Identification of genes involved in haevy metals tolerance and hyperaccumulation in Arabidopsis halleri and characterisation of a bZIP transcription factor responsible for Cd uptake and translocation to the shoot in Arabidopsis thaliana

Il cadmio (Cd) rappresenta uno dei principali fattori di rischio sia per la salute umana che per l\u2019ambiente: a causa della sua elevata solubilit\ue0 in acqua, si ha una vasta distribuzione nell\u2019ecosistema, insieme ad un\u2019immediata disponibilit\ue0 all\u2019assorbimento da parte delle piante e quindi l\u2019ingresso nella catena alimentare. Un\u2019alternativa ai tradizionali sistemi di risanamento ambientale da metalli pesanti, tra cui il Cd, \ue8 rappresentata dalla phytoremediation: una tecnica in situ, eco-compatibile ed a basso impatto economico che si pone come obiettivo la rimozione dall\u2019ambiente di agenti inquinanti, sia di natura organica che inorganica, attraverso l\u2019uso di organismi vegetali. In particolar modo, la fitoestrazione prevede l\u2019utilizzo di piante in grado di rimuovere tali inquinanti da siti contaminati e accumularli nei propri tessuti epigei (Pilon-Smits, 2005). L\u2019identificazione di numerose specie vegetali iperaccumulatrici in grado di tollerare, ma soprattutto di accumulare, elevate quantit\ue0 di metalli pesanti nei propri tessuti, dimostra che le piante possiedono il potenziale genetico per tollerarli e rimuoverli da matrici contaminate. Un esempio \ue8 rappresentato da Arabidopsis halleri (appartenente alla famiglia delle Brassicaceae) in grado di tollerare elevate concentrazioni di Cd, Zn e Pb ed iperaccumulare Cd e Zn (van Rossum et al., 2004). Essendo vicina dal punto di vista filogenetico ad Arabidopsis thaliana, specie modello per studi di genetica molecolare in ambito vegetale, A. halleri riveste un particolare interesse per lo studio dei meccanismi responsabili dell\u2019accumulo e tolleranza ai metalli pesanti. Negli ultimi anni, grazie a studi di genomica funzionale, sono stati identificati numerosi componenti molecolari responsabili della tolleranza e dell\u2019accumulo, ma rimangono ancora da chiarire molti aspetti di fondamentale importanza alla base della regolazione dell\u2019espressione genica, in cui i fattori di trascrizione (TFs), ad esempio, giocano un ruolo chiave. Inoltre, \ue8 necessario considerare il contributo apportato dai microorganismi della rizosfera della specie vegetale interessata. \uc8 noto infatti che tali microorganismi sono in grado di alterare la mobilit\ue0 dei metalli presenti nell\u2019ambiente, influenzandone di conseguenza il loro assorbimento da parte dell\u2019apparato radicale della pianta (Lovley, 1995).Cadmium (Cd) is a main risk for human health and agriculture: this is due to its high solubility in water, which causes its rapid distribution into the environment, an immediate availability to plants and its access into the food-chain. An alternative strategy of environmental remediation from heavy metals, for example Cd, is the phytoremediation: a process applied in situ, ecologically safe (environment friendly) and inexpensive, which has as aim the strip of organic and inorganic contaminants from sites by plants. Particularly, the phytoextraction provide the use of plants able to remove heavy metals and accumulate them in the above-ground tissues (Pilon-Smits, 2005). The identification of numerous hyperaccumulator plants capable to tolerate and accumulate high heavy metal amounts in their tissues, demonstrates that plants own the genetic capacity to tolerate and remove heavy metals from contaminated sites. An example is Arabidopsis halleri (belonging to Brassicaceae family), a plant species tolerant to Cd, Zn and Pb and hyperaccumulator of Cd and Zn (van Rossum et al., 2004). Being phylogenetically related to Arabidopsis thaliana, A. halleri is considered an important model system in studies that concern phytoremediation. Much remains still unknown about the molecular components of the metal-induced signal transduction, and only recently, thanks to differential-expression analyses, it has been possible to identify several genes, for example transcription factors (TFs), involved in heavy metal stress response. Moreover it important to consider the role of microbial community of rhizosphere in heavy metal uptake and translocation to the shoot processes: rhizosphere microorganisms, in fact, are able to modify (alter), directly or indirectly, the heavy metal mobility in soil, influencing their absorption by plant roots (Lovley, 1995)

