184 results on '"Rossini, Laura"'
Search Results
152. Additional file 21: Table S5. of Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch)
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Cirilli, Marco, Rossini, Laura, Geuna, Filippo, Palmisano, Francesco, Angelantonio Minafra, Castrignanò, Tiziana, Gattolin, Stefano, Ciacciulli, Angelo, Babini, Anna, Liverani, Alessandro, and Bassi, Daniele
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3. Good health - Abstract
List of primers used in this study. (DOCX 8 kb)
153. Integrative genomics approaches validate <italic>PpYUC11-like</italic> as candidate gene for the stony hard trait in peach (<italic>P. persica</italic> L. Batsch).
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Cirilli, Marco, Ciacciulli, Angelo, Chiozzotto, Remo, Rossini, Laura, Bassi, Daniele, Giovannini, Daniela, Liverani, Alessandro, and Gattolin, Stefano
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FRUIT quality ,PEACH ,INDOLEACETIC acid ,GENOMICS ,TRANSCRIPTOMES ,NUCLEOTIDE sequencing ,FRUIT ripening - Abstract
Background: Texture is one of the most important fruit quality attributes. In peach, stony hard (SH) is a recessive monogenic trait (
hd/hd ) that confers exceptionally prolonged firm flesh to fully ripe fruit. Previous studies have shown that the SH mutation affects the fruit ability to synthesize appropriate amounts of indol-3-acetic acid (IAA), which orchestrates the ripening processes through the activation of system 2 ethylene pathway. Allelic variation in a TC microsatellite located within the first intron ofPpYUC11-like (a YUCCA-like auxin-biosynthesis gene) has been recently proposed as the causal mutation of the SH phenotype. Results: The simple genetic determinism of the SH trait has been clarified through genome-wide association and LD analyses in a diverse set of accessions, restricting thehd locus to an interval of about 1.8 Mbp in chromosome 6. The comparison of fruit transcriptome data from non-SH (melting flesh) and SH accessions provided an expression patterns overview of the annotated transcripts within thehd locus, confirming the absence ofPpYUC11-like expression in SH fruits. To explore further possible associations between genomic variants at thehd locus and the SH phenotype, re-sequencing data of the SH accession 'D41–62' were compared with several SH and non-SH accessions with different genetic backgrounds. A further step of validation was provided through the evaluation of variant-trait association in two bi-parental F2 populations issued from the SH accession 'D41–62' and a panel of advanced breeding selections, showing perfect co-segregation of thePpYUC11-like intron TC20 allele and the SH phenotype. Conclusions: In this study, we provide a multi-level validation of the genetic control of the SH trait through the integration of genome-wide association mapping, transcriptome analysis and whole-genome resequencing data for SH and non-SH accessions, and marker-trait association in a panel of advanced breeding selections and segregating progenies. Collectively, our data confirm with high confidence the role of allelic variation atPpYUC11-like locus as the genetic determinant of the SH trait, opening interesting perspectives at both biological and applied research level. [ABSTRACT FROM AUTHOR]- Published
- 2018
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154. Genetic dissection of fruit maturity date in apricot (P. armeniaca L.) through a Single Primer Enrichment Technology (SPET) approach.
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Baccichet, Irina, Chiozzotto, Remo, Scaglione, Davide, Bassi, Daniele, Rossini, Laura, and Cirilli, Marco
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APRICOT , *DATES (Fruit) , *FRUIT trees , *PHENOTYPIC plasticity , *NUCLEOTIDE sequencing , *MISSING data (Statistics) - Abstract
Background: Single primer enrichment technology (SPET) is an emerging and increasingly popular solution for high-throughput targeted genotyping in plants. Although SPET requires a priori identification of polymorphisms for probe design, this technology has potentially higher reproducibility and transferability compared to other reduced representation sequencing (RRS) approaches, also enabling the discovery of closely linked polymorphisms surrounding the target one. Results: The potential for SPET application in fruit trees was evaluated by developing a 25K target SNPs assay to genotype a panel of apricot accessions and progenies. A total of 32,492 polymorphic sites were genotyped in 128 accessions (including 8,188 accessory non-target SNPs) with extremely low levels of missing data and a significant correlation of allelic frequencies compared to whole-genome sequencing data used for array design. Assay performance was further validated by estimating genotyping errors in two biparental progenies, resulting in an overall 1.8% rate. SPET genotyping data were used to infer population structure and to dissect the architecture of fruit maturity date (MD), a quantitative reproductive phenological trait of great agronomical interest in apricot species. Depending on the year, GWAS revealed loci associated to MD on several chromosomes. The QTLs on chromosomes 1 and 4 (the latter explaining most of the phenotypic variability in the panel) were the most consistent over years and were further confirmed by linkage mapping in two segregating progenies. Conclusions: Besides the utility for marker assisted selection and for paving the way to in-depth studies to clarify the molecular bases of MD trait variation in apricot, the results provide an overview of the performance and reliability of SPET for fruit tree genetics. [ABSTRACT FROM AUTHOR]
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- 2022
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155. A semi-automatic registration protocol to match ex-vivo high-field 7T MR images and histological slices in surgical samples from patients with drug-resistant epilepsy.
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Aquino, Domenico, Garbelli, Rita, Rossini, Laura, De Santis, Dalia, Spreafico, Roberto, d'Orio, Piergiorgio, Tassi, Laura, and Padelli, Francesco
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MAGNETIC resonance imaging , *PEOPLE with epilepsy , *BLAND-Altman plot , *EPILEPSY , *RIGID bodies , *RECORDING & registration , *INTRAVASCULAR ultrasonography , *PEDIATRIC surgery - Abstract
MRI is a fundamental tool to detect brain structural anomalies and improvement in this technique has the potential to visualize subtle abnormalities currently undetected. Correlation between pre-operative MRI and histopathology is required to validate the neurobiological basis of MRI abnormalities. However, precise MRI-histology matching is very challenging with the surgical samples. We previously developed a coregistration protocol to match the in-vivo MRI with ex-vivo MRI obtained from surgical specimens. Now, we complete the process to successfully align ex-vivo MRI data with the proper digitalized histological sections in an automatic way. The implemented pipeline is composed by the following steps: a) image pre-processing made of MRI and histology volumes conversion and masking; b) gross rigid body alignment between MRI volume and histology virtual slides; c) rigid alignment between each MRI section and histology slice and estimate of the correlation coefficient for each step to select the MRI slice that best matches histology; d) final linear registration of the selected slices. This method is fully automatic, except for the first masking step, fast and reliable in comparison to the manual one, as assessed using a Bland-Altman plot. The visual assessment usually employed for choosing the best fitting ex-vivo MRI slice for each stained section takes hours and requires practice. Goubran et al. (2015) proposed an iterative registration protocol but its aim and methods were different from ours. No others similar methods are reported in the literature. This protocol completes our previous pipeline. The ultimate goal will be to apply the entire process to finely investigate the relationship between clinical MRI data and histopathological features in patients with drug-resistant epilepsy. • MRI-histology coregistration might improve the in-vivo MRI lesion detection. • This coregistration is very challenging with post-surgical samples. • Ex-vivo MRI of the sample is a useful step between histology and in-vivo MRI. • We develop a pipeline to align ex-vivo MRI with digitalized histological sections. • This protocol, coupled with in-vivo / ex-vivo MRI registration, completes the process. [ABSTRACT FROM AUTHOR]
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- 2022
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156. Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions.
