Pasquale Tripodi

Polyphenol Oxidases in Crops: Biochemical, Physiological and Genetic Aspects

Enzymatic browning is a colour reaction occurring in plants, including cereals, fruit and horticultural crops, due to oxidation during postharvest processing and storage. This has a negative impact on the colour, flavour, nutritional properties and shelf life of food products. Browning is usually caused by polyphenol oxidases (PPOs), following cell damage caused by senescence, wounding and the attack of pests and pathogens. Several studies indicated that PPOs play a role in plant immunity, and emerging evidence suggested that PPOs might also be involved in other physiological processes. Genomic investigations ultimately led to the isolation of PPO homologs in several crops, which will be possibly characterized at the functional level in the near future. Here, focusing on the botanic families of Poaceae and Solanaceae, we provide an overview on available scientific literature on PPOs, resulting in useful information on biochemical, physiological and genetic aspects.

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing.

BackgroundKnowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes.ResultsGBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features.ConclusionsGBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs.

Genetic Transformation and Genomic Resources for Next-Generation Precise Genome Engineering in Vegetable Crops

In the frame of modern agriculture facing the predicted increase of population and general environmental changes, the securement of high quality food remains a major challenge to deal with. Vegetable crops include a large number of species, characterized by multiple geographical origins, large genetic variability and diverse reproductive features. Due to their nutritional value, they have an important place in human diet. In recent years, many crop genomes have been sequenced permitting the identification of genes and superior alleles associated with desirable traits. Furthermore, innovative biotechnological approaches allow to take a step forward towards the development of new improved cultivars harboring precise genome modifications. Sequence-based knowledge coupled with advanced biotechnologies is supporting the widespread application of new plant breeding techniques to enhance the success in modification and transfer of useful alleles into target varieties. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system, zinc-finger nucleases, and transcription activator-like effector nucleases represent the main methods available for plant genome engineering through targeted modifications. Such technologies, however, require efficient transformation protocols as well as extensive genomic resources and accurate knowledge before they can be efficiently exploited in practical breeding programs. In this review, we revise the state of the art in relation to availability of such scientific and technological resources in various groups of vegetables, describe genome editing results obtained so far and discuss the implications for future applications.

A multi-trait characterization of the ‘Friariello’ landrace: a Mediterranean resource for sweet pepper breeding

Landraces are an important resource for crop breeding, due to their resilience and content of quality traits. However, genetic and phenotypic variability needs to be carefully characterized for proper direct and indirect use. In the present study, a multidisciplinary approach was carried out to assess the Italian sweet pepper landrace ‘Friariello’. A total of 18 traditional accessions were compared with five hybrids and two ecotypes with similar fruit typology. Genetic and morpho-agronomic characterization allowed us to distinguish five different group types of ‘Friariello’. Accessions showing two/three lobes at the blossom end of the fruit were found to be the most productive, whereas the genotypes showing one/two lobes at the blossom end were the most homogeneous. A total of 167 volatile organic compounds (VOCs) were identified in the collection analysed. Moreover, of the 37 targeted VOCs, 29 showed significant differences in content among the pepper genotypes studied. Of such VOCs related to main flavours described for pepper in the literature, ten were found to be the major determinants of variability among the derived ‘Friariello’ groups. A slightly negative, albeit not significant, correlation was observed between ascorbic acid (AsA) content and agronomic traits, suggesting a better quality for less productive accessions, but also the possibility to improve yield without significantly reducing the AsA levels. The approach used allowed us to define how the different typologies can be used for different breeding purposes, integrating the peculiar properties in order to establish a desirable landrace ideotype. Furthermore, valuable sources for improving quality traits in pepper breeding were identified.

An Overview of Genotyping by Sequencing in Crop Species and Its Application in Pepper

The exploitation of genetic variation in crops is essential to establish innovative breeding programs in the frame of global population increase and the sustainable intensification of agriculture. The advent of next generation sequencing technologies and the availability of complete or draft genome sequences of many crops allowed the development of several methods for SNP discovery. Genotyping by sequencing (GBS) has recently emerged as a promising approach to simultaneously allow SNP identification and genotyping. GBS provides a rapid, highly informative, high-throughput and cost-effective tool for exploring plant genetic diversity on a genome-wide scale and does not require any a priori knowledge on the genome of the species of interest. The features of GBS make it an attractive technology for (1) the assessment of population structure of germplasm collections; (2) the development of high density linkage maps and (3) genetic mapping studies. Herein, we present an overview of the GBS method and describe the main protocols in use, the principal methods for genetic diversity analysis and potential applications of the results in crop breeding programs. Finally, we illustrate the strategy we adopted to investigate the genetic diversity in cultivated pepper (Capsicum annuum).

