Alternative splicing (AS) significantly enhances transcriptome complexity. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes.

In light of ongoing climate changes in wine-growing regions, the selection of drought-tolerant rootstocks is becoming a crucial factor for developing a sustainable viticulture. In this study, M4, a new rootstock genotype that shows tolerance to drought, was compared from a genomic and transcriptomic point of view with the less drought-tolerant genotype 101.14. The root and leaf transcriptome of both 101.14 and the M4 rootstock genotype was analysed, following exposure to progressive drought conditions. Multifactorial analyses indicated that stress treatment represents the main factor driving differential gene expression in roots, whereas in leaves the genotype is the prominent factor. Upon stress, M4 roots and leaves showed a higher induction of resveratrol and flavonoid biosynthetic genes, respectively. The higher expression of VvSTS genes in M4, confirmed by the accumulation of higher levels of resveratrol in M4 roots compared with 101.14, was coupled to an up-regulation of several VvWRKY transcription factors. Interestingly, VvSTS promoter analyses performed on both the resequenced genomes highlighted a significantly higher number of W-BOX elements in the tolerant genotype. It is proposed that the elevated synthesis of resveratrol in M4 roots upon water stress could enhance the plant’s ability to cope with the oxidative stress usually associated with water deficit.

Two peach genes homologous to the Arabidopsis ethylene receptor genes ETR1 and ERS1, named Pp‐ETR1 and Pp‐ERS1 respectively, have been isolated and characterized. Pp‐ETR1 and Pp‐ERS1 are conserved in terms of exon numbers and intron positions, although the first and fifth introns of Pp‐ETR1 have an unusual length. In addition, two putative polyadenylation sites, that may cause an incomplete splicing at the 3′ terminus, are present in the fifth intron. A motif of 28 nt, which shows high homology with ethylene responsive elements found in promoters of genes up‐regulated by ethylene, is present in the promoter region of Pp‐ERS1. Expression analysis, carried out by quantitative RT‐PCR, was performed during fruit development and ripening, and leaf and fruitlet abscission. The level of Pp‐ETR1 transcripts remained unchanged in all the tissues and developmental stages examined, whereas Pp‐ERS1 mRNA abundance increased in ripening mesocarp, in leaf and fruitlet activated abscission zones, and following propylene application. 1‐methylcyclopropene (1‐MCP), an inhibitor of ethylene action, did not affect Pp‐ETR1 transcription, while it down‐regulated Pp‐ERS1. A rise in ethylene evolution, accompanied by an increase of Pp‐ERS1 transcript accumulation occurred within 24 h from the end of 1‐MCP treatment. These results indicate that Pp‐ERS1 might play a role in abscission and ripening.

Background: Auxins act as repressors of ripening inception in grape (véraison), while ethylene and abscisic acid (ABA) play a positive role as inducers of the syndrome. Despite the increasing amount of information made available on this topic, the complex network of interactions among these hormones remains elusive. In order to shed light on these aspects, a holistic approach was adopted to evaluate, at the transcriptomic level, the crosstalk between hormones in grape berries, whose ripening progression was delayed by applying naphtalenacetic acid (NAA) one week before véraison. Results: The NAA treatment caused significant changes in the transcription rate of about 1,500 genes, indicating that auxin delayed grape berry ripening also at the transcriptional level, along with the recovery of a steady state of its intracellular concentration. Hormone indices analysis carried out with the HORMONOMETER tool suggests that biologically active concentrations of auxins were achieved throughout a homeostatic recovery. This occurred within 7 days after the treatment, during which the physiological response was mainly unspecific and due to a likely pharmacological effect of NAA. This hypothesis is strongly supported by the up-regulation of genes involved in auxin conjugation (GH3-like) and action (IAA4- and IAA31-like). A strong antagonistic effect between auxin and ethylene was also observed, along with a substantial ‘synergism’ between auxins and ABA, although to a lesser extent. Conclusions: This study suggests that, in presence of altered levels of auxins, the crosstalk between hormones involves diverse mechanisms, acting at both the hormone response and biosynthesis levels, creating a complex response network.