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Prof. Gianni Barcaccia
University of Padova - Dept. of Agronomy Food Natural resources Animals and Environment (DAFNAE)

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0 Genotyping
0 Molecular Markers
0 Plant Breeding
0 Population Genetics
0 barcoding

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Molecular Markers
Genotyping
barcoding
Plant Breeding
Population Genetics
plant genomics and transcriptomics

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Short Biography

Since 2017 Full Professor of Genetics and Genomics at the University of Padova (Italy) and Adjunct Professor of Plant Breeding at the University of Georgia (USA). PhD title on Plant Reproductive Systems and Population Genetics at the University of Perugia in 1995. Tenured Professor of Genetics and Genomics at the University of Padova from 2001 to 2016. Professor in charge of Genomics Applied to Plant Breeding and Genetic Traceability of Food Products at the University of Padova. Vice-Director of the Department of Agronomy Food Natural resources Animals and Environment (DAFNAE) since 2014 and Coordinator of the Department Commission for Technology Transfer and Third Mission (http://www.dafnae.unipd.it). Recently elected as new Director of Department for the academic years 2019-2023. Research expertise on plant reproductive systems and barriers (male-sterility, self-incompatibility and apomixis), use of molecular markers for population genetics and genomics, and marker-assisted breeding. Principal investigator of BreedOmics, a laboratory service of genomics for breeding populations and for genetic identification of varieties and genetic authentication of their foodstuffs (Molecular tools: DNA fingerprinting, SSR genotyping, SNP haplotyping, DNA barcoding, NGS sequencing). For further information visit my personal webpage: http://www.giannibarcaccia.com

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Journal article
Published: 03 June 2021 in Agronomy
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Low temperature is a major limiting factor for the growth and reproduction of some plant species, such as tomato. So far, few studies have been conducted on the effects of low temperature, and the mechanisms of plants’ response to this type of stress is not fully clear. In the current study, the effects of low, nonfreezing temperature (10 °C for three days) on the hormone content, antioxidant activity, and expression patterns of cold-related genes in the leaves of cold-tolerant species (Solanum habrochaites Accession ‘LA1777′) and cold-susceptible species (Solanum lycopersicum cultivar ‘Moneymaker’) were investigated. Low temperature increased the abscisic acid (ABA) content in both tomato species, while the content of zeatin-type cytokinins (ZT) increased in the cold-tolerant species. However, the content of indole-3-acetic acid (IAA) and gibberellic acid (GA) reduced in response to low temperature in susceptible species. Accordingly, cytokinin (CK) is identified as an important hormone associated with low-temperature stress in tomato. In addition, our results indicate that the C-repeat/DRE binding factor 1 (CBF1) gene is less induced in response to low temperature in tomato, although transcription of the inducer of CBF expression 1 (ICE1) gene was upregulated under low temperature in both tomato species. It seems that ICE1 may modulate cold-regulated (COR) genes in a CBF-independent way. In addition, in response to low temperature, the malondialdehyde (MDA) level and membrane stability index (MSI) increased in the susceptible species, indicating that low temperature induces oxidative stress. Additionally, we found that glutathione peroxidase is highly involved in reactive oxygen species (ROS) scavenging induced by low temperature, and antioxidants are more induced in tolerant species. Overall, our results suggest that sub-optimal temperatures promote oxidative stress in tomato and CK is introduced as a factor related to the response to low temperature that requires deeper attention in future breeding programs of tomato.

ACS Style

Parviz Heidari; Mohammad Reza Amerian; Gianni Barcaccia. Hormone Profiles and Antioxidant Activity of Cultivated and Wild Tomato Seedlings under Low-Temperature Stress. Agronomy 2021, 11, 1146 .

AMA Style

Parviz Heidari, Mohammad Reza Amerian, Gianni Barcaccia. Hormone Profiles and Antioxidant Activity of Cultivated and Wild Tomato Seedlings under Low-Temperature Stress. Agronomy. 2021; 11 (6):1146.

Chicago/Turabian Style

Parviz Heidari; Mohammad Reza Amerian; Gianni Barcaccia. 2021. "Hormone Profiles and Antioxidant Activity of Cultivated and Wild Tomato Seedlings under Low-Temperature Stress." Agronomy 11, no. 6: 1146.

Original research article
Published: 25 May 2021 in Frontiers in Plant Science
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Common bean (Phaseolus vulgaris L.) is an essential source of food proteins and an important component of sustainable agriculture systems around the world. Thus, conserving and exploiting the genetic materials of this crop species play an important role in achieving global food safety and security through the preservation of functional and serependic opportunities afforded by plant species diversity. Our research aimed to collect and perform agronomic, morpho-phenological, molecular-genetic, and nutraceutical characterizations of common bean accessions, including lowland and mountain Venetian niche landraces (ancient farmer populations) and Italian elite lineages (old breeder selections). Molecular characterization with SSR and SNP markers grouped these accessions into two well-separated clusters that were linked to the original Andean and Mesoamerican gene pools, which was consistent with the outputs of ancestral analysis. Genetic diversity in the two main clusters was not distributed equally the Andean gene pool was found to be much more uniform than the Mesoamerican pool. Additional subdivision resulted in subclusters, supporting the existence of six varietal groups. Accessions were selected according to preliminary investigations and historical records and cultivated in two contrasting Venetian environments: sea-level and mountain territories. We found that the environment significantly affected some nutraceutical properties of the seeds, mainly protein and starch contents. The antioxidant capacity was found significantly greater at sea level for climbing accessions and in the mountains for dwarf accessions. The seed yield at sea level was halved than mountain due to a seeds reduction in weight, volume, size and density. At sea level, bean landraces tended to have extended flowering periods and shorter fresh pod periods. The seed yield was positively correlated with the length of the period during which plants had fresh pods and negatively correlated with the length of the flowering period. Thus, the agronomic performance of these genetic resources showed their strong connection and adaptation to mountainous environments. On the whole, the genetic-molecular information put together for these univocal bean entries was combined with overall results from plant and seed analyses to select and transform the best accessions into commercial varieties (i.e., pure lines) suitable for wider cultivation.

