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Fine mapping and identification of candidate genes for the peach powdery mildew resistance gene Vr3

Horticulture Research 2020年第1期7卷 343-351页

作者： Neus Marimon Jordi Luque pere arús Iban Eduardo Centre for Research in Agricultural Genomics(CRAG)CsIC-IRTA-UAB-UB Campus UAB08193 BellaterraBarcelonaSpain IRTA(Institut de Recerca i Tecnologia Agroalimentàries) BarcelonaSpain Plant Pathology IRTA CabrilsCarretera de Cabrils km 208348 CabrilsSpain

Powdery mildew is one of the major diseases of peach(Prunus persica),caused by the ascomycete Podosphaera ***,it is controlled through calendar-based fungicide treatments starting at petal fall,but an alternative is to develop resistant peach *** studies mapped a resistance gene(Vr3)in interspecific populations between almond(‘Texas’)and peach(‘Earlygold’).To obtain molecular markers highly linked to Vr3 and to reduce the number of candidate genes,we fine-mapped Vr3 to a genomic region of 270 kb with 27 annotated *** find evidence supporting one of these positional candidate genes as being responsible of Vr3,we analyzed the polymorphisms of the resequences of both parents and used near-isogenic lines(NILs)for expression analysis of the positional candidate genes in symptomatic or asymptomatic *** differentially expressed between resistant and susceptible individuals were annotated as a Disease Resistance Protein RGA2(Prupe2G111700)or an Eceriferum 1 protein involved in epicuticular wax biosynthesis(Prupe2G112800).Only Prupe2G111700 contained a variant predicted to have a disruptive effect on the encoded protein,and was overexpressed in both heterozygous and homozygous individuals containing the Vr3 almond allele,compared with susceptible *** information was also useful to identify and validate molecular markers tightly linked and flanking *** addition,the NILs used in this work will facilitate the introgression of this gene into peach elite materials,alone or pyramided with other known resistance genes such as peach powdery mildew resistance gene Vr2.

关键词： resistance peach mapping

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High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond×peach progenies

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Horticulture Research 2015年第1期2卷 234-241页

作者： JoséManuel Donoso Iban Eduardo Roger Picañol Ignasi Batlle Werner Howad María Joséaranzana pere arús IRTA Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB Campus UAB Bellaterra(Cerdanyola del Vallès)08193 BarcelonaSpain IRTA.Centre de Mas de Bover.Crta.De Reus–El Morell Km 3.8.43120 Constantί TarragonaSpain INIA Av.Salamanca s/nSector Los ChoapinosRengoChile Rijk Zwaan Finca La Marina-Pj Lo Contreras s/n30395 La PueblaCartagenaSpain

Peach(Prunus persica)and almond(Prunus dulcis)are two sexually compatible species that produce fertile ***,a highly polymorphic species,is a potential source of new genes for peach that has a strongly eroded gene *** we describe the genetics of a male sterile phenotype that segregated in two almond(‘Texas’)×peach(‘Earlygold’)progenies:an F2(T×E)and a backcross one(T1E)to the‘Earlygold’***-density maps were developed using a 9k peach sNP chip and 135 simple-sequence *** highly syntenic and collinear maps were obtained:one for the F2(T×E)and two for the backcross,T1E(for the hybrid)and E(for‘Earlygold’).A major reduction of recombination was observed in the interspecific maps(T×E and T1E)compared to the intraspecific parent(E).The E map also had extensive monomorphic genomic regions suggesting the presence of large DNA fragments identical by *** data for the male sterility character were consistent with the existence of cytoplasmic male sterility,where individuals having the almond cytoplasm required the almond allele in at least one of two independent restorer genes,Rf1 and Rf2,to be *** restorer genes were located in a 3.4 Mbp fragment of linkage group 2(Rf1)and 1.4 Mbp of linkage group 6(Rf2).Both fragments contained several genes coding for pentatricopeptide proteins,demonstrated to be responsible for restoring fertility in other *** implications of these results for using almond as a source of novel variability in peach are discussed.

