Michele Morgante

The large phenotypic variability characterizing the sweet orange [ Citrus sinensis (L.) Osbeck] germplasm arose from spontaneous somatic mutations and led to the diversification of major groups (common, acidless, Navel, and pigmented). Substantial divergence also occurred within each varietal group. The genetic basis of such variability (i.e., ripening time, fruit shape, color, acidity, and sugar content) is largely uncharacterized, and therefore not exploitable for molecular breeding. Moreover, the clonal nature of all sweet orange accessions hinders the traceability of propagation material and fruit juice using low‐density molecular markers. To build a catalog of somatic mutations in Italian varieties, 20 accessions were sequenced at high coverage. This allowed the identification of single nucleotide polymorphisms (SNPs), structural variants (SVs), and large hemizygous deletions, specific to clones or varietal groups. A panel of 239 SNPs was successfully used for genotyping 221 sweet orange accessions, allowing them to be clustered into varietal groups. Furthermore, genotyping of SNPs and SVs was extended to leaf and juice samples of commercial varieties belonging to two varietal groups (Moro and Tarocco) collected from 26 sites in Southern Italy, confirming the usefulness of the identified markers for the identification of specific clones. Interestingly, we found that the insertion of the transposable element VANDAL in the gene exons significantly affected the level of allelic‐specific expression. Finally, the markers developed in the present work contribute to unraveling the origin and diversification of sweet oranges, representing a reliable and efficient molecular tool for the unambiguous fingerprint of somatic mutants and an asset for the traceability of orange plant material and fruit juice.

The stress that the space environment can induce on plant physiology is of both abiotic and biotic nature. The abiotic space environment is characterized by ionizing radiation and altered gravity, geomagnetic field (GMF), pressure, and light conditions. Biotic interactions include both pathogenic and beneficial interactions. Here, we provide an overall picture of the effects of abiotic and biotic space-related factors on plant physiology. The knowledge required for the success of future space missions will lead to a better understanding of fundamental aspects of plant physiological responses, thus providing useful tools for plant breeding and agricultural practices on Earth.

In order to better understand the mechanisms generating genetic diversity in the recent allotetraploid speciesCoffea arabica, here we present a chromosome-level assembly obtained with long read technology. Two genomic compartments with different structural and functional properties are identified in the two homoeologous genomes. The resequencing data from a large set of accessions reveals low intraspecific diversity in the center of origin of the species. Across a limited number of genomic regions, diversity increases in some cultivated genotypes to levels similar to those observed within one of the progenitor species,Coffea canephora, presumably as a consequence of introgressions deriving from the so-called Timor hybrid. It also reveals that, in addition to few, early-occurring exchanges between homoeologous chromosomes, there are numerous recent chromosomal aberrations including aneuploidies, deletions, duplications and exchanges. These events are still polymorphic in the germplasm and could represent a fundamental source of genetic variation in such a lowly variable species.

Il Parlamento italiano ha alcuni giorni fa approvato un emendamento che apre alla sperimentazione in campo delle piante ottenute tramite le cosiddette TEA, Tecnologie di Evoluzione Assistita, che in Europa vengono chiamate New Genomic Techniques e che in passato erano chiamate New Breeding Techniques.Perché dobbiamo essere felici di questa decisione? Cisgenesi e il genome editing tramite CRISPR/Cas, che sono le due tecniche che in Italia abbiamo ricompreso nella definizione di TEA, ci permettono di modificare in maniera mirata singoli geni o addirittura singole basi del DNA all’interno dei geni ottenendo risultati che sono indistinguibili da quelli che potremmo ottenere per incrocio o per mutazione spontanea ma molto più velocemente e in maniera più precisa, ossia senza effetti collaterali indesiderati. E possiamo usare queste tecnologie per rendere le piante più resistenti ai patogeni, per renderle più tolleranti alla siccità, per renderle capaci di meglio sfruttare i fertilizzanti azotati ed anche per renderle capaci di meglio sfruttare l’energia solare attraverso il processo della fotosintesi. Tutte modificazioni che ci possono permettere di migliorare la sostenibilità delle produzioni agricole e diminuire l’impatto ambientale dell’agricoltura.Noi oggi stiamo sfruttando il capitale di risorse naturali del nostro pianeta in maniera non sostenibile, ossia stiamo consumando più risorse naturali di quante non se ne rigenerino spontaneamente. Ce lo fa capire in maniera formale l’equazione dell’impatto globale che mette a confronto l’impronta ecologica delle attività umane con la capacità rigenerativa della biosfera. Oggi l’impronta è pari a 1,6 volte la capacità rigenerativa della biosfera. Ciò vuol dire che stiamo intaccando profondamente il nostro capitale di risorse naturali e più lo intacchiamo più la diseguaglianza aumenta. Dell’impatto sull’ambiente delle attività umane una grossa parte è legata alla produzione di alimenti, anche se comunemente tendiamo a pensare ad altre attività economiche come principali responsabili del degrado ambientale. Il sistema agroalimentare è responsabile, secondo stime recenti, del 34% delle emissioni totali di gas clima-alteranti. Di questo 34% il 71% è dovuto alla sola produzione primaria, cioè alle attività agricole. A ciò si devono assommare, fra gli altri, gli effetti sulla perdita di biodiversità dovuti principalmente alla messa a coltura di superfici che vengono sottratte al loro ruolo di ospiti di ecosistemi naturali che sono sempre molto più ricchi in biodiversità di quanto non lo possa essere un sistema agricolo e gli effetti sulla fertilità dei suoli che tende a diminuire per effetto di molte delle attuali pratiche agricole.Come possiamo fare per riportare almeno in parità l’equazione? Visto che diminuire la popolazione non si può e diminuire l’attività economica sarebbe assai impopolare, non ci resta che giocare sull’efficienza con cui sfruttiamo le nostre risorse naturali per produrre beni e servizi, in altre parole ricchezza o nel caso specifico cibo. E a cosa corrisponde l’efficienza? A scelte politiche e soprattutto ad innovazione tecnologica.