ACS Style

Pietro Sica; Francesco Scariolo; Aline Galvao; Domiziana Battaggia; Carlo Nicoletto; Carmelo Maucieri; Fabio Palumbo; Dorcas Franklin; Miguel Cabrera; Maurizio Borin; Paolo Sambo; Gianni Barcaccia. Molecular Hallmarks, Agronomic Performances and Seed Nutraceutical Properties to Exploit Neglected Genetic Resources of Common Beans Grown by Organic Farming in Two Contrasting Environments. Frontiers in Plant Science 2021, 12, 1 .

AMA Style

Pietro Sica, Francesco Scariolo, Aline Galvao, Domiziana Battaggia, Carlo Nicoletto, Carmelo Maucieri, Fabio Palumbo, Dorcas Franklin, Miguel Cabrera, Maurizio Borin, Paolo Sambo, Gianni Barcaccia. Molecular Hallmarks, Agronomic Performances and Seed Nutraceutical Properties to Exploit Neglected Genetic Resources of Common Beans Grown by Organic Farming in Two Contrasting Environments. Frontiers in Plant Science. 2021; 12 ():1.

Chicago/Turabian Style

Pietro Sica; Francesco Scariolo; Aline Galvao; Domiziana Battaggia; Carlo Nicoletto; Carmelo Maucieri; Fabio Palumbo; Dorcas Franklin; Miguel Cabrera; Maurizio Borin; Paolo Sambo; Gianni Barcaccia. 2021. "Molecular Hallmarks, Agronomic Performances and Seed Nutraceutical Properties to Exploit Neglected Genetic Resources of Common Beans Grown by Organic Farming in Two Contrasting Environments." Frontiers in Plant Science 12, no. : 1.

Journal article
Published: 20 May 2021 in Genes
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Potassium (K+), as a vital element, is involved in regulating important cellular processes such as enzyme activity, cell turgor, and nutrient movement in plant cells, which affects plant growth and production. Potassium channels are involved in the transport and release of potassium in plant cells. In the current study, three OsKAT genes and two OsAKT genes, along with 11 nonredundant putative potassium channel genes in the rice genome, were characterized based on their physiochemical properties, protein structure, evolution, duplication, in silico gene expression, and protein–protein interactions. In addition, the expression patterns of OsAKTs and OsKATs were studied in root and shoot tissues under salt stress using real-time PCR in three rice cultivars. K+ channel genes were found to have diverse functions and structures, and OsKATs showed high genetic divergence from other K+ channel genes. Furthermore, the Ka/Ks ratios of duplicated gene pairs from the K+ channel gene family in rice suggested that these genes underwent purifying selection. Among the studied K+ channel proteins, OsKAT1 and OsAKT1 were identified as proteins with high potential N-glycosylation and phosphorylation sites, and LEU, VAL, SER, PRO, HIS, GLY, LYS, TYR, CYC, and ARG amino acids were predicted as the binding residues in the ligand-binding sites of K+ channel proteins. Regarding the coexpression network and KEGG ontology results, several metabolic pathways, including sugar metabolism, purine metabolism, carbon metabolism, glycerophospholipid metabolism, monoterpenoid biosynthesis, and folate biosynthesis, were recognized in the coexpression network of K+ channel proteins. Based on the available RNA-seq data, the K+ channel genes showed differential expression levels in rice tissues in response to biotic and abiotic stresses. In addition, the real-time PCR results revealed that OsAKTs and OsKATs are induced by salt stress in root and shoot tissues of rice cultivars, and OsKAT1 was identified as a key gene involved in the rice response to salt stress. In the present study, we found that the repression of OsAKTs, OsKAT2, and OsKAT2 in roots was related to salinity tolerance in rice. Our findings provide valuable insights for further structural and functional assays of K+ channel genes in rice.

ACS Style

Zahra Musavizadeh; Hamid Najafi-Zarrini; Seyed Kazemitabar; Seyed Hashemi; Sahar Faraji; Gianni Barcaccia; Parviz Heidari. Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress. Genes 2021, 12, 784 .

AMA Style

Zahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kazemitabar, Seyed Hashemi, Sahar Faraji, Gianni Barcaccia, Parviz Heidari. Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress. Genes. 2021; 12 (5):784.

Chicago/Turabian Style

Zahra Musavizadeh; Hamid Najafi-Zarrini; Seyed Kazemitabar; Seyed Hashemi; Sahar Faraji; Gianni Barcaccia; Parviz Heidari. 2021. "Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress." Genes 12, no. 5: 784.

