To gain statistical evidence of miRNA differential expression driven by the environment and/or genotype, we made pairwise comparisons, keeping constant the developmental stage, and evaluating the miRNA modulation among vineyards or between cultivars . The analyses reveal that some miRNAs are differentially expressed between the two genotypes grown in the same environment, but also that a number of miRNAs are modulated by the environment. In particular the number of differentially expressed miRNAs is higher in ripened berries , while no miRNAs are differentially expressed at bunch closure stage . In details, 14 reads are differentially expressed at pea size stage, in at least one comparison, corresponding to 6 distinct miRNA families; 27 reads are modulated at 19 ◦Brix stage, corresponding to 12 miRNA families and 35 reads are differentially expressed in berries at harvest, corresponding to 12 miRNA families. It is worth noting that 4 of the 6 families modulated in the berries at pea size, are still present among the miRNAs differentially expressed in the berries sampled at 19 ◦Brix and at harvest , even though not always in the same comparisons. Some of the modulated miRNAs, both novel and known are intriguingly connected to berry development and secondary metabolism, even though most of the modulated families are still uncharacterized, or with targets not clearly involved in berry ripening and development, and deserve further studies to fully understand their biological roles. Using high throughput sequencing coupled with robust bioinformatics pipelines we analyzed small RNAs derived from the berries of Cabernet Sauvignon and Sangiovese, grown sideby-side in three vineyards, representative of different grapevine cultivation areas in Italy . The size distribution profiles of our libraries were in general consistent with previous reports in berry grapevine, black plastic pots for plants where the 21-nt class was more abundant than the 24-nt class .
Our analysis revealed dynamic features of the regulatory network mediated by miRNAs and other small RNAs, at the basis of genotype-environment interactions. Plants evolved a series of pathways that generate small RNAs of different sizes with dedicated functions . Although the various small RNA classes have been intensively studied, we are still far from understanding how many small RNA pathways exist, and how they are connected . Additionally, new classes of small non-coding RNAs continue to be discovered and many studies demonstrate a substantial redundancy and cross-talk between known small RNA pathways . Estimating the exact percentage of the plant genome covered by small RNA-generating loci still remains a challenge. By applying static cluster analysis, we investigated small RNA abundances across the genome, identifying 4408 small RNAs producing hotspots. We analyzed their expression in different cultivars, environments and developmental stages, highlighting that the majority of the considered small RNA producing regions was modulated in different conditions. This suggests a strong influence of small RNAs in the response to environment in grapevine berries. Only 462 small RNA-generating loci, corresponding to about 10% of the total, were expressed in all the analyzed libraries, possibly involved in essential biological pathways. Comparing the two cultivars, we observed, with few exceptions, that Cabernet Sauvignon berries have a higher number of expressed sRNA-generating loci than Sangiovese berries when collected in the same conditions . Considering the fact that small RNAs are implicated in the regulation of gene expression in several processes , the higher number of small RNAs expressed in Cabernet Sauvignon compared to Sangiovese berries may reflect a buffering effect of small RNAs influencing grapevine response to diverse growing environments. We believe that these characteristics may have contributed to the wide diffusion of Cabernet Sauvignon, allowing its wide cultivation in almost all wine producing countries. This is not the case for Sangiovese whose cultivation is more restricted.
It is worth noting that Sangiovese is considered a very unsettled grapevine cultivar , showing a wide range of variability in response to year, clone and bunch exposure . Differently, Cabernet Sauvignon is a cultivars showing less inter-annual differences in terms, for example, of concentration of secondary metabolites . To better evaluate varietal differences in response to the environment, we calculated the CS/SG ratio for the small RNA producing hotspots in the three vineyards. An interesting example is found in green berries sampled in Riccione. A region on chromosome 4 showed a 390-fold change in the small RNA abundance, when comparing Cabernet vs. Sangiovese . Most of the reads produced in this region are 21 nt long and are also phased in intervals of 21 nt from both strands, typical of a phased locus . The gene in this locus, also known as VvRD22g, encodes a BURP domaincontaining protein, involved in an ABA-mediated abiotic stress response, which persists still after long periods of stress . The small RNAs profile suggests that the locus is regulated by phased siRNAs similarly to the mechanisms already described for PPR, NB-LRR, and MYB gene families . This is a clear example of GxE interactions since the BURP domain gene modulates phased siRNAs production in the two cultivars only when grown in Riccione. When removing the threshold of minimum cluster abundance set to 5 HNA, in the CS/SG ratio, a high number of clusters with fold change greater than 50 was found, where one of the libraries has 0 HNA and the other any number greater than 30 HNA. This fact suggests a very strong modulation of the expression of small RNAs between the two cultivars, which is more or less pronounced depending on the vineyard where the berries were cultivated. A similar situation was observed comparing the expression level of small RNAs between reciprocal hybrids of Solanum lycopersicum and S. pimpinellifolium . The ripening process of grapevine berries is highly affected by the environment and we observed the impact of the environment on the ripening process in the expression of small RNAs.
