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An integrated approach for increasing breeding efficiency in apple and peach in Europe

Horticulture Research 2018年第1期5卷 825-838页

作者： Francois Laurens Maria JoséAranzana Pere Arus Daniele Bassi Marco Bink Joan Bonany Andrea Caprera Luca Corelli-Grappadelli Evelyne Costes Charles-Eric Durel Jehan-Baptiste Mauroux Hélène Muranty Nelson Nazzicari Thierry Pascal Andrea Patocchi Andreas Peil Bénédicte Quilot-Turion Laura Rossini Alessandra Stella michela troggio Riccardo Velasco Eric van de Weg IRHS INRAAgrocampus-OuestUniversitéd’AngersSFR 4207 QuaSaVUniversitéBretagne Loire42 rue Georges MorelBeaucouzé49071France IRTA(Institut de Recerca i Tecnologia Agroalimentàries) BarcelonaSpain Centre for Research in Agricultural Genomics(CRAG)CSIC-IRTA-UAB-UB Campus UABBellaterraBarcelonaSpain Universitàdegli Studi di Milano-DiSAA Via Celoria 2Milan20133Italy Biometris Wageningen University and ResearchDroevendaalsesteeg 1Wageningen6708PBThe Netherlands IRTA-Mas Badia Mas BadiaLa Tallada17134Spain Parco Tecnologico Padano Via EinsteinLoc.Cascina CodazzaLodi26900Italy Dipartimento di Scienze Agrarie Alma Mater Studiorum-Universitàdi BolognaBolognaItaly UMR AGAP INRAMontpellier34398France GAFL INRAMontfavet84143France Agroscope Research Division Plant BreedingSchloss 1Wädenswil8820Switzerland Julius Kühn-Institute(JKI) Federal Research Centre for Cultivated Plants Institute for Breeding Research on Fruit CropsPillnitzer Platz 3aDresden01326Germany Research and Innovation Center Fondazione Edmund MachSan Michele all’AdigeTrentoItaly CREA-VE Center of Viticulture and Enologyvia XXVIII Aprile 26Conegliano(TV)31015Italy Plant Breeding Wageningen University and ResearchDroevendaalsesteeg 1P.O.Box 386Wageningen6700AJThe Netherlands Hendrix Genetics Research Technology&ServicesBoxmeer5830 ACThe Netherlands

Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and breeding.To bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private companies.Three complementary approaches were pursued:(i)tool and software development,(ii)deciphering genetic control of main horticultural traits taking into account allelic diversity and(iii)developing plant materials,tools and methodologies for breeders.Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding,development of new,dense SNP arrays in apple and peach,new phenotypic methods for some complex traits,software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis(PBA).This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies(GWAS)on several European genebank collections.FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities.Through FruitBreedomics,significant progresses were made in the field of apple and peach breeding,genetics,genomics and bioinformatics of which advantage will be made by breeders,germplasm curators and scientists.A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public.This review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond.

关键词： breeding germplasm breed

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Accuracy and responses of genomic selection on key traits in apple breeding

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Horticulture Research 2015年第1期2卷 1-12页

作者： Hélène Muranty michela troggio Inès Ben Sadok Mehdi Al Rifaï Annemarie Auwerkerken Elisa Banchi Riccardo Velasco Piergiorgio Stevanato W.Eric van de Weg Mario Di Guardo Satish Kumar François Laurens Marco C.A.M.Bink Institut de Recherche en Horticulture et Semences UMR1345 INRASFR 4207 QUASAVF-49071 BeaucouzeFrance Research and Innovation Center Fondazione Edmund MachSan Michele all’AdigeTrentoItaly Better 3 Fruit RillaarBelgium DAFNAE Dipartimentodi Agronomia Animali Alimenti Risorse Naturalie Ambienteviale Università1635020 Legnaro(PD)Universitàdegli Studi di PadovaItaly Wageningen UR Plant Breeding Wageningen University and Research CenterWageningenThe Netherlands The New Zealand Institute for Plant&Food Research Limited Private Bag 1401Havelock North 4157New Zealand Biometris Wageningen University and Research CenterWageningenThe Netherlands

