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Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple

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Horticulture Research 2020年第1期7卷 889-902页

作者： Morgane Roth Hélène Muranty Mario Di Guardo Walter Guerra Andrea Patocchi fabrizio costa Plant Breeding Research Division AgroscopeWädenswilZurichSwitzerland IRHS INRAEAgrocampus-OuestUniversitéd’AngersSFR 4207 QuaSaVBeaucouzéFrance Department of Genomics and Biology of Fruit Crops Research and Innovation CentreFondazione Edmund Mach(FEM)Via E.Mach 138010 San Michele all’AdigeItaly Department of Agriculture Food and Environment(Di3A)University of CataniaCataniaItaly Research Centre Laimburg Laimburg 639040 AuerItaly Center Agriculture Food Environment University of TrentoVia Mach 138010 San Michele all’AdigeItaly Present address:GAFL INRAE84140 MontfavetFrance

Texture is a complex trait and a major component of fruit quality in apple.While the major effect of MdPG1,a gene controlling firmness,has already been exploited in elite cultivars,the genetic basis of crispness remains poorly understood.To further improve fruit texture,harnessing loci with minor effects via genomic selection is therefore necessary.In this study,we measured acoustic and mechanical features in 537 genotypes to dissect the firmness and crispness components of fruit texture.Predictions of across-year phenotypic values for these components were calculated using a model calibrated with 8,294 SNP markers.The best prediction accuracies following cross-validations within the training set of 259 genotypes were obtained for the acoustic linear distance(0.64).Predictions for biparental families using the entire training set varied from low to high accuracy,depending on the family considered.While adding siblings or half-siblings into the training set did not clearly improve predictions,we performed an optimization of the training set size and composition for each validation set.This allowed us to increase prediction accuracies by 0.17 on average,with a maximal accuracy of 0.81 when predicting firmness in the‘Gala’×‘Pink Lady’family.Our results therefore identified key genetic parameters to consider when deploying genomic selection for texture in apple.In particular,we advise to rely on a large training population,with high phenotypic variability from which a‘tailored training population’can be extracted using a priori information on genetic relatedness,in order to predict a specific target population.

关键词： prediction optimization fir

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Investigation of the transcriptomic and metabolic changes associated with superficial scald physiology impaired by lovastatin and 1-methylcyclopropene in pear fruit(cv.“Blanquilla”)

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Horticulture Research 2020年第1期7卷 2229-2245页

作者： Jordi Giné-Bordonaba Nicola Busatto Christian Larrigaudière Violeta Lindo-García Gemma Echeverria Urska Vrhovsek Brian Farneti Franco Biasioli Concetta De Quattro Marzia Rossato Massimo Delledonne fabrizio costa XaRTA-Postharvest Institute for Food and Agricultural Research and Technology(IRTA)Edifici FruitcentreParc Científic i Tecnològic Agroalimentari de Lleida25003 LleidaSpain Department of Genomics and Biology of Fruit Crops Research and Innovation CentreFondazione Edmund Machvia Mach 138010 San Michele all’AdigeTrentoItaly Department of Food Quality and Nutrition Research and Innovation CentreFondazione Edmund Machvia Mach 138010 San Michele all’AdigeTrentoItaly Department of Biotechnology University of VeronaStrada le Grazie 1537134 VeronaItaly Center Agriculture Food Environment University of Trentovia Mach 138010 San Michele all’AdigeTrentoItaly

