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1. Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts

Author

Zheng, Zheng, Sun, Ziqi, Qi, Feiyan, Fang, Yuanjin, Lin, Ke, Pavan, Stefano, Huang, Bingyan, Dong, Wenzhao, Du, Pei, Tian, Mengdi, Shi, Lei, Xu, Jing, Han, Suoyi, Liu, Hua, Qin, Li, Zhang, Zhongxin, Dai, Xiaodong, Miao, Lijuan, Zhao, Ruifang, Wang, Juan, Liao, Yanlin, Li, Alun, Ruan, Jue, Delvento, Chiara, Aiese Cigliano, Riccardo, Maliepaard, Chris, Bai, Yuling, Visser, Richard G. F., and Zhang, Xinyou

Published
2024
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5. A telomere-to-telomere genome assembly of the cultivated peanut

Author

Wang, Xiaobo, Sun, Ziqi, Qi, Feiyan, Zhou, Zhiyuan, Du, Pei, Shi, Lei, Dong, Wenzhao, Huang, Bingyan, Han, Suoyi, Pavan, Stefano, Zhang, Meng, Cui, Mengjie, Xu, Jing, Liu, Hua, Qin, Li, Zhang, Zhongxin, Dai, Xiaodong, Gao, Wei, Miao, Lijuan, Zhao, Ruifang, Wang, Juan, Wang, Mengmeng, Zhi, Chenyang, Hu, Yaojun, Zhao, Huanhuan, Chen, Linjie, Jin, Xiaodong, Sun, Yanhui, Zheng, Zheng, and Zhang, Xinyou

Published
2025
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8. Supplementary Material. Detection and distribution of two alleles of the Sk gene, controlling the kernel taste in almond [Prunus dulcis Miller (D.A. Webb)]

Author

Sánchez-Pérez, Raquel [0000-0003-1606-3121], Pavan, Stefano [stefano.pavan@uniba.it], Lotti, Concetta, Minervini, Anna Paola, Delvento, Chiara, Losciale, Pasquale, Gaeta, Liliana, Sánchez-Pérez, Raquel, Ricciardi, Luigi, Pavan, Stefano, Sánchez-Pérez, Raquel [0000-0003-1606-3121], Pavan, Stefano [stefano.pavan@uniba.it], Lotti, Concetta, Minervini, Anna Paola, Delvento, Chiara, Losciale, Pasquale, Gaeta, Liliana, Sánchez-Pérez, Raquel, Ricciardi, Luigi, and Pavan, Stefano

Abstract

Almond [Prunus dulcis Miller (D. A. Webb), syn. Prunus amygdalus L.)] is the major tree nut crop worldwide in terms of production and cultivated area. Almond domestication was enabled by the selection of individuals bearing sweet kernels, which do not accumulate high levels of the toxic cyanogenic glucoside amygdalin. Previously, we showed that the Sweet kernel (Sk) gene, controlling the kernel taste in almond, encodes a basic helix loop helix (bHLH) transcription factor regulating the amygdalin biosynthetic pathway. In addition, we characterized a dominant allele of this gene, further referred to as Sk-1, which originates from a C1036→T missense mutation and confers the sweet kernel phenotype. Here we provide evidence indicating that the allele further referred to as Sk-2, originally detected in the cultivar “Atocha” and arising from a T989→G missense mutation, is also dominantly inherited and confers the sweet kernel phenotype in almond cultivated germplasm. The use of single nucleotide polymorphism (SNP) data from genotyping by sequencing (GBS) for population structure and hierarchical clustering analyses indicated that Sk-2 occurs in a group of related genotypes, including the widespread cultivar “Texas”, descending from the same ancestral population. KASP and dual label functional markers were developed for the accurate and high-throughput selection of the Sk-1 and Sk-2 alleles, and the genotyping of a panel of 134 almond cultivars. Overall, our results provide further insights on the understanding of the almond cultivation history. In addition, molecular marker assays and genotypic data presented in this study are expected to be of major interest for the conduction of almond breeding programs, which often need to select sweet kernel individuals in segregant populations

Published
2023

10. Erythrodermic psoriasis

Author

PATUZZO, Giuseppe, primary, GRAZZI, Niccolò, additional, DE LUCA, Tiziana, additional, FIN, Monica, additional, LEARDINI, Nicola, additional, PAVAN, Stefano, additional, and TENCI, Andrea, additional

Published
2024
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12. Explainable artificial intelligence for genotype-to-phenotype prediction in plant breeding: a case study with a dataset from an almond germplasm collection.