Review
Published: 17 May 2021 in Plants
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The gene flow mediated by unreduced gametes between diploid and tetraploid plants of the Medicagosativa-coerulea-falcata complex is pivotal for alfalfa breeding. Sexually tetraploidized hybrids could represent the best way to exploit progressive heterosis simultaneously derived from gene diversity, heterozygosity, and polyploidy. Moreover, unreduced gametes combined with parthenogenesis (i.e., apomixis) would enable the cloning of plants through seeds, providing a unique opportunity for the selection of superior genotypes with permanently fixed heterosis. This reproductive strategy has never been detected in the genus Medicago, but features of apomixis, such as restitutional apomeiosis and haploid parthenogenesis, have been reported. By means of an original case study, we demonstrated that sexually tetraploidized plants maintain apomeiosis, but this trait is developmentally independent from parthenogenesis. Alfalfa meiotic mutants producing unreduced egg cells revealed a null or very low capacity for parthenogenesis. The overall achievements reached so far are reviewed and discussed along with the efforts and strategies made for exploiting reproductive mutants that express apomictic elements in alfalfa breeding programs. Although several studies have investigated the cytological mechanisms responsible for 2n gamete formation and the inheritance of this trait, only a very small number of molecular markers and candidate genes putatively linked to unreduced gamete formation have been identified. Furthermore, this scenario has remained almost unchanged over the last two decades. Here, we propose a reverse genetics approach, by exploiting the genomic and transcriptomic resources available in alfalfa. Through a comparison with 9 proteins belonging to Arabidopsisthaliana known for their involvement in 2n gamete production, we identified 47 orthologous genes and evaluated their expression in several tissues, paving the way for novel candidate gene characterization studies. An overall view on strategies suitable to fill the gap between well-established meiotic mutants and next-generation genomic resources is presented and discussed.

ACS Style

Fabio Palumbo; Elisa Pasquali; Emidio Albertini; Gianni Barcaccia. A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources. Plants 2021, 10, 999 .

AMA Style

Fabio Palumbo, Elisa Pasquali, Emidio Albertini, Gianni Barcaccia. A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources. Plants. 2021; 10 (5):999.

Chicago/Turabian Style

Fabio Palumbo; Elisa Pasquali; Emidio Albertini; Gianni Barcaccia. 2021. "A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources." Plants 10, no. 5: 999.

Journal article
Published: 17 April 2021 in Horticulturae
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Low-temperature stress is a type of abiotic stress that limits plant growth and production in both subtropical and tropical climate conditions. In the current study, the effects of 24-epi-brassinolide (EBR) as analogs of brassinosteroids (BRs) were investigated, in terms of hormone content, antioxidant enzyme activity, and transcription of several cold-responsive genes, under low-temperature stress (9 °C) in two different tomato species (cold-sensitive and cold-tolerant species). Results indicated that the treatment with exogenous EBR increases the content of gibberellic acid (GA3) and indole-3-acetic acid (IAA), whose accumulation is reduced by low temperatures in cold-sensitive species. Furthermore, the combination or contribution of BR and abscisic acid (ABA) as a synergetic interaction was recognized between BR and ABA in response to low temperatures. The content of malondialdehyde (MDA) and proline was significantly increased in both species, in response to low-temperature stress; however, EBR treatment did not affect the MDA and proline content. Moreover, in the present study, the effect of EBR application was different in the tomato species under low-temperature stress, which increased the catalase (CAT) activity in the cold-tolerant species and increased the glutathione peroxidase (GPX) activity in the cold-sensitive species. Furthermore, expression levels of cold-responsive genes were influenced by low-temperature stress and EBR treatment. Overall, our findings revealed that a low temperature causes oxidative stress while EBR treatment may decrease the reactive oxygen species (ROS) damage into increasing antioxidant enzymes, and improve the growth rate of the tomato by affecting auxin and gibberellin content. This study provides insight into the mechanism by which BRs regulate stress-dependent processes in tomatoes, and provides a theoretical basis for promoting cold resistance of the tomato.

ACS Style

Parviz Heidari; Mahdi Entazari; Amin Ebrahimi; Mostafa Ahmadizadeh; Alessandro Vannozzi; Fabio Palumbo; Gianni Barcaccia. Exogenous EBR Ameliorates Endogenous Hormone Contents in Tomato Species under Low-Temperature Stress. Horticulturae 2021, 7, 84 .

AMA Style

Parviz Heidari, Mahdi Entazari, Amin Ebrahimi, Mostafa Ahmadizadeh, Alessandro Vannozzi, Fabio Palumbo, Gianni Barcaccia. Exogenous EBR Ameliorates Endogenous Hormone Contents in Tomato Species under Low-Temperature Stress. Horticulturae. 2021; 7 (4):84.

Chicago/Turabian Style

Parviz Heidari; Mahdi Entazari; Amin Ebrahimi; Mostafa Ahmadizadeh; Alessandro Vannozzi; Fabio Palumbo; Gianni Barcaccia. 2021. "Exogenous EBR Ameliorates Endogenous Hormone Contents in Tomato Species under Low-Temperature Stress." Horticulturae 7, no. 4: 84.

Author correction
Published: 22 March 2021 in Scientific Reports
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.

ACS Style

Gianni Barcaccia; Giulio Galla; Alessandro Achilli; Anna Olivieri; Antonio Torroni. Author Correction: Uncovering the sources of DNA found on the Turin Shroud. Scientific Reports 2021, 11, 1 -1.

AMA Style

Gianni Barcaccia, Giulio Galla, Alessandro Achilli, Anna Olivieri, Antonio Torroni. Author Correction: Uncovering the sources of DNA found on the Turin Shroud. Scientific Reports. 2021; 11 (1):1-1.

Chicago/Turabian Style

Gianni Barcaccia; Giulio Galla; Alessandro Achilli; Anna Olivieri; Antonio Torroni. 2021. "Author Correction: Uncovering the sources of DNA found on the Turin Shroud." Scientific Reports 11, no. 1: 1-1.