To elucidate the physiology underlying the development of superficial scald in pears,susceptible“Blanquilla”fruit was treated with different compounds that either promoted(ethylene)or repressed(1-methylcyclopropene and lovastatin)the incidence of this disorder after 4 months of cold storage.Our data show that scald was negligible for the fruit treated with 1-methylcyclopropene or lovastatin,but highly manifested in untreated(78%incidence)or ethylenetreated fruit(97%incidence).The comparison between the fruit metabolomic profile and transcriptome evidenced a distinct reprogramming associated with each treatment.In all treated samples,cold storage led to an activation of a cold-acclimation-resistance mechanism,including the biosynthesis of very-long-chain fatty acids,which was especially evident in 1-methylcyclopropane-treated fruit.Among the treatments applied,only 1-methylcyclopropene inhibited ethylene production,hence supporting the involvement of this hormone in the development of scald.However,a common repression effect on the PPO gene combined with higher sorbitol content was found for both lovastatin and 1-methylcyclopropene-treated samples,suggesting also a non-ethylene-mediated process preventing the development of this disorder.The results presented in this work represent a step forward to better understand the physiological mechanisms governing the etiology of superficial scald in pears.

关键词： superficial impaired hence

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Ethylene-auxin crosstalk regulates postharvest fruit ripening process in apple

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Fruit Research 2021年第1期1卷 116-128页

作者： Nicola Busatto Alice Tadiello Marco Moretto Brian Farneti Francesca Populin Urska Vrhovsek Mauro Commisso Elisa Sartori Paolo Sonego Franco Biasioli Guglielmo costa Flavia Guzzo Paolo Fontana Kristof Engelen fabrizio costa Research and Innovation Centre Fondazione Edmund Machvia Mach 138098 San Michele all'AdigeTrentoItaly Department of Biotechnology University of VeronaStrada le Grazie 15CàVignal 137134 VeronaItaly Department of Agricultural Science University of BolognaVia Fanin 4640127BolognaItaly Center Agriculture Food Environment C3A University of TrentoVia Mach 138098 San Michele all'AdigeTrentoItaly

The ripening of climacteric fruits,such as apple,is represented by a series of genetically programmed events orchestrated by the action of several hormones.In this study,we investigated the existence of a hormonal crosstalk between ethylene and auxin during the post-harvest ripening of three internationally known apple cultivars:‘Golden Delicious',‘Granny Smith'and‘Fuji'.The normal climacteric ripening was impaired by the exogenous application of 1-methylcyclopropene(1-MCP)that affected the production of ethylene and the physiological behaviour of specific ethylene-related quality traits,such as fruit texture and the production of volatile organic compounds.The application of 1-MCP induced,moreover,a de-novo accumulation of auxin.The RNA-Seq wide-transcriptome analysis evidenced as the competition at the level of the ethylene receptors induced a cultivar-dependent transcriptional re-programming.The DEGs annotation carried out through the KEGG database identified as most genes were assigned to the plant hormone signaling transduction category,and specifically related to auxin and ethylene.The interplay between these two hormones was further assessed through a candidate gene analysis that highlighted a specific activation of GH3 and ILL genes,encoding key steps in the process of the auxin homeostasis mechanism.Our results showed that a compromised ethylene metabolism at the onset of the climacteric ripening in apple can stimulate,in a cultivar-dependent fashion,an initial de-novo synthesis and de-conjugation of auxin as a tentative to restore a normal ripening progression.

关键词： crosstalk cultivar process

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Wide transcriptional investigation unravel novel insights of the on-tree maturation and postharvest ripening of‘Abate Fetel’pear fruit

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Horticulture Research 2019年第1期6卷 1378-1392页

作者： Nicola Busatto Brian Farneti Alice Tadiello Vicky Oberkofler Antonio Cellini Franco Biasioli Massimo Delledonne Alessandro Cestaro Christos Noutsos fabrizio costa Department of Genomics and Biology of Fruit Crops Research and Innovation CentreFondazione Edmund Mach(FEM)Via E.Mach 138010 San Michele all’AdigeItaly Department of Biology University of PadovaVia G.Colombo 335121 PadovaItaly Institute for Biochemistry and Biology Karl-Liebknecht-Str.24-2514476 PotsdamGermany Department of Agricultural and Food Science University of BolognaVia Fanin 4640127 BolognaItaly Department of Food Quality and Nutrition Research and Innovation CentreFondazione Edmund Mach(FEM)Via E.Mach 138010 San Michele all’AdigeItaly Department of Biotecnology University of VeronaStrada le Grazie 15CàVignal 137134 VeronaItaly Unit of Computational Biology Research and Innovation CentreFondazione Edmund Mach(FEM)Via E.Mach 138010 San Michele all’AdigeItaly Biology Department SUNY College at Old WestburyOld WestburyNY 11568USA

