Dissecting the genetic diversity of cultivated tomato () germplasm resources: a comparison of ddRADseq genotyping and microsatellite analysis via capillary electrophoresis and high-resolution melting.

Unlabelled: Understanding the genetic diversity of crops is of fundamental importance for the efficient use and improvement of germplasm resources. Different molecular genotyping systems have been implemented for population structure and phylogenetic relationships analyses, among which, microsatellites (SSRs) and single nucleotide polymorphisms (SNPs) markers have been the most widely used. This study reports the efficacy of SNPs detected via double-digest restriction-site-associated DNA sequencing (ddRADseq) and SSRs analyzed via capillary electrophoresis (CE) and high-resolution melting (HRM) in tomato.

Genomic structure and marker-trait association for plant and fruit traits in Capsicum chinense and Capsicum baccatum germplasm.

Objectives: Capsicum baccatum and C. chinense are domesticated pepper species originating from Latin America recognized for their unique flavor and taste and widely diffused as spicy food for fresh uses or for processing. Owing to their capacity for adaptation to diverse habitats in tropical regions, these species serve as a valuable resource for agronomic traits and tolerance to both biotic and abiotic challenges in breeding projects.

Development and application of Single Primer Enrichment Technology (SPET) SNP assay for population genomics analysis and candidate gene discovery in lettuce.

Single primer enrichment technology (SPET) is a novel high-throughput genotyping method based on short-read sequencing of specific genomic regions harboring polymorphisms. SPET provides an efficient and reproducible method for genotyping target loci, overcoming the limits associated with other reduced representation library sequencing methods that are based on a random sampling of genomic loci. The possibility to sequence regions surrounding a target SNP allows the discovery of thousands of closely linked, novel SNPs.

Application of High-Resolution Melting and DNA Barcoding for Discrimination and Taxonomy Definition of Rocket Salad ( spp.) Species.

Nuclear and cytoplasmic DNA barcoding regions are useful for plant identification, breeding, and phylogenesis. In this study, the genetic diversity of 17 species, was investigated with 5 barcode markers. The allelic variation was based on the sequences of chloroplast DNA markers including the spacer between and and gene (), the rubisco (), the maturase K (), as well as the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA.

Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection.

Investigating crop diversity through genome-wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P-SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype-by-environment (G × E) interactions, multi-environment GWAS with a 10 195-marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries.

Harnessing Crop Diversity through Genetics, Genomics and Phenomics Approaches.

Developing resilient cultivars ensuring adequate productions will be the agriculture industry's primary challenge in the coming decades to ensure food security, especially with climate change and a growing global population [...

Genetic Analyses of Seed Longevity in L. in Cold Storage Conditions.

Seed longevity is the most important trait in the genebank management system. No seed can remain infinitely viable. There are 1241 accessions of L.

An integrated genomic and biochemical approach to investigate the potentiality of heirloom tomatoes: Breeding resources for food quality and sustainable agriculture.

A revival of interest in traditional varieties reflects the change in consumer preferences and the greater awareness of the quality of locally grown products. As ancient cultivars, heirlooms have been selected for decades in specific habitats and represent nowadays potential germplasm sources to consider for breeding high-quality products and cultivation in sustainable agriculture. In this study, 60 heirloom tomato ( L.

Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.

Tomato is one of the major vegetable crops grown worldwide and a model species for genetic and biological research. Progress in genomic technologies made possible the development of forefront methods for high-scale sequencing, providing comprehensive insight into the genetic architecture of germplasm resources. This review revisits next-generation sequencing strategies and applications to investigate the diversity of tomato, describing the common platforms used for SNP genotyping of large collections, sequencing, and whole genome resequencing.

Occurrence of on Chickpea in Italy: Pathogen Identification and Characterization.

Climate change has led to the spread of plant pathogens in novel environments, causing dramatic crop losses and economic damage. represents a massive fungal family, containing a huge number of plant pathogens, which are able to infect several hosts. Among them, is a necrotrophic fungus, responsible for several plant diseases, including the soft stem rot of common bean, crown rot on strawberry and charcoal rot of several legumes.

Genotypic and Environmental Effects on Morpho-Physiological and Agronomic Performances of a Tomato Diversity Panel in Relation to Nitrogen and Water Stress Under Organic Farming.

The agricultural scenario of the upcoming decades will face major challenges for the increased and sustainable agricultural production and the optimization of the efficiency of water and fertilizer inputs. Considering the current and foreseen water scarcity in several marginal and arid areas and the need for a more sustainable farming production, the selection and development of cultivars suitable to grow under low-input conditions is an urgent need. In this study, we assayed 42 tomato genotypes for thirty-two morpho-physiological and agronomic traits related to plant, fruit, and root characteristics under standard (control) and no-nitrogen fertilization or water deficit (30% of the amount given to non-stressed trials) treatments in two sites (environments), which corresponded to organic farms located in Italy and Spain.

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.

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.

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.

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.

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.

Methods of Development of Biparental Mapping Populations in Horticultural Crops.

Biparental mapping populations consist of a set of individuals derived from crosses between two parents often belonging to diverse species of a botanical genus and differing in terms of phenotype and traits to share. The development of such recombinant libraries represents a powerful strategy for dissection of the genetic basis of complex traits in crops and these are largely utilized to develop pre-breeding sources to use in crop improvement. This chapter provides an overview of methods and strategies to follow, for the construction of different types of populations, from a plant breeder point of view.

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.

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.

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.