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Khahani, Bahman, Tavakol, Elahe, Shariati, Vahid, and Rossini, Laura
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RICE yields , *LOCUS in plant genetics , *PLANT genetics , *PLANT breeders , *PLANT water requirements - Abstract
Meta-QTL (MQTL) analysis is a robust approach for genetic dissection of complex quantitative traits. Rice varieties adapted to non-flooded cultivation are highly desirable in breeding programs due to the water deficit global problem. In order to identify stable QTLs for major agronomic traits under water deficit conditions, we performed a comprehensive MQTL analysis on 563 QTLs from 67 rice populations published from 2001 to 2019. Yield and yield-related traits including grain weight, heading date, plant height, tiller number as well as root architecture-related traits including root dry weight, root length, root number, root thickness, the ratio of deep rooting and plant water content under water deficit condition were investigated. A total of 61 stable MQTLs over different genetic backgrounds and environments were identified. The average confidence interval of MQTLs was considerably refined compared to the initial QTLs, resulted in the identification of some well-known functionally characterized genes and several putative novel CGs for investigated traits. Ortho-MQTL mining based on genomic collinearity between rice and maize allowed identification of five ortho-MQTLs between these two cereals. The results can help breeders to improve yield under water deficit conditions. [ABSTRACT FROM AUTHOR]
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- 2021
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157. The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity.
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Verde, Ignazio, Jenkins, Jerry, Dondini, Luca, Micali, Sabrina, Pagliarani, Giulia, Vendramin, Elisa, Paris, Roberta, Aramini, Valeria, Gazza, Laura, Rossini, Laura, Bassi, Daniele, Troggio, Michela, Shu, Shengqiang, Grimwood, Jane, Tartarini, Stefano, Dettori, Maria Teresa, and Schmutz, Jeremy
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PRUNUS , *HORTICULTURE , *CHROMOSOMES , *GENOMES , *NUCLEOTIDE sequencing - Abstract
Background: The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. Results: Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. Conclusions: The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes. [ABSTRACT FROM AUTHOR]
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- 2017
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158. Genetic dissection of heading date and yield under Mediterranean dry climate in barley ( Hordeum vulgare L.).
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Tavakol, Elahe, Elbadry, Nader, Tondelli, Alessandro, Cattivelli, Luigi, and Rossini, Laura
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BARLEY yields , *DROUGHT tolerance , *PLANT breeders , *CLIMATE change , *MEDITERRANEAN climate - Abstract
Understanding the genetics of drought tolerance is a major goal of plant breeders, especially in the Mediterranean region due to its sensitivity to drought and climate changes. Here we investigated genomic regions associated with heading date and yield under rainfed (R) and irrigated (I) conditions, along with some drought tolerance indices derived from phenotypic data collected on a panel of 83 European barley cultivars evaluated in field trials in Foggia, southern Italy, for three growing seasons. A genome wide association analysis (GWAS) was carried out using gene-based SNPs incorporated in the Illumina iSELECT Chip with known map position. A total of 4169 polymorphic SNPs were considered after filtering out SNPs with >10 % missing data and <10 % minimum allele frequency. Heritability was high for heading date and moderate for yield. Principle components analysis partitioned the barley germplasm in three subgroups characterized by different row-type and growth habit. A significant association with heading date was detected on chromosome 2HS, where the different alleles of associated markers were able to significantly affect heading date in different cultivars. Moreover, GWAS uncovered a significant association with yield and relative yield under R conditions on chromosome 5HS. These results provide a clue for further analysis on genetic control of barley flowering time and production in response to water stress under Mediterranean dry climate. [ABSTRACT FROM AUTHOR]
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- 2016
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159. Photoperiod-H1 (Ppd-H1) Controls Leaf Size.
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Digel, Benedikt, Tavakol, Elahe, Verderio, Gabriele, Tondelli, Alessandro, Xin Xu, Cattivelli, Luigi, Rossini, Laura, and von Korff, Maria
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Leaf size is a major determinant of plant photosynthetic activity and biomass; however, it is poorly understood how leaf size is genetically controlled in cereal crop plants like barley (Hordeum vulgare). We conducted a genome-wide association scan for flowering time, leaf width, and leaf length in a diverse panel of European winter cultivars grown in the field and genotyped with a single-nucleotide polymorphism array. The genome-wide association scan identified PHOTOPERIOD-H1 (Ppd-H1) as a candidate gene underlying the major quantitative trait loci for flowering time and leaf size in the barley population. Microscopic phenotyping of three independent introgression lines confirmed the effect of Ppd-H1 on leaf size. Differences in the duration of leaf growth and consequent variation in leaf cell number were responsible for the leaf size differences between the Ppd-H1 variants. The Ppd-H1-dependent induction of the BARLEY MADS BOX genes BM3 and BM8 in the leaf correlated with reductions in leaf size and leaf number. Our results indicate that leaf size is controlled by the Ppd-H1- and photoperiod-dependent progression of plant development. The coordination of leaf growth with flowering may be part of a reproductive strategy to optimize resource allocation to the developing inflorescences and seeds. [ABSTRACT FROM AUTHOR]
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- 2016
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160. The barley mutant happy under the sun 1 (hus1): An additional contribution to pale green crops.
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Rotasperti, Lisa, Tadini, Luca, Chiara, Matteo, Crosatti, Cristina, Guerra, Davide, Tagliani, Andrea, Forlani, Sara, Ezquer, Ignacio, Horner, David S., Jahns, Peter, Gajek, Katarzyna, García, Addy, Savin, Roxana, Rossini, Laura, Tondelli, Alessandro, Janiak, Agnieszka, and Pesaresi, Paolo
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CLIMATE change mitigation , *CROPS , *BIOMASS production , *PLANT performance , *GRAIN yields , *BARLEY - Abstract
Truncated antenna size of photosystems and lower leaf chlorophyll content has been shown to increase photosynthetic efficiency and biomass accumulation in microalgae, cyanobacteria and higher plants grown under high-density cultivation conditions. Here, we have asked whether this strategy is also applicable to a major crop by characterizing the barley mutant happy under the sun 1 (hus1). The pale green phenotype of hus1 is due to a 50% reduction in the chlorophyll content of leaves, owing to a premature stop codon in the HvcpSRP43 gene for the 43-kDa chloroplast Signal Recognition Particle (cpSRP43). The Hv cpSRP43 protein is responsible for the uploading of photosystem antenna proteins into the thylakoid membranes, and its truncation results in a smaller photosystem antenna size. Besides a detailed molecular and physiological characterization of the mutant grown under controlled greenhouse conditions, we show that the agronomic performance of hus1 plants, in terms of total biomass production and grain yield under standard field conditions, is comparable to that of control plants. The results are discussed in terms of the potential benefits of the hus1 phenotype, and of natural allelic variants of the HvcpSRP43 locus, with respect to productivity and mitigation of climate change. • The hus1 barley mutant is characterized by a 50% reduction of leaf chlorophyll content; • The chlorophyll reduction is caused by a premature stop codon in the HvcpSRP43 gene; • The mutation is responsible for the reduced accumulation of photosystem antenna proteins; • The leaf pale green phenotype does not impair photosynthesis under field conditions. [ABSTRACT FROM AUTHOR]
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- 2022
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161. Saturating the Prunus (stone fruits) genome with candidate genes for fruit quality.