The Maize PIN Gene Family of Auxin Transporters

Auxin is a key regulator of plant development and its differential distribution in plant tissues, established by a polar cell to cell transport, can trigger a wide range of developmental processes. A few members of the two families of auxin efflux transport proteins, PIN-formed (PIN) and P-glycoprotein (ABCB/PGP), have so far been characterized in maize. Nine new Zea mays auxin efflux carriers PIN family members and two maize PIN-like genes have now been identified. Four members of PIN1 (named ZmPIN1a–d) cluster, one gene homologous to AtPIN2 (ZmPIN2), three orthologs of PIN5 (ZmPIN5a–c), one gene paired with AtPIN8 (ZmPIN8), and three monocot-specific PINs (ZmPIN9, ZmPIN10a, and ZmPIN10b) were cloned and the phylogenetic relationships between early-land plants, monocots, and eudicots PIN proteins investigated, including the new maize PIN proteins. Tissue-specific expression patterns of the 12 maize PIN genes, 2 PIN-like genes and ZmABCB1, an ABCB auxin efflux carrier, were analyzed together with protein localization and auxin accumulation patterns in normal conditions and in response to drug applications. ZmPIN gene transcripts have overlapping expression domains in the root apex, during male and female inflorescence differentiation and kernel development. However, some PIN family members have specific tissue localization: ZmPIN1d transcript marks the L1 layer of the shoot apical meristem and inflorescence meristem during the flowering transition and the monocot-specific ZmPIN9 is expressed in the root endodermis and pericycle. The phylogenetic and gene structure analyses together with the expression pattern of the ZmPIN gene family indicate that subfunctionalization of some maize PINs can be associated to the differentiation and development of monocot-specific organs and tissues and might have occurred after the divergence between dicots and monocots

Time course of biochemical, physiological, and molecular responses to field-mimicked conditions of drought, salinity, and recovery in two maize lines

Drought and salinity stresses will have a high impact on future crop productivity, due to climate change and the increased competition for land, water, and energy. The response to drought (WS), salinity (SS), and the combined stresses (WS+SS) was monitored in two maize lines: the inbred B73 and an F1 commercial stress-tolerant hybrid. A protocol mimicking field progressive stress conditions was developed and its effect on plant growth analyzed at different time points. The results indicated that the stresses limited growth in the hybrid and arrested it in the inbred line. In SS, the two genotypes had different ion accumulation and translocation capacity, particularly for Na+ and Cl 12. Moreover, the hybrid perceived the stress, reduced all the analyzed physiological parameters, and kept them reduced until the recovery. B73 decreased all physiological parameters more gradually, being affected mainly by SS. Both lines recovered better from WS than the other stresses. Molecular analysis revealed a diverse modulation of some stress markers in the two genotypes, reflecting their different response to stresses. Combining biochemical and physiological data with expression analyses yielded insight into the mechanisms regulating the different stress tolerance of the two lines

Development of a non-chemical RNAi-based strategy for Amaranthus hybridus L. weed management

Weeds are one of the major issues in cropping systems, responsible for significant yield losses. Herbicide applications are the most effective strategy to control weeds, but stricter legislation has resulted in a significant reduction in the number of herbicides available on the market. Furthermore, the recent European legislation on the sustainable use of pesticides will require farmers to drastically reduce chemical use over the next ten years while promoting integrated weed management strategies that improve environmental sustainability and lower the risks to animal and human health. In addition, the over-reliance on chemical control has resulted in the evolution of resistant biotypes. As a result, new technologies to effectively manage weeds and weed resistance should be developed. In this regard, the development of a non-chemical weed control strategy based on RNA interference (RNAi) technology could: i) represent a potential non-chemical weed control strategy, ii) provide an emerging GMO-free strategy for managing invasive and resistant weeds, and iii) provide a valid opportunity to go inside the molecular mechanisms of weed biology. In this study, the acetolactate synthase (ALS) gene of Amaranthus hybridus L. has been used as the target to assess the effectiveness and applicability of in-vitro synthesized double-stranded RNAs (dsRNAs) direct application for endogenous gene silencing and weed control. A. hybridus is a monoecious and self-pollinated weed that has evolved multiple resistance to herbicides with different sites of action, including ALS inhibitors, which are the most used herbicides in soybean. ALS represents an ideal target for the development and future application of dsRNA-mediated gene silencing because it is an intronless, nucleotide-stable, and single-copy gene. We have produced dsRNAs of various lengths (ranging from 218 to 460bp) targeting three distinct ALS regions: the 5’- and 3’-ends, and a central region. dsRNAs molecules were transcribed in-vitro by T7 RNA polymerase and externally applied to the abaxial leaf surface of A. hybridus plants at 4-6 true leaves developmental stage by: i) mechanical inoculation, or ii) high-pressure spraying. Despite the expression of ALS gene transcripts was found to be lightly downregulated when synthetic 2 ALS-dsRNAs were applied, no phenotypic effects were observed. Our current research focuses on the determination of the effectiveness of ALS-dsRNAs silencing using agroinfiltration techniques, and on dsRNAs delivery techniques through the use of nanomaterials to maximize the effectiveness of gene silencing by exogenous dsRNAs application. This second approach was preliminary studied by RNA electrophoretic mobility of functionalized nanomaterial and by means of confocal microscopy on A. hybridus leaves. In parallel, we are examining the expression patterns of genes thought to be involved in the RNAi pathway in A. hybridus to verify if their expression is triggered by dsRNA applications