To decipher the transcriptomic regulation of the on-tree fruit maturation in pear cv.‘Abate Fetel’,a RNA-seq transcription analysis identified 8939 genes differentially expressed across four harvesting stages.These genes were grouped into 11 SOTA clusters based on their transcriptional pattern,of which three included genes upregulated while the other four were represented by downregulated genes.Fruit ripening was furthermore investigated after 1 month of postharvest cold storage.The most important variation in fruit firmness,production of ethylene and volatile organic compounds were observed after 5 days of shelf-life at room temperature following cold storage.The role of ethylene in controlling the ripening of‘Abate Fetel’pears was furthermore investigated through the application of 1-methylcyclopropene,which efficiently delayed the progression of ripening by reducing fruit softening and repressing both ethylene and volatile production.The physiological response of the interference at the ethylene receptor level was moreover unraveled investigating the expression pattern of 12 candidate genes,initially selected to validate the RNA-seq profile.This analysis confirmed the effective role of the ethylene competitor in downregulating the expression of cell wall(PG)and ethylene-related genes(ACS,ACO,ERS1,and ERS2),as well as inducing one element involved in the auxin signaling pathway(Aux/IAA),highlighting a possible cross-talk between these two hormones.The expression patterns of these six elements suggest their use as molecular toolkit to monitor at molecular level the progression of the fruit on-tree maturation and postharvest ripening.

关键词： furthermore tree insight

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Electrical storm in systemic sclerosis: Inside the electroanatomic substrate

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World Journal of Cardiology 2014年第10期6卷 1127-1130页

作者： Michela Casella Corrado Carbucicchio Eleonora Russo Francesca Pizzamiglio Paolo Golia Sergio Conti fabrizio costa Antonio Dello Russo Claudio Tondo Francesca Pizzamiglio Sergio Conti Antonio Dello Russo Claudio Tondo Cardiac Arrhythmia Research Centre Centro Cardiologico Monzino IRCCS 20138 Milan Italy Department of Cardiovascular Disease Morgagni-Pierantoni Hospital 27121 Forlì Italy Biosense-Webster 00040 Pomezia Italy

We report the case of a 63-year-old woman affected by a severe form of systemic scleroderma with pul-monary involvement(interstitial fibrosis diagnosed by biopsy and moderate pulmonary hypertension) and cardiac involvement(paroxysmal atrial fibrillation, right atrial flutter treated by catheter ablation, ventricular tachyarrhythmias, previous dual chamber implantable cardioverter defibrillator implant). Because of recurrent electrical storms refractory to iv antiarrhythmic drugs the patient was referred to our institution to undergo catheter ablation. During electrophysiological proce-dure a 3D shell of cardiac anatomy was created with intracardiac echocardiography pointing out a significant right ventricular dilatation with a complex aneurysmal lesion characterized by thin walls and irregular multiple trabeculae. A substrate-guided strategy of catheter ab-lation was accomplished leading to a complete electri-cal isolation of the aneurism and to the abolishment of all abnormal electrical activities. The use of advanced strategies of imaging together with electroanatomical mapping added important information to the complex arrhythmogenic substrate and improved efficacy and safety.