Occurrence of variable levels of health-promoting fruit compounds in horn-shaped Italian sweet pepper varieties assessed by a comprehensive approach: Health promoting compounds in horn-shaped italian sweet pepper varieties

BACKGROUND Cultivated pepper is a rich source of diverse bioactive compounds with potential properties related to the prevention of major degenerative and proliferative diseases. In the present study, 15 sweet pepper varieties, highly appreciated on the Italian market, were assessed for variation in the content of ascorbic acid, isoprenoids and flavonoids, as well as morpho-agronomic performances and molecular diversity. RESULTS The collection under study showed a wide variability for all traits considered. Traditional cultivars, although less productive, were characterized by a high content of β-carotene and ascorbic acid, reaching maximum concentrations of 230.5 mg kg-1 fresh weight (fw) and 2750 mg kg-1 fw, respectively. Strong correlations were demonstrated between neoxanthin and luteolins. Fruit weight was positively correlated with α-tocopherol content and negatively correlated with luteolins content. The genotyping by sequencing platform allowed the identification of 1833 single nucleotide polymorphism, which better defined the relationships among cultivars, based on provenance and improvement rate. CONCLUSIONS The present study provides an overview of the variability in the expression of fruit nutritional traits in a collection of horn-shaped pepper cultivars, integrating agronomic and molecular data. The impact for breeding and consumers is discussed.

Genetic and environmental factors underlying variation in yield performance and bioactive compound content of hot pepper varieties (Capsicum annuum) cultivated in two contrasting Italian locations

Hot pepper (Capsicum spp.) is an economically considerable crop, particularly appreciated for its nutritional properties and antioxidants content. Levels of the latter depend on several factors including the cultivar and the environment. In the present study, diversity in morpho-agronomic traits and phytochemical compounds was investigated in 14 hot pepper accessions cultivated in two different pedoclimatic locations. The main source of variation was due to the genotype which showed significant differences for all traits at both locations. With regard to the bioactive compounds, the environment accounted for over 30% of variation for carotenoids, ascorbic acid and tocopherols and less than 0.5% for capsaicinoids. A strong genotype × environment interaction (p < 0.01) was observed in all traits with the exception of those related to fruit weight and shape. Genotyping by sequencing was used for molecular analysis revealing a total of 2120 single-nucleotide polymorphisms. Diversity on the basis of hierarchical clustering and structure analysis elucidated the relationships among accessions on the basis of their biological status and common ancestors, suggesting their contribution to the phenotypic performances observed. The comprehensive approach of this study provides useful information on the variability of phytochemicals mediated by the environment, revealing the challenge related to the genetic improvement of bioactive compounds. The integration of phenotypic and molecular data provides information to identify interesting hot pepper accessions to select for breeding programmes.

Response of rocket salad germplasm (Eruca and Diplotaxis spp.) to major pathogens causing damping-off, wilting and leaf spot diseases

Abstract In the present study, 26 accessions of rocket salad belonging to four species (Eruca sativa Mill., Diplotaxis tenuifolia (L.) DC., Diplotaxis muralis (L.) DC. and Erucastrum spp.) were tested for resistance to damping-off, wilting and leaf spot disease causal agents. High susceptibility to Rhizoctonia solani was detected in all accessions while variability in rocket seedling susceptibility for Sclerotinia assays was observed. Susceptibility to wilting caused by the fungus Fusarium oxysporum f. sp. raphani was tested. E. sativa varieties exhibited a lower severity degree associated to yellowing-related symptoms compared to D. tenuifolia. Resistance assay using the bacterium Xanthomonas campestris pv. campestris was also performed. Five E. sativa varieties showed a disease incidence lower than 60% while all the D. tenuifolia accessions, showed a susceptibility of 100%. The present study represents a step towards the identification of genetic resources useful in breeding for the selections of novel resistant varieties.