The application of genomic selection in fruit tree crops is expected to enhance breeding eficiency by increasing prediction accuracy,increasing selection intensity and decreasing generation interval.The objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key traits.The training population comprised 977 individuals derived from 20 pedigreed fllsib families.Historic phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an llumina 20K SNP array.From these data,a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application fllsib families.The application families had genotypes at 364 SNPs from a dedicated 512 SNP array,and these genotypic data were extended to the high-density level by imputation.These five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding values.Accuracy of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of 0.19.The accuracies were strongly affected by the phenotypic distribution and heritability of traits.In the largest family,significant selection response was observed for traits with high heritability and symmetric phenotypic distribution.Traits that showed non-significant response often had reduced and skewed phenotypic variation or low heritability.Among the five application families the accuracies were uncorrelated to the degree of relatedness to the training population.The results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.

关键词： breeding crops traits

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Mitochondria replacement from transplanted amniotic fluid stem cells:a promising therapy for non-neuronal defects in spinal muscular atrophy

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Neural Regeneration Research 2024年第5期19卷 971-972页

作者： michela Pozzobon Camilla Bean Women’s and Children’s Health Department University of Padova Foundation Institute of Pediatric Research Cittàdella Speranza PadovaItaly Department of Medicine University of UdineUdineItaly

Spinal muscular atrophy(SMA)is a genetic disorder that primarily affects infants and leads to muscle weakness,atrophy,and paralysis.The main cause is the homozygous mutation or deletion of the SMN1 gene,resulting in inadequate levels of the survival motor neuron(SMN)protein.Approved treatments focus on restoring SMN levels through various approaches,but there is a need for“SMN-independent”therapies that target other pathological processes.Skeletal muscle is closely involved in SMA pathology,with impaired muscle function observed before motor neuron degeneration.Studies have revealed that SMN loss leads to skeletal muscle mitochondrial structural abnormalities,impaired respiration,and accumulation of reactive oxygen species.

关键词： impaired atrophy muscular

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A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species

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Horticulture Research 2016年第1期3卷 30-42页

作者： Erica A Di Pierro Luca Gianfranceschi Mario Di Guardo Herma JJ Koehorst-van Putten Johannes W Kruisselbrink Sara Longhi michela troggio Luca Bianco Hélène Muranty Giulia Pagliarani Stefano Tartarini Thomas Letschka Lidia Lozano Luis Larisa Garkava-Gustavsson Diego Micheletti Marco CAM Bink Roeland E Voorrips Ebrahimi Aziz Riccardo Velasco François Laurens W Eric van de Weg Department of Biosciences University of MilanMilan20133Italy Plant Breeding Wageningen University and ResearchWageningen6700AJThe Netherlands Research and Innovation Centre Edmund Mach FoundationSan Michele all’Adige38010Italy Biometris Wageningen University and ResearchWageningen6700AAThe Netherlands IRHS INRAAGROCAMPUS-OuestUniversitéd’AngersSFR 4207 QUASAVBeaucouzé49071France Department of Agricultural Sciences University of BolognaBologna40127Italy Department of Molecular Biology Laimburg Research Centre for Agriculture and ForestryOra39040Italy Department of Plant Breeding Swedish University of Agricultural SciencesAlnarp23053Sweden Hendrix Genetics Research Technology&ServicesBoxmeer 5830 ACThe Netherlands

Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus domestica Borkh),the genome sequence v1 and v2 could not meet this need;therefore,a novel approach was devised to develop a dense genetic linkage map,providing the most reliable marker-loci order for the highest possible number of markers.The approach was based on four strategies:(i)the use of multiple full-sib families,(ii)the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism(SNP)markers,(iii)the construction of a single backcross-type data set including all families,and(iv)a two-step map generation procedure based on the sequential inclusion of markers.The map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM.Moreover,chromosome 5 was oriented according to its homoeologous chromosome 10.This map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies.Its collinearity with the genome sequences v1 and v3 are reported.To our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and individuals.This result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species.

关键词： breeding linkage mapping

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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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How to identify early complications in patients undergoing distal gastrectomy?