Journal article
Published: 26 January 2021 in Horticulturae
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Beans are often grown in regions with climates that are susceptible to drought during the cultivation period. Consequently, it is important to identify bean accessions tolerant to drought conditions and assess the effect of drought on seeds’ nutraceutical properties. This study evaluated the effect of drought during different development stages (NES = never stressed; ALS = always stressed; SBF = stressed before flowering; SAF = stressed after flowering) on the yield and nutraceutical properties of six local bean varieties: Fasolo del Diavolo, Gialet, Posenati, Secle, D’oro, and Maron. Analysis of variance indicated that Gialet was not significantly affected by drought treatments, and Posenati under SBF and NES treatments had greater yields than under ALS and SAF treatments, whereas Secle under SBF produced 80% more seeds than under NES. Total phenols, antioxidant capacity, and calcium content were significantly different among the local varieties. Yield was significantly and positively correlated with seed calcium content and significantly and negatively correlated with protein, total phenols, and antioxidant capacity. The interaction between local varieties and treatment significantly affected seeds’ Zn content. Gialet and Maron seeds’ Zn contents were about 60 mg kg−1, almost double the average of commercial varieties. In summary, this study paves the way to the identification of potential bean varieties resistant to drought. Further molecular studies will help support these findings.

ACS Style

Pietro Sica; Aline Galvao; Francesco Scariolo; Carmelo Maucieri; Carlo Nicoletto; Cristiane Pilon; Paolo Sambo; Gianni Barcaccia; Maurizio Borin; Miguel Cabrera; Dorcas Franklin. Effects of Drought on Yield and Nutraceutical Properties of Beans (Phaseolus spp.) Traditionally Cultivated in Veneto, Italy. Horticulturae 2021, 7, 17 .

AMA Style

Pietro Sica, Aline Galvao, Francesco Scariolo, Carmelo Maucieri, Carlo Nicoletto, Cristiane Pilon, Paolo Sambo, Gianni Barcaccia, Maurizio Borin, Miguel Cabrera, Dorcas Franklin. Effects of Drought on Yield and Nutraceutical Properties of Beans (Phaseolus spp.) Traditionally Cultivated in Veneto, Italy. Horticulturae. 2021; 7 (2):17.

Chicago/Turabian Style

Pietro Sica; Aline Galvao; Francesco Scariolo; Carmelo Maucieri; Carlo Nicoletto; Cristiane Pilon; Paolo Sambo; Gianni Barcaccia; Maurizio Borin; Miguel Cabrera; Dorcas Franklin. 2021. "Effects of Drought on Yield and Nutraceutical Properties of Beans (Phaseolus spp.) Traditionally Cultivated in Veneto, Italy." Horticulturae 7, no. 2: 17.

Journal article
Published: 07 December 2020 in Genes
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Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.

ACS Style

Sahar Faraji; Ertugrul Filiz; Seyed Kamal Kazemitabar; Alessandro Vannozzi; Fabio Palumbo; Gianni Barcaccia; Parviz Heidari. The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses. Genes 2020, 11, 1464 .

AMA Style

Sahar Faraji, Ertugrul Filiz, Seyed Kamal Kazemitabar, Alessandro Vannozzi, Fabio Palumbo, Gianni Barcaccia, Parviz Heidari. The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses. Genes. 2020; 11 (12):1464.

Chicago/Turabian Style

Sahar Faraji; Ertugrul Filiz; Seyed Kamal Kazemitabar; Alessandro Vannozzi; Fabio Palumbo; Gianni Barcaccia; Parviz Heidari. 2020. "The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses." Genes 11, no. 12: 1464.

Journal article
Published: 20 October 2020 in Scientific Reports
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Pet food industry has grown considerably in the last few years and it is expected to continue with this rate. Despite the economic impact of this sector and the consumer concerns for the increasing number of food and feed adulteration cases, few studies have been published on mislabelling in pet foods. We therefore investigated the capability of a next generation sequencing-based mini-barcoding approach to identify animal species in pet food products. In a preliminary analysis, a 127 bp fragment of the COI gene was tested on both individual specimens and ad hoc mixed fresh samples used as testers, to evaluate its discrimination power and primers effectiveness. Eighteen pet food products of different price categories and forms available on the market (i.e. kibbles, bites, pâté and strips) were analysed through an NGS approach in biological replicates. At least one of the species listed in the ingredients was not detected in half of the products, while seven products showed supplementary species in addition to those stated on the label. Due to the accuracy, sensitivity and specificity demonstrated, this method can be proposed as food genetic traceability system to evaluate both the feed and food quality timely along the supply chain.

ACS Style

Fabio Palumbo; Francesco Scariolo; Alessandro Vannozzi; Gianni Barcaccia. NGS-based barcoding with mini-COI gene target is useful for pet food market surveys aimed at mislabelling detection. Scientific Reports 2020, 10, 1 -8.

AMA Style

Fabio Palumbo, Francesco Scariolo, Alessandro Vannozzi, Gianni Barcaccia. NGS-based barcoding with mini-COI gene target is useful for pet food market surveys aimed at mislabelling detection. Scientific Reports. 2020; 10 (1):1-8.

Chicago/Turabian Style

Fabio Palumbo; Francesco Scariolo; Alessandro Vannozzi; Gianni Barcaccia. 2020. "NGS-based barcoding with mini-COI gene target is useful for pet food market surveys aimed at mislabelling detection." Scientific Reports 10, no. 1: 1-8.

