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Characterization and QTL identification in eggplant introgression lines under two N fertilization levels

Horticultural Plant Journal(园艺学报:英文版) 2023年第5期9卷 971-985页

作者： Elena Rosa-Martínez Gloria Villanueva Ahmet Sahin Pietro Gramazio María Dolores García-Martínez María Dolores Raig on Santiago Vilanova Jaime Prohens Mariola Plazas instituto de conservacion y mejora de la agrodiversidad valenciana Universitat Politecnica de ValenciaCamino de Vera 1446022 ValenciaSpain instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas-Universitat Politecnica de ValenciaCamino de Vera 1446022 ValenciaSpain

Lowering nitrogen inputs is a major goal for sustainable *** the present study,a set of 10 Solanum melongena introgression lines(ILs)developed using Solanum incanum as the exotic donor parent were grown under two nitrogen fertilization doses supplied with the irrigation system:1)8.25 mmol·L-1NH4NO3,corresponding to the high nitrogen treatment(HN),and 2)no external nitrogen supply,corresponding to the low nitrogen treatment(LN).Twenty traits,including plant growth and yield parameters,fruit size and morphology,nitrogen and carbon content in leaf and fruit,and phenolics content in fruit,were *** aim was to select of potential materials for eggplant breeding under low N inputs,as well as to identify and locate putative QTLs associated with the traits *** significant differences were observed between the soil characteristics of the HN and LN treatments,except for nitrogen and iron content,which was slightly lower in the HN,probably as a consequence of higher nutrient removal from soil by plants in the latter *** of variance showed that lowering nitrogen inputs did not significantly affect the final yield,fruit morphology,size and phenolics *** agronomic traits were highly and positively correlated with each other under both treatments,as well as total phenolics with chlorogenic acid *** assessment of the differences between each IL and the recipient parent resulted in the identification of 36 QTLs associated with most of the traits—12 were specific to the HN,17 specific to the LN,and 7 were stable across *** introgressed fragment of *** generally had a negative effect on the trait,except for QTLs for fruit dry matter,for fruit length on chromosome 10 under the HN,and for fruit pedicel length on chromosome 9 under the *** increase over AN-S-26 of the allele of *** for the QTLs detected ranged between-73.98% and 26.03% in HN and-73.67%and 34.43% in *** findings provide useful tools fo

关键词： Solanum melongena Solanum incanum Wild relatives N fertilization Abiotic stress QTL

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Evaluation of three sets of advanced backcrosses of eggplant with wild relatives from different gene pools under low N fertilization conditions

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Horticulture Research 2023年第8期10卷 295-309页

作者： Gloria Villanueva Mariola Plazas Pietro Gramazio Reyes D.Moya Jaime Prohens Santiago Vilanova instituto de conservación y mejora de la agrodiversidad valenciana Universitat Politècnica de ValènciaCamino de Vera 1446022ValenciaSpain

The development of new cultivars with improved nitrogen use efficiency(NUE)is key for implementing sustainable agriculture *** wild relatives(CWRs)provide valuable genetic resources for breeding programs aimed at achieving this *** this study,three eggplant(Solanum melongena)accessions together with their advanced backcrosses(ABs;BC3 to BC5 generations)were evaluated for 22 morpho-agronomic,physiological,and NUE traits under low nitrogen(LN)fertilization *** ABs were developed with introgressions from the wild relatives Solanum insanum,Solanum dasyphyllum,and Solanum *** AB population comprised a total of 25,59,and 59 genotypes,respectively,with overall donor wild relative genome coverage percentages of 58.8%,46.3%,and 99.2%.The three *** recurrent parents were also evaluated under control(normal)N *** of N fertilization in the parents resulted in decreased chlorophyll content-related traits,aerial biomass,stem diameter,and yield and increased NUE,nitrogen uptake efficiency(NUpE),and nitrogen utilization efficiency(NUtE).However,the decrease in yield was moderate,ranging between 62.6%and 72.6%.A high phenotypic variation was observed within each of the three sets of ABs under LN conditions,with some individuals displaying improved transgressive characteristics over the recurrent *** the single primer enrichment technology 5 k probes platform for high-throughput genotyping,we observed a variable but high degree of recurrent parent genome recovery in the ABs attributable to the lines recombination,allowing the successful identification of 16 quantitative trait loci(QTL).Different allelic effects were observed for the introgressed QTL *** candidate genes were identified in the QTL regions associated with plant growth,yield,fruit size,and NUE-related *** results show that eggplant materials with introgressions from CWRs can result in a dramatic impact in eggplant breedi

