Ezio Portis

• University of Turin

Eggplant ( Solanum melongena ) is one of the four most important Solanaceous crops, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. We studied the genome‐wide association of historical genebank phenotypic data on a genotyped worldwide collection of 3449 eggplant accessions. Overall, 334 significant association...

Eggplant ( Solanum melongena ) is one of the four most important Solanaceous crops, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. We studied the Genome-wide association (GWA) of historical genebank phenotypic data on a genotyped worldwide collection of 3,449 eggplant accessions. Overall, 334 significant asso...

The distribution of chlorophylls in eggplant (Solanum melongena) peel exhibits either a uniform pattern or an irregular green netting pattern. The latter, manifested as a gradient of dark green netting that is intensified in the proximal part of the fruit on a pale green background, is common in wild relatives and some eggplant landraces. Despite t...

Globe artichoke (Cynara cardunculus var. scolymus; 2n = 2x = 34) is a food crop consumed for its immature flower heads. Traditionally, globe artichoke varietal types are vegetatively propagated. However, seed propagation makes it possible to treat the crop as annual, increasing field uniformity and reducing farmers costs, as well as pathogens diffu...

This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience me...

The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On...

Eggplant (Solanum melongena) is an important Solanaceous crop, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. Its domestication centers and migration and diversification routes are still a matter of debate. We report the largest georeferenced and genotyped collection to this date for eggplant and its wild rel...

Recovery, characterization, and sanitization of traditional Italian local landraces/varieties of potatoes that are at risk of extinction

Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. Eggplant is closely related to over 500 species of Solanum subgenus Leptostemonum, belonging to its primary, secondary, and tertiary genepools, and exhibits a wide range of characteristics, in...

The distribution of chlorophylls in the eggplant ( Solanum melongena ) fruit peel can be uniform or display an irregular green netting pattern. The fruit green netting phenotype, manifested as a gradient of dark green netting, more intense in the proximal part of the fruit on a pale green background, is commonly present in eggplant wild relatives a...

Persian buttercup (Ranunculus asiaticus L.) and poppy anemone (Anemone coronaria L.) are ornamental, outcrossing, perennial species belonging to the Ranunculaceae family, characterized by large and highly repetitive genomes. We applied K-seq protocol in both species to generate high-throughput sequencing data and produce a large number of genetic p...

The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the co...

Understanding the mechanisms by which chlorophylls are synthesized in the eggplant (Solanum melongena) fruit peel is of great relevance for eggplant breeding. A multi-parent advanced generation inter-cross (MAGIC) population and a germplasm collection have been screened for green pigmentation in the fruit peel and used to identify candidate genes f...

Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating,...

Understanding the mechanisms by which chlorophylls are synthesized in the eggplant (Solanum melongena) fruit peel is of great relevance for eggplant breeding. A multi-parent advanced generation inter-cross (MAGIC) population and a germplasm collection have been screened for green pigmentation in the fruit peel and used to identify candidate genes f...

The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichok...

The Solanaceae family, also referred to as nightshades or the tomato family, includes a wide variety of morphologies and habits. It has a distinct evolutionary history driven by natural selection, among other processes, which has resulted in unique adaptations and rewarding biochemical pathways for pollinators. The Solanaceae family contains 99 gen...

Anemone coronaria L. (2n = 2x = 16) is a perennial, allogamous, highly heterozygous plant marketed as a cut flower or in gardens. Due to its large genome size, limited efforts have been made in order to develop species-specific molecular markers. We obtained the first draft genome of the species by Illumina sequencing an androgenetic haploid plant...

An increasing interest in the cultivation of (European) hazelnut (Corylus avellana) is driving a demand to breed cultivars adapted to non-conventional environments, particularly in the context of incipient climate change. Given that plant phenology is so strongly determined by genotype, a rational approach to support these breeding efforts will be...

In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms drivin...

Significance This study provides a deep population genomic analysis of 10,000 Capsicum accessions held in genebanks and representing a frame of the global diversity of the genus. By combining single nucleotide polymorphisms (SNPs) based data and passport information, we investigated the genomic diversity and population structure of wild and domesti...

The European hazelnut (Corylus avellana L.; 2n=2x=22) is a worldwide economically important tree nut that is cross-pollinated due to sporophytic incompatibility. Therefore, any individual plant is highly heterozygous. Cultivars are clonally propagated using mound layering, rooted suckers and micropropagation. In recent years, the interest in this c...

Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non‐anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant ‘67/3’ reference line, by Hi‐C retrofitti...

Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as “sweet”, “smoky”, or “fruity” aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceive...

Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest an...

Globe artichoke ( Cynara cardunculus var. scolymus; 2n=2x= 34) is cropped largely in the Mediterranean region, being Italy the leading world producer; however, over time, its cultivation has spread to the Americas and China. In 2016, we released the first (v1.0) globe artichoke genome sequence (http://www.artichokegenome.unito.it/). Its assembly wa...