Review
Published: 25 September 2020 in Frontiers in Plant Science
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Cannabis (Cannabis sativa L.) is an influential yet controversial agricultural plant with a very long and prominent history of recreational, medicinal, and industrial usages. Given the importance of this species, we deepened some of the main challenges—along with potential solutions—behind the breeding of new cannabis cultivars. One of the main issues that should be fixed before starting new breeding programs is the uncertain taxonomic classification of the two main taxa (e.g., indica and sativa) of the Cannabis genus. We tried therefore to examine this topic from a molecular perspective through the use of DNA barcoding. Our findings seem to support a unique species system (C. sativa) based on two subspecies: C. sativa subsp. sativa and C. sativa subsp. indica. The second key issue in a breeding program is related to the dioecy behavior of this species and to the comprehension of those molecular mechanisms underlying flower development, the main cannabis product. Given the role of MADS box genes in flower identity, we analyzed and reorganized all the genomic and transcriptomic data available for homeotic genes, trying to decipher the applicability of the ABCDE model in Cannabis. Finally, reviewing the limits of the conventional breeding methods traditionally applied for developing new varieties, we proposed a new breeding scheme for the constitution of F1 hybrids, without ignoring the indisputable contribution offered by genomics. In this sense, in parallel, we resumed the main advances in the genomic field of this species and, ascertained the lack of a robust set of SNP markers, provided a discriminant and polymorphic panel of SSR markers as a valuable tool for future marker assisted breeding programs.

ACS Style

Gianni Barcaccia; Fabio Palumbo; Francesco Scariolo; Alessandro Vannozzi; Marcello Borin; Stefano Bona. Potentials and Challenges of Genomics for Breeding Cannabis Cultivars. Frontiers in Plant Science 2020, 11, 1 .

AMA Style

Gianni Barcaccia, Fabio Palumbo, Francesco Scariolo, Alessandro Vannozzi, Marcello Borin, Stefano Bona. Potentials and Challenges of Genomics for Breeding Cannabis Cultivars. Frontiers in Plant Science. 2020; 11 ():1.

Chicago/Turabian Style

Gianni Barcaccia; Fabio Palumbo; Francesco Scariolo; Alessandro Vannozzi; Marcello Borin; Stefano Bona. 2020. "Potentials and Challenges of Genomics for Breeding Cannabis Cultivars." Frontiers in Plant Science 11, no. : 1.

Review
Published: 23 September 2020 in Agriculture
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Flowering time, abiotic stress tolerance and disease resistance are important agronomic traits of forage species like Lolium spp. Understanding the genetic control of these traits is enabled by the combination of genomic tools with conventional breeding techniques. Flowering time in this genus represents a complex trait due to the differences in the primary induction requirements among the species. In total, 36 QTLs (Quantitative Trait Locus) were identified across all seven linkage groups of Italian and perennial ryegrass involved in the flowering pathways, with several putative orthologous/homologous genes that have been characterized in other major crops. From the perspective of climate change, abiotic stress tolerance has become an essential feature; many QTLs that are involved in the control of plant responses have been identified, and transcriptional studies focusing on drought tolerance reported several DEGs (Differentially Expressed Genes) involved in carbon and lipid metabolism and signal transduction. Due to the incidence of microbial diseases, QTLs useful to developing cultivars resistant to bacterial wilt (Xanthomonas translucens pv. graminis), ryegrass crown rust (Puccinia coronata f. sp. Lolii) and gray leaf spot (Magnaporthe grisea/oryzae) have been mapped in both L. perenne and L. multiflorum populations. Due to the great importance of Lolium species, especially as forage crops, additional information about the three aforementioned agronomic traits is needed.

ACS Style

Elisa Pasquali; Gianni Barcaccia. Genomics Applied to the Analysis of Flowering Time, Abiotic Stress Tolerance and Disease Resistance: A Review of What We Have Learned in Lolium spp. Agriculture 2020, 10, 425 .

AMA Style

Elisa Pasquali, Gianni Barcaccia. Genomics Applied to the Analysis of Flowering Time, Abiotic Stress Tolerance and Disease Resistance: A Review of What We Have Learned in Lolium spp. Agriculture. 2020; 10 (10):425.

Chicago/Turabian Style

Elisa Pasquali; Gianni Barcaccia. 2020. "Genomics Applied to the Analysis of Flowering Time, Abiotic Stress Tolerance and Disease Resistance: A Review of What We Have Learned in Lolium spp." Agriculture 10, no. 10: 425.

Review
Published: 28 July 2020 in Genes
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Apomixis sensu stricto (agamospermy) is asexual reproduction by seed. In angiosperms it represents an easy byway of life cycle renewal through gamete-like cells that give rise to maternal embryos without ploidy reduction (meiosis) and ploidy restitution (syngamy). The origin of apomixis still represents an unsolved problem, as it may be either evolved from sex or the other way around. This review deals with a reappraisal of the origin of apomixis in order to deepen knowledge on such asexual mode of reproduction which seems mainly lacking in the most basal angiosperm orders (i.e., Amborellales, Nymphaeales and Austrobaileyales, also known as ANA-grade), while it clearly occurs in different forms and variants in many unrelated families of monocots and eudicots. Overall findings strengthen the hypothesis that apomixis as a whole may have evolved multiple times in angiosperm evolution following different developmental pathways deviating to different extents from sexuality. Recent developments on the genetic control of apomixis in model species are also presented and adequately discussed in order to shed additional light on the antagonist theories of gain- and loss-of-function over sexuality.

ACS Style

Gianni Barcaccia; Fabio Palumbo; Sergio Sgorbati; Emidio Albertini; Fulvio Pupilli. A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms. Genes 2020, 11, 859 .

AMA Style

Gianni Barcaccia, Fabio Palumbo, Sergio Sgorbati, Emidio Albertini, Fulvio Pupilli. A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms. Genes. 2020; 11 (8):859.

Chicago/Turabian Style

Gianni Barcaccia; Fabio Palumbo; Sergio Sgorbati; Emidio Albertini; Fulvio Pupilli. 2020. "A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms." Genes 11, no. 8: 859.

