Use of Microsatellites to Study Agricultural Biodiversity and Food Traceability

Molecular markers are useful tools for measuring the genetic diversity among agricultural species. In plants, microsatellites are still the most used markers for germplasm characterization, conservation, and traceability purposes, while in the livestock sector, although having represented the standard for at least two decades, they are still used only for minor farm animal species. In this work, together with a review on the use of microsatellites in livestock, we also illustrate the use of these markers for the characterization of agricultural diversity and food traceability through two case studies: (i) the analysis of genetic diversity in ancient fruit tree cultivars of apple (Malus × domestica Borkh.), pear (Pyrus communis L.), sweet cherry (Prunus avium L.), and sour cherry (Prunus cerasus L.) from Northern Italy and (ii) the molecular authentication of wheat food chain. In the former case, a high genetic variability as well as the presence of different ploidy levels were detected, while in the latter microsatellite markers were shown to be useful for traceability and product authentication along the whole food chain. Overall, the presented evidence confirms the versatility of microsatellites as markers for both agrobiodiversity characterization and food traceability in cultivated plants and farm animals

Current perspectives on the hormonal control of seed development in Arabidopsis and maize: a focus on auxin.

The seed represents the unit of reproduction of flowering plants, capable of developing into another plant, and to ensure the survival of the species under unfavorable environmental conditions. It is composed of three compartments: seed coat, endosperm and embryo. Proper seed development depends on the coordination of the processes that lead to seed compartments differentiation, development and maturation.Funded by the Ministry for Education and University, Italy(FIRB grant no. RBFR08UG7)Postprint (published version

Current perspectives on the hormonal control of seed development in Arabidopsis and maize: a focus on auxin

The seed represents the unit of reproduction of flowering plants, capable of developing into another plant, and to ensure the survival of the species under unfavorable environmental conditions. It is composed of three compartments: seed coat, endosperm and embryo. Proper seed development depends on the coordination of the processes that lead to seed compartments differentiation, development and maturation. The coordination of these processes is based on the constant transmission/perception of signals by the three compartments. Phytohormones constitute one of these signals; gradients of hormones are generated in the different seed compartments, and their ratios comprise the signals that induce/inhibit particular processes in seed development. Among the hormones, auxin seems to exert a central role, as it is the only one in maintaining high levels of accumulation from fertilization to seed maturation. The gradient of auxin generated by its PIN carriers affects several processes of seed development, including pattern formation, cell division and expansion. Despite the high degree of conservation in the regulatory mechanisms that lead to seed development within the Spermatophytes, remarkable differences exist during seed maturation between Monocots and Eudicots species. For instance, in Monocots the endosperm persists until maturation, and constitutes an important compartment for nutrients storage, while in Eudicots it is reduced to a single cell layer, as the expanding embryo gradually replaces it during the maturation. This review provides an overview of the current knowledge on hormonal control of seed development, by considering the data available in two model plants: Arabidopsis thaliana, for Eudicots and Zea mays L., for Monocots. We will emphasize the control exerted by auxin on the correct progress of seed development comparing, when possible, the two species.Antonella Locascio, Irma Roig-Villanova, and Jamila Bernardi were funded by the Ministry for Education and University, Italy (FIRB grant no. RBFR08UG7).Peer reviewedPeer Reviewe

Mild Potassium Chloride Stress Alters the Mineral Composition, Hormone Network, and Phenolic Profile in Artichoke Leaves

There is a growing interest among consumers and researchers in the globe artichoke [Cynara cardunculus L. subsp. scolymus (L.) Hegi] leaf extract due to its nutraceutical and therapeutic properties. The application of an abiotic stress such as salinity can activate the stress-signaling pathways, thus enhancing the content of valuable phytochemicals. The aim of this study was to assess the metabolic changes in artichokes by probing the leaf metabolome of artichoke plants grown in a floating system and exposed to a relatively mild (30 mM) potassium chloride (KCl) salt stress. Potassium chloride treatment decreased the leaf dry biomass of artichoke, macro- and microelements in leaves (e.g., Ca, Mg, Mn, Zn, and B) but increased the concentrations of K and Cl. Metabolomics highlighted that the hormonal network of artichokes was strongly imbalanced by KCl. The indole-3-acetic acid conjugates, the brassinosteroids hormone 6-deoxocastasterone, and even more the cytokinin precursor N(6)-(Delta-2-isopentenyl)-adenosine-5'-triphosphate, strongly increased in leaves of KCl-treated plants. Moreover, KCl saline treatment induced accumulation of GA4, a bioactive form additional to the already known GA3. Another specific response to salinity was changes in the phenolic compounds profile, with flavones and isoflavones being decreased by KCl treatment, whereas flavonoid glycosides increased. The osmotic/oxidative stress that salinity generates also induced some expected changes at the biochemical level (e.g., ascorbate degradation, membrane lipid peroxidation, and accumulation of mannitol phosphate). These latter results help explain the molecular/physiological mechanisms that the plant uses to cope with potassium chloride stress exposure

Auxin effects on maize seed transciptome during the early stages of endosperm development