Author

Novielli, Pierfrancesco, Romano, Donato, Pavan, Stefano, Losciale, Pasquale, Stellacci, Anna Maria, Diacono, Domenico, Bellotti, Roberto, and Tangaro, Sabina

Subjects
SUSTAINABILITY, PLANT breeding, ARTIFICIAL intelligence, SUSTAINABLE agriculture, FEATURE selection
Abstract

Background: Advances in DNA sequencing revolutionized plant genomics and significantly contributed to the study of genetic diversity. However, predicting phenotypes from genomic data remains a challenge, particularly in the context of plant breeding. Despite significant progress, accurately predicting phenotypes from high-dimensional genomic data remains a challenge, particularly in identifying the key genetic factors influencing these predictions. This study aims to bridge this gap by integrating explainable artificial intelligence (XAI) techniques with advanced machine learning models. This approach is intended to enhance both the predictive accuracy and interpretability of genotype-to-phenotype models, thereby improving their reliability and supportingmore informed breeding decisions. Results: This study compares several ML methods for genotype-to-phenotype prediction, using data available from an almond germplasm collection. After preprocessing and feature selection, regression models are employed to predict almond shelling fraction. Best predictions were obtained by the Random Forest method (correlation = 0.727 ± 0.020, an R2 = 0.511 ± 0.025, and an RMSE = 7.746 ± 0.199). Notably, the application of the SHAP (SHapley Additive exPlanations) values algorithm to explain the results highlighted several genomic regions associated with the trait, including one, having the highest feature importance, located in a gene potentially involved in seed development. Conclusions: Employing explainable artificial intelligence algorithms enhances model interpretability, identifying genetic polymorphisms associated with the shelling percentage. These findings underscore XAI's efficacy in predicting phenotypic traits from genomic data, highlighting its significance in optimizing crop production for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Detection and distribution of two dominant alleles associated with the sweet kernel phenotype in almond cultivated germplasm

Author

Ministero dell'Istruzione, dell'Università e della Ricerca, European Commission, Regione Puglia, Ministerio de Economía y Competitividad (España), Sánchez-Pérez, Raquel [0000-0003-1606-3121], Lotti, Concetta, Minervini, Anna Paola, Delvento, Chiara, Losciale, Pasquale, Gaeta, Liliana, Sánchez-Pérez, Raquel, Ricciardi, Luigi, Pavan, Stefano, Ministero dell'Istruzione, dell'Università e della Ricerca, European Commission, Regione Puglia, Ministerio de Economía y Competitividad (España), Sánchez-Pérez, Raquel [0000-0003-1606-3121], Lotti, Concetta, Minervini, Anna Paola, Delvento, Chiara, Losciale, Pasquale, Gaeta, Liliana, Sánchez-Pérez, Raquel, Ricciardi, Luigi, and Pavan, Stefano

Abstract

Almond [Prunus dulcis Miller (D. A. Webb), syn. Prunus amygdalus L.)] is the major tree nut crop worldwide in terms of production and cultivated area. Almond domestication was enabled by the selection of individuals bearing sweet kernels, which do not accumulate high levels of the toxic cyanogenic glucoside amygdalin. Previously, we showed that the Sweet kernel (Sk) gene, controlling the kernel taste in almond, encodes a basic helix loop helix (bHLH) transcription factor regulating the amygdalin biosynthetic pathway. In addition, we characterized a dominant allele of this gene, further referred to as Sk-1, which originates from a C1036!T missense mutation and confers the sweet kernel phenotype. Here we provide evidence indicating that the allele further referred to as Sk-2, originally detected in the cultivar “Atocha” and arising from a T989!G missense mutation, is also dominantly inherited and confers the sweet kernel phenotype in almond cultivated germplasm. The use of single nucleotide polymorphism (SNP) data from genotyping by sequencing (GBS) for population structure and hierarchical clustering analyses indicated that Sk-2 occurs in a group of related genotypes, including the widespread cultivar “Texas”, descending from the same ancestral population. KASP and dual label functional markers were developed for the accurate and high-throughput selection of the Sk-1 and Sk-2 alleles, and the genotyping of a panel of 134 almond cultivars. Overall, our results provide further insights on the understanding of the almond cultivation history. In addition, molecular marker assays and genotypic data presented in this study are expected to be of major interest for the conduction of almond breeding programs, which often need to select sweet kernel individuals in segregant populations

Published
2023

19. Overexpression of the C4 protein of tomato yellow leaf curl Sardinia virus increases tomato resistance to powdery mildew

Author

D’Errico, Chiara, Forgia, Marco, Pisani, Marco, Pavan, Stefano, Noris, Emanuela, and Matić, Slavica

