Whole-genome resequencing reveals genomic footprints of Italian sweet and hot pepper heirlooms giving insight into genes underlying key agronomic and qualitative traits.

Background: Pepper is a major crop species of the Solanaceae family, largely appreciated for its high nutritional and healthy contribution to human diets. In the Mediterranean basin, the favorable pedoclimatic conditions enhanced the selection of several diversified landraces cultivated pepper (Capsicum annuum), for whom Italy can be considered a main pole of diversification. Hence, a survey of traditional C.

Combined effect of silicon and non-thermal plasma treatments on yield, mineral content, and nutraceutical proprieties of edible flowers of Begonia cucullata.

Edible flowers are becoming popular as a nutraceutical and functional food that can contribute to human nutrition with high antioxidant molecules and mineral elements. While comparative studies between different flower species have been performed, less is known about the best agronomical practices to increase yield and nutraceutical proprieties of blooms. Silicon stimulates plant resistance against stress and promotes plant growth while non-thermal plasma (NTP) technology has been applied for the disinfection and decontamination of water, as well as for increasing plant production and quality.

Whole-Genome Doubling Affects Pre-miRNA Expression in Plants.

Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling.

New Insight into Justicidin B Pathway and Production in .

Lignans are the main secondary metabolites synthetized by species as plant defense compounds but they are also valuable for human health, in particular, for novel therapeutics. In this work, in vitro cultures, cells (Cc), adventitious roots (ARc) and hairy roots (HRc) were developed for the production of justicidin B through elicitation with methyl jasmonate (MeJA) and coronatine (COR). The performances of the cultures were evaluated for their stability, total phenols content and antioxidant ability.

Protoplast-Based Method for Genome Editing in Tetraploid Potato.

The cultivated potato is tetraploid with four probably equivalent loci for each gene. A potato variety is furthermore commonly genetically heterogeneous and selected based on a beneficial genetic context which is maintained by clonal propagation. When introducing genetic changes by genome editing it is then desirable to achieve edits in all four loci for a certain gene target.

Guidelines for Setting Up a mRNA Sequencing Experiment and Best Practices for Bioinformatic Data Analysis.

RNA-sequencing, commonly referred to as RNA-seq, is the most recently developed method for the analysis of transcriptomes. It uses high-throughput next-generation sequencing technologies and has revolutionized our understanding of the complexity and dynamics of whole transcriptomes.In this chapter, we recall the key developments in transcriptome analysis and dissect the different steps of the general workflow that can be run by users to design and perform a mRNA-seq experiment as well as to process mRNA-seq data obtained by the Illumina technology.

Practical Workflow from High-Throughput Genotyping to Genomic Estimated Breeding Values (GEBVs).

The global climate is changing, resulting in significant economic losses worldwide. It is thus necessary to speed up the plant selection process, especially for complex traits such as biotic and abiotic stresses. Nowadays, genomic selection (GS) is paving new ways to boost plant breeding, facilitating the rapid selection of superior genotypes based on the genomic estimated breeding value (GEBV).

High-Throughput DNA Isolation in Vegetable Crops for Genomics Applications.

Isolating high-quality DNA is essential for several applications in molecular biology and genomics. Performing whole-genome sequencing in crops and development of reduced representation genomic libraries for genotyping require precise standard on DNA in terms of concentration and purity. For screening large populations it is essential to increase the extraction throughput at affordable costs.

Cultivated Tomato ( L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes.

In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and two wild species among the closest () and most distantly related () species to cultivated tomatoes. Comparative analyses among the chloroplast genomes sequenced in this work and those available in GenBank allowed evaluating the variability of plastomes and defining phylogenetic relationships.

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions.

Background: Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority.

Phytochemical Profile, Mineral Content, and Bioactive Compounds in Leaves of Seed-Propagated Artichoke Hybrid Cultivars.

The globe artichoke ( L. subsp. (L.

Optimizing N Fertilization to Improve Yield, Technological and Nutritional Quality of Tomato Grown in High Fertility Soil Conditions.

Processing tomato is the second most important worldwide cash crop, generally produced in high-input systems. However, fruit yield and quality are affected by agronomic management, particularly nitrogen (N) fertilization, whose application to indeterminate growth genotypes for canning has yet to be investigated in depth. Hence, the objective of this work was to assess the effects of different N rates (0, 50, 125, 200, 275, and 350 kg ha) on fruit yield and quality characteristics of processing tomato 'San Marzano' landrace.

Genome-Wide HMG Family Investigation and Its Role in Glycoalkaloid Accumulation in Wild Tuber-Bearing .

Steroidal glycoalkaloids (SGAs) are a class of nitrogen-containing glycosides occurring in several plant families and biosynthesized through a specific pathway. HMG-CoA reductase is the first enzyme of this pathway, and its transcription can be regulated by biotic and abiotic stressors and even in a tissue-specific manner. This study aimed to characterize the genes family in a tuber-bearing potato species, , using transcriptional and functional approaches.

Overview of Biotic Stresses in Pepper ( spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics.

Pepper ( spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant.

Genome Sequencing of C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals.

Distinctive strains of are used as soil inoculants for their ability to promote plant growth. strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as . In this paper, the complete genome sequence of strain C1 is reported.

Applications and Trends of Machine Learning in Genomics and Phenomics for Next-Generation Breeding.

Crops are the major source of food supply and raw materials for the processing industry. A balance between crop production and food consumption is continually threatened by plant diseases and adverse environmental conditions. This leads to serious losses every year and results in food shortages, particularly in developing countries.

Characterization and Antioxidant Activity of Essential Oil of Four Sympatric Orchid Species.

The volatile fractions from fresh inflorescences of naturally growing orchids (L.) R. M.

Antioxidant and Mineral Composition of Three Wild Leafy Species: A Comparison Between Microgreens and Baby Greens.

Wild plants may play an important role in human nutrition and health and, among them, many are the leafy species. We hypothesized that the wild greens could be profitably grown as microgreens and baby greens, specialty products whose market is increasing. We compared three wild leafy species ( Scop.

Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Mitochondrial Genome.

Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions.

Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites.

Capsicum is one of the major vegetable crops grown worldwide. Current subdivision in clades and species is based on morphological traits and coarse sets of genetic markers. Broad variability of fruits has been driven by breeding programs and has been mainly studied by linkage analysis.

Mycorrhiza-mediated interference between cover crop and weed in organic winter cereal agroecosystems: The mycorrhizal colonization intensity indicator.

The mycorrhizal fungi are symbiotic organisms able to provide many benefits to crop production by supplying a set of ecosystem functions. A recent ecological approach based on the ability of the fungi community to influence plant-plant interactions by extraradical mycelium development may be applied to diversified, herbaceous agroecosystems. Our hypothesis is that the introduction of a winter cereal cover crop (CC) as arbuscular mycorrhizal fungi (AMF)-host plant in an organic rotation can boosts the AMF colonization of the other plants, influencing crop-weed interference.