic loci). We used patterns of gene expression to identify candidates for genes with a role in TSD and other developmental processes without making a priori assumptions about the identity of these genes (ortholog-based approach). We identified genes with sexually dimorphic mRNA accumulation during the temperature sensitive period of development in the Red-eared slider turtle (Trachemys scripta), a turtle with TSD. Genes with differential mRNA accumulation in response to estrogen (estradiol-17β; E(2)) exposure and developmental stages were also identified.ResultsSequencing 767 clones from three suppression-subtractive hybridization libraries yielded a total of 581 unique sequences. Screening a macroarray with a subset of those sequences revealed a total of 26 genes that exhibited differential mRNA accumulation: 16 female biased and 10 male biased. Additional analyses revealed that C16ORF62 (an unknown gene) and MALAT1 (a long noncoding RNA) exhibited increased mRNA accumulation at the male producing temperature relative to the female producing temperature during embryonic sexual development. Finally, we identified four genes (C16ORF62, CCT3, MMP2, and NFIB) that exhibited a stage effect and five genes (C16ORF62, CCT3, MMP2, NFIB and NOTCH2) showed a response to E(2) exposure.ConclusionsHere we report a survey of genes identified using patterns of mRNA accumulation during embryonic development in a turtle with TSD. Many previous studies have focused on examining the turtle orthologs of genes involved in mammalian development. Although valuable, the limitations of this approach are exemplified by our identification of two genes (MALAT1 and C16ORF62) that are sexually dimorphic during embryonic development. MALAT1 is a noncoding RNA that has not been implicated in sexual differentiation in other vertebrates and C16ORF62 has an unknown function. Our results revealed genes that are candidates for having roles in turtle embryonic development, including TSD, and highlight the need to expand our search parameters beyond protein-coding genes.

Project description:Background Field observations and a few physiological studies pointed out that peach embryogenesis and fruit development are strictly related. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools failed. Moreover, physiological disturbances during the early embryo development lead to seed abortion and fruitlet abscission. Later on, the interactions between seed and fruit development become less stringent. Genetic and molecular information about seed and fruit development in peach is limited. Results The isolation of 455 genes differentially expressed in seed and fruit was done by means of a comparative analysis of the transcription profiles carried out in peach (Prunus persica, cv Fantasia) seed and mesocarp throughout development by means of µPEACH 1.0, the first peach microarray. Genes differentially expressed in the two organs and specific of developmental stages had been identified, and some were validated as markers. Genes representative of the main functional categories are present, among which several transcription factors such as MADS-box, bZIP, Aux/IAA, AP2, WRKY, and HD. Some of these showed a similar transcription profile in the two organs, while others displayed an opposite pattern, being more expressed in embryo at early development and in mesocarp at ripening. Conclusions The µPEACH1.0, although developed from ripe fruit ESTs, resulted in being suitable for studying seed/mesocarp interactions. Among the differentially expressed genes, marker genes specific for organ and stage of development have been selected. Comparisons were carried out by pooling stage 1 and 2 (named early development, e) and stage 3 and 4 (named late development, l), separately for mesocarp (M) and seed (S) of cultivar Fantasia, and using a simple loop experimental design. RNA has been extracted from fruit harvest at above-mentioned stages of development. At least four hybridizations have been conducted for a total of four technical replicates (with dye-swap).

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A cross-species transcriptomics approach to identify genes involved in leaf development.

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A cross-species transcriptomics approach to identify genes involved in leaf development.

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