Summary: Coffee is one of the most traded commodities world‐wide. As with 70% of land plants, coffee is associated with arbuscular mycorrhizal (AM) fungi, but the molecular bases of this interaction are unknown. We studied the mycorrhizal phenotype of two commercially important Coffea arabica cultivars (‘Typica National’ and ‘Catimor Amarillo’), upon Funnelliformis mosseae colonisation grown under phosphorus limitation, using an integrated functional approach based on multi‐omics, physiology and biochemistry. The two cultivars revealed a strong biomass increase upon mycorrhization, even at low level of fungal colonisation, improving photosynthetic efficiency and plant nutrition. The more important iconic markers of AM symbiosis were activated: We detected two gene copies of AM‐inducible phosphate (Pt4), ammonium (AM2) and nitrate (NPF4.5) transporters, which were identified as belonging to the C. arabica parental species (C. canephora and C. eugenioides) with both copies being upregulated. Transcriptomics data were confirmed by ions and metabolomics analyses, which highlighted an increased amount of glucose, fructose and flavonoid glycosides. In conclusion, both coffee cultivars revealed a high responsiveness to the AM fungus along their root‐shoot axis, showing a clear‐cut re‐organisation of the major metabolic pathways, which involve nutrient acquisition, carbon fixation, and primary and secondary metabolism.

We have sequenced the chloroplast genome of red spruce (Picea rubens) for the first time using the single-end, short-reads (44 bp) Illumina sequences, assembled and functionally annotated it, and identified simple sequence repeats (SSRs). The contigs were assembled using SOAPdenovo2 following the retrieval of chloroplast genome sequences using the black spruce (Picea mariana) chloroplast genome as the reference. The assembled genome length was 122,115 bp (gaps included). Comparatively, the P. rubens chloroplast genome reported here may be considered a near-complete draft. Global genome alignment and phylogenetic analysis based on the whole chloroplast genome sequences of Picea rubens and 10 other Picea species revealed high sequence synteny and conservation among 11 Picea species and phylogenetic relationships consistent with their known classical interrelationships and published molecular phylogeny. The P. rubens chloroplast genome sequence showed the highest similarity with that of P. mariana and the lowest with that of P. sitchensis. We have annotated 107 genes including 69 protein-coding genes, 28 tRNAs, 4 rRNAs, few pseudogenes, identified 42 SSRs, and successfully designed primers for 26 SSRs. Mononucleotide A/T repeats were the most common followed by dinucleotide AT repeats. A similar pattern of microsatellite repeats occurrence was found in the chloroplast genomes of 11 Picea species.

Background: Brown trout is one of the most widespread fresh-water fish species in Europe. The evolutionary history of and phylogenetic relationships between brown trout populations are complex, and this is especially true for Italian populations, which are heavily influenced in different ways by stocking practices. The characterization of the genetic structure of Italian brown trout populations may give information on the risk of losing endemic Italian populations due to lack of genetic diversity or to admixture with stocking populations. The identification of signatures of selection, and the information deriving from dense genotyping data will help genotype-informed breeding programs. We used a ddRAD-seq approach to obtain more than 100,000 single nucleotide polymorphisms (SNPs), and to characterize the population structure and signatures of selection in 90 brown trout samples. Results: Italian brown trout populations are genetically differentiated, although the stocking practices have introduced strong admixture in endemic Italian trout, especially with the Atlantic lineage. Most of the analysed populations showed high levels of kinship and inbreeding. We detected putative signatures of selection using different approaches, and investigated if the regions were enriched for functional categories. Several regions putatively under selection and characterized by a reduction in heterozygosity across all the studied populations are enriched for genes involved in the response to viral infections. Conclusions: Our results, which show evidence of admixture with the Atlantic lineage (commonly used for stocking), confirm the need for controlling stocking practices, in order to avoid the erosion of the endemic gene pool; given the apparently high levels of kinship and inbreeding in local populations, our results also show the need to take action for increasing gene diversity. In addition, we used the genetically-distinct lineages to detect signatures of selection and we identified putative signatures of selection in several regions associated with resistance to infectious diseases. These constitute candidate regions for the study of resistance to infections in wild and farmed trout.