关键词： Ventricular tachycardia Electrical storm Radiofrequency catheter ablation Systemic sclerosis

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Brain dysfunctions and neurotoxicity induced by psychostimulants in experimental models and humans:an overview of recent findings

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Neural Regeneration Research 2024年第9期19卷 1908-1918页

作者： Marcello Serra Nicola Simola Alexia E.Pollack Giulia costa Department of Biomedical Sciences Section of NeuroscienceUniversity of CagliariCagliariItaly Department of Biology University of Massachusetts-BostonBostonMAUSA

Preclinical and clinical studies indicate that psychostimulants,in addition to having abuse potential,may elicit brain dysfunctions and/or neurotoxic effects.Central toxicity induced by psychostimulants may pose serious health risks since the recreational use of these substances is on the rise among young people and adults.The present review provides an overview of recent research,conducted between 2018 and 2023,focusing on brain dysfunctions and neurotoxic effects elicited in experimental models and humans by amphetamine,cocaine,methamphetamine,3,4-methylenedioxymethamphetamine,methylphenidate,caffeine,and nicotine.Detailed elucidation of factors and mechanisms that underlie psychostimulant-induced brain dysfunction and neurotoxicity is crucial for understanding the acute and enduring noxious brain effects that may occur in individuals who use psychostimulants for recreational and/or therapeutic purposes.

关键词： 3,4-methylenedioxymethamphetamine amphetamine caffeine cell cultures cocaine methamphetamine methylphenidate neurotoxicity nicotine

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Could mammalian inorganic polyphosphate be a crucial signaling molecule in neurological disorders?

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Neural Regeneration Research 2024年第4期19卷 701-702页

作者： Renata Torres Da costa Maria E.Solesio Rutgers University Department of BiologyCamdenNJUSA

Since the early stages of life on earth,cellular metabolism has evolved to adapt to fluctuations in nutrient and oxygen availability.In this context,mammals,which are probably the organisms that show one of the highest levels of metabolic complexity,have developed an elegant system that uses constant and rechargeable energy sources of modulate their metabolism.This homeostasis is especially important in the central nervous system,as neurons and other cells in the brain are highly susceptible to fluctuations in nutrients and oxygen availability.

关键词： metabolism homeostasis neurological

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Apple whole genome sequences:recent advances and new prospects

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Horticulture Research 2019年第1期6卷 1247-1270页

作者： Cameron P.Peace Luca Bianco Michela Troggio Eric van de Weg Nicholas P.Howard Amandine Cornille Charles-Eric Durel Sean Myles ZoëMigicovsky Robert J.Schaffer Evelyne Costes Gennaro Fazio Hisayo Yamane Steve van Nocker Chris Gottschalk fabrizio costa David Chagné Xinzhong Zhang Andrea Patocchi Susan E.Gardiner Craig Hardner Satish Kumar Francois Laurens Etienne Bucher Dorrie Main Sook Jung Stijn Vanderzande Department of Horticulture Washington State UniversityPullmanWA 99164USA Computational Biology Fondazione Edmund MachSan Michele all’AdigeTN 38010Italy Department of Genomics and Biology of Fruit Crops Fondazione Edmund MachSan Michele all’AdigeTN 38010Italy Plant Breeding Wageningen University and ResearchWageningen 6708PBThe Netherlands Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Institut für Biologie und Umweltwissenschaften Carl von Ossietzky Universität26129 OldenburgGermany GQE-Le Moulon Institut National de la Recherche AgronomiqueUniversity of Paris-SudCNRSAgroParisTechUniversitéParis-Saclay91190 Gif-sur-YvetteFrance Institut National de la Recherche Agronomique Institut de Recherche en Horticulture et SemencesUMR 134549071 BeaucouzéFrance Department of Plant Food and Environmental SciencesFaculty of AgricultureDalhousie UniversityTruroNS B2N 5E3Canada The New Zealand Institute for Plant and Food Research Ltd Motueka 7198New Zealand School of Biological Sciences University of AucklandAuckland 1142New Zealand AGAP INRACIRADMontpellier SupAgroUniversity of MontpellierMontpellierFrance Plant Genetic Resources Unit USDA ARSGenevaNY 14456USA Laboratory of Pomology Graduate School of AgricultureKyoto UniversityKyoto 606-8502Japan Department of Horticulture Michigan State UniversityEast LansingMI 48824USA The New Zealand Institute for Plant and Food Research Ltd(Plant&Food Research) Palmerston North Research CentrePalmerston North 4474New Zealand College of Horticulture China Agricultural University100193 BeijingChina Agroscope 8820 WädenswilSwitzerland Queensland Alliance of Agriculture and Food Innovation University of QueenslandSt Lucia 4072Australia New Cultivar Innovation Plant and Food ResearchHavelock North 4130New Zealand Agroscope 1260 ChanginsSwitzerland

