Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

Abstract Background Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N2-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins. Results Adopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases. Conclusion An extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties.

Evaluación integrada de la sostenibilidad ambiental, económica y social del cultivo de maíz en Chiapas, México

En este estudio se evaluó la sostenibilidad de los agroecosistemas tradicionales y alternativos de producción de maíz en tres Ejidos de la Región Selva de Chiapas, mediante la aplicación del enfoque agroecológico (MESMIS). El estudio se realizó en dos ciclos agrícolas: milpa y tornamil. En el primero se evaluaron los sistemas de roza-tumba-quema (R‑T‑Q), sin quema y en sucesión de nescafé (Mucuna deeringiana Bort.). En el segundo ciclo se analizaron tres sistemas sin quema con diferentes periodos de nescafé, y se modificó la densidad poblacional para analizar su efecto sobre la producción. Los valores de los indicadores económicos y sociales se obtuvieron a través de técnicas participativas. En la milpa se determinó el efecto positivo del fuego en el control de las arvenses y de la plaga Diatraea liniolata (Walker). Los sistemas alternativos con uso de abono verde presentaron mejores resultados en los aspectos agronómicos. Los sistemas con modificación de la densidad poblacional obtuvieron un mayor rendimiento de grano y una mayor rentabilidad financiera. En el análisis final integrado, los sistemas alternativos obtuvieron mejores resultados, aunque los sistemas de R‑T‑Q, por la adaptación al medio ambiente, obtuvieron resultados positivos en algunas variables. Por tanto, su uso en la región constituye una realidad etnocultural lejos de desaparecer en el futuro cercano.

Sugarcane moth borers (Lepidoptera: Noctuidae and Pyraloidea): phylogenetics constructed using COII and 16S mitochondrial partial gene sequences

Sugarcane moth borers are a diverse group of species occurring in several genera, but predominately within the Noctuidae and Pyraloidea. They cause economic loss in sugarcane and other crops through damage to stems and stalks by larval boring. Partial sequence data from two mitochondrial genes, COII and 16S, were used to construct a molecular phylogeny based on 26 species from ten genera and six tribes. The Noctuidae were found to be monophyletic, providing molecular support for the taxonomy within this subfamily. However, the Pyraloidea are paraphyletic, with the noctuids splitting Galleriinae and Schoenobiinae from the Crambinae. This supports the separation of the Pyralidae and Crambinae, but does not support the concept of the incorporation of the Schoenobiinae in the Crambidae. Of the three crambine genera examined, Diatraea was monophyletic, Chilo paraphyletic, and Eoreuma was basal to the other two genera. Within the Noctuidae, Sesamia and Bathytricha were monophyletic, with Busseola basal to Bathytricha. Many species in this study (both noctuids and pyraloids) had different biotypes within collection localities and across their distribution; however the individual biotypes were not phylogenetically informative. These data highlight the need for taxonomic revisions at all taxon levels and provide a basis for the development of DNA-based diagnostics for rapidly identifying many species at any developmental stage. This ability is vital, as the species are an incursion threat to Australia and have the potential to cause significant losses to the sugar industry.