关键词： breeding cultivar fertilization

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A review on re-emerging bacteriophage therapy in the era of XDR

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生物细胞(英文) 2023年第9期47卷 1915-1930页

作者： POOJA BHADORIYA RICHA SHARMA REKHA MEHROTRA SIMRAN KAUR ISHA SRIVASTAVA MUKUL JAIN PRASHANT KAUSHIK department of Microbiology Shaheed Rajguru College of Applied Sciences for WomenUniversity of DelhiVasundhara EnclaveNew Delhi110096India lab-209 Cell&Developmental biology labCenter of Research for DevelopmentParul UniversityVadodara391760GujaratIndia instituto de conservacióny mejora de la agrodiversidad valenciana Universitat Politècnica de ValènciaValencia46022Spain

In the present medicine world antibiotic resistance is one of the key threats to universal health *** continue to work hard to combat this global health *** therapy,an age-old practice during the early twentieth century,was outshined by the discovery of *** the advent of widespread antibiotic resistance,phage therapy has again redeemed itself as a potential alternative owing to its adeptness to target bacteria *** side effects,the ability to migrate to different body organs,a distinct mode of action,and proliferation at the infection site,make phages a profitable candidate to replace conventional *** progressive outcome of numerous in vitro studies and case reports has validated the clinical efficacy of phage *** bright perspective of using phages to treat bacterial infections has fueled enormous medical research to exploit their potential as *** gaps in the information about phages and the lack of consent for clinical trials is major hurdle for consideration of phage *** phage therapy as a reality in medicine requires a coordinated effort from different *** this review,we aim to emphasize the importance of phage therapy in modern *** review explains their historical journey,basic phage biology,cross-talk with the host immunity,obstacles with phage therapy,and their possible *** data on the various significant clinical trials of phage therapy has been *** evaluated the efficacy of antibiotics and phage therapy in part and in combination,along with recent progress and future perspectives of phage therapy.

关键词： Bacteriophages Antibiotic resistance Phage biology Phage therapy Phage therapy clinical trials Phage therapy in India

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ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean‘da serbo’type long shelf-life germplasm

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Horticulture Research 2020年第1期7卷 1047-1060页

作者： Salvatore Esposito Teodoro Cardi Gabriele Campanelli Sara Sestili María JoséDíez Salvador Soler Jaime Prohens Pasquale Tripodi CREA Research Centre for Vegetable and Ornamental Crops Pontecagnano(SA)Italy CREA Research Centre for Vegetable and Ornamental Crops Monsampolo del Tronto(AP)TrontoItaly instituto de conservación y mejora de la agrodiversidad valenciana Universitat Politècnica de València46022 ValenciaSpain

Double digest restriction-site associated sequencing(ddRAD-seq)is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm *** this methodology,we investigated the genomic diversity of a panel of 288 diverse tomato(Solanum lycopersicum L.)accessions enriched in‘da serbo’(called‘de penjar’in Spain)long shelf life(LSL)materials(152 accessions)mostly originating from Italy and *** rest of the materials originate from different countries and include landraces for fresh consumption,elite cultivars,heirlooms,and breeding *** from their LSL trait,‘da serbo’landraces are of remarkable interest for their *** identified 32,799 high-quality SNPs,which were used for model ancestry population structure and non-parametric hierarchical *** genetic subgroups were revealed,clearly separating most‘da serbo’landraces,but also the Spanish germplasm,suggesting a subdivision of the population based on type and geographical *** disequilibrium(LD)in the collection decayed very rapidly withindentification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such as CTR1 and ***,a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key *** findings suggest the presence of a genetic footprint of the‘da serbo’germplasm selected in the Mediterranean ***,we provide novel insights on LSL‘da serbo’germplasm as a promising source of alleles for tolerance to stresses.