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Illa, Eudald, Eduardo, Iban, Audergon, Jean, Barale, Francesca, Dirlewanger, Elisabeth, Li, Xiongwei, Moing, Annick, Lambert, Patrick, Dantec, Loick, Gao, Zhongshan, Poëssel, Jean-Luc, Pozzi, Carlo, Rossini, Laura, Vecchietti, Alberto, Arús, Pere, and Howad, Werner
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PRUNUS , *FRUIT quality , *PLANT genetics , *GENE expression in plants , *LOCUS (Genetics) , *GENETIC polymorphisms , *GENE mapping - Abstract
To identify genes involved in the expression of a trait using the candidate gene (CG) approach, the genome positions of the maximum number of genes which potentially cause the observed phenotypic variability needs to be known. This position is compared with that of major genes or quantitative trait loci (QTL) for this character, with the co-location of the CG and major gene or QTL indicating a possible cause and effect relationship. In the present study we selected 273 sequences from expressed sequence tag collections, corresponding to CGs from metabolic pathways affecting fruit growth and maturity, texture, sugar and organic acid content, aroma and color, and mapped them in the Prunus reference map (T × E) based on an interspecific almond × peach F2 population. We used the bin-mapping approach, where only eight plants, six of the T × E progeny plus one of the parents and the F1 hybrid, are used to determine the position of a marker. This strategy was very efficient, with 206 CGs mapped, based mainly on the segregation of one or more single-nucleotide polymorphisms. These CGs were located throughout the Prunus genome and are a resource for genetic analysis in stone fruit (peach, plum, apricot and cherry) and almond. Co-locations between CGs and major genes or QTL responsible for natural variability of fruit quality characters in Prunus were identified using the available information on their positions. [ABSTRACT FROM AUTHOR]
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- 2011
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162. Cross Talk between the KNOX and Ethylene Pathways Is Mediated by Intron-Binding Transcription Factors in Barley.
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Osnato, Michela, Stile, Maria Rosaria, Yamei Wang, Meynard, Donaldo, Curiale, Serena, Guiderdoni, Emmanuel, Yongxiu Liu, Horner, David S., Ouwerkerk, Pieter B. F., Pozzi, Carlo, Müller, Kai J., Salamini, Francesco, and Rossini, Laura
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INTRONS , *TRANSCRIPTION factors , *NUCLEOTIDE sequence , *GENE expression , *ETHYLENE , *BARLEY - Abstract
In the barley (Hordeum vulgare) Hooded (Kap) mutant, the duplication of a 305-bp intron sequence leads to the overexpression of the Barley knox3 (Bkn3) gene, resulting in the development of an extra flower in the spikelet. We used a one-hybrid screen to identify four proteins that bind the intron-located regulatory element (Kap intron-binding proteins). Three of these, Barley Ethylene Response Factor1 (BERF1), Barley Ethylene Insensitive Like1 (BEIL1), and Barley Growth Regulating Factor1 (BGRF1), were characterized and their in vitro DNA-binding capacities verified. Given the homology of BERF1 and BEIL1 to ethylene signaling proteins, we investigated if these factors might play a dual role in intron-mediated regulation and ethylene response. In transgenic rice (Oryza sativa), constitutive expression of the corresponding genes produced phenotypic alterations consistent with perturbations in ethylene levels and variations in the expression of a key gene of ethylene biosynthesis. In barley, ethylene treatment results in partial suppression of the Kap phenotype, accompanied by up-regulation of BERF1 and BEILI expression, followed by down-regulation of Bkn3 mRNA levels. In rice protoplasts, BEIL1 activates the expression of a reporter gene driven by the 305-bp intron element, while BERF1 can counteract this activation. Thus, BEIL1 and BERF1, likely in association with other Kap intron-binding proteins, should mediate the fine-tuning of Bkn3 expression by ethylene. We propose a hypothesis for the cross talk between the KNOX and ethylene pathways. [ABSTRACT FROM AUTHOR]
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- 2010
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163. Integrated QTL detection for key breeding traits in multiple peach progenies
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Daniele Bassi, Sabrina Micali, José Antonio Campoy, Elisabeth Dirlewanger, François Laurens, Laura Rossini, Pere Arús, Nelson Nazzicari, Ignazio Verde, Celia M. Cantín, Patrick Lambert, Marco C. A. M. Bink, Thierry Pascal, Jose Ramon Hernandez Mora, Diego Micheletti, Andrea Caprera, Maria José Aranzana, Maria Teresa Dettori, Michela Troggio, Elisa Banchi, Bénédicte Quilot-Turion, Eric van de Weg, European Commission, Agencia Estatal de Investigación (España), Generalitat de Catalunya, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Institute of Research and Technology, Food and Agriculture (IRTA), Research and Innovation Centre, Edmund Mach Foundation (FEM), Technology & Services, Hendrix Genetics, Plant Breeding, Wageningen University and Research Center (WUR), Fruit CentreParc Cientific i Tecnològic Agroalimentari de Lleida (PCiTAL), Research Centre for Fodder Crops and Dairy Productions, Council for Agricultural Research and Economics (CREA), PTP Science Park, Centro di Ricerca per la Frutticoltura, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Institut National de la Recherche Agronomique (INRA), DiSAA, Università degli studi di Milano [Milano], Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Severo Ochoa Programme for Centres of Excellence in R&D' 2016–2019 (SEV-2015-0533)', project AGL2015-68329-R, CERCA Programme/Generalitat de Catalunya., European Project: 265582, Producció Vegetal, Fructicultura, Genòmica i Biotecnologia, Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Hernández Mora, José R, Micheletti, Diego, Bink, Marco, Van de Weg, Eric, Cantín, Celia, Nazzicari, Nelson, Caprera, Andrea, Dettori, Maria Teresa, Micali, Sabrina, Banchi, Elisa, Campoy, José Antonio, Dirlewanger, Elisabeth, Lambert, Patrick, Pascal, Thierry, Troggio, Michela, Bassi, Daniele, Rossini, Laura, Verde, Ignazio, Quilot Turion, Bénédicte, Laurens, Françoi, Arús, Pere, Aranzana, Maria José, Wageningen University and Research [Wageningen] (WUR), Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Génétique et Amélioration des Fruits et Légumes (GAFL), Università degli Studi di Milano [Milano] (UNIMI), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), and Università degli Studi di Milano = University of Milan (UNIMI)
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0106 biological sciences ,0301 basic medicine ,PBA ,variabilité génétique ,Breeding ,détection qtl ,01 natural sciences ,Prunus ,pédigrée ,fishery management ,genetic variability ,Cultivar ,Pedigre-based Analysis ,2. Zero hunger ,Genetics ,Vegetal Biology ,FlexQTLTM ,Peach QTL ,Peach breeding ,food and beverages ,PE&RC ,Settore AGR/07 - GENETICA AGRARIA ,génotype végétal ,Gene pool ,PBR Biodiversity and genetic variation ,FlexQTL ,Biotechnology ,Research Article ,lcsh:QH426-470 ,Genotype ,lcsh:Biotechnology ,Quantitative Trait Loci ,Flowers ,Biology ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,PBR Biodiversiteit en Genetische Variatie ,03 medical and health sciences ,lcsh:TP248.13-248.65 ,phase reproductrice ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Genetic variability ,Allele ,Selection (genetic algorithm) ,gestion des pêches ,Probability ,Prunus persica ,Heritability ,lcsh:Genetics ,030104 developmental biology ,Solubility ,pépinière fruitière ,Fruit ,EPS ,Biologie végétale ,010606 plant biology & botany - Abstract
[Background]: Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability., [Results]: Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value., [Conclusions]: The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality., This work has been funded under the EU seventh Framework Programme by the FruitBreedomics project Nu. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops. IRTA-CRAG group received financial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016–2019 (SEV-2015-0533)” and through the project AGL2015-68329-R, and from the CERCA Programme/Generalitat de Catalunya.