Eggplant is the second most important solanaceous berry-producing crop after tomato. Despite mapping studies based on bi-parental progenies and GWAS approaches having been performed, an eggplant intraspecific high-resolution map is still lacking. We developed a RIL population from the intraspecific cross ‘305E40’, (androgenetic introgressed line ca...

Sweet pepper (Capsicum annuum L.) is a high value crop and one of the most widely grown vegetables belonging to the Solanaceae family. In addition to commercial varieties and F1 hybrids, a multitude of landraces are grown, whose genetic combination is the result of hundreds of years of random, environmental, and farmer selection. High genetic diver...

In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Despite its wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Gi...

Methods for investigating DNA methylation nowadays either require a reference genome and high coverage, or investigate only CG methylation. Moreover, no large-scale analysis can be performed for N⁶-methyladenosine (6 mA) at an affordable price. Here we describe the methylation content sensitive enzyme double-digest restriction-site-associated DNA (...

With approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the...

Single primer enrichment technology (SPET) is a new, robust, and customizable solution for targeted genotyping. Unlike genotyping by sequencing (GBS), and like DNA chips, SPET is a targeted genotyping technology, relying on the sequencing of a region flanking a primer. Its reliance on single primers, rather than on primer pairs, greatly simplifies...

Genetic variation within globe artichoke landraces contributes to the variable yield performance detected in cultivation. It was built up over many generations of vegetative propagation as a consequence of the limited selection applied by farmers as well as the accumulation of mutations. This chapter reports the results obtained by applying clonal...

Understanding the population genetic structure of crop gene pool is a fundamental prerequisite in plant evolutionary biology and plant breeding. Based on this consideration, in this chapter we pursued two main aims. The first was to review the status of the research pointed at deciphering the population structure of the gene pools of globe artichok...

A first assembly of globe artichoke genome was released in 2016 and the project required the adoption of a set of strategies to overcome the lack of a homozygous reference genotype. Moreover, the inability to exploit standard genotyping methods, normally adopted in inbred species where homozygous segregating progenies can be more easily obtained, p...

The first reference genome sequence of the highly heterozygous globe artichoke has been recently released (January 2016, www.artichokegenome.unito.it), organized in 17 pseudomolecules and including about 27,000 predicted genes. Since the release of the first genome draft, it was clear that, due to the its homozygous profile, the plant selected for...

The availability of the genome sequence of globe artichoke and cultivated cardoon, and the development of physical maps in both taxa, have provided new opportunities to study genetic variation between varietal types to an unprecedented scale, thus contributing to dissect the path from sequence variation to phenotype. Furthermore, they have also pro...

The first high-quality genome assembly of the globe artichoke has been produced within the Compositae Genome Project and the resequencing analyses of four globe artichoke genotypes, representative of the core varietal types, as well as a genotype of the related taxa cultivated cardoon was, later on, carried out. The Web site “www.artichokegenome.un...

Both inter- and intraspecific maps have been developed in eggplant. The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. The first maps developed could be defined as ‘first generation,’ built up by means of pre-NGS (next-generation sequencing) molecular biology techni...

Methods for investigating DNA methylation nowadays either require a reference genome and high coverage, or investigate only CG methylation. Moreover, no large-scale analysis can be performed for N6-methyladenosine (6mA). Here we describe the methylation content sensitive enzyme double-digest restriction-site-associated DNA (ddRAD) technique (MCSeEd...

Globe artichoke represents one of the main horticultural species of the Mediterranean basin, and ‘Spinoso sardo’ is the most widespread and economically relevant varietal type in Sardinia, Italy. In the last decades, in vitro culture of meristematic apices has increased the frequency of aberrant plants in open-field production. These off-type pheno...

This book presents the latest information on the genetics and genomics of the globe artichoke. It focuses on the latest findings, tools and strategies employed in genome sequencing, physical map development and QTL analyses, as well as genomic resources. The re-sequencing of four globe artichoke genotypes, representative of the core varietal types...

In the last 50 years the nut production of Castanea sativa in Europe has strongly declined due to various factors: the aging of the population in the areas of growing changes in the structure of society, and the spread of diseases and pests, including the chestnut gall wasp (Dryocosmus kuriphilus, Yasumatsu). Yet, recently, the interest for the pla...

Cynara cardunculus L. (family Asteraceae, a.k.a. Compositae; 2n=2x=34) is an outcrossing species that includes three fully cross-compatible botanical taxa: globe artichoke (var. scolymus (L.) Fiori), cultivated cardoon (var. altilis D.C.) and their common ancestor wild cardoon (var. sylvestris (Lam.) Fiori). Recently, we published the sequence of t...

Cynara cardunculus, a member of the Asteraceae family, comprises the three taxa var. scolymus (globe artichoke), var. altilis (cultivated cardoon) and the ancestral var. sylvestris (wild cardoon). The substantial quantities of lignocellulosic biomass produced by these plants (up to 30.0 t/ha year⁻¹ dry matter by the cultivated cardoon) can be used...

