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Genetic variation in three forms of asexually propagated Agave tequilana Weber var. 'Azul' plants namely offsets, bulbils and in vitro cultured individuals was studied by AFLP analysis. Low levels of variation were observed between mother plants and offsets and a higher level between mother plant and bulbils. Families obtained from commercial plantations showed lower levels of variation in comparison to families grown as ornamentals. No variation was observed between the original explant and four generations of in vitro cultured plants. Epigenetic variation was also studied by analyzing changes in methylation patterns between mother plants and offspring in each form of asexual reproduction. Offsets and bulbils showed an overall decrease in methylation whereas in vitro cultured plants showed patterns specific to each generation: Generations 1 and 4 showed overall demethylation whereas Generations 2 and 3 showed increased methylation. Analysis of ESTs associated with transposable elements revealed higher proportions of ESTs from Ty1-copia-like, Gypsy and CACTA transposable elements in cDNA libraries obtained from pluripotent tissue suggesting a possible correlation between methylation patterns, expression of transposable element associated genes and somaclonal variation.

Roots are vital for the uptake of water and nutrients, and for anchorage in the soil. They are highly plastic, able to adapt developmentally and physiologically to changing environmental conditions. Understanding the molecular mechanisms behind this growth and development requires knowledge of root transcriptomics, proteomics, and metabolomics. Genomics approaches, including the recent publication of a root expression map, root proteome, and environment-specific root expression studies, are uncovering complex transcriptional and post-transcriptional networks underlying root development. The challenge is in further capitalizing on the information in these datasets to understand the fundamental principles of root growth and development. In this review, we highlight progress researchers have made toward this goal.

Several varieties of Agave tequilana Weber have been described, but only A. tequilana Weber var. “azul” is accepted for the production of tequila. Discrimination between the different varieties is difficult and the relationships between them at the genotype level are unclear. In addition genetic diversity within and between populations of A. tequilana Weber var. “azul” has been shown to be low. AFLP analysis of nine A. tequilana varieties indicated that certain varieties were genotypically close to A. tequilana Weber var. “azul”. A significant level of diversity was also observed among A. tequilana Weber var. “azul” samples obtained from the same plantation and from different plantations in Guanajuato State, Mexico.

Sucrose phosphate synthase (SPS) is a key enzyme in the translocation of photoassimilates from sink-to-source tissues and the remobilization of reserves from storage tissues during seed germination. The tissue specific distribution of SPS is mainly determined by transcriptional mechanisms. To gain further insight into the mechanisms that regulate the transcriptional activity of SPS genes, we carried out a deletion analysis of the rice sps1 promoter using transient expression assays and transgenic rice plants. The sps1 promoter is atypical since it lacks recognizable TATA and initiator sequences near the transcription start site. It was found that the minimal active sps1 promoter consists of a 146 bp 5′ flanking sequence that is capable of directing activity in photosynthetic tissues in rice. No positive or negative regulatory elements upstream to position −146 influencing expression in photosynthetic tissues were found. It was also observed that the sps1 promoter fragment containing 5′ sequences upstream to position −1830 conferred expression only in the scutellum of germinating seeds, whereas shorter promoter versions directed expression in the scutellum but also in the aleurone layer, suggesting the presence of a negative element upstream of position −1188 that suppresses expression in the aleurone. Gain of function experiments suggest that the negative element present upstream of position −1188 is necessary but not sufficient to suppress expression in the aleurone.

Alterations in water relations, growth and histopathology caused by Macrophomina phaseolina , causal agent of charcoal rot, and drought stress were characterized in Phaseolus vulgaris L. under controlled conditions. P. vulgaris cultivars BAT 477 and TLP 19 (resistant) and Pinto UI-114 and Rio Tibagi (susceptible) were cultivated under irrigation and drought stress conditions in infested or uninfested pots with a highly virulent isolate of M. phaseolina . Drought stress showed higher negative effects than M. phaseolina on water relations, vegetative growth and histopathology in P. vulgaris . Drought stress decreased transpiration rate, water potential, osmotic potential, turgor potential, relative water content, leaf area and dry weight of all vegetative structures of P. vulgaris . Drought stress increased charcoal rot development and stomatal resistance, and increased the association among physiological and growth characteristics and charcoal rot development. M. phaseolina invaded between epidermal cells of BAT 477 and Pinto UI-114 hypocotyls. The fungus infected cortex tissues, vascular cylinder, and pith cells of Pinto UI-114, but only epidermal and parenchyma cells of BAT 477. Typical symptoms caused by M. phaseolina were found to be associated with damage caused by the fungus on host tissues, and they were related to drought stress.

Macrophomina phaseolina infects a wide range of plant species. In the case of Phaseolus vulgaris (the common bean), the fungus causes charcoal rot which can lead to severe losses especially under arid conditions. In order to combat the disease, it is necessary to have information on the population structure of the pathogen in terms of pathogenesis on different species which may be grown simultaneously or successively within a region. Previous reports have demonstrated the heterogeneity of the pathogen both in terms of morphological characteristics and molecular genotype; however no systematic attempt has been made to compare pathogenesis of different isolates in relation to genotype, species of origin or geographical location. With this aim 84 isolates of M. phaseolina from different plant species in different geographical regions of Mexico were analysed by inoculation on a set of P. vulgaris cultivars differing in reaction to the fungus and by determination of their amplified fragment length polymorphism (AFLP) genotype. Forty three distinct pathotypes were identified, only two of which were found in more than one species. All 84 isolates had distinct AFLP genotypes and cluster analysis showed a tendency of the isolates to form groups related to geographical origin or species of origin.