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- 2017
164. The Peach v2.0 release: High-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity
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Jeremy Schmutz, Sabrina Micali, Laura Rossini, Giulia Pagliarani, Shengqiang Shu, Jane Grimwood, Valeria Aramini, Michela Troggio, Daniele Bassi, Jerry Jenkins, Stefano Tartarini, Roberta Paris, Elisa Vendramin, Maria Teresa Dettori, Luca Dondini, Laura Gazza, Ignazio Verde, Verde, Ignazio, Jenkins, Jerry, Dondini, Luca, Micali, Sabrina, Pagliarani, Giulia, Vendramin, Elisa, Paris, Roberta, Aramini, Valeria, Gazza, Laura, Rossini, Laura, Bassi, Daniele, Troggio, Michela, Shu, Shengqiang, Grimwood, Jane, Tartarini, Stefano, Dettori, Maria Teresa, and Schmutz, Jeremy
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0301 basic medicine ,Genotyping Techniques ,Bioinformatics ,Genetic Linkage ,Sequence assembly ,SNP ,Gap patching ,Computational biology ,Biology ,Centromeric region ,Medical and Health Sciences ,Polymorphism, Single Nucleotide ,Genome ,Recombination rates ,03 medical and health sciences ,NGS resequencing ,Information and Computing Sciences ,WGS assembly ,Genetics ,Polymorphism ,Indel ,Recombination rate ,2. Zero hunger ,Whole genome sequencing ,Comparative genomics ,Prunus persica ,Genetic diversity ,Contig ,Shotgun sequencing ,Human Genome ,Chromosome Mapping ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Single Nucleotide ,Genomics ,Biological Sciences ,15. Life on land ,SSR ,Centromeric regions ,Settore AGR/07 - GENETICA AGRARIA ,SSRs ,030104 developmental biology ,Linkage mapping ,Generic health relevance ,Microsatellite Repeats ,Research Article ,SNPs ,Biotechnology - Abstract
Background The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. Results Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. Conclusions The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3606-9) contains supplementary material, which is available to authorized users.
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- 2017
165. The genetic basis of composite spike form in barley and ‘miracle-wheat’
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Gizaw M. Wolde, Nese Sreenivasulu, Twan Rutten, Carlo Pozzi, Thomas Nussbaumer, Takao Komatsuda, Piotr Gawroński, Ravi Koppolu, Abdulhamit Battal, Corinna Trautewig, Federica Bini, Tiziana Fusca, Tina Seidensticker, Laura Rossini, Geetha Govind, Helmy M. Youssef, Shun Sakuma, Stefano Ciannamea, Silvio Salvi, Akemi Tagiri, Andreas Börner, Roberto Tuberosa, Cristobal Uauy, Udda Lundqvist, Thorsten Schnurbusch, Naser Poursarebani, Poursarebani, Naser, Seidensticker, Tina, Koppolu, Ravi, Trautewig, Corinna, Gawroński, Piotr, Bini, Federica, Govind, Geetha, Rutten, Twan, Sakuma, Shun, Tagiri, Akemi, Wolde, Gizaw M., Youssef, Helmy M., Battal, Abdulhamit, Ciannamea, Stefano, Fusca, Tiziana, Nussbaumer, Thoma, Pozzi, Carlo, Börner, Andrea, Lundqvist, Udda, Komatsuda, Takao, Salvi, Silvio, Tuberosa, Roberto, Uauy, Cristobal, Sreenivasulu, Nese, Rossini, Laura, and Schnurbusch, Thorsten
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Developmental and Behavioral Genetics ,‘Wunder-Weizen’ ,Sequence analysis ,Mutant ,Locus (genetics) ,Investigations ,‘Compositum-Barley’ ,Chromosomes, Plant ,Gene Expression Regulation, Plant ,Sequence Homology, Nucleic Acid ,Botany ,Genetics ,Yield potential ,Triticeae ,Gene ,Triticum ,Panicle ,Plant Proteins ,Inflorescence branching ,biology ,"compositum-barley" ,"miracle-wheat" ,"wunder-weizen" ,Inflorescence Branching ,Yield Potential ,Gene Expression Profiling ,Chromosome Mapping ,food and beverages ,Hordeum ,‘Miracle-Wheat’ ,biology.organism_classification ,Inflorescence ,Hordeum vulgare ,Transcription Factors - Abstract
Inflorescences of the tribe Triticeae, which includes wheat (Triticum sp. L.) and barley (Hordeum vulgare L.) are characterized by sessile spikelets directly borne on the main axis, thus forming a branchless spike. "Compositum-Barley" and tetraploid "Miracle-Wheat" (T. turgidum convar. compositum (L.f.) Filat.) display non-canonical spike-branching in which spikelets are replaced by lateral branch-like structures resembling small-sized secondary spikes. As a result of this branch formation "Miracle-Wheat" produces significantly more grains per spike, leading to higher spike yield. In this study, we first isolated the gene underlying spike-branching in "Compositum-Barley", i.e. compositum 2 (com2). Moreover, we found that COM2 is orthologous to the branched head(t) (bh(t)) locus regulating spike-branching in tetraploid "Miracle-Wheat". Both genes possess orthologs with similar functions in maize BRANCHED SILKLESS 1 (BD1) and rice FRIZZY PANICLE/BRANCHED FLORETLESS 1 (FZP/BFL1) encoding AP2/ERF transcription factors. Sequence analysis of the bh(t) locus in a collection of mutant and wild type tetraploid wheat accessions revealed that a single amino acid substitution in the DNA-binding domain gave rise to the domestication of "Miracle-Wheat". mRNA in situ hybridization, microarray experiments, and independent qRT-PCR validation analyses revealed that the branch repression pathway in barley is governed through the spike architecture gene Six-rowed spike 4 regulating COM2 expression, while HvIDS1 (barley ortholog of maize INDETERMINATE SPIKELET 1) is a putative down-stream target of COM2. These findings presented here provide new insights into the genetic basis of spike architecture in Triticeae, and have disclosed new targets for genetic manipulations aiming at boosting wheat's yield potential.
