Lorenzo Barchi

Università degli Studi di Torino | UNITO

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...

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 represent...

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...

Recently, there has been a substantial increase in high‐throughput technologies that generate highly complex large datasets for use in the sciences. Plant breeding and genetics have benefited from this data explosion where many public and private institutions now implement genomic and phenomic data to predict performance thus informing germplasm se...

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...

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...

Eggplant (Solanum melongena L.) is a worldwide cultivated vegetable crop from the Solanaceae family whose berries are an important component of human’s daily diet and are rich in health-related compounds. As it happens with many domesticates, this species is sensitive to many abiotic stresses including drought, extreme temperatures, salinity, and s...

Eggplant (Solanum melongena L.), similar to many other crops, suffers from soil-borne diseases, including Fusarium oxysporum f. sp. melongenae (Fom), causing wilting and heavy yield loss. To date, the genetic factors underlying plant responses to Fom are not well known. We previously developed a Recombinant Inbred Lines (RILs) population using as a...

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...

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...

Capsicum annuum L. is one of the most cultivated Solanaceae species, and in the open field, water limitation leading to drought stress affects its fruit quality, fruit setting, fruit size and ultimately yield. We identified stage-specific and a common core set of differentially expressed genes, following RNA-seq transcriptome analyses of a breeding...

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...

Eggplant ( Solanum melongena L.) represents the third most important crop of the Solanaceae family and is an important component of our daily diet. A population of 164 F6 recombinant inbred lines (RILs), derived from two eggplant lines differing with respect to several key agronomic traits, “305E40” and “67/3,” was grown to the commercial maturatio...

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...

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...

Here we focus on the highly conserved MYB-bHLH-WD repeat (MBW) transcriptional complex model in eggplant, which is pivotal in the transcriptional regulation of the anthocyanin biosynthetic pathway. Through a genome-wide approach performed on the recently released Eggplant Genome (cv. 67/3) previously identified, and reconfirmed by us, members belon...

Here we focus on the highly conserved MYB-bHLH-WD repeat (MBW) transcriptional complex model in eggplant, which is pivotal in the transcriptional regulation of the anthocyanin biosynthetic pathway. Through a genome-wide approach performed on the recently released Eggplant Genome (cv. 67/3) previously identified, and reconfirmed by us, members belon...

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...

The recently constructed eggplant genome provides an opportunity for genome-wide marker exploration to be used for variety identification and genetic analysis. SNPs with high density across the genome and genetic stability are suitable for DNA fingerprint and genetic analysis. In this study, we used the eggplant reference genome of line 63/7 and re...

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...

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...

MicroRNAs in plants are endogenous small non-coding RNAs involved in many biological processes related to growth, development and stress response, through post-transcriptional silencing of key target genes. Only a few studies have described the miRNome of globe artichoke. In a very first attempt, 122 new miRNAs were mined through miRNA transcriptom...

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...

Thanks to the recent development of NGS technologies, draft genomes are at present available for many crops. However, most of the genome sequences are incomplete and highly fragmented because they rely on the alignment of billions of short-sequence reads and do not comprehensively report on genomic elements such as highly variable regions and DNA r...

Genome annotation makes it possible to identify the coding and non-coding regions of a genome, such as exons-introns, regulatory elements, repeats as well as gene functions and locations. The newly developed eggplant genome sequence (see Chap. 7) was masked using RepeatMasker, by combining homology-based and de novo approaches, and ~73% of the eggp...

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...

Poster abstract

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...

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...

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...

The butyrogenic capability of Lactobacillus (L.) plantarum is highly dependent on the substrate type and so far not assigned to any specific metabolic pathway. Accordingly, we compared three genomes of L. plantarum that showed a strain-specific capability to produce butyric acid in human cells growth media. Based on the genomic analysis, butyric ac...

Endogenous housekeeping genes are traditionally employed to normalize the expression of target genes in RT-qPCR studies. Assuming that a perfect housekeeping suitable for every condition does not exist, expression stability of the chosen reference gene should be evaluated at every new experiment. The housekeeping selection process reveals furthermo...

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 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...

Eggplant berries are a source of health-promoting metabolites including antioxidant and nutraceutical compounds, mainly anthocyanins and chlorogenic acid; however, they also contain some anti-nutritional compounds such as steroidal glycoalkaloids (SGA) and saponins, which are responsible for the bitter taste of the flesh and with potential toxic ef...

Eggplant is a source of health-promoting metabolites including antioxidant and nutraceutical compounds such as peel anthocyanins and chlorogenic acid of the flesh with anti-diabetic, hypotensive, cardioprotective, and hepatoprotective properties. On the other hand, it is also characterized by the presence of some anti-nutritional compounds such as...

An eggplant ( Solanum melongena ) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which ta...

Given the attention drawn since several decades by arbuscular mycorrhizal fungi (AMF) as poten-tial biological alternatives to chemicals in a low-input agriculture, much effort has been spent in the investigation of mechanisms influencing the dynamics inside AMF communities. In the present study we evaluated the influence of different crop rotation...

The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the genome, and seek to establish correlations between phenotype and genotype. The major advantages of GWA lie in being able to sample a much wid...

Globe artichoke (Cynara cardunculus var. scolymus), whose immature inflorescences (capitula) are consumed as a vegetable all over the world, contributes significantly to the agricultural economy of the Mediterranean basin. Here, we describe a QTL (quantitative trait loci) analysis aimed at elucidating the mode of inheritance of seven main and first...