关键词： linkage restore mapping

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Almond population genomics and non-additive GWAs reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time

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Horticulture Research 2023年第10期10卷 262-272页

作者： Felipe Pérez de los Cobos Eva Coindre Naima Dlalah Bénédicte Quilot-Turion Ignasi Batlle pere arús Iban Eduardo Henri Duval Fruticultura Institut de Recerca i Tecnologia Agroalimentàries(IRTA)Mas BovéCtra.Reus-El Morell Km 3843120 ConstantíTarragonaSpain Centre de Recerca en Agrigenòmica(CRAG) CSIC-IRTA-UAB-UB.Institut de Recerca i Tecnologia Agroalimentàries(IRTA)Cerdanyola del Vallès(Bellaterra)08193 BarcelonaSpain Centre for Research in Agricultural Genomics(CRAG)CsIC-IRTA-UAB-UB Campus UABEdifici CRAGCerdanyola del Vallès(Bellaterra)08193 BarcelonaSpain INRAE GAFLF-84143MontfavetFrance

Domestication drastically changed crop genomes,fixing alleles of interest and creating different genetic ***-wide association studies(GWAss)are a powerful tool to detect these alleles of interest(and so QTLs).In this study,we explored the genetic structure as well as additive and non-additive genotype-phenotype associations in a collection of 243 almond *** genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups,all formed by accessions with a common *** of these groups was formed exclusively by spanish accessions,while the rest were mainly formed by accessions from China,Italy,France,and the *** results agree with archaeological and historical evidence that separate modern almond dissemination into four phases:Asiatic,Mediterranean,Californian,and southern *** total,we found 13 independent QTLs for nut weight,crack-out percentage,double kernels percentage,and blooming *** the 13 QTLs found,only one had an additive *** candidate gene analysis,we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage,Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage,and Prudul26A000954 as a candidate gene for the QTL found in blooming *** study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding.

关键词： additive GWAs traits

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Prunus genetics and applications after de novo genome sequencing:achievements and prospects

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Horticulture Research 2019年第1期6卷 1222-1246页

作者： Maria Joséaranzana Véronique Decroocq Elisabeth Dirlewanger Iban Eduardo Zhong shan Gao Ksenija Gasic Amy Iezzoni sook Jung Cameron Peace Humberto Prieto Ryutaro Tao Ignazio Verde Albert G.Abbott pere arús IRTA Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UBCampus UABEdifici CRAGCerdanyola del Vallès(Bellaterra)08193 BarcelonaSpain UMR 1332 BFP INRAUniversity of BordeauxA3C and Virology Teams33882 Villenave-d’Ornon CedexFrance Allergy Research Center Zhejiang University310058 HangzhouChina Clemson University ClemsonSC 29634USA Department of Horticulture Michigan State University1066 Bogue StreetEast LansingMI 48824-1325USA Department of Horticulture Washington State UniversityPullmanWA 99164-6414USA Biotechnology Laboratory La Platina Research StationInstituto de Investigaciones AgropecuariasSanta Rosa11610 La PintanaSantiagoChile Laboratory of Pomology Graduate School of AgricultureKyoto UniversityKyoto 606-8502Japan Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria(CREA)-Centro di ricerca Olivicoltura Frutticoltura e Agrumicoltura(CREA-OFA)RomeItaly University of Kentucky 106 T.P.Cooper HallLexingtonKY 40546-0073USA

Prior to the availability of whole-genome sequences,our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EsT *** public release of the peach genome and others that followed,significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits *** this review,we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome *** the structural and evolutionary contexts,we summarize:(1)the current status of Prunus whole-genome sequences;(2)preliminary and ongoing work on the sequence structure and diversity of the genomes;(3)the analyses of Prunus genome evolution driven by natural and man-made selection;and(4)provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs ***,we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus *** include phenology,fruit quality,allergens,disease resistance,tree architecture,and ***,we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop ***,we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae(GDR)and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.