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- 2015
166. Whole-genome analysis of diversity and SNP-major gene association in peach germplasm
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Cassia da Silva Linge, Ruijuan Ma, Daniele Bassi, Teresa Barreneche, Thierry Pascal, Nelson Nazzicari, Igor Pacheco, Sabrina Micali, S. Foschi, I. Iglesias, Laura Rossini, Diego Micheletti, Valeria Aramini, Pere Arús, Zhongshan Gao, Lirong Wang, Bénédicte Quilot-Turion, Ignazio Verde, Maria José Aranzana, Patrick Lambert, Elisa Banchi, Michela Troggio, Xiong-wei Li, Maria Teresa Dettori, J. Carbó, François Laurens, European Commission, Ministero delle Politiche Agricole Alimentari e Forestali, Ministerio de Ciencia e Innovación (España), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Institute of Research and Technology, Food and Agriculture (IRTA), Centro di Ricerca per la Frutticoltura, Agricultural Research Council (CRA), DISAA, Università degli Studi di Milano [Milano] (UNIMI), Centro Ricerca Produzione Vegetale (CRPV), Fondazione Edmund Mach (FEM), Research and Innovation Centre, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Estació Experimental de Lleida, Estacio Experimental Mas Badia, Zhenzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Horticultural Institute, Jiangsu Academy of Agricultural Sciences, Department of Horticulture, Zhejiang University, Parco Tecnologico Padano, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), This work has been funded by the EU seventh Framework Programme (http://ec.europa.eu/ research/fp7/index_en.cfm) through the project 'FruitBreedomics: Integrated Approach for increasing breeding efficiency in fruit tree crops' (Grant #FP7- 265582, by the Ministero delle Politiche Agricole Alimentari e Forestali -Italy, European Project: 265582,EC:FP7:KBBE,FP7-KBBE-2010-4,FRUIT BREEDOMICS(2011), Università degli studi di Milano [Milano], Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Micheletti, Diego, Dettori, Maria Teresa, Micali, Sabrina, Aramini, Valeria, Pacheco, Igor, Da Silva Linge, Cassia, Foschi, Stefano, Banchi, Elisa, Barreneche, Teresa, Quilot Turion, Bénédicte, Lambert, Patrick, Pascal, Thierry, Iglesias, Ignasi, Carbó, Joaquim, Wang, Li Rong, Ma, Rui Juan, Li, Xiong Wei, Gao, Zhong Shan, Nazzicari, Nelson, Troggio, Michela, Bassi, Daniele, Rossini, Laura, Verde, Ignazio, Laurens, Françoi, Arús, Pere, Joséaranzana, Maria, Università degli Studi di Milano = University of Milan (UNIMI), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)
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Genetics and Molecular Biology (all) ,0106 biological sciences ,Germplasm ,[SDV.SA]Life Sciences [q-bio]/Agricultural sciences ,Linkage disequilibrium ,variabilité génétique ,lcsh:Medicine ,Genome-wide association study ,Biochemistry ,01 natural sciences ,Chromosome Mapping ,Genetic Variation ,Genome-Wide Association Study ,Haplotypes ,Phenotype ,Phylogeny ,Prunus persica ,Chromosomes, Plant ,Genome, Plant ,Genotype ,Polymorphism, Single Nucleotide ,Agricultural and Biological Sciences (all) ,Biochemistry, Genetics and Molecular Biology (all) ,Medicine (all) ,Haplotype ,lcsh:Science ,prunus persica ,2. Zero hunger ,Genetics ,0303 health sciences ,Genome ,Multidisciplinary ,Vegetal Biology ,Single Nucleotide ,Major gene ,Agricultural sciences ,Settore AGR/07 - GENETICA AGRARIA ,genome wide association study (GWAS) ,Gene pool ,génotype ,Research Article ,polymorphisme nucléotidique simple (SNP) ,Biology ,Chromosomes ,03 medical and health sciences ,Genetic variation ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Genetic variability ,Polymorphism ,Domestication ,030304 developmental biology ,lcsh:R ,Plant ,lcsh:Q ,Sciences agricoles ,Biologie végétale ,010606 plant biology & botany - Abstract
Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs., This work has been funded by the EU seventh Framework Programme (http://ec.europa.eu/research/fp7/index_en.cfm) through the project “FruitBreedomics: Integrated Approach for increasing breeding efficiency in fruit tree crops” (Grant #FP7- 265582; http://fruitbreedomics.com/); by the Ministero delle Politiche Agricole Alimentari e Forestali -Italy (MiPAAF, http://www.politicheagricole.it) through the project ‘‘DRUPOMICS: Sequenziamento del genoma del pesco ed utilizzo della sequenza in programmi di miglioramento della qualita` del frutto del pesco e della resistenza alle malattie’’ (Grant # DM14999/7303/08) and “ESPLORA: Esplorazione della biodiversità vegetale ed animale alla ricerca di alleli superiori da inserire nei programmi avanzati di miglioramento genetico a sostegno dell’agricoltura nazionale” (Grant #DM 14658/7303/10); by the Spanish Ministry of Science and Innovation (http://www.micinn.es/) through the project AGL2012-40228-C02-01 (uso de la secuencia genomica para la caracterizacion de la variabilidad intraclonal e interespecifica en Melocotonero y almendro) and by the INIA (http://www.inia.es/) through the Project RF2012-00024-C04-04 (“conservación y caracterización de germoplasma introducido”).
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- 2015
167. Peach fruit resisteance to brown rot (monilinia spp): a genomic approach disciplinary sector : genetics (agr07)
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Pacheco-Cruz, Igor A, Bassi, Daniele, Rossini, Laura, and Universita Degli Studi Di Milano
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food and beverages - Abstract
Brown Rot disease (BR) caused by the necrotrophic fungus Monilinia spp. is a majar problem for the peach fruit market, causing significant losses at post-harvest level. Previous work demonstrated the possibility of discriminating between susceptible and tolerant peach genotypes, suggesting a quantitative nature of the BR resistance. In arder to uncover genomic regions associated with this trait and identify molecular markers for marker assisted selection (MAS), an F1 segregating population from the intra-specific Contender (tolerant cultivar) x Elegant Lady (susceptible cultivar) peach cross has been chosen for QTL analysis. Phenotypic analysis was performed over two harvest seasons, using an artificial infection procedure that measured skin and flesh resistance to a M. fructigena field isolate. Significant correlations were found between the data obtained in the two years and between the two traits. Maturity date (MD) was also highly correlated with resistan ce traits. Genotyping 11 O CxEL individuals allowed the construction of a linkage map (CxEL map), containing 78 SSR, covering a total genetic distance of 317.7 cM, and having an average marker density of 4.7 cM/marker. 8oth parametric (interval mapping) and non-parametric (Kruskai-Wallis analysis) QTL analysis using genotypic and phenotypic data from CxEL revealed two QTL clusters: a QTL underlying skin resistance located on LG CxEL-2 (explaining a 15% - 22% of the total phenotypic variability), and a QTL associated with flesh resistance (explaining a 30% - 35.2% of the total phenotypic variability), collocating with a majar MD QTL on LG CxEL-4. These results suggest that resistance to BR has at least two main components: the first related to avoidance of fungal penetration, anda second earliness-associated factor associated with fungal spread after penetration. Furthermore, markers M 1 a (CxEL-2) and UDAp-439 (CxEL-4) may provide useful tools for MAS for BR-resistance breeding programmes. Doctorado TERMINADA PFCHA-Becas 102p. PFCHA-Becas
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- 2010
168. Genetic dissection of aroma volatile compounds from the essential oil of peach fruit: QTL analysis and identification of candidate genes using dense SNP maps
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Raul Pirona, Iban Eduardo, Alberto Vecchietti, Igor Pacheco, Laura Rossini, Daniele Bassi, Carlo Pozzi, Elisa Banchi, G. Chietera, Michela Troggio, Ministero dell'Istruzione, dell'Università e della Ricerca, European Commission, Eduardo, Iban, Chietera, Giorgiana, Pirona, Raul, Pacheco, Igor, Troggio, Michela, Banchi, Elisa, Bassi, Daniele, Rossini, Laura, Vecchietti, Alberto, and Pozzi, Carlo