The most relevant observation is that Riccione is very peculiar in relation to the activation of sRNA hotspots, as indicated by the high number of Riccionespecific clusters and by the extreme modification it induces in the CS/SG ratio : in Riccione in fact this ratio decreases in green berries and increases in ripened berries, and this is not observed in any other vineyard; in addition to this the already discussed example of BURP domain gene, is observed in Riccione, as well. Riccione is the most diverse environment when compared to Montalcino and Bolgheri. Riccione is located at the Adriatic coast and has a temperate sub-littoral climate, while Montalcino and Bolgheri are both located in Tuscany with typically Mediterranean climate. Moreover, both cultivars show a peculiar profile of small RNA loci during berries ripening, in Riccione. The expression of small RNA loci in Cabernet Sauvignon berries drastically changed during development, especially when collected in Riccione , not only in the number of active loci but also in the different genic or intergenic disposition: ripened berries have a 2.6-fold increase in small RNA loci active in genic regions. Differently, when Sangiovese is grown in Riccione, there is a very high number of small RNA loci active in green berries, mainly associated to transposable elements that remains almost stable during development although the proportion of intergenic loci is reduced. Sangiovese berries collected in Montalcino show a 2.5- fold increase of small RNA producing loci during development. Differences during berry development between the cultivars may explain their different behavior in different environments, and the characteristics of each vineyard may favor one or other variety according to their demands. For example, Sangiovese needs a long growing season with sufficient warmth to fully ripen . Consequently, drainage pot cooler environments will require a reprograming of Sangiovese gene expression in order to achieve ripening. Other factors such as composition of soil, level of humidity, photoperiod and density of cultivation may be exerting the same influence on the ripening of the berries triggering the activation of different small RNA loci. Applying a conservative pipeline to the analysis of our 48 small RNA libraries, we recognized 89 known and annotated grapevine miRNAs. In addition, when compared to previous reports in grapevine we identified 7 completely novel miRNAs plus 26 homologous to other plant species, but novel to grapevine. This is a remarkable number considering the stringency of our pipeline and that our study is based only on four developmental stages of berries. The outline of miRNA accumulation across samples is different from that of sRNA-producing loci. While the expression of sRNA-generating regions allows distinguishing very well between ripened and green berries and also between cultivars , the accumulation of miRNAs shows a clear distinction only between ripened and green berries, and when the berries were green, we observe a further dichotomy separating the two cultivars and the two green developmental stages. The same pattern of miRNA accumulation among green and ripened berries of grapevine was observed when we described the miRNA expression atlas of Vitis vinifera . Comparing the distribution of miRNAs expressed throughout our samples, we found a set of 39 miRNAs ubiquitous or nearly ubiquitous to all the libraries, and very few miRNAs specific of a cultivar, vineyard or developmental stage.
All these 39 miRNAs belong to known vvi-miRNA families. With few exceptions, the same set of miRNAs was also found expressed in all the small RNA libraries constructed with different tissues of the grapevine cv. Corvina , where the population of expressed miRNAs appears highly variable apart from a well-defined group of miRNAs, probably related to the basal metabolism. These findings are also consistent with previous report in grapevine where a small number of known tissue-specific miRNAs was described . Considering the ripening process as shown in the heat maps , and the correlation dendrogram, it is clear that most miRNAs are modulated during the developmental process. For some miRNA families, we observed the same peculiar patterns of miRNA accumulation, previously described in the grapevine miRNA atlas , e.g., an increase of accumulation toward ripening for miR156 f/g/i, and a decrease for miR166c/e, miR172d, miR319, and miR396a/b, but this is not the main focus of our paper. To establish genotype and environmental influence on miRNA modulation, we performed a statistical analysis that revealed a number of miRNAs differentially expressed. Being aware of the fact that we had only two biological replicates, we applied the exact test as implemented in the EdgeR package. This test has been recently judged a very robust tool that can be used in experiments similar to our, because of its low false positive rate and relative high true positive ratein the presence of a fold change higher than 4 . Considering berries at the same developmental stages, we compared Sangiovese vs. Cabernet Sauvignon in a given vineyard and Montalcino vs. Bolgheri, Montalcino vs. Riccione, and Bolgheri vs. Riccione keeping the cultivar fixed. In total we performed 9 pairwise comparisons for each developmental stage. In general, we observed that berries at 19 ◦Brix and at harvest show a higher number of differentially expressed miRNAs. The most interesting examples are represented by two novel miRNAs, whose predicted targets are related to the biosynthesis and accumulation of secondary metabolites, which are of crucial importance in grapevine berries, since its quality depends mainly on its metabolites . The candidate grapem1191 is differentially expressed in Sangiovese between Riccione and Bolgheri and was predicted to target the transparent-testa 12 gene that encodes a multidrug secondary transporter-like protein involved in the vacuolar accumulation of the flavonoid proanthocyanidin in different species including grapevine . Also, in grapevine some studies provide evidences that the intracellular transport of acylated anthocyanins is catalyzed by a MATE transporter . The grape-m1355 seems to be involved in four different pathways, all related to secondary metabolites. It is differentially expressed in Montalcino between the two varieties and was predicted to target a cinnamoyl reductase-like protein , which is part of the of the polyphenol biosynthetic pathway ; a cinnamyl alcohol dehydrogenase involved in the lignin biosynthesis ; a phenylacetaldehyde reductase , which catalyzes, in tomato, the last step in the synthesis of the volatile 2-phenylethanol, important for the aroma and flavor of many foods ; and different bifunctional dihydroflavonol 4-reductases . DFR catalyzes the first step in the conversion of dihydroflavonols to anthocyanins and are responsible for the production of colored anthocyanins .