Review
Published: 14 July 2020 in Sustainability
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The recent outbreak of a new Coronavirus has developed into a global pandemic with about 10.5 million reported cases and over 500,000 deaths worldwide. Our prospective paper reports an updated analysis of the impact that this pandemic had on the Italian agri-food sector during the national lockdown and discusses why and how this unprecedented economic crisis could be a turning point to deal with the overall sustainability of food and agricultural systems in the frame of the forthcoming European Green Deal. Its introductory part includes a wide-ranging examination of the first quarter of pandemic emergency, with a specific focus on the primary production, to be understood as agriculture (i.e., crops and livestock, and their food products), fisheries, and forestry. The effect on the typical food and wine exports, and the local environment tourism segments is also taken into account in this analysis, because of their old and deep roots into the cultural and historical heritage of the country. The subsequent part of the paper is centered on strategic lines and research networks for an efficient socio-economic and territorial restart, and a faster transition to sustainability in the frame of a circular bio-economy. Particular emphasis is given to the urgent need of investments in research and development concerning agriculture, in terms of not only a fruitful penetration of the agro-tech for a next-generation agri-food era, but also a deeper attention to the natural and environmental resources, including forestry. As for the rest of Europe, Italy demands actions to expand knowledge and strengthen research applied to technology transfer for innovation activities aimed at providing solutions for a climate neutral and resilient society, in reference to primary production to ensure food security and nutrition quality. Our expectation is that science and culture return to play a central role in national society, as their main actors are capable of making a pivotal contribution to renew and restart the whole primary sector and agri-food industry, addressing also social and environmental issues, and so accelerating the transition to sustainability.

ACS Style

Gianni Barcaccia; Vincenzo D’Agostino; Alessandro Zotti; Bruno Cozzi. Impact of the SARS-CoV-2 on the Italian Agri-Food Sector: An Analysis of the Quarter of Pandemic Lockdown and Clues for a Socio-Economic and Territorial Restart. Sustainability 2020, 12, 5651 .

AMA Style

Gianni Barcaccia, Vincenzo D’Agostino, Alessandro Zotti, Bruno Cozzi. Impact of the SARS-CoV-2 on the Italian Agri-Food Sector: An Analysis of the Quarter of Pandemic Lockdown and Clues for a Socio-Economic and Territorial Restart. Sustainability. 2020; 12 (14):5651.

Chicago/Turabian Style

Gianni Barcaccia; Vincenzo D’Agostino; Alessandro Zotti; Bruno Cozzi. 2020. "Impact of the SARS-CoV-2 on the Italian Agri-Food Sector: An Analysis of the Quarter of Pandemic Lockdown and Clues for a Socio-Economic and Territorial Restart." Sustainability 12, no. 14: 5651.

Preprint
Published: 06 July 2020
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The recent outbreak of a new Coronavirus has developed into a global pandemic with about 10,5 million reported cases and over 500,000 deaths worldwide. Our prospective paper reports an updated analysis of the impact that this pandemic had on the Italian agri-food sector during the national lockdown and discusses why and how this unprecedented economic crisis could be a turning point to deal with the overall sustainability of food and agricultural systems in the frame of the forthcoming European Green Deal. Its introductory part includes a wide-ranging examination of the first quarter of pandemic emergency, with a specific focus on the primary production, to be understood as agriculture (i.e. crops and livestock, and their food products), fisheries and forestry. The effect on the typical food and wine exports, and the local environment tourism segments is also taken into account in this analysis, because of their old and deep roots into the cultural and historical heritage of the country. The subsequent part of the paper is centered on strategic lines and research networks for an efficient socio-economic and territorial restart, and a faster transition to sustainability in the frame of a circular bio-economy. Particular emphasis is given to the urgent need of investments in research and development concerning agriculture, in terms of not only a fruitful penetration of the agro-tech for a next-generation agri-food era, but also a deeper attention to the natural and environmental resources, including forestry. As for the rest of Europe, Italy demands actions to expand knowledge and strengthen research applied to technology transfer for innovation activities aimed at providing solutions for a climate neutral and resilient society, in reference to primary production to ensure food security and nutrition quality. Our expectation is that science and culture return to play a central role in national society, as their main actors are capable of making a pivotal contribution to renew and restart the whole primary sector and agri-food industry, addressing also social and environmental issues, and so accelerating the transition to sustainability.

ACS Style

Gianni Barcaccia; Vincenzo D'agostino; Alessandro Zotti; Bruno Cozzi. Impact of the SARS-CoV-2 on the Italian Agri-food Sector: An Analysis of the Quarter of Pandemic Lockdown and Clues for a Socio-Economic and Territorial Restart. 2020, 1 .

AMA Style

Gianni Barcaccia, Vincenzo D'agostino, Alessandro Zotti, Bruno Cozzi. Impact of the SARS-CoV-2 on the Italian Agri-food Sector: An Analysis of the Quarter of Pandemic Lockdown and Clues for a Socio-Economic and Territorial Restart. . 2020; ():1.

Chicago/Turabian Style

Gianni Barcaccia; Vincenzo D'agostino; Alessandro Zotti; Bruno Cozzi. 2020. "Impact of the SARS-CoV-2 on the Italian Agri-food Sector: An Analysis of the Quarter of Pandemic Lockdown and Clues for a Socio-Economic and Territorial Restart." , no. : 1.