The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the ident...

Accessory SNP markers. A full list of additional accessory SNP markers for TGdL and MB, excluding from map construction because they were in excess since only one marker per scaffold was chosen. (XLSX)

Detailed genetic maps of the Corylus avellana cultivars Tonda Gentile delle Langhe (TGdL) and Merveille de Bollwiller (MB). TGdL (female parent, blue LGs on the left) and MB (male parent, yellow LGs on the right), and location of QTL responsible for time of leaf budburst. Homologues LGs are presented side-by-side and aligned on the base of markers...

Complete list of all SNPs identified in this study. SNPs are categorized in five types: I) both parents homozygous, monomorphic; II) both parents homozygous, polymorphic; III) both parents heterozygous, monomorphic, IV) TGdL heterozygous, MB homozygous; V) TGdL homozygous, MB heterozygous. (XLSX)

LOD curves for the major QTL responsible for time of leaf budburst detected on TGdL_02 in five years of observations (2012–2016). The estimated LODs at the QTL peak is reported and the dashed line indicates the genome-wide LOD Thresholds (GW) as determined by a permutation test at p ≤ 0.05. (TIF)

We have characterized the simple sequence repeat (SSR) markers of the eggplant (Solanum melongena) using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were complex, with two stretches of repeats separated by an...

Globe artichoke (Cynara cardunculus var. scolymus) is a cross-pollinated, highly heterozygous species, which is conventionally propagated vegetatively. A scheme is described here which combines phenotypic with genotypic selection to fast track the development of a seed-propagated variety. The scheme was tested by making three selections, on a pheno...

Fusarium spp. and Verticillium spp. are widespread soil pathogens responsible for vascular wilts causing heavy yield losses in eggplant (Solanum melongena) as well as in many other crops. Here we report on the identification of QTLs affecting the resistance to Fusarium and Verticillium in an F2 intraspecific population of 156 individuals bred from...

The genome sequence of globe artichoke (Cynara cardunculus L. var. scolymus, 2n = 2x = 34) is now available for use. A survey of C. cardunculus genetic resources is essential for understanding the evolution of the species, carrying out genetic studies and for application of breeding strategies. We report on the resequencing analyses (~35×) of four...

Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltrans...

Conserved motifs in the globe artichoke demethylases (1, 2, 3). Motif 1 included Perm-CXXC (PF15629) domain, motif 2 included HhH-GPD (PF00730), while motif 3 included part of the RRM DME (PF15628). (TIF)

Protein models of the globe artichoke DRM-like proteins. Their three dimensional structures have been compared to that of A. thaliana AtDRM2. MTase domains are highlighted in green and BAH domains in purple. (TIF)

Primer sequences used in the qRT-PCR assays. (DOCX)

Conserved motifs in the globe artichoke C5-MTases. (TIF)

Protein models of the globe artichoke demethylase-like proteins. Their three dimensional structures have been compared to that of A. thaliana AtDME. RRM DME domains are highlighted in orange, Perm-CXXC domains in light blue and HhH-GPD domains in magenta. (TIF)

Demethylase sequences used for tree construction. A. thaliana and S. lycopersicum sequences have also been used for searching for globe artichoke homologs. (DOCX)

Methyltransferase sequences used for tree construction. A. thaliana and S. lycopersicum sequences have also been used for searching for globe artichoke homologs. (DOCX)

Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) usin...

The technology in which a gene(s) is moved between unrelated species has been termed ‘genetic transformation,’ ‘gene technology,’ or ‘genetic engineering.’ Its result is a ‘genetically modified (GM) organism.’ The principal GM food crops grown commercially to date are herbicide-tolerant and insecticide-producing soybean, maize, and canola (oilseed...

The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. scolymus) has been used to catalog the genome’s content of simple sequence repeat (SSR) markers. More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. A...

Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage o...

List of eggplant QTL identified by Barchi et al. (2012) and Portis et al. (2014, 2015).

The pepper QTL identified by Yarnes et al. (2013).

The pepper markers aligned on pepper genome sequence.

The eggplant and pepper markers grouped by clusters.

The table shows the clusters observed in the alignment of eggplant and pepper markers. The eggplant traits are given in the left column while on the right the pepper traits included in each cluster are reported.

Details of chromosome synteny between tomato CDS and pepper genome. Physical positions of tomato CDS matching pepper genome in detail. The relative position of tomato CDS is shown on the ordinate axis while on the abscissa axis there are the normalized pepper chromosomes. The captions on the right show the chromosome of origin of tomato CDS. Physic...

The eggplant markers aligned on pepper genome sequence.

QTL location (only loci harboring QTL are shown). The figure is complementary with the Supplementary Table S5 and shows the loci bearing both eggplant and pepper markers. The scale shown on the Y axis indicates the LOD score. The scale on the X axis indicates the position on pepper chromosome in Mbps. Map positions of the QTL are given by the peaks...