In 2010,a major scientific milestone was achieved for tree fruit crops:publication of the first draft whole genome sequence(WGS)for apple(Malus domestica).This WGS,v1.0,was valuable as the initial reference for sequence information,fine mapping,gene discovery,variant discovery,and tool development.A new,high quality apple WGS,GDDH13 v1.1,was released in 2017 and now serves as the reference genome for apple.Over the past decade,these apple WGSs have had an enormous impact on our understanding of apple biological functioning,trait physiology and inheritance,leading to practical applications for improving this highly valued crop.Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly.Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees.High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders.We understand the species,geographical,and genomic origins of domesticated apple more precisely,as well as its relationship to wild relatives.The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable,environmentally sound,productive,and consumer-desirable apple production.This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs.Recommendations for“what’s next”focus on necessary upgrades to the genome sequence data pool,as well as for use of the data,to reach new frontiers in genomics-based scientific understanding of apple.

关键词： breakthrough hundreds frontier

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Sensing of membrane tensions:the pleiotropic functions of OscA/TMEM63 mechanosensitive ion channels

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Journal of Genetics and Genomics 2024年第6期51卷 579-582页

作者： Bo Yu Alex costa Yang Zhao Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China Key Laboratory of Plant Carbon Capture Chinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100049China Department of Biosciences University of MilanVia Celoria 26Milan 20133Italy

Organisms sense and respond to environmental and developmental signals to drive adaptive responses(Kefauver et al.,2020;Yu et al.,2024).These stimuli can be mainly divided into physical and chemical stimuli,and the physical stimuli include light,temperature,sound,vibration,pressure,stretch,shear stress,osmotic stress,and substrate deformation.Some of these physical stimuli trigger physical forces and alter membrane tension,which in turn activates mechanosensitive channels(MsCs)and converts the mechanical cues into biochemical signals.

关键词： deformation. convert mec

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Colorectal cancer screening:A review of current knowledge and progress in research

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World Journal of Gastrointestinal Oncology 2024年第4期16卷 1119-1133页

作者： Sara Ramos Lopes Claudio Martins Inês costa Santos Madalena Teixeira Élia Gamito Ana Luisa Alves Department of Gastroenterology Centro Hospitalar de SetúbalSetúbal 2910-446Portugal

Colorectal cancer(CRC)is one of the most prevalent malignancies worldwide,being the third most commonly diagnosed malignancy and the second leading cause of cancer-related deaths globally.Despite the progress in screening,early diagnosis,and treatment,approximately 20%-25%of CRC patients still present with metastatic disease at the time of their initial diagnosis.Furthermore,the burden of disease is still expected to increase,especially in individuals younger than 50 years old,among whom early-onset CRC incidence has been increasing.Screening and early detection are pivotal to improve CRC-related outcomes.It is well established that CRC screening not only reduces incidence,but also decreases deaths from CRC.Diverse screening strategies have proven effective in decreasing both CRC incidence and mortality,though variations in efficacy have been reported across the literature.However,uncertainties persist regarding the optimal screening method,age intervals and periodicity.Moreover,adherence to CRC screening remains globally low.In recent years,emerging technologies,notably artificial intelligence,and non-invasive biomarkers,have been developed to overcome these barriers.However,controversy exists over the actual impact of some of the new discoveries on CRC-related outcomes and how to effectively integrate them into daily practice.In this review,we aim to cover the current evidence surrounding CRC screening.We will further critically assess novel approaches under investigation,in an effort to differentiate promising inno-vations from mere novelties.

关键词： Colorectal cancer Screening Review Oncology Artificial intelligence

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