Inheritance patterns in metabolism and growth in diallel crosses of Arabidopsis thaliana from a single growth habitat.

Metabolism is a key determinant of plant growth and modulates plant adaptive responses. Increased metabolic variation due to heterozygosity may be beneficial for highly homozygous plants if their progeny is to respond to sudden changes in the habitat. Here, we investigate the extent to which heterozygosity contributes to the variation in metabolism and size of hybrids of Arabidopsis thaliana whose parents are from a single growth habitat. We created full diallel crosses among seven parents, originating from Southern Germany, and analysed the inheritance patterns in primary and secondary metabolism as well as in rosette size in situ. In comparison to primary metabolites, compounds from secondary metabolism were more variable and showed more pronounced non-additive inheritance patterns which could be attributed to epistasis. In addition, we showed that glucosinolates, among other secondary metabolites, were positively correlated with a proxy for plant size. Therefore, our study demonstrates that heterozygosity in local A. thaliana population generates metabolic variation and may impact several tasks directly linked to metabolism.

Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana.

Hybrid necrosis is a common type of hybrid incompatibility in plants. This phenomenon is caused by deleterious epistatic interactions, resulting in spontaneous activation of plant defenses associated with leaf necrosis, stunted growth and reduced fertility in hybrids. Specific combinations of alleles of ACCELERATED CELL DEATH 6 (ACD6) have been shown to be a common cause of hybrid necrosis in Arabidopsis thaliana. Increased ACD6 activity confers broad-spectrum resistance against biotrophic pathogens but reduces biomass production. We generated 996 crosses among individuals derived from a single collection area around Tübingen (Germany) and screened them for hybrid necrosis. Necrotic hybrids were further investigated by genetic linkage, amiRNA silencing, genomic complementation and metabolic profiling. Restriction site associated DNA (RAD)-sequencing was used to understand genetic diversity in the collection sites containing necrosis-inducing alleles. Novel combinations of ACD6 alleles found in neighbouring stands were found to activate the A. thaliana immune system. In contrast to what we observed in controlled conditions, necrotic hybrids did not show reduced fitness in the field. Metabolic profiling revealed changes associated with the activation of the immune system in ACD6-dependent hybrid necrosis. This study expands our current understanding of the active role of ACD6 in mediating trade-offs between defense responses and growth in A.  thaliana.

ANALIZANDO DATOS DE RNA-Seq EN PROCARIOTAS: UNA REVISIÓN PARA NO EXPERTOS: A Review for Non-experts / RNA-Seq Data Analysis in Prokaryotes

La secuenciación de transcritos con RNA-Seq es hoy en día una de las técnicas más populares en los estudios transcriptómicos. Relativamente reciente, esta técnica ha permitido la secuenciación de transcritos de RNA en una escala y profundidad no alcanzada por otras técnicas anteriores. Sin embargo, el alcance de las conclusiones que se pueden sacar depende estrictamente de un proceso adecuado, desde el diseño experimental hasta el análisis bioinformático de los datos. Dadas las diferencias en el proceso transcripcional de las células eucariotas y procariotas, el análisis de RNA-Seq deberá tener ciertas consideraciones dependiendo del tipo de organismo estudiado. En esta revisión se exponen los principales factores a tener en cuenta para lograr un análisis de RNA-Seq consistente, replicable y concluyente, enfocándose específicamente en organismos procariotas.

RNA-Seq is nowadays the method of choice for the sequencing of transcripts and transcriptomes in the field of molecular biology and gene expression assays. Until recently, this technique has allowed for the sequencing of RNA transcripts in an unprecedented scale and depth never reached in previous years; nevertheless, the reach and validity of the conclusions generated will depend strictly on an adequate experimental design and a robust analysis of the data. Given the inherent differences between prokaryotes and eukaryotes, the RNA-Seq analysis should take into account the type of organism studied. In this review we present the main factors to take into consideration when designing a consistent analysis for this type of data in prokaryotes, from the experimental design to the in silico analysis of the generated data.