Journal article
Published: 30 June 2020 in International Journal of Molecular Sciences
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Cytoplasmic male sterility (CMS) has always aroused interest among researchers and breeders, being a valuable resource widely exploited not only to breed F1 hybrid varieties but also to investigate genes that control stamen and pollen development. With the aim of identifying candidate genes for CMS in fennel, we adopted an effective strategy relying on the comparison between mitochondrial genomes (mtDNA) of both fertile and sterile genotypes. mtDNA raw reads derived from a CMS genotype were assembled in a single molecule (296,483 bp), while a draft mtDNA assembly (166,124 nucleotides, 94 contigs) was performed using male fertile sample (MF) sequences. From their annotation and alignment, two atp6-like sequences were identified. atp6-, the putative mutant copy with a 300 bp truncation at the 5’-end, was found only in the mtDNA of CMS samples, while the wild type copy (atp6+) was detected only in the MF mtDNA. Further analyses (i.e., reads mapping and Sanger sequencing), revealed an atp6+ copy also in CMS samples, probably in the nuclear DNA. However, qPCRs performed on different tissues proved that, despite its availability, atp6+ is expressed only in MF samples, while apt6- mRNA was always detected in CMS individuals. In the light of these findings, the energy deficiency model could explain the pollen deficiency observed in male sterile flower. atp6- could represent a gene whose mRNA is translated into a not-fully functional protein leading to suboptimal ATP production that guarantees essential cellular processes but not a high energy demand process such as pollen development. Our study provides novel insights into the fennel mtDNA genome and its atp6 genes, and paves the way for further studies aimed at understanding their functional roles in the determination of male sterility.

ACS Style

Fabio Palumbo; Nicola Vitulo; Alessandro Vannozzi; Gabriele Magon; Gianni Barcaccia. The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions. International Journal of Molecular Sciences 2020, 21, 4664 .

AMA Style

Fabio Palumbo, Nicola Vitulo, Alessandro Vannozzi, Gabriele Magon, Gianni Barcaccia. The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions. International Journal of Molecular Sciences. 2020; 21 (13):4664.

Chicago/Turabian Style

Fabio Palumbo; Nicola Vitulo; Alessandro Vannozzi; Gabriele Magon; Gianni Barcaccia. 2020. "The Mitochondrial Genome Assembly of Fennel (Foeniculum vulgare) Reveals Two Different atp6 Gene Sequences in Cytoplasmic Male Sterile Accessions." International Journal of Molecular Sciences 21, no. 13: 4664.

Journal article
Published: 04 May 2020 in Plants
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S-Adenosyl-L-methionine (SAM) is a key enzyme involved in many important biological processes, such as ethylene and polyamine biosynthesis, transmethylation, and transsulfuration. Here, the SAM synthetase (SAMS) gene family was studied in ten different plants (Arabidopsis, tomato, eggplant, sunflower, Medicago truncatula, soybean, rice, barley, Triticum urartu and sorghum) with respect to its physical structure, physicochemical characteristics, and post-transcriptional and post-translational modifications. Additionally, the expression patterns of SAMS genes in tomato were analyzed based on a real-time quantitative PCR assay and an analysis of a public expression dataset. SAMS genes of monocots were more conserved according to the results of a phylogenetic analysis and the prediction of phosphorylation and glycosylation patterns. SAMS genes showed differential expression in response to abiotic stresses and exogenous hormone treatments. Solyc01g101060 was especially expressed in fruit and root tissues, while Solyc09g008280 was expressed in leaves. Additionally, our results revealed that exogenous BR and ABA treatments strongly reduced the expression of tomato SAMS genes. Our research provides new insights and clues about the role of SAMS genes. In particular, these results can inform future functional analyses aimed at revealing the molecular mechanisms underlying the functions of SAMS genes in plants.

ACS Style

Parviz Heidari; Faezeeh Mazloomi; Thomas Nussbaumer; Gianni Barcaccia. Insights into the SAM Synthetase Gene Family and Its Roles in Tomato Seedlings under Abiotic Stresses and Hormone Treatments. Plants 2020, 9, 586 .

AMA Style

Parviz Heidari, Faezeeh Mazloomi, Thomas Nussbaumer, Gianni Barcaccia. Insights into the SAM Synthetase Gene Family and Its Roles in Tomato Seedlings under Abiotic Stresses and Hormone Treatments. Plants. 2020; 9 (5):586.

Chicago/Turabian Style

Parviz Heidari; Faezeeh Mazloomi; Thomas Nussbaumer; Gianni Barcaccia. 2020. "Insights into the SAM Synthetase Gene Family and Its Roles in Tomato Seedlings under Abiotic Stresses and Hormone Treatments." Plants 9, no. 5: 586.

Journal article
Published: 23 April 2020 in Genes
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The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive (Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce (Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.

ACS Style

Alice Patella; Fabio Palumbo; Samathmika Ravi; Piergiorgio Stevanato; Gianni Barcaccia. Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.). Genes 2020, 11, 462 .

AMA Style

Alice Patella, Fabio Palumbo, Samathmika Ravi, Piergiorgio Stevanato, Gianni Barcaccia. Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.). Genes. 2020; 11 (4):462.

Chicago/Turabian Style

Alice Patella; Fabio Palumbo; Samathmika Ravi; Piergiorgio Stevanato; Gianni Barcaccia. 2020. "Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed down the Genomic Region Responsible for Leaf Shape in Endive (Cichorium endivia L.)." Genes 11, no. 4: 462.

Journal article
Published: 09 November 2019 in Genes
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The development of new varieties of horticultural crops benefits from the integration of conventional and molecular marker-assisted breeding schemes in order to combine phenotyping and genotyping information. In this study, a selected panel of 16 microsatellite markers were used in different steps of a breeding programme of lettuce (Lactuca sativa L., 2 n = 18). Molecular markers were first used to genotype 71 putative parental lines and to plan 89 controlled crosses designed to maximise recombination potentials. The resulting 871 progeny plants were then molecularly screened, and their marker allele profiles were compared with the profiles expected based on the parental lines. The average cross-pollination success rate was 68 ± 33%, so 602 F1 hybrids were completely identified. Unexpected genotypes were detected in 5% of cases, consistent with this species’ spontaneous out-pollination rate. Finally, in a later step of the breeding programme, 47 different F3 progenies, selected by phenotyping for a number of morphological descriptors, were characterised in terms of their observed homozygosity and within-population genetic uniformity and stability. Ten of these populations had a median homozygosity above 90% and a median genetic similarity above 95% and are, therefore, particularly suitable for pre-commercial trials. In conclusion, this study shows the synergistic effects and advantages of conventional and molecular methods of selection applied in different steps of a breeding programme aimed at developing new varieties of lettuce.

