Bioinformatic identification of a putative microRNA-transcription factor network motif in the regulation of laccase genes in peach (Prunus persica)

Laccase proteins are multicopper glycoprotein oxidases expressed in plant tissues under biotic and abiotic stress conditions. They are able to catalyze oxidation of a broad range of substrates including phenols and amines. The regulation of expression of such genes is crucial for proper reaction to stress. At the DNA level, this modulation is mediated by the recruitment of specific transcription factors (TF) to suitable transcription factor binding sites (TFBS), usually located upstream of a gene. At the RNA level, the short microRNAs molecules (miRs) interfere with the translation of target proteins through base‐pairing with messenger RNAs. Complex regulatory circuits combining those interactions fine‐tune protein expression and enhance plant responses to environmental change. In this case study we performed a phylogenetic analysis of peach laccases and characterized specific peach miRs (miR397a and miR408), reported previously as posttranscriptional regulatory elemen ts of laccase genes. Using a bioinformatic approach we identified unique TFBS for abscisic acid (ABA) response elements in promoter regions of both miR and laccase genes. The signaling molecule ABA plays a major role in plant responses to stress. We propose a feed‐forward loop motif in the stress response network involving ABA action in peach by integrating the TF‐mediated regulation of miR and laccase genes at the transcriptional level with the miR regulation of laccase target genes at the post‐transcriptional level

Assessment of diversity and genetic structure is an essential step for effective use of grape germplasm collections

The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. The FEM grape germplasm resources (2273 accessions) were characterised using 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) to examine the structure of genetic diversity and to propose a core set of grape accessions representing the allelic diversity of the whole collection. Retention of the maximum genetic and phenotypic variability was tested for two genetic core collections and one larger core set established based on phenological records. These results can be combined to the definition of inter- and intraspecific levels of germplasm stratification, and make possible to design studies dissecting the genetic basis of agronomic and domestication-related trait