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0106 biological sciences ,Candidate gene ,Nonanal ,Linalool ,p-Menth-1-en-9-al ,Peach ,QTLs ,VOCs ,Forestry ,Horticulture ,Genetics ,Molecular Biology ,QTL ,Population ,Single-nucleotide polymorphism ,Quantitative trait locus ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Genetic ,Botany ,education ,Aroma ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,education.field_of_study ,biology ,VOC ,food and beverages ,biology.organism_classification ,Settore AGR/07 - GENETICA AGRARIA ,chemistry ,010606 plant biology & botany ,SNP array - Abstract
Volatile organic compounds (VOCs) in plants are involved in aroma and pest resistance. These compounds form a complex mixture whose composition is specific to species and often to varieties. Despite their importance as essential factors that determine peach fruit quality, understanding of molecular, genetic, and physiological mechanisms underlying aroma formation is limited. The aim of this study was the identification in peach of quantitative trait loci (QTLs) for fruit VOCs to understand their genetic basis using an F1 population of 126 seedlings deriving from the cross between “Bolero” (B) and “OroA” (O), two peach cultivars differing in their aroma profile. Dense single nucleotide polymorphism (SNP) and SSR maps covering the eight linkage groups of the peach genome were constructed by genotyping with the International Peach SNP Consortium peach SNP array v1, and data for 23 VOCs with high or unknown “odor activity value” were obtained by gas chromatography–mass spectrometry analysis of fruit essential oil in the years 2007 and 2008. A total of 72 QTLs were identified, most consistent in both years. QTLs were identified for the 23 VOCs studied, including three major QTLs for nonanal, linalool, and for p-menth-1-en-9-al stable in both years. Collocations between candidate genes and major QTLs were identified taking advantage of the peach genome sequence: genes encoding two putative terpene synthases and one lipoxygenase (Lox) might be involved in the biosynthesis of linalool and p-menth-1-en-9-al, and nonanal, respectively. Implications for marker-assisted selection and future research on the subject are discussed., This work was supported by a grant from Ministero dell’Istruzione, dell’Università e della Ricerca (MIUR) to PTP (Progetto industriale “Sviluppo di sistemi integrati per la caratterizzazione, il miglioramento, la selezione e la propagazione di razze animali e vegetali. Utilizzazione di sistemi molecolari avanzati per la diagnostica dei prodotti agrari”) and by an Italian grant to DB funded by private and public agencies “MAS.PES: apricot and peach breeding by molecular-assisted selection”. Construction of the linkage map was partly funded under the EU seventh Framework Programme by the FruitBreedomics project no. 265582: “Integrated approach for increasing breeding efficiency in fruit tree crops.” GC was supported by two grants from MIUR, PRIN project numbers 2005074520, 20074AX5CA. RP was supported by MIUR FIRB grant RBIP06CTBR.
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169. A missense mutation in the barley Xan-h gene encoding the Mg-chelatase subunit I leads to a viable pale green line with reduced daily transpiration rate.
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Persello A, Tadini L, Rotasperti L, Ballabio F, Tagliani A, Torricella V, Jahns P, Dalal A, Moshelion M, Camilloni C, Rosignoli S, Hansson M, Cattivelli L, Horner DS, Rossini L, Tondelli A, Salvi S, and Pesaresi P
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- Photosynthesis genetics, Phenotype, Photosystem II Protein Complex metabolism, Photosystem II Protein Complex genetics, Hordeum genetics, Hordeum physiology, Hordeum enzymology, Chlorophyll metabolism, Mutation, Missense, Plant Transpiration genetics, Plant Proteins genetics, Plant Proteins metabolism, Plant Leaves genetics, Plant Leaves physiology, Lyases genetics, Lyases metabolism
- Abstract
Key Message: The barley mutant xan-h.chli-1 shows phenotypic features, such as reduced leaf chlorophyll content and daily transpiration rate, typical of wild barley accessions and landraces adapted to arid climatic conditions. The pale green trait, i.e. reduced chlorophyll content, has been shown to increase the efficiency of photosynthesis and biomass accumulation when photosynthetic microorganisms and tobacco plants are cultivated at high densities. Here, we assess the effects of reducing leaf chlorophyll content in barley by altering the chlorophyll biosynthesis pathway (CBP). To this end, we have isolated and characterised the pale green barley mutant xan-h.chli-1, which carries a missense mutation in the Xan-h gene for subunit I of Mg-chelatase (HvCHLI), the first enzyme in the CBP. Intriguingly, xan-h.chli-1 is the only known viable homozygous mutant at the Xan-h locus in barley. The Arg298Lys amino-acid substitution in the ATP-binding cleft causes a slight decrease in HvCHLI protein abundance and a marked reduction in Mg-chelatase activity. Under controlled growth conditions, mutant plants display reduced accumulation of antenna and photosystem core subunits, together with reduced photosystem II yield relative to wild-type under moderate illumination, and consistently higher than wild-type levels at high light intensities. Moreover, the reduced content of leaf chlorophyll is associated with a stable reduction in daily transpiration rate, and slight decreases in total biomass accumulation and water-use efficiency, reminiscent of phenotypic features of wild barley accessions and landraces that thrive under arid climatic conditions., (© 2024. The Author(s).)
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- 2024
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170. Dendritic spine loss in epileptogenic Type II focal cortical dysplasia: Role of enhanced classical complement pathway activation.
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Rossini L, De Santis D, Cecchini E, Cagnoli C, Maderna E, Cartelli D, Morgan BP, Torvell M, Spreafico R, di Giacomo R, Tassi L, de Curtis M, and Garbelli R
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- Adult, Humans, Dendritic Spines pathology, Complement Pathway, Classical, Focal Cortical Dysplasia, Malformations of Cortical Development pathology, Epilepsy pathology, Drug Resistant Epilepsy pathology
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Dendritic spines are the postsynaptic sites for most excitatory glutamatergic synapses. We previously demonstrated a severe spine loss and synaptic reorganization in human neocortices presenting Type II focal cortical dysplasia (FCD), a developmental malformation and frequent cause of drug-resistant focal epilepsy. We extend the findings, investigating the potential role of complement components C1q and C3 in synaptic pruning imbalance. Data from Type II FCD were compared with those obtained in focal epilepsies with different etiologies. Neocortical tissues were collected from 20 subjects, mainly adults with a mean age at surgery of 31 years, admitted to epilepsy surgery with a neuropathological diagnosis of: cryptogenic, temporal lobe epilepsy with hippocampal sclerosis, and Type IIa/b FCD. Dendritic spine density quantitation, evaluated in a previous paper using Golgi impregnation, was available in a subgroup. Immunohistochemistry, in situ hybridization, electron microscopy, and organotypic cultures were utilized to study complement/microglial activation patterns. FCD Type II samples presenting dendritic spine loss were characterized by an activation of the classical complement pathway and microglial reactivity. In the same samples, a close relationship between microglial cells and dendritic segments/synapses was found. These features were consistently observed in Type IIb FCD and in 1 of 3 Type IIa cases. In other patient groups and in perilesional areas outside the dysplasia, not presenting spine loss, these features were not observed. In vitro treatment with complement proteins of organotypic slices of cortical tissue with no sign of FCD induced a reduction in dendritic spine density. These data suggest that dysregulation of the complement system plays a role in microglia-mediated spine loss. This mechanism, known to be involved in the removal of redundant synapses during development, is likely reactivated in Type II FCD, particularly in Type IIb; local treatment with anticomplement drugs could in principle modify the course of disease in these patients., (© 2022 The Authors. Brain Pathology published by John Wiley & Sons Ltd on behalf of International Society of Neuropathology.)