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World Journal of Gastrointestinal Surgery 2024年第4期16卷 974-981页

作者： Giuseppe Tropeano Maria michela Chiarello Valeria Fico Giuseppe Brisinda Emergency Surgery and Trauma Center Fondazione Policlinico Universitario A Gemelli IRCCSRome 00168Italy Department of Surgery Azienda Sanitaria Provinciale di CosenzaCosenza 87100Italy Department of Medical and Surgical Sciences UniversitàCattolica del Sacro CuoreRome 00168Italy

In this editorial we comment on the article by Zhang et al published in a recent issue of the World Journal of Gastrointestinal Surgery.Gastrectomy with appropriate lymph node dissection is still standard curative treatment in locally advanced gastric cancer.Several studies point out that gastric cancer surgery is a complex procedure that leads to a high risk of morbidity and mortality.Many factors can contribute to the onset of complications with consequent effects on prognosis and increased mortality.The complications can be divided in complications related to anastomosis,to motility and to surgical site infection.The study presented by Zhang B et al represent an interesting analysis on the possibility to prevent postoperative morbidity.The study was performed on 131 patients with distal gastric cancer who underwent gastrectomy with D2 lymph node dissection.Of these patients,16%developed early postoperative complications.The univariate analysis showed that prealbumin level,hypertension,diabetes,history of abdominal surgery,R0 resection,and blood transfusion were factors influencing early postoperative complications after distal gastrectomy.Moreover,the inclusion of the above significant variables in the logistic regression analysis revealed that hypertension,diabetes,a history of abdominal surgery,and blood transfusion were independent predictors of postoperative complications.In conclusion,preoperative and intraoperative factors can be used to establish an early postoperative nomogram model.The results of the study presented by Zhang et al suggest that the prediction model can be used to guide the detection of postoperative complications and has clinical reference value.

关键词： Gastric cancer Gastrectomy Lymph node dissection Morbidity Mortality Surgical site infections

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Indocyanine green:The guide to safer and more effective surgery

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World Journal of Gastrointestinal Surgery 2024年第3期16卷 641-649页

作者： Pietro Fransvea Maria michela Chiarello Valeria Fico Maria Cariati Giuseppe Brisinda Emergency Surgery and Trauma Center Fondazione Policlinico Universitario Agostino Gemelli IRCCSRome 00168Italy Department of Surgery Azienda Sanitaria Provinciale di CosenzaCosenza 87100Italy Department of Surgery Azienda Sanitaria Provinciale di CrotoneCrotone 88900Italy Department of Abdominal and Endocrine Metabolic Medical and Surgical Sciences Fondazione Policlinico Universitario A Gemelli IRCCSRome 00168Italy

In this editorial we comment on the article by Kalayarasan and co-workers published in the recent issue of the World Journal of Gastrointestinal Surgery.The authors present an interesting review on the use of indocyanine green fluo-rescence in different aspects of abdominal surgery.They also highlight future perspectives of the use of indocyanine green in mini-invasive surgery.Indo-cyanine green,used for fluorescence imaging,has been approved by the Food and Drug Administration and is safe for use in humans.It can be administered in-travenously or intra-arterially.Since its advent,there have been several advance-ments in the applications of indocyanine green,especially in the surgical field,such as intraoperative mapping and biopsy of sentinel lymph node,measurement of hepatic function prior to resection,in neurosurgical cases to detect vascular anomalies,in cardiovascular cases for patency and assessment of vascular ab-normalities,in predicting healing following amputations,in helping visualization of hepatobiliary anatomy and blood vessels,in reconstructive surgery,to assess flap viability and for the evaluation of tissue perfusion following major trauma and burns.For these reasons,the intraoperative use of indocyanine green has become common in a variety of surgical specialties and transplant surgery.Co-lorectal surgery has just lately begun to adopt this technique,particularly for perfusion visualization to prevent anastomotic leakage.The regular use of in-docyanine green coupled with fluorescence angiography has recently been pro-posed as a feasible tool to help improve patient outcomes.Using the best available data,it has been shown that routine use of indocyanine green in colorectal surgery reduces the rates of anastomotic leak.The use of indocyanine green is proven to be safe,feasible,and effective in both elective and emergency scenarios.However,additional robust evidence from larger-scale,high-quality studies is essential before incorporating indocyanine green guided surgery into standard practice.