In angiosperms, the endosperm is the primary nourishing tissue that provides nutrients for seed germination and in monocots it represents the main constituent of the seed. Cereal seed, and in particular maize seed, could be used as a model for the study of the endosperm tissue. To discover the genes involved in early seed development we performed a time course experiment of the transcriptome of the maize endosperm at 8, 12 and 16 DAP. Endosperm transcript profiling was extended to a mutant impaired in auxin biosynthesis, defective endosperm 18 (de18), to study the hormone-dependent transcriptional network and in particular the auxin effect on transcriptome. The number of transcripts aligned to the reference genome progressively decreased from 8 to 16 DAP and the majority of them were up-regulated in the earliest stage. This evidences a more dynamic transcriptional regulation at 8 DAP, as expected for endosperm that is a tissue that undergoes cell death at maturation. Gene Ontology (GO) analysis of annotated genes showed that these genes were enriched in biological process terms such as cellular and metabolic processes, regulation of biological process, localization and response to stimulus. As regards the molecular function category, the most representative belong to the binding and catalytic activity terms. The main GO term found up regulated during development was the nutrient reservoir activity that is in agreement with the storage accumulation function of endosperm. The regulation of RNA metabolic process, transcription and signaling were the main GO terms down regulated together with the RNA transport, mRNA surveillance and biosynthesis of secondary metabolites pathways. DEGs belonging to hormones signaling pathways, cell cycle and epigenetic effectors were evidenced and validated by real time PCR and in situ hybridization. A morphological description of the mutant and wild type together with the in situ hybridization of the most interesting genes will allow localizing genes related to early endosperm development

Molecular Characterization of Citrus Cultivars: Insight from Recent Sudies

Citrus fruits are an important nutritional source for human health and have immense economic value. Fruit development and ripening are key processes in the production of the phytonutrients, which are essential for a balanced diet and for disease prevention. The anthocyanins are respon-sible for red pigmentation in the flesh of sweet orange and one of the most important antioxidant compounds together with carotenoids (in particular lycopene) and ascorbic acid. These compounds contribute to protect against certain cancers, cardiovascular diseases, and other degene-rative processes. The anthocyanin pathway is well described, and gene coding enzymes of the biosynthesis sequenced and analyzed at the molecular level. The generally identical structure and composition of genes taking part to anthocyanins pathway and their higher expression in blood oranges compared to common ones, suggested the investigation on regu-latory network, in particular MYB transcription factors that play an important role in activation of the biosynthesis. In a recent study, the association of a long terminal repeat (LTR) to a Myb-like gene was found correlated to the red pigmentation in the flesh fruits of sweet orange cultivars. Citrus fruits are important also for their content of ascorbic acid. The gene transcription of key enzymes involved in the four known biosynthesis pathways of the vitamin C resulted up-regulated specifically in fruit, contributing to the high vitamin C accumulation in juice sacs. Moreover, new data related to the GalUR gene family in the citrus genome may suggest its involvement. The expected variability within Citrus species is low, due to the origin by spontaneous mutation and vegetative propagation, leading to a narrow genetic basis. Sweet orange, lemon, lime and grapefruit, are characterized by high heterozygosis, but nearly all cultivars are similar, as they originate from a common ancestor hybrid. Single nucleotide polymorphisms (SNPs) identification performed on various accessions of Citrus clementine and C. sinensis, confirmed the higher heterozygosity of sweet orange respect to clementine; and the presence of very few SNPs linked to agronomical characteristics. The development of next generation sequencing technologies will provide precise description of the genetic composition of citrus accessions and species. In particular, the availability of the citrus genome will permit to increase the opportunity identifying SNP markers to be used to develop citrus assay platforms for breeders. The further step will be to exploit both transcriptome and genome information to map the location of natural genetic variants that confer economically important traits mostly in the fruit

Communicating across generations: the Bsister Language

Bsister proteins form a clade of MADS-box transcription factors that originated 300 million years ago, after ferns diverged but before Angiosperms and Gymnosperms lineages did. Thus, Bsister proteins have been found in both Gymnosperm and Angiosperm species such as paddy oat (Gnetum gnemon), ginkgo, yew (Taxus baccata), rape seed, rice, maize, wheat, petunia, snapdragon, tomato and Arabidopsis. In all these species, they are expressed in female reproductive organs. In this review we go over the evolution and pattern of expression of the Bsister proteins, and we have a glance on their interaction patterns in the form of high order MADS-box complexes in different species. We describe the functions that have been assigned to them according to the analysis of mutants and RNA interference data. We finish this review discussing from a novel point of view the role that Bsister proteins might have, also in tetramer combinations with other MADS-box proteins, on the regulation of tissues communication occurring during reproduction. It is known that a cross-talk is essential for a proper ovule and seed development and Bsister and their target genes might play key roles in these communication processes

Auxin content, cell size and endoreduplication level in the mutant defective endosperm-18.

In this work, we investigated the relationship between auxin level, cell division and endoreduplication in developing endosperms of the mutant de18. The most significant difference between de18 and De18 were detected at 8 days after pollination, where the mutant showed a deficiency in the polidy level, number and volume of the endosperm cells

Isolating resistance genes against Fusarium ear rot in maize.

We investigated global gene expression in maize ears at several time points after infection with Fusarium verticillioides. In kernels at 48 h post infection with a fumonisin-producing strain, about 800 differentially expressed sequences were identified and nearly 10% assigned to the category cell rescue, defence and virulence. The expression analysis was extended to early (12, 24 h) and late (72, 96 h) phases after infection with a fumonisin-nonproducing strain. The mutant strain was able to activate host defence genes later than the wild type strain. When resistant and susceptible maize genotypes were compared, in the resistant lines the expression of defence genes were induced upon infection, indicative of a basal defence response against the fungus. In the susceptible genotypes defence genes were induced specifically after pathogen infection. The basal defence response was also active against several fungal species invading maize kernels. The differentially expressed genes were selected as candidate genes for mapping. SNP markers were developed for resistant and susceptible maize lines. SSR markers were selected according to their chromosomal positions on the maize reference map with the aim to test the polymorphisms in the two parental lines and in a segregating F2 population. The molecular markers associated to resistance will be localized on a high density molecular map and exploited to detect quantitative trait loci (QTLs)