Development, Preparation, and Curation of High-Throughput Phenotypic Data for Genome-Wide Association Studies: A Sample Pipeline in R.

Genome-wide association studies (GWAS) have benefited from the advances of sequencing methods for the generation of high-density genomic data. By bridging genotype to phenotype, several genes have been associated with traits of agricultural interest. Despite this, there is still a gap between genotyping and phenotyping due to the large difference in throughput between the two disciplines.

Optimized Ultrasound-Assisted Extraction of Lignans from Species with Green Solvents.

Lignans are plant phenols derived from phenylpropanoids. They play a significant role in plant defense and have features that make them appealing for pharmaceutical applications. Lignans can be obtained by plant in vitro cultures; their production by adventitious and hairy roots of species seems to be a promising alternative to chemical synthesis.

Influence of year, genotype and cultivation system on nutritional values and bioactive compounds in tomato (Solanum lycopersicum L.).

Two tomato genotypes were grown in open field by three cultivation systems (one conventional and two distinct organic for mulching) in three years, 2015, 2016 and 2017. Yields, sugars, organic acids, amino acids, ascorbic acid, biothiols, carotenoids and phenols were measured. Weather conditions largely differed among harvest years, with summer 2016 rainier and less warm, and an opposite summer 2017.

Sorting biotic and abiotic stresses on wild rocket by leaf-image hyperspectral data mining with an artificial intelligence model.

Background: Wild rocket (Diplotaxis tenuifolia) is prone to soil-borne stresses under intensive cultivation systems devoted to ready-to-eat salad chain, increasing needs for external inputs. Early detection of the abiotic and biotic stresses by using digital reflectance-based probes may allow optimization and enhance performances of the mitigation strategies.

Methods: Hyperspectral image analysis was applied to D.

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.

Surveying soil-borne disease development on wild rocket salad crop by proximal sensing based on high-resolution hyperspectral features.

Wild rocket (Diplotaxis tenuifolia, Brassicaceae) is a baby-leaf vegetable crop of high economic interest, used in ready-to-eat minimally processed salads, with an appreciated taste and nutraceutical features. Disease management is key to achieving the sustainability of the entire production chain in intensive systems, where synthetic fungicides are limited or not permitted. In this context, soil-borne pathologies, much feared by growers, are becoming a real emergency.

Hyperspectral Reflectance Response of Wild Rocket () Baby-Leaf to Bio-Based Disease Resistance Inducers Using a Linear Mixed Effect Model.

Baby leaf wild rocket cropping systems feeding the high convenience salad chain are prone to a set of disease agents that require management measures compatible with the sustainability-own features of the ready-to-eat food segment. In this light, bio-based disease resistance inducers able to elicit the plant's defense mechanism(s) against a wide-spectrum of pathogens are proposed as safe and effective remedies as alternatives to synthetic fungicides, to be, however, implemented under practical field applications. Hyperspectral-based proximal sensing was applied here to detect plant reflectance response to treatment of wild rocket beds with strain TA35, laminarin-based Vacciplant, and strain LAS117 cell wall extract-based Romeo, compared to a local standard approach including synthetic fungicides (i.

Anti-Multiple Myeloma Potential of Secondary Metabolites from -Part 2.

Multiple Myeloma (MM) is an aggressive tumor causing millions of deaths every year and currently available therapies are often unsuccessful or correlated with severe side effects. In our previous work we demonstrated that the hydroalcoholic extract inhibits the growth of the MM cell line and we isolated two metabolites responsible for the activity: and . Herein we report their interaction with proteasome, one of the main targets in the fight against MM.

The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems.

Food legumes are crucial for all agriculture-related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system.

Global range expansion history of pepper ( spp.) revealed by over 10,000 genebank accessions.

Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker-trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper ( spp.

Isolation and Characterization of Strain ST9; Rhizomicrobiota and in Planta Studies.

The development of biotechnologies based on beneficial microorganisms for improving soil fertility and crop yields could help to address many current agriculture challenges, such as food security, climate change, pest control, soil depletion while decreasing the use of chemical fertilizers and pesticides. Plant growth-promoting (PGP) microbes can be used as probiotics in order to increase plant tolerance/resistance to abiotic/biotic stresses and in this context strains belonging to the group have shown to have potential as PGP candidates. In this study a new isolate is reported and tested for (i) in vitro PGP features, (ii) whole-genome sequence analysis, and (iii) its effects on the rhizosphere microbiota composition, plant growth, and different plant genes expression levels in greenhouse experiments.

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.

Plastid Transformation in Potato: An Important Source of Nutrition and Industrial Materials.

For a long time, plastid transformation has been a routine technology only in tobacco due to lack of effective selection and regeneration protocols, and, for some species, due to inefficient recombination using heterologous flanking regions in transformation vectors. Nevertheless, the availability of this technology to economically important crops offers new possibilities in plant breeding to manage pathogen resistance or improve nutritional value. Herein we describe an efficient plastid transformation protocol for potato (Solanum tuberosum subsp.

Liquid Chromatographic Quadrupole Time-of-Flight Mass Spectrometric Untargeted Profiling of (Poly)phenolic Compounds in L. and L. Fruits and Their Comparative Evaluation.

This study provided a detailed profiling of the antioxidant and bioactive compounds occurring in three varieties of L. fruits ("Fall Gold", "Glen Ample" and "Tulameen") compared to L. black raspberry ("Jewel" cultivar), adopting a comprehensive untargeted metabolomics approach developed with UHPLC analysis coupled with quadrupole/time-of-flight high resolution mass spectrometry, using the SWATH acquisition protocol.

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.

Past and Future of Plant Stress Detection: An Overview From Remote Sensing to Positron Emission Tomography.

Plant stress detection is considered one of the most critical areas for the improvement of crop yield in the compelling worldwide scenario, dictated by both the climate change and the geopolitical consequences of the Covid-19 epidemics. A complicated interconnection of biotic and abiotic stressors affect plant growth, including water, salt, temperature, light exposure, nutrients availability, agrochemicals, air and soil pollutants, pests and diseases. In facing this extended panorama, the technology choice is manifold.

Genes and genome editing tools for breeding desirable phenotypes in ornamentals.

We review the main genes underlying commercial traits in cut flower species and critically discuss the possibility to apply genome editing approaches to produce novel variation and phenotypes. Promoting flowering and flower longevity as well as creating novelty in flower structure, colour range and fragrances are major objectives of ornamental plant breeding. The novel genome editing techniques add new possibilities to study gene function and breed new varieties.

Phytonutritional Content and Aroma Profile Changes During Postharvest Storage of Edible Flowers.

Edible flowers are niche horticultural products, routinely used as cooking ingredients in the food industry. Currently, new species are required with the aim of enlarging the number of species with a long shelf-life, healthy nutraceutical compounds, and new fragrance and tastes. Mill, A.

The Double-Layer Method to the Genesis of Androgenic Plants in Anemone coronaria.

Homozygous lines occur for plant breeding programs and for studies about gene expression and genetic mapping and they can be derived from anther culture. In this chapter, the method to obtain androgenic plants from an ornamental cut flower, Anemone coronaria belonging to the Ranunculaceae family, is described. In this species, androgenic plants were obtained culturing anthers with responsive microspores in Petri dishes containing a double layer of substrate with specific composition.

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).