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- 2023
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171. Why are type II focal cortical dysplasias frequently located at the bottom of sulcus? A neurodevelopmental hypothesis.
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Studer M, Rossini L, Spreafico R, Pelliccia V, Tassi L, de Curtis M, and Garbelli R
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- Humans, Magnetic Resonance Imaging, Epilepsy, Malformations of Cortical Development complications, Malformations of Cortical Development diagnostic imaging, Malformations of Cortical Development, Group I
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- 2022
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172. Multi-environment genome -wide association mapping of culm morphology traits in barley.
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Bretani G, Shaaf S, Tondelli A, Cattivelli L, Delbono S, Waugh R, Thomas W, Russell J, Bull H, Igartua E, Casas AM, Gracia P, Rossi R, Schulman AH, and Rossini L
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In cereals with hollow internodes, lodging resistance is influenced by morphological characteristics such as internode diameter and culm wall thickness. Despite their relevance, knowledge of the genetic control of these traits and their relationship with lodging is lacking in temperate cereals such as barley. To fill this gap, we developed an image analysis-based protocol to accurately phenotype culm diameters and culm wall thickness across 261 barley accessions. Analysis of culm trait data collected from field trials in seven different environments revealed high heritability values (>50%) for most traits except thickness and stiffness, as well as genotype-by-environment interactions. The collection was structured mainly according to row-type, which had a confounding effect on culm traits as evidenced by phenotypic correlations. Within both row-type subsets, outer diameter and section modulus showed significant negative correlations with lodging (<-0.52 and <-0.45, respectively), but no correlation with plant height, indicating the possibility of improving lodging resistance independent of plant height. Using 50k iSelect SNP genotyping data, we conducted multi-environment genome-wide association studies using mixed model approach across the whole panel and row-type subsets: we identified a total of 192 quantitative trait loci (QTLs) for the studied traits, including subpopulation-specific QTLs and 21 main effect loci for culm diameter and/or section modulus showing effects on lodging without impacting plant height. Providing insights into the genetic architecture of culm morphology in barley and the possible role of candidate genes involved in hormone and cell wall-related pathways, this work supports the potential of loci underpinning culm features to improve lodging resistance and increase barley yield stability under changing environments., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Bretani, Shaaf, Tondelli, Cattivelli, Delbono, Waugh, Thomas, Russell, Bull, Igartua, Casas, Gracia, Rossi, Schulman and Rossini.)
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- 2022
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173. Less is more: natural variation disrupting a miR172 gene at the di locus underlies the recessive double-flower trait in peach (P. persica L. Batsch).
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Cirilli M, Rossini L, Chiozzotto R, Baccichet I, Florio FE, Mazzaglia A, Turco S, Bassi D, and Gattolin S
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- Flowers genetics, Genes, Plant genetics, Genotype, Phenotype, Prunus persica genetics
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Background: With the domestication of ornamental plants, artificial selective pressure favored the propagation of mutations affecting flower shape, and double-flower varieties are now readily available for many species. In peach two distinct loci control the double-flower phenotype: the dominant Di2 locus, regulated by the deletion of the binding site for miR172 in the euAP2 PETALOSA gene Prupe.6G242400, and the recessive di locus, of which the underlying factor is still unknown., Results: Based on its genomic location a candidate gene approach was used to identify genetic variants in a diverse panel of ornamental peach accessions and uncovered three independent mutations in Prupe.2G237700, the gene encoding the transcript for microRNA miR172d: a ~5.0 Kb LTR transposable element and a ~1.2 Kb insertion both positioned upstream of the sequence encoding the pre-miR172d within the transcribed region of Prupe.2G237700, and a ~9.5 Kb deletion encompassing the whole gene sequence. qRT-PCR analysis confirmed that expression of pre-miR172d was abolished in di/di genotypes homozygous for the three variants., Conclusions: Collectively, PETALOSA and the mutations in micro-RNA miR172d identified in this work provide a comprehensive collection of the genetic determinants at the base of the double-flower trait in the peach germplasms., (© 2022. The Author(s).)
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- 2022
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174. Role of NODDI in the MRI Characterization of Hippocampal Abnormalities in Temporal Lobe Epilepsy: Clinico-histopathologic Correlations.
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Giachetti I, Padelli F, Aquino D, Garbelli R, De Santis D, Rossini L, Deleo F, Pascuzzo R, Coras R, Marucci G, Tringali G, Maccagnano C, De Curtis M, Bruzzone MG, and Didato G
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- Adult, Atrophy pathology, Diffusion Tensor Imaging methods, Hippocampus diagnostic imaging, Hippocampus pathology, Humans, Magnetic Resonance Imaging, Neurites, Sclerosis diagnostic imaging, Sclerosis pathology, Epilepsy, Temporal Lobe diagnostic imaging, Epilepsy, Temporal Lobe pathology
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Background and Objectives: The identification of possible hippocampal alterations is a crucial point for the diagnosis and therapy of patients with unilateral temporal lobe epilepsy (TLE). This study aims to investigate the role of neurite orientation dispersion and density imaging (NODDI) compared to diffusion tensor imaging (DTI) in the comprehension of hippocampal microstructure in TLE., Methods: DTI and NODDI metrics were calculated in the hippocampi of adult patients with TLE, with and without histology-confirmed hippocampal sclerosis (HS), and in age/sex-matched healthy controls (HC). Diffusion metrics and hippocampal volumes of the pathologic side were compared within participants and between participants among the HS, non-HS, and HC groups. Diffusion metrics were also correlated with hippocampal volume and patients' clinical features. After surgery, hippocampal specimens were processed for neuropathology examinations., Results: Fifteen patients with TLE (9 with and 6 without HS) and 11 HC were included. Hippocampal analyses resulted in a significant increase in fractional anisotropy (FA) and mean diffusivity (MD; mm
2 /s × 10-3 ) and decrease in orientation dispersion index (ODI) comparing the pathologic side of patients with HS and their relative nonpathologic side (0.203 vs 0.183, 0.825 vs 0.724, 0.366 vs 0.443, respectively), the pathologic side of patients without HS (0.203 vs 0.169, 0.825 vs 0.745, 0.366 vs 0.453, respectively), and HC (0.203 vs 0.172, 0.825 vs 0.729, 0.366 vs 0.447, respectively). Moreover, neurite density (ND) was significantly decreased comparing both hippocampi of patients with HS (0.416 vs 0.460). A significant increase in free-water isotropic volume fraction (fiso) was found in the comparison of pathologic hippocampi of patients with HS and nonpathologic hippocampi of patients with HS (0.323 vs 0.258) and HC (0.323 vs 0.226). Hippocampal volume of all patients with TLE negatively correlated with MD ( r = -0.746, p = 0.0145) and positively correlated with ODI ( r = 0.719, p = 0.0145). Fiso and ND of sclerotic hippocampi positively correlated with disease duration ( r = 0.684, p = 0.0424 and r = 0.670, p = 0.0486, respectively). Immunohistochemistry in sclerotic hippocampal specimens revealed neuronal loss in the pyramidal layer and fiber reorganization at the level of stratum lacunosum-moleculare, confirming ODI and ND metrics., Discussion: This study shows the capability of diffusion MRI metrics to detect hippocampal microstructural alterations. Among them, ODI seems to better highlight the fiber reorganization observed by neuropathology in sclerotic hippocampi., (© 2022 American Academy of Neurology.)- Published
- 2022
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175. Genetic and phenotypic analyses reveal major quantitative loci associated to fruit size and shape traits in a non-flat peach collection (P. persica L. Batsch).