MIK2 is a candidate gene of the S-locus for sporophytic self-incompatibility (SSI) in chicory (Cichorium intybus, Asteraceae)

The Cichorium genus offers a unique opportunity to study the sporophytic self incompatibility (SSI) system, being composed of species characterized by highly efficient SI (C. intybus) and complete self compatibility (C. endivia). The chicory genome was used to map 7 previously identified SSI locus-associated markers. The region containing the S locus was restricted to an 4 M bp window on chromosome 5. Among the genes predicted in this region, MDIS1 INTERACTING RECEPTOR LIKE KINASE 2 (MIK2) was promising as a candidate for SSI. Its ortholog in Arabidopsis is involved in pollen stigma recognition reactions, and its protein structure is similar to that of S-receptor kinase (SRK), a key component of the SSI in the Brassica genus. The sequencing of MIK2 in chicory and endive accessions revealed two contrasting scenarios. In C. endivia, MIK2 was fully conserved even comparing different botanical varieties (smooth and curly). In C. intybus, 387 SNPs and 3 INDELs were identified when comparing accessions of different biotypes from the same botanical variety (radicchio). The SNP distribution throughout the gene was uneven, with hypervariable domains preferentially localized in the LRR-rich extracellular region, putatively identified as the receptor domain. The gene was hypothesized to be under positive selection, as the nonsynonymous mutations were more than double the synonymous ones (dN / dS = 2.17). An analogous situation was observed analyzing the first 500 bp of the MIK2 promoter: no SNPs were observed among the endive samples, whereas 44 SNPs and 6 INDELs were detected among the chicory samples. Further analyses are needed to confirm the role of MIK2 in SSI and to demonstrate whether the 23 species-specific nonsynonymous SNPs in the CDS and/or the species-specific 10 bp INDEL found in a CCAAT box region of the promoter are responsible for the contrasting sexual behaviors of the two species

Heterosis in horticultural crop breeding: combining old theoretical bases with modern genomic views

Heterosis in plants has been among the challenging topics for plant scientists worldwide. The production of F1 hybrid varieties of seed-propagated horticultural species is one of the most successful applications of plant breeding techniques. The exploitation of the heterosis phenomenon promotes homogeneity and maximizes crop yields and is a way for breeders to legally control and protect their commercial products. In the past heterosis has been largely studied and explored in cereal crop systems, considering maize as a model for understanding the genetic bases of this phenomenon. To date, crossbreeding in horticultural vegetables has also rapidly progressed. F1 hybrid varieties are available for many horticultural crops, including both allogamous and autogamous species. Several genetic and nongenetic mechanisms have been applied to facilitate the large-scale production of F1 hybrid seeds in vegetable crops to prevent undesirable selfing. Although the development and commercialization of F1 hybrids is currently common in agriculture, this phenomenon is still being investigated at different levels. With the rapid accumulation of knowledge on plant genome structures and gene activities and the advancement of new genomics platforms and methodologies, significant progress has been achieved in recent years in the study of the genetic and molecular bases of heterosis. This paper provides a brief overview of current theoretical advances and practical predictions of the molecular mechanisms underlying heterosis in plants. The aim is to carefully summarize the fundamental mechanisms of heterosis in plants, focusing on horticultural plant breeding, to improve the existing knowledge in this research area. We describe the quantitative genetic model of phenotypic variation and combine evolutionary, phenotypic and molecular genetic views to explain the origin and manifestation of heterosis and its significance for breeding F1 hybrid varieties in horticultural crops. The principles of genomic prediction and its applications in genomic selection are then covered

Current insights and advances into plant male sterility: new precision breeding technology based on genome editing applications