Subjects
Plant Science
Abstract

Powdery mildew (PM) is one of the most important diseases of greenhouse and field-grown tomatoes. Viruses can intervene beneficially on plant performance in coping with biotic and abiotic stresses. Tomato yellow leaf curl Sardinia virus (TYLCSV) has been reported recently to induce tolerance against drought stress in tomato, and its C4 protein acts as the main causal factor of tolerance. However, its role in response to biotic stresses is still unknown. In this study, transgenic tomato plants carrying the TYLCSV C4 protein were exposed to biotic stress following the inoculation with Oidium neolycopersici, the causal agent of tomato PM. Phytopathological, anatomic, molecular, and physiological parameters were evaluated in this plant pathosystem. Heterologous TYLCSV C4 expression increased the tolerance of transgenic tomato plants to PM, not only reducing symptom occurrence, but also counteracting conidia adhesion and secondary hyphae elongation. Pathogenesis-related gene expression and salicylic acid production were found to be higher in tomato transgenic plants able to cope with PM compared to infected wild-type tomato plants. Our study contributes to unraveling the mechanism leading to PM tolerance in TYLCSV C4-expressing tomato plants. In a larger context, the findings of TYLCSV C4 as a novel PM defense inducer could have important implications in deepening the mechanisms regulating the management of this kind of protein to both biotic and abiotic stresses.

Published
2023
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21. High-density linkage mapping and genetic dissection of resistance to broomrape (Orobanche crenata Forsk.) in pea (Pisum sativum L.).

Author

Delvento, Chiara, Arcieri, Francesco, Marcotrigiano, Angelo Raffaele, Guerriero, Marzia, Fanelli, Valentina, Dellino, Maria, Curci, Pasquale Luca, Bouwmeester, Harro, Lotti, Concetta, Ricciardi, Luigi, and Pavan, Stefano

Subjects
LOCUS (Genetics), BROOMRAPES, GENE mapping, PEAS, AGRICULTURE, SINGLE nucleotide polymorphisms
Abstract

Pea (Pisum sativum L.) is a widely cultivated legume of major importance for global food security and agricultural sustainability. Crenate broomrape (Orobanche crenata Forsk.) (Oc) is a parasitic weed severely affecting legumes, including pea, in the Mediterranean Basin and the Middle East. Previously, the identification of the pea line "ROR12", displaying resistance to Oc, was reported. Two-year field trials on a segregant population of 148 F7 recombinant inbred lines (RILs), originating from a cross between "ROR12" and the susceptible cultivar "Sprinter", revealed high heritability (0.84) of the "ROR12" resistance source. Genotyping-by-sequencing (GBS) on the same RIL population allowed the construction of a high-density pea linkage map, which was compared with the pea reference genome and used for quantitative trait locus (QTL) mapping. Three QTLs associated with the response to Oc infection, named PsOcr-1, PsOcr-2, and PsOcr-3, were identified, with PsOcr-1 explaining 69.3% of the genotypic variance. Evaluation of the effects of different genotypic combinations indicated additivity between PsOcr-1 and PsOcr-2, and between PsOcr-1 and PsOcr-3, and epistasis between PsOcr-2 and PsOcr-3. Finally, three Kompetitive Allele Specific PCR (KASP) marker assays were designed on the single-nucleotide polymorphisms (SNPs) associated with the QTL significance peaks. Besides contributing to the development of pea genomic resources, this work lays the foundation for the obtainment of pea cultivars resistant to Oc and the identification of genes involved in resistance to parasitic Orobanchaceae. [ABSTRACT FROM AUTHOR]

Published
2023
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24. DNA sequencing sheds light on the evolutionary history of peanut and identifies genes associated with phenotypic diversification

Author

Zheng, Zheng, primary, Sun, Ziqi, additional, Qi, Feiyan, additional, Fang, Yuanjin, additional, Lin, Ke, additional, Pavan, Stefano, additional, Huang, Bingyan, additional, Dong, Wenzhao, additional, Du, Pei, additional, Tian, Mengdi, additional, Shi, Lei, additional, Xu, Jing, additional, Han, Suoyi, additional, Liu, Hua, additional, Qin, Li, additional, Zhang, Zhongxin, additional, Dai, Xiaodong, additional, Miao, Lijuan, additional, Zhao, Ruifang, additional, Wang, Juan, additional, Bai, Yuling, additional, Visser, Richard, additional, and Zhang, Xinyou, additional

Published
2022
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29. DESINFORMAÇÃO, PÓS-VERDADE E DEMOCRACIA: UMA ANÁLISE NO CONTEXTO DO ESTADO DEMOCRÁTICO DE DIREITO

