Transcription Profiling of Signal Transduction-Related Genes in Sugarcane Tissues

Abstract

A collection of 237,954 sugarcane ESTs was examined in search of signal transduction genes. Over 3500 components involved in several aspects of signal transduction, transcription, development, cell cycle, stress responses and pathogen interaction were compiled into the Sugarcane Signal Transduction (SUCAST) Catalogue. Sequence comparisons and protein domain analysis revealed 477 receptors, 510 protein kinases, 107 protein phosphatases, 75 small GTPases, 17 G-proteins, 114 calcium and inositol metabolism proteins, and over 600 transcription factors. The elements were distributed into 29 main categories subdivided into 409 sub-categories. Genes with no matches in the public databases and of unknown function were also catalogued. A cDNA microarray was constructed to profile individual variation of plants cultivated in the field and transcript abundance in six plant organs (flowers, roots, leaves, lateral buds, and 1st and 4th internodes). From 1280 distinct elements analyzed, 217 (17%) presented differential expression in two biological samples of at least one of the tissues tested. A total of 153 genes (12%) presented highly similar expression levels in all tissues. A virtual profile matrix was constructed and the expression profiles were validated by real-time PCR. The expression data presented can aid in assigning function for the sugarcane genes and be useful for promoter characterization of this and other economically important grasses.

De novo transcriptome assembly of sugarcane leaves submitted to prolonged water-deficit stress

“…The largest EST collection of sugarcane was obtained by the SUCEST project (Vettore et al, 2001(Vettore et al, , 2003. The database generated by this project permitted to identify genes associated with cold stress (Nogueira et al, 2003), oxidative stress (Kurama et al, 2002), and protease inhibitor genes associated with pathogen resistance (Soares-Costa et al, 2002;Falco and Silva-Filho, 2003;Mello et al, 2003), as well as to evaluate the tissue specificity involved in signal transduction (Papini-Terzi et al, 2005) and the tissue specificity of transposons (de Araujo et al, 2005). The SUCEST project provided a basic and fundamental set of data for a better understanding of the physiological and biochemical processes that occur in sugarcane.…”

Sugarcane Responses at Water Deficit Conditions

“…Around 238,000 ESTs were produced from plants of different vegetative or reproductive stages grown in vitro and in vivo under diverse conditions. Data obtained from this project was used to support studies of biotic (Barsalobres-Cavallari et al, 2006) and abiotic stresses (Kurama et al, 2002;Nogueira et al, 2003), as well as other researches with sugarcane (Camargo et al, 2007;Papini-Terzi et al, 2005;Rocha et al, 2007;Rosa et al, 2005). To perform a collection of ESTs from Brazilian sugarcane cultivars expressed specifically under water deficit conditions, the data provided by www.intechopen.com Sucest project was also applied in a large scale gene expression study using sugarcane cultivars with different tolerance to drought (Rocha et al, 2007;Rodrigues et al, 2009Rodrigues et al, , 2011.…”

Challenges, Opportunities and Recent Advances in Sugarcane Breeding

“…Microarrays data have showed a change in gene expression by drought conditions. In sugarcane 93 genes were differentially expressed, including orthologs of NAC and DREB transcription factors and the cysteine proteinase RD19A (Koizumi et al, 1993;Papini-Terzi et al, 2005;Tran et al, 2004;Yamaguchi & Shinozaki, 2006). Indeed, this knowledge led to the development of transgenic sugarcane more tolerant to drought (see section on Biotechnology).…”

“…Transcriptome efforts in sugarcane had a landmark in the late 1990s, when the large-scale cDNA libraries sequencing project SUCEST was set (Vettore et al, 2001(Vettore et al, , 2003, and from which almost 300,000 EST (ESTs: expressed sequence tags) were obtained, assembled into ~43,000 unique transcribed sequences, the closest picture of sugarcane transcriptional units. Most functional genomics projects performed in the 1990's focused on sucrose content, disease resistance and stress tolerance, and involved several techniques, such as EST characterization, microarray and SAGE analyses (Vettore et al, 2003;Papini-Terzi et al, 2005;Calsa Jr & Figueira 2007;Rocha et al, 2007;Menossi et al, 2008;Papini-Terzi et al, 2009;Waclawovsky et al, 2010;Iskandar et al, 2011). The post-genomic era comprises the use of this information into breeding programs, with the identified markers that reveal expression profile of genes in different environmental conditions (Moore, 2005;Waclawovsky et al, 2010;Khan et al, 2011).…”