关键词： germplasm breeding shelf

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Characteristics and in-hospital mortality of elderly patients with heart failure in Spanish hospitals

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Journal of Geriatric Cardiology 2023年第4期20卷 247-255页

作者： Alberto Esteban-Fernández Manuel Anguita-Sánchez Juan Luis Bonilla-Palomas María Anguita-Gámez María García JoséLuis Bernal Náyade del Prado Cristina Fernández-Pérez Julián Pérez-Villacastin Juan JoséGómez-Doblas Francisco Javier Elola Cardiology department Hospital Universitario Severo OchoaMadridSpain Cardiology department Hospital Universitario Reina SofíaCórdobaSpain Cardiology department Hospital San Juan de la CruzÚbedaSpain Cardiology department Hospital Clínico San CarlosMadridSpain Fundación instituto para la mejora de la Asistencia Sanitaria MadridSpain Management Control department Hospital Universitario 12 de OctubreMadridSpain department of Preventive Medicine Área Sanitaria de Santiago de Compostela y BarbanzaInstituto de Investigación de SantiagoSantiago de CompostelaSpain Cardiology department Hospital Universitario Virgen de la VictoriaMálagaSpain

BACKGROUND The prevalence of heart failure(HF)increases with age,and it is one of the leading causes of hospitalization and death in older ***,there are little data on in-hospital mortality in patients with HF≥75 years in *** A retrospective analysis of the Spanish Minimum Basic Data Set was performed,including all HF episodes discharged from public hospitals in Spain between 2016 and *** was performed using the International Classification of Diseases,10th ***≥75 years with HF as the principal diagnosis were *** calculated:(1)the crude in-hospital mortality rate and its distribution according to age and sex;(2)the risk-standardized in-hospital mortality ratio;and(3)the association between in-hospital mortality and the availability of an intensive cardiac care unit(ICCU)in the *** We included 354,792 HF episodes of patients over 75 *** mean age was 85.2±5.5 years,and 59.2%of patients were *** most frequent comorbidities were renal failure(46.1%),diabetes mellitus(35.5%),valvular disease(33.9%),cardiorespiratory failure(29.8%),and hypertension(26.9%).In-hospital mortality was 12.7%,and increased with age[odds ratio(OR)=1.07,95%CI:1.07–1.07,Pded to be lower(OR=0.85,95%CI:0.72–1.00,P=0.053).CONCLUSIONS In-hospital mortality in patients with HF≥75 years between 2016 and 2019 was 12.7%,higher in males and elderly *** main predictors of mortality were cardiogenic shock,stroke,and advanced *** was a trend toward lower mortality in centers with an ICCU.

关键词： patients mortality diagnosis

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Exploiting the diversity of tomato:the development of a phenotypically and genetically detailed germplasm collection

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Horticulture Research 2020年第1期7卷 1941-1954页

作者： Estefanía Mata-Nicolás Javier Montero-Pau Esther Gimeno-Paez Víctor Garcia-Carpintero Peio Ziarsolo Naama Menda Lukas A.Mueller JoséBlanca Joaquín Cañizares Esther van der Knaap María JoséDíez instituto Universitario de conservación y mejora de la agrodiversidad valenciana.COMAV.Universitat Politècnica de València ValenciaSpain department of Biochemistry and Molecular Biology Universitat de ValènciaValenciaSpain Boyce Thompson Institute IthacaNYUSA Institute of Plant Breeding Genetics and GenomicsUniversity of GeorgiaGeorgiaGAUSA department of Horticulture University of GeorgiaGeorgiaGAUSA

A collection of 163 accessions,including Solanum pimpinellifolium,Solanum lycopersicum *** and Solanum lycopersicum ***,was selected to represent the genetic and morphological variability of tomato at its centers of origin and domestication:Andean regions of Peru and Ecuador and *** collection is enriched with *** *** from the Amazonian region that has not been analyzed previously nor used *** collection has been morphologically characterized showing diversity for fruit,flower and vegetative *** genomes were sequenced in the Varitome project and are publicly available(***/projects/varitome).The identified SNPs have been annotated with respect to their impact and a total number of 37,974 out of 19,364,146 SNPs have been described as high impact by the SnpEeff *** has shown associations for different traits,demonstrating the potential of this collection for this kind of *** have not only identified known QTLs and genes,but also new regions associated with traits such as fruit color,number of flowers per inflorescence or inflorescence *** speed up and facilitate the use of this information,F2 populations were constructed by crossing the whole collection with three different *** F2 collection is useful for testing SNPs identified by GWAs,selection sweeps or any other candidate *** data is available on Solanaceae Genomics Network and the accession and F2 seeds are freely available at COMAV and at TGRC *** these resources together make this collection a good candidate for genetic studies.