Author

PANSIERI, Flávio, KRAUS, Mariella, and PAVAN, Stefano Avila

Subjects
desinformação, fake news, pós-verdade, democracia
Abstract

Objetivo: Com as novas formas de comunicação possibilitadas com a internet, a desinformação se apresenta como uma nova realidade cada vez mais presente na sociedade de diversos países, constatando-se um período de pós-verdade que reflete nos contextos democráticos de diversas maneiras. Assim, o presente artigo tem o objetivo de traçar um panorama a respeito da forma como a desinformação nos tempos atuais traz reflexos no Estado Democrático de Direito, notadamente à moderação de conteúdo em plataformas digitais.Metodologia: Por meio do método de abordagem dedutivo e técnica de pesquisa bibliográfica.Resultados: Conclui-se que é preciso traçar estratégias jurídicas para conviver nesta nova realidade posta e, ainda, que a imprecisão do termo fake news não traduz o problema da pós-verdade.Contribuições: Refletir sobre as formas de moderação dos conteúdos de desinformação no contexto de pós-verdade e os reflexos disto no Estado Democrático de Direito.Palavras-chave: desinformação; fake news; pós-verdade; democracia. ABSTRACTObjective: With the new forms of communication made possible with the internet, misinformation presents itself as a new reality that is increasingly present in society in different countries, revealing a period of post-truth that reflects on democratic contexts in different ways. Thus, this article aims to draw an overview of how misinformation in current times, reflections on the Democratic Rule of Law, notably the moderation of content on digital platforms.Methodology: Through the method of deductive approach and bibliographic research technique.Results: It is concluded that it is necessary to trace legal strategies to live in this new reality, and also that the imprecision of the term fake news does not reflect the problem of post-truth.Contributions: To reflect on the ways of moderating disinformation content in the context of post-truth and its reflexes on the Democratic Rule of Law.Keywords: disinformation; fake news; post-truth; democracy.

Published
2021

33. Screening of Olive Biodiversity Defines Genotypes Potentially Resistant to Xylella fastidiosa

Author

Pavan, Stefano, primary, Vergine, Marzia, additional, Nicolì, Francesca, additional, Sabella, Erika, additional, Aprile, Alessio, additional, Negro, Carmine, additional, Fanelli, Valentina, additional, Savoia, Michele Antonio, additional, Montilon, Vito, additional, Susca, Leonardo, additional, Delvento, Chiara, additional, Lotti, Concetta, additional, Nigro, Franco, additional, Montemurro, Cinzia, additional, Ricciardi, Luigi, additional, De Bellis, Luigi, additional, and Luvisi, Andrea, additional

Published
2021
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41. In Vitro and In Vivo Nutraceutical Characterization of Two Chickpea Accessions: Differential Effects on Hepatic Lipid Over-Accumulation

Author

Centrone, Mariangela, primary, Gena, Patrizia, additional, Ranieri, Marianna, additional, Di Mise, Annarita, additional, D’Agostino, Mariagrazia, additional, Mastrodonato, Maria, additional, Venneri, Maria, additional, De Angelis, Davide, additional, Pavan, Stefano, additional, Pasqualone, Antonella, additional, Summo, Carmine, additional, Fanelli, Valentina, additional, Valenti, Giovanna, additional, Calamita, Giuseppe, additional, and Tamma, Grazia, additional

Published
2020
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44. Genotyping by Sequencing of Cultivated Lentil (Lens culinaris Medik.) Highlights Population Structure in the Mediterranean Gene Pool Associated With Geographic Patterns and Phenotypic Variables

Author

Pavan, Stefano, primary, Bardaro, Nicoletta, additional, Fanelli, Valentina, additional, Marcotrigiano, Angelo Raffaele, additional, Mangini, Giacomo, additional, Taranto, Francesca, additional, Catalano, Domenico, additional, Montemurro, Cinzia, additional, De Giovanni, Claudio, additional, Lotti, Concetta, additional, and Ricciardi, Luigi, additional

Published
2019
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50. Synteny-Based Development of CAPS Markers Linked to the Sweet kernel LOCUS, Controlling Amygdalin Accumulation in Almond (Prunus dulcis (Mill.) D.A.Webb)

Author

Ricciardi, Francesca, Del Cueto, Jorge, Bardaro, Nicoletta, Mazzeo, Rosa, Ricciardi, Luigi, Dicenta, Federico, Sánchez-pérez, Raquel, Pavan, Stefano, Lotti, Concetta, Ricciardi, Francesca, Del Cueto, Jorge, Bardaro, Nicoletta, Mazzeo, Rosa, Ricciardi, Luigi, Dicenta, Federico, Sánchez-pérez, Raquel, Pavan, Stefano, and Lotti, Concetta

Published
2018

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