关键词： Prunus breeding achievements

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桃品种特异性荧光ssR分子标记数据库构建

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果树学报 2013年第6期30卷 924-932页

作者：李雄伟孟宪桥贾惠娟王力荣王志强马瑞娟吴大军董冰 Maria Jose aranzana pere arús 高中山浙江大学果树科学研究所·农业部园艺植物生长发育与生物技术重点开放实验室杭州310058 中国农业科学院郑州果树研究所郑州450009 江苏省农业科学院园艺研究所南京210014 浙江奉化水蜜桃研究所浙江奉化315521 山西省农业科学研究院果树研究所山西太谷030815 Centre de Recerca en Agrigenomica CsIC-IRTA-UAB Campus UAB-Edifici CRAG Bellaterra-Cerdanyola del Valles 08193BarcelonaSpain

【目的】选择通用的荧光ssR分子标记建立桃种质资源基因型数据库便于进行种质特异性鉴定、资源交换、管理和利用。【方法】根据48个ssR标记对国内外669份桃品系的遗传多样性测试结果，从中选择出一部分多态信息含量较高、适合品种鉴别... 详细信息

【目的】选择通用的荧光ssR分子标记建立桃种质资源基因型数据库便于进行种质特异性鉴定、资源交换、管理和利用。【方法】根据48个ssR标记对国内外669份桃品系的遗传多样性测试结果，从中选择出一部分多态信息含量较高、适合品种鉴别的标记，采用不同荧光标识组合在ABI3130测序仪测试，为了使不同批次的测试结果准确可靠，6—8个参照品种纳入每次的测试中。结果用16个ssR标记基本可以判断品种的特异性，它们可以用4种荧光标识进行标记，便于分为4组在ABI遗传分析仪上测试。目前数据库包含641份材料．基因型一致的品系多为同一品种突变体和自交系演化的地方品种。文中列出了100份中国代表性种质资源分子标记数据库，并建议8个中国品系为参照。对17个桃品种进行系谱验证发现，我国资源圃所育成的7个品种系谱信息正确，但日本桃品种系谱信息与文献出现偏差。【结论】应用16个多态性高的ssR荧光标记可以构建精确的桃品种分子指纹数据库，测试方法及结果对品种特异性和系谱鉴定提供重要的参考．推动资源分子指纹数据库标准化建设工作。

关键词：桃荧光标记ssR 指纹图谱数据库品种鉴定系谱鉴定

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Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

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Horticulture Research 2021年第1期8卷 72-82页

作者： Felipe perez de los Cobos Pedro J.Martinez-Garcia Agusti Romero Xavier Miarnau Iban Eduardo Werner Howad Mourad Mnejja Federico Dicenta Rafel socias i Company Maria J.Rubio-Cabetas Thomas M.Gradziel Michelle Wirthensohn Henri Duval Doron Holland pere arus Francisco J.Vargas Ignasi Batlle Institut de Recerca i Tecnologia Agroalimentaries(IRTA) Mas BoveCtra.Reus-El Morell Km 3843120 ConstantiTarragonaSpain Institut de Recerca i Tecnologia Agroalimentaries(IRTA) Centre de Recerca en Agrigenomica(CRAG)CSIC-IRTA-UAB-UB.Cerdanyola del Valles(Bellaterra)08193 BarcelonaSpain Centro de Edafologia y Biologia Aplicada del segura Consejo Superior de Investigaciones Cientificas(CEBAS-CSIC)P.O.Box 16430100 EspinardoMurciaSpain Institut de Recerca i Tecnologia Agroalimentaries(IRTA) FruitcentrePCiTALGardeny ParkFruitcentre Building25003 LleidaSpain Centro de Investigacion y Tecnologia Agroalimentaria de aragon(CITA) Avda.Montanana 93050059ZaragozaInstituto Agroalimentario de Aragon IA2(CITA-Universidad de Zaragoza)ZaragozaSpain University of California 1 Shields AvenueDavisCA 95616USA University of Adelaide Waite ResearchSchool of AgricultureFood and WinePMB 1Glen OsmondAdelaideSA 5064Australia Institut National de la Recherche Agronomique(INRA) Domain St.Maurice CS 6009484143 Montfavet CedexFrance Agricultural Research Organization Newe-Ya’ar Research CenterP.O.Box 1021Ramat Yishad 30095Israel

Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder ***,in almond,little is known about the genetic variability in current breeding stocks,although several cases of inbreeding depression have been *** gain insights into the genetic structure in modern breeding programs worldwide,marker-verified pedigree data of 220 almond cultivars and breeding selections were *** coefficients,pairwise relatedness,and genetic contribution were calculated for these *** results reveal two mainstream breeding lines based on three cultivars:“Tuono”,“Cristomorto”,and“Nonpareil”.Descendants from“Tuono”or“Cristomorto”number 76(sharing 34 descendants),while“Nonpareil”has 71 *** mean inbreeding coefficient of the analyzed genotypes was 0.041,with 14 genotypes presenting a high inbreeding coefficient,over *** programs from France,the UsA,and spain showed inbreeding coefficients of 0.075,0.070,and 0.037,*** to their genetic contribution,modern cultivars from Israel,France,the UsA,spain,and Australia trace back to a maximum of six main founding *** the group of 65 genotypes carrying the s f allele for self-compatibility,the mean relatedness coefficient was 0.125,with“Tuono”as the main founding genotype(24.7%of total genetic contribution).The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process *** current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.

关键词： breeding cultivar founding

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True cicadas (Cicadidae) as prey for the birds of the Western Palearctic: a review

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Avian Research 2020年第2期11卷 174-182页

作者： pere Pons Departament de Ciències Ambientals Universitat de Girona

Background:True cicadas(Cicadidae)are large and temporarily abundant *** availability may produce demographic and behavioural effects on bird populations,as happens with forest avifauna feeding on periodical cicadas in North *** Europe,the Near East and North Africa,knowledge of cicada predation by birds is ***:To help fill this gap,I consulted Cramp’s Birds of the Western Palearctic,conducted a search of online databases and used search engines to generate a database of Western Palearctic birds known to eat ***:A total of 105 species(16%of those occurring in the region)belonging to 13 orders,and comprising 20 of the 33 passerine families,were found to consume cicadas.I estimated that 69 of these bird species are known to consume cicadas within the limits of the Western *** terrestrial birds predate on cicadas,preferably on *** predators include cuckoos,owls,bee-eaters,woodpeckers,falcons,reed-warblers,larks,crows and jays,buntings,shrikes,pipits and wagtails,flycatchers and chats,tits,sparrows,leaf-warblers,starlings,warblers and thrushes,but also terns and *** are consumed by some passerines,owls and *** can make up as much as 70%of food items delivered to *** of stomach contents and neck collar samples are the most common methods used in diet ***:Available knowledge is biased towards species that have been more intensively studied,and often lack proper quantification of prey *** studies about the relative importance of cicadas as prey for birds in the Western Palearctic are needed.I suggest using non-invasive studies based on pellets and droppings and prioritizing declining bird species.

关键词： Bird species Cicadidae Cramp’s handbook Diet studies Predator-prey relationships

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Phylobone: a comprehensive database of bone extracellular matrix proteins in human and model organisms

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Bone Research 2023年第3期11卷 617-624页

作者： Margalida Fontcuberta-Rigo Miho Nakamura pere Puigbò Medicity Research Laboratory Faculty of MedicineUniversity of TurkuTykistökatu 620520 TurkuFinland Institute of Biomaterials and Bioengineering Tokyo Medical and Dental University2-3-10 Kanda-SurugadaiChiyodaTokyo 1010062Japan Graduate school of Engineering Tohoku University6-6 Aramaki Aza AobaAoba-kuSendaiMiyagi 9808579Japan Department of Biology University of Turku20500 TurkuFinland Eurecat Technology Center of Catalonia.Nutrition and Health UnitReus 43204 CataloniaSpain Department of Biochemistry and Biotechnology University Rovira i Virgili43007 TarragonaCataloniaSpain

The bone extracellular matrix(ECM) contains minerals deposited on highly crosslinked collagen fibrils and hundreds of noncollagenous proteins. some of these proteins are key to the regulation of bone formation and regeneration via signaling pathways,and play important regulatory and structural roles. However, the complete list of bone extracellular matrix proteins, their roles, and the extent of individual and cross-species variations have not been fully captured in both humans and model organisms. Here, we introduce the most comprehensive resource of bone extracellular matrix(ECM) proteins that can be used in research fields such as bone regeneration, osteoporosis, and mechanobiology. The Phylobone database(available at https://***) includes 255proteins potentially expressed in the bone extracellular matrix(ECM) of humans and 30 species of vertebrates. A bioinformatics pipeline was used to identify the evolutionary relationships of bone ECM proteins. The analysis facilitated the identification of potential model organisms to study the molecular mechanisms of bone regeneration. A network analysis showed high connectivity of bone ECM proteins. A total of 214 functional protein domains were identified, including collagen and the domains involved in bone formation and resorption. Information from public drug repositories was used to identify potential repurposing of existing drugs. The Phylobone database provides a platform to study bone regeneration and osteoporosis in light of(biological) evolution,and will substantially contribute to the identification of molecular mechanisms and drug targets.