关键词： germplasm collection traits

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Genetic diversity,population structure,and relationships in a collection of pepper(Capsicum spp.)landraces from the Spanish centre of diversity revealed by genotypingby-sequencing(GBS)

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Horticulture Research 2019年第1期6卷 1030-1042页

作者： Leandro Pereira-Dias Santiago Vilanova Ana Fita Jaime Prohens Adrián Rodríguez-Burruezo instituto de conservación y mejora de la agrodiversidad valenciana Universitat Politècnica de València46022 ValenciaSpain

Pepper(Capsicum spp.)is one of the most important vegetable crops;however,pepper genomic studies lag behind those of other important *** we present the results of a high-throughput genotyping-by-sequencing(GBS)study of a collection of 190 Capsicum ***,including 183 of five cultivated species(***,***,***,***,and ***)and seven of the wild form *** *** generated 6,766,231 high-quality read tags,of which 40.7%were successfully aligned to the reference *** calling yielded 4083 highly informative segregating *** diversity and relationships of a subset of 148 accessions,of which a complete passport information was available,was studied using principal components analysis(PCA),discriminant analysis of principal components(DAPC),and phylogeny ***,***,and *** were successfully separated by all *** population was divided into seven clusters by DAPC,where *** accessions were clustered together with *** *** accessions were spread into two distinct genetic pools,while European accessions were admixed and closely *** of accessions was mainly associated to differences in fruit characteristics and *** studies showed a close relation between Spanish and Mexican accessions,supporting the hypothesis that the first arose from a main genetic flow from the ***’s D statistic values were consistent with positive selection in the *** clusters,possibly related to domestication or selection towards traits of *** work provides comprehensive and relevant information on the origin and relationships of Spanish landraces and for future association mapping studies in pepper.

关键词： crops pepper GBS

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Morphoagronomic characterization and wholegenome resequencing of eight highly diverse wild and weedy *** and *** *** accessions used for the first interspecific tomato MAGIC population

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Horticulture Research 2020年第1期7卷 477-492页

作者： Pietro Gramazio Leandro Pereira-Dias Santiago Vilanova Jaime Prohens Salvador Soler Javier Esteras Alfonso Garmendia María JoséDíez Faculty of Life and Environmental Sciences University of Tsukuba1-1-1 Tennodai305-8572 TsukubaJapan instituto de conservación y mejora de la agrodiversidad valenciana Universitat Politècnica de ValènciaCamino de Vera 1446022 ValenciaSpain departamento de Ecosistemas Agroforestales Universitat Politècnica de ValènciaCamino de Vera 1446022 ValenciaSpain instituto Agroforestal Mediterráneo Universitat Politècnica de ValènciaCamino de Vera 1446022 ValenciaSpain

The wild Solanum pimpinellifolium(SP)and the weedy *** ***(SLC)are largely unexploited genetic reservoirs easily accessible to breeders,as they are fully cross-compatible with cultivated tomato(*** ***).We performed a comprehensive morphological and genomic characterization of four wild SP and four weedy SLC accessions,selected to maximize the range of variation of both *** eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross(MAGIC)*** morphoagronomic characterization was carried out with 39 descriptors to assess plant,inflorescence,fruit and agronomic traits,revealing the broad range of diversity *** of the morphological variation observed in SP was likely associated to the adaptation of the accessions to different environments,while in the case of SLC to both human activity and adaptation to the ***-genome resequencing of the eight accessions revealed over 12 million variants,ranging from 1.2 to 1.9 million variants in SLC and from 3.1 to 4.8 million in SP,being 46.3%of them(4,897,803)private *** genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of *** was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two *** functional characterization of the variants revealed a significative enrichment of GO terms related to changes in cell walls that would have been negatively selected during domestication and *** comprehensive morphoagronomic and genetic characterization of these accessions will be of great relevance for the genetic analysis of the first interspecific MAGIC population of tomato and provides valuable knowledge and tools to the tomato community for genetic and genomic studies and for breeding purposes.