ACS Style

Alice Patella; Fabio Palumbo; Giulio Galla; Gianni Barcaccia. The Molecular Determination of Hybridity and Homozygosity Estimates in Breeding Populations of Lettuce (Lactuca sativa L.). Genes 2019, 10, 916 .

AMA Style

Alice Patella, Fabio Palumbo, Giulio Galla, Gianni Barcaccia. The Molecular Determination of Hybridity and Homozygosity Estimates in Breeding Populations of Lettuce (Lactuca sativa L.). Genes. 2019; 10 (11):916.

Chicago/Turabian Style

Alice Patella; Fabio Palumbo; Giulio Galla; Gianni Barcaccia. 2019. "The Molecular Determination of Hybridity and Homozygosity Estimates in Breeding Populations of Lettuce (Lactuca sativa L.)." Genes 10, no. 11: 916.

Journal article
Published: 24 October 2019 in Genes
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The European Union (EU) market for sweet potatoes has increased by 100% over the last five years, and sweet potato cultivation in southern European countries is a new opportunity for the EU to exploit and introduce new genotypes. In view of this demand, the origins of the principal Italian sweet potato clones, compared with a core collection of genotypes from Central and Southern America, were investigated for the first time. This was accomplished by combining a genetic analysis, exploiting 14 hypervariable microsatellite markers, with morphological and chemical measurements based on 16 parameters. From the molecular analyses, Italian accessions were determined to be genetically very similar to the South American germplasm, but they were sub-clustered into two groups. This finding was subsequently confirmed by the morphological and chemical measurements. Moreover, the analysis of the genetic structure of the population suggested that one of the two groups of Italian genotypes may have descended from one of the South American accessions, as predicted on the basis of the shared morphological characteristics and molecular fingerprints. Overall, the combination of two different characterization methods, genetic markers and agronomic traits, was effective in differentiating or clustering the sweet potato genotypes, in agreement with their geographical origin or phenotypic descriptors. This information could be exploited by both breeders and farmers to detect and protect commercial varieties, and hence for traceability purposes.

ACS Style

Fabio Palumbo; Aline Carolina Galvao; Carlo Nicoletto; Paolo Sambo; Gianni Barcaccia. Diversity Analysis of Sweet Potato Genetic Resources Using Morphological and Qualitative Traits and Molecular Markers. Genes 2019, 10, 840 .

AMA Style

Fabio Palumbo, Aline Carolina Galvao, Carlo Nicoletto, Paolo Sambo, Gianni Barcaccia. Diversity Analysis of Sweet Potato Genetic Resources Using Morphological and Qualitative Traits and Molecular Markers. Genes. 2019; 10 (11):840.

Chicago/Turabian Style

Fabio Palumbo; Aline Carolina Galvao; Carlo Nicoletto; Paolo Sambo; Gianni Barcaccia. 2019. "Diversity Analysis of Sweet Potato Genetic Resources Using Morphological and Qualitative Traits and Molecular Markers." Genes 10, no. 11: 840.

Journal article
Published: 10 July 2019 in Plants
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Cichorium intybus L., well known in Italy with the common name "Radicchio", is an important leafy vegetable that is prevalently reproduced by allogamy due to very efficient barriers of self-incompatibility. Marker-assisted breeding is widely used by seed firms to develop new hybrid varieties that manifest genetic distinctiveness, uniformity and stability. A total of 29 mapped microsatellite markers were used for genotyping 504 samples of the Red of Chioggia biotype: First, two synthetics, four F1 hybrids and two derived F2 populations were compared to assess the distinctiveness of their gene pool and structure; then, the uniformity and stability of 3 years of production of a commercial F1 variety were also investigated. Genetic similarity and diversity statistics as well as the genetic structure of populations were analysed, including allele and genotype frequencies. The mean estimates and ranges of genetic similarity enabled the molecular discrimination of OP synthetics from F1 varieties and their F2 progenies and the determination of individual plant memberships. Moreover, the genetic structure of F1 hybrids produced in 3 years unexpectedly revealed two main clusters that discriminate the first 2 years from the 3rd, mainly because of the presence of uncommon specific alleles and different allele frequencies. Overall, this molecular information will enable breeders to determine the genetic distinctness, uniformity and stability of commercial and experimental varieties, as well as their genetic relationships and relatedness. Hence, this work provides a useful tool for achieving the molecular characterisation and genetic identification of different radicchio populations.

ACS Style

Alice Patella; Francesco Scariolo; Fabio Palumbo; Gianni Barcaccia. Genetic Structure of Cultivated Varieties of Radicchio (Cichorium intybus L.): A Comparison between F1 Hybrids and Synthetics. Plants 2019, 8, 213 .

AMA Style

Alice Patella, Francesco Scariolo, Fabio Palumbo, Gianni Barcaccia. Genetic Structure of Cultivated Varieties of Radicchio (Cichorium intybus L.): A Comparison between F1 Hybrids and Synthetics. Plants. 2019; 8 (7):213.

Chicago/Turabian Style

Alice Patella; Francesco Scariolo; Fabio Palumbo; Gianni Barcaccia. 2019. "Genetic Structure of Cultivated Varieties of Radicchio (Cichorium intybus L.): A Comparison between F1 Hybrids and Synthetics." Plants 8, no. 7: 213.