关键词： drugs matrix database

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Comparison Between Modal Analysis and Impedance-based Methods for Analysing stability of Unbalanced Microgrids with Grid-forming Electronic Power Converters

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Journal of Modern Power systems and Clean Energy 2023年第4期11卷 1269-1281页

作者： sauro J.Yague Aurelio García-Cerrada pere Palacín Farré IQs school of Engineering Ramón Llull UniversityVia Augusta 39008017 BarcelonaSpain Institute for Research in Technology ICAI School of EngineeringComillas Pontifical UniversityAlberto Aguilera 2328015 MadridSpain

stability in unbalanced power systems has deserved little attention in the *** the importance of this scenario in distribution systems with distributed generation,this paper revisits modal analysis techniques for stability studies in power systems,and explains how to tackle unbalanced power systems with voltage-dependent *** procedure is described in detail and applied to a low-voltage(LV)simple case study with two grid-forming electronic power converters and unbalanced *** are then compared with those obtained with the popular impedance-based *** the latter is easier to implement using simulation or field data,the former requires complete information of the system,but gives a better insight into the *** both methods are based on a small-signal approximation of the system,they provide similar results,but they discern different information.A larger second case study based on an LV CIGRE distribution system is also *** are obtained using a detailed simulink model of the microgrids with electronic power converters.

关键词： stability microgrid modal analysis impedancebased method unbalanced distribution system

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Late Miocene/Early Pliocene vertebrate fauna from Mallorca(Balearic Islands,Western Mediterranean):an update

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Integrative Zoology 2014年第2期9卷 183-196页

作者： pere BOVER Juan ROFEs salvador BAILON Jordi AGUsTÍ Gloria CUENCA-BEsCÓs Enric TORREs Josep Antoni ALCOVER IMEDEA(CsIC-UIB) Mediterranean Institute for Advanced StudiesDepartment of Biodiversity and ConservationBalearic IslandsSpain Research Associate Division of Vertebrate Zoology/Mammalogy Department American Museum of Natural HistoryNew YorkNYUSA Department of stratigraphy and Paleontology University of the Basque CountryLeioaSpain Grupo aragosaurus-IUCA Area of PaleontologíaEarth Sciences DepartmentUniversity of ZaragozaZaragozaSpain UMR 7209-7194 of CNRs Department of Ecology and Biodiversity ManagementNational Museum of Natural HistoryParisFrance ICREA Institut Catalàde Paleoecologia Humana i EvolucióSocial(IPHES)Universitat Rovira i VirgiliTarragonaSpain

The vertebrate fossil record from the Balearic Islands(western Mediterranean)has improved considerably over the past decade,especially in Mallorca and *** Menorca,the Pliocene terrestrial fauna was updated by the discovery and description of the large-sized leporid Nuralagus,several reptiles and an *** Mal-lorca,paleontological exploration yielded 2 deposits with a Late Miocene/Early Pliocene chronology,Calóden Rafelino(CdR)and Na Burguesa-1(NB-1).so far,4 new mammalian taxa and 2 new reptiles have been iden-tified for the CdR deposit,whereas the faunal assemblage from the recently discovered deposit(Apr 2012)of NB-1 is currently composed of,at least,6 terrestrial mammals,8 reptiles and an *** faunal composi-tion and some primitive characteristics of the obtained taxa suggest that the chronology of this deposit is slight-ly earlier than the *** terrestrial vertebrates recorded in these 2 Mallorcan deposits are changing the view of the paleofaunal assemblage previously known for the Plio-Pleistocene of the *** charac-teristics displayed by some of the taxa suggest that these faunas would be at the beginning of an isolated *** this paper we present a preliminary report on the fossils recovered from the NB-1 deposit,as well as some unpublished data from CdR,and we analyze the whole fauna from both Mallorcan deposits,focusing on taxonomical and paleobiogeographical aspects.

关键词： Early Pliocene Late Miocene Mallorca new fauna paleobiogeography

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