关键词： agronomic breeding MAGIC

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Global longitudinal strain is superior to ejection fraction for detecting myocardial dysfunction in end-stage renal disease with hyperparathyroidism

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World Journal of Cardiology 2022年第4期14卷 239-249页

作者： Maria Fernanda Carrasco-Ruiz Antonio Ruiz-Rivera Marvin A Soriano-Ursúa Carlos Martinez-Hernandez Leticia Manuel-Apolinar Carmen Castillo-Hernandez Gustavo Guevara-Balcazar Eunice D Farfán-García Ana Mejia-Ruiz Ivan Rubio-Gayosso Teresa Perez-Capistran department of Physiology Escuela Superior de MedicinaInstituto Politécnico NacionalCiudad de México 11340Mexico department of Cardiology Instituto Mexicano del Seguro SocialCiudad de México 06720Mexico Endocrine Research Unit Instituto Mexicano del Seguro SocialCiudad de México 06720Mexico department of Cardiovascular Pharmacology Instituto Politécnico NacionalCiudad de México 11340Mexico department of Biochemistry Escuela Superior de MedicinaInstituto Politécnico NacionalCiudad de México 11340Mexico Education Research Comisión Nacional Para la Mejora Continua de la EducaciónCiudad de México 03900Mexico Postgraduate Studies and Research Section Escuela Superior de MedicinaInstituto Politécnico NacionalCiudad de México 11340Mexico department of Physiology Instituto Politécnico NacionalMexico City 11340Ciudad de MéxicoMexico

BACKGROUND The estimation of left ventricular ejection fraction(LVEF)by 2D echocardiography(2D-ECHO)is the most used tool to assess LV systolic function(LVSF).Global longitudinal strain(GLS)has recently been suggested as a superior method for several *** study explored the association and prevalence of LV systolic dysfunction(LVSD)by using these methods in patients with end-stage renal disease(ESRD)and severe hyperparathyroidism(SHPTH);both associated with cardiovascular events(CEs).AIM To evaluate the myocardial function in patients with ESRD and SHPTH by using the GLS and LVEF measured through conventional *** In 62 patients with ESRD and SHPTH,asymptomatic,and without a history of CEs,LVSF was evaluated by 2D-ECHO,obtaining the EF,by the Simpson biplane method,and GLS by speckle *** The total patients with ESRD had a preserved LVEF(>50%)but abnormal GLS(dependent association of GLS and serum parathyroid hormone(PTH),LV mass index,and ***,PTH was independently associated with lateral e'wave and tricuspid regurgitation *** In patients with SHPTH linked to ESRD,the use of GLS by 2D-ECHO is a more sensitive tool than LVEF for detecting LVSD.

关键词： Left ventricular hypertrophy Systolic dysfunction Global longitudinal strain End-stage renal disease Parathormone

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Evaluating the potential of(epi)genotype‑by‑low pass nanopore sequencing in dairy cattle:a study on direct genomic value and methylation analysis

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Journal of Animal Science and Biotechnology 2023年第6期14卷 2276-2289页

作者： Oscar Gonzalez‑Recio Adrian Lopez‑Catalina Ramon Peiro‑Pastor Alicia Nieto‑Valle Monica Castro Almudena Fernandez Dpt.mejora Genetica Animal INIA-CSICCtra La Coruna Km 7.528040 MadridSpain. ETSIAAB Universidad Politecnica de Madrid.Ciudad Universitaria S/N28040 MadridSpain.

Background Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the *** requires a low sequencing depth to be cost effective,which may increase the error at the genotype *** generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation,which provides added value to *** aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle,and the possibility to obtain methylation marks *** latest nanopore chemistry(LSK14 and Q20)achieved a modal base calling accuracy of 99.55%,whereas previous kit(LSK109)achieved slightly lower accuracy(99.1%).The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99,depending on the trait(milk,fat or protein yield),with a sequencing depth as low as 2×and using the latest chemistry(LSK114).Lower sequencing depth led to biased estimates,yet with high rank *** LSK109 and Q20 achieved lower accuracies(0.57-0.93).More than one million high reliable methylated sites were obtained,even at low sequencing depth,located mainly in distal intergenic(87%)and promoter(5%)*** This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high *** may provide advantages in populations with no available SNP chip,or when a large density of markers with a wide range of allele frequencies is *** addition,low pass sequencing provided nucleotide methylation status of>1 million nucleotides at≥10×,which is an added value for epigenetic studies.

关键词： Genomic selection Genomic values Low pass sequencing Low sequencing imputation Polygenic risk score

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