关键词： Indocyanine green Colorectal surgery Fluorescence-guided surgery Gastrointestinal surgery Hepato-biliary surgery Pancreatic surgery Surgical oncology

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外推法导引及应用

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数学进展 2024年第1期53卷 13-40页

作者： Claude BREZINSKI michela REDIVO-ZAGLIA 保罗·潘勒韦实验室法国国家科学研究中心混合研究单位8524里尔大学法国里尔59655 帕多瓦大学意大利帕多瓦35122

在数值科学和应用科学中,人们经常需要考虑多种类型的序列:标量、向量、四元数、矩阵以及后来出现的张量.这些序列可能收敛,也可能发散.当它们收敛时,其收敛速度可能会非常缓慢,以至于其实际用途十分有限.在某些情况下,可以修改建立这... 详细信息

在数值科学和应用科学中,人们经常需要考虑多种类型的序列:标量、向量、四元数、矩阵以及后来出现的张量.这些序列可能收敛,也可能发散.当它们收敛时,其收敛速度可能会非常缓慢,以至于其实际用途十分有限.在某些情况下,可以修改建立这些序列的过程,但在其他情况下,这个过程是一个无法进入的黑箱.那么,规避这一困难的一个可行方法就是将序列变换成另一个序列,希望它能收敛到相同的极限,并且收敛得更快.这种序列变换背后的思想就是外推法.本文是关于这些方法中最重要的方法以及其理论基础和算法方面的导引.本文还介绍了一些应用.

关键词：外推法收敛加速序列变换安德森加速张量非线性方程吉布斯现象

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Enhancing sensitivity of triple-negative breast cancer to DNA-damaging therapy through chemical inhibition of the m6A methyltransferase METTL3

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Cancer Communications 2024年第2期44卷 282-286页

作者： Bianca Cesaro Alessia Iaiza Fabio Piscopo Marco Tarullo Eleonora Cesari Dante Rotili Antonello Mai Alberto Diana michela Londero Luca Del Giacco Riccardo Masetti Alba Di Leone Chiara Naro Silvia Masciarelli Giulia Fontemaggi Claudio Sette Francesco Fazi Alessandro Fatica Department of Anatomical HistologicalForensic&Orthopedic SciencesSection of Histology&Medical EmbryologySapienza University of RomeRomeItaly Department of Biology and Biotechnologies“Charles Darwin” Sapienza University of RomeRomeItaly GSTeP Organoids Research Core Facility Fondazione Policlinico A.Gemelli Istituto di Ricovero e Cura a Carattere Scientifico(IRCCS)RomeItaly Department of Drug Chemistry and Technologies Sapienza University of RomeRomeItaly Pasteur Institute Cenci-Bolognetti FoundationSapienza University of RomeRomeItaly Department of BioSciences University of MilanMilanItaly Multidisciplinary Breast Center Dipartimento Scienze della Salute della Donna e del Bambino e di SanitàPubblicaCatholic University of the Sacred HeartRomeItaly Department of Neuroscience Section of Human AnatomyCatholic University of the Sacred HeartRomeItaly Oncogenomic and Epigenetic Unit IRCCS Regina Elena National Cancer InstituteRomeItaly

Dear Editor,N 6-methyladenosine(m^(6)A)is a critical mRNA modi-fication catalyzed by the enzyme methyltransferase-like 3(METTL3),with implications in RNA metabolism.METTL3 upregulation is associated with cancer progre... 详细信息

关键词： cancer methyltransferase metastasis

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Estrogens still represent an attractive therapeutic approach for Alzheimer’s disease

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Neural Regeneration Research 2022年第1期17卷 93-94页

作者： Elena Tamagno michela Guglielmotto Department of Neuroscience University of TorinoTorinoItaly(Tamagno EGuglielmotto M)Neuroscience Institute of Cavalieri Ottolenghi Foundation(NICO)University of TorinoTorinoItaly

Alzheimer’s disease(AD)is a progressive neurodegenerative condition that goes f rom mild cogni t ive impai rment in prodromal disease to severely disabling deficits in advanced stages.The risk for AD development,as well as progression and severity,clearly differ between men and women(Pike,2017).Epidemiological studies have shown that there is a significantly increased prevalence in the development of AD in women compared to men,which is usually explained by the longer lifespan of women.This increased frequency may be due to the interplay between age and sex,in which genetic factors together with hormonal and metabolic patterns play a crucial role.Moreover,cognitive impairment has been confirmed to be greater in women than in men at the same stage of AD,likely due to reduced estrogen levels in postmenopausal women(Laws et al.,2016).

关键词： Alzheimer attractive therapeutic

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