Plant male sterility (MS) represents the inability of the plant to generate functional anthers, pollen, or male gametes. Developing MS lines represents one of the most important challenges in plant breeding programs, since the establishment of MS lines is a major goal in F1 hybrid production. For these reasons, MS lines have been developed in several species of economic interest, particularly in horticultural crops and ornamental plants. Over the years, MS has been accomplished through many different techniques ranging from approaches based on cross-mediated conventional breeding methods, to advanced devices based on knowledge of genetics and genomics to the most advanced molecular technologies based on genome editing (GE). GE methods, in particular gene knockout mediated by CRISPR/Cas-related tools, have resulted in flexible and successful strategic ideas used to alter the function of key genes, regulating numerous biological processes including MS. These precision breeding technologies are less time-consuming and can accelerate the creation of new genetic variability with the accumulation of favorable alleles, able to dramatically change the biological process and resulting in a potential efficiency of cultivar development bypassing sexual crosses. The main goal of this manuscript is to provide a general overview of insights and advances into plant male sterility, focusing the attention on the recent new breeding GE-based applications capable of inducing MS by targeting specific nuclear genic loci. A summary of the mechanisms underlying the recent CRISPR technology and relative success applications are described for the main crop and ornamental species. The future challenges and new potential applications of CRISPR/Cas systems in MS mutant production and other potential opportunities will be discussed, as generating CRISPR-edited DNA-free by transient transformation system and transgenerational gene editing for introducing desirable alleles and for precision breeding strategies

Dissecting the effect of soil on plant phenology and berry transcriptional plasticity in two Italian grapevine varieties (Vitis vinifera L.)

Grapevine embodies a fascinating species as regards phenotypic plasticity and genotype-per-environment interactions. The terroir, namely the set of agri-environmental factors to which a variety is subjected, can influence the phenotype at the physiological, molecular, and biochemical level, representing an important phenomenon connected to the typicality of productions. We investigated the determinants of plasticity by conducting a field-experiment where all terroir variables, except soil, were kept as constant as possible. We isolated the effect of soils collected from different areas, on phenology, physiology, and transcriptional responses of skin and flesh of a red and a white variety of great economic value: Corvina and Glera. Molecular results, together with physio-phenological parameters, suggest a specific effect of soil on grapevine plastic response, highlighting a higher transcriptional plasticity of Glera in respect to Corvina and a marked response of skin compared to flesh. Using a novel statistical approach, we identified clusters of plastic genes subjected to the specific influence of soil. These findings could represent an issue of applicative value, posing the basis for targeted agricultural practices to enhance the desired characteristics for any soil/cultivar combination, to improve vineyards management for a better resource usage and to valorize vineyards uniqueness maximizing the terroir-effect

MIK2 is a candidate gene of the S-locus for sporophytic self-incompatibility in chicory (Cichorium intybus, Asteraceae)

The Cichorium genus offers a unique opportunity to study the sporophytic self-incompatibility (SSI) system, being composed of species characterized by highly efficient self-incompatibility (e.g., C. intybus) and complete self-compatibility (e.g., C. endivia). To this end, the chicory genome was used to map seven previously identified SSI locus-associated markers. The region containing the S-locus was therefore restricted to an ~4 M bp window on chromosome 5. Among the genes predicted in this region, MDIS1 INTERACTING RECEPTOR LIKE KINASE 2 (ciMIK2) was particularly promising as a candidate for SSI. Its ortholog in Arabidopsis (atMIK2) is involved in pollen−stigma recognition reactions, and its protein structure is similar to that of S-receptor kinase (SRK), a key component of the SSI system in the Brassica genus. The amplification and sequencing of MIK2 in chicory and endive accessions revealed two contrasting scenarios. In C. endivia, MIK2 was fully conserved even when comparing different botanical varieties (i.e., smooth and curly endive). In C. intybus, 387 polymorphic positions and 3 INDELs were identified when comparing accessions of different biotypes all belonging to the same botanical variety (i.e., radicchio). The polymorphism distribution throughout the gene was uneven, with hypervariable domains preferentially localized in the LRR-rich extracellular region, putatively identified as the receptor domain. The gene was hypothesized to be under positive selection, as the nonsynonymous mutations were more than double the synonymous ones (dN/dS = 2.17). An analogous situation was observed when analyzing the first 500 bp of the MIK2 promoter: no SNPs were observed among the endive samples, whereas 44 SNPs and 6 INDELs were detected among the chicory samples. Further analyses are needed to confirm the role of MIK2 in SSI and to demonstrate whether the 23 species-specific nonsynonymous SNPs in the CDS and/or the species-specific 10 bp-INDEL found in a CCAAT box region of the promoter are responsible for the contrasting sexual behaviors of chicory and endive