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Cirilli M, Baccichet I, Chiozzotto R, Silvestri C, Rossini L, and Bassi D
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Fruit size and shape are critical agronomical and pomological attributes and prime targets in peach breeding programs. Apart from the flat peach type, a Mendelian trait well-characterized at the genetic level, ample diversity of fruit size and shapes is present across peach germplasms. Nevertheless, knowledge of the underlying genomic loci remains limited. In this work, fruit size and shape were assessed in a collection of non-flat peach accessions and selections, under controlled fruit load conditions. The architecture of these traits was then dissected by combining association and linkage mapping, revealing a major locus on the proximal end of chromosome 6 (qSHL/Fs6.1) explaining a large proportion of phenotypic variability for longitudinal shape and also affecting fruit size. A second major locus for fruit longitudinal shape (qSHL5.1), probably also affecting fruit size, was found co-localizing at locus G, suggesting pleiotropic effects of peach/nectarine traits. An additional QTL for fruit longitudinal shape (qSHL6.2) was identified in the distal end of chromosome 6 in a cross with an ornamental double-flower peach and co-localized with the Di2 locus, controlling flower morphology. Besides assisting breeding activities, knowledge of loci controlling fruit size and shape paves the way for more in-depth studies aimed at the identification of underlying genetic variant(s)., (© 2021. The Author(s).)
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- 2021
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176. Dynamic expression of NR2F1 and SOX2 in developing and adult human cortex: comparison with cortical malformations.
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Foglio B, Rossini L, Garbelli R, Regondi MC, Mercurio S, Bertacchi M, Avagliano L, Bulfamante G, Coras R, Maiorana A, Nicolis S, Studer M, and Frassoni C
- Subjects
- Adult, Animals, Humans, Interneurons metabolism, Mice, Neocortex metabolism, Neurogenesis, Neurons metabolism, SOXB1 Transcription Factors genetics, COUP Transcription Factor I metabolism, SOXB1 Transcription Factors metabolism
- Abstract
The neocortex, the most recently evolved brain region in mammals, is characterized by its unique areal and laminar organization. Distinct cortical layers and areas can be identified by the presence of graded expression of transcription factors and molecular determinants defining neuronal identity. However, little is known about the expression of key master genes orchestrating human cortical development. In this study, we explored the expression dynamics of NR2F1 and SOX2, key cortical genes whose mutations in human patients cause severe neurodevelopmental syndromes. We focused on physiological conditions, spanning from mid-late gestational ages to adulthood in unaffected specimens, but also investigated gene expression in a pathological context, a developmental cortical malformation termed focal cortical dysplasia (FCD). We found that NR2F1 follows an antero-dorsal
low to postero-ventralhigh gradient as in the murine cortex, suggesting high evolutionary conservation. While SOX2 is mainly expressed in neural progenitors next to the ventricular surface, NR2F1 is found in both mitotic progenitors and post-mitotic neurons at GW18. Interestingly, both proteins are highly co-expressed in basal radial glia progenitors of the outer sub-ventricular zone (OSVZ), a proliferative region known to contribute to cortical expansion and complexity in humans. Later on, SOX2 becomes largely restricted to astrocytes and oligodendrocytes although it is also detected in scattered mature interneurons. Differently, NR2F1 maintains its distinct neuronal expression during the whole process of cortical development. Notably, we report here high levels of NR2F1 in dysmorphic neurons and NR2F1 and SOX2 in balloon cells of surgical samples from patients with FCD, suggesting their potential use in the histopathological characterization of this dysplasia.- Published
- 2021
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177. Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses.
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Hennet L, Berger A, Trabanco N, Ricciuti E, Dufayard JF, Bocs S, Bastianelli D, Bonnal L, Roques S, Rossini L, Luquet D, Terrier N, and Pot D
- Abstract
Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels., (Copyright © 2020 Hennet, Berger, Trabanco, Ricciuti, Dufayard, Bocs, Bastianelli, Bonnal, Roques, Rossini, Luquet, Terrier and Pot.)
- Published
- 2020
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178. Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch).
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Cirilli M, Giovannini D, Ciacciulli A, Chiozzotto R, Gattolin S, Rossini L, Liverani A, and Bassi D
- Subjects
- Fruit anatomy & histology, Gene Expression Profiling, Genes, Plant physiology, Genetic Loci genetics, Genetic Markers, Genome, Plant genetics, Genome-Wide Association Study, Genomics, Linkage Disequilibrium, Prunus persica anatomy & histology, Quantitative Trait, Heritable, Real-Time Polymerase Chain Reaction, Sequence Analysis, DNA, Fruit genetics, Genes, Plant genetics, Prunus persica genetics
- Abstract
Background: Texture is one of the most important fruit quality attributes. In peach, stony hard (SH) is a recessive monogenic trait (hd/hd) that confers exceptionally prolonged firm flesh to fully ripe fruit. Previous studies have shown that the SH mutation affects the fruit ability to synthesize appropriate amounts of indol-3-acetic acid (IAA), which orchestrates the ripening processes through the activation of system 2 ethylene pathway. Allelic variation in a TC microsatellite located within the first intron of PpYUC11-like (a YUCCA-like auxin-biosynthesis gene) has been recently proposed as the causal mutation of the SH phenotype., Results: The simple genetic determinism of the SH trait has been clarified through genome-wide association and LD analyses in a diverse set of accessions, restricting the hd locus to an interval of about 1.8 Mbp in chromosome 6. The comparison of fruit transcriptome data from non-SH (melting flesh) and SH accessions provided an expression patterns overview of the annotated transcripts within the hd locus, confirming the absence of PpYUC11-like expression in SH fruits. To explore further possible associations between genomic variants at the hd locus and the SH phenotype, re-sequencing data of the SH accession 'D41-62' were compared with several SH and non-SH accessions with different genetic backgrounds. A further step of validation was provided through the evaluation of variant-trait association in two bi-parental F
2 populations issued from the SH accession 'D41-62' and a panel of advanced breeding selections, showing perfect co-segregation of the PpYUC11-like intron TC20 allele and the SH phenotype., Conclusions: In this study, we provide a multi-level validation of the genetic control of the SH trait through the integration of genome-wide association mapping, transcriptome analysis and whole-genome resequencing data for SH and non-SH accessions, and marker-trait association in a panel of advanced breeding selections and segregating progenies. Collectively, our data confirm with high confidence the role of allelic variation at PpYUC11-like locus as the genetic determinant of the SH trait, opening interesting perspectives at both biological and applied research level.- Published
- 2018
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179. An integrated approach for increasing breeding efficiency in apple and peach in Europe.
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Laurens F, Aranzana MJ, Arus P, Bassi D, Bink M, Bonany J, Caprera A, Corelli-Grappadelli L, Costes E, Durel CE, Mauroux JB, Muranty H, Nazzicari N, Pascal T, Patocchi A, Peil A, Quilot-Turion B, Rossini L, Stella A, Troggio M, Velasco R, and van de Weg E
- Abstract
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., Competing Interests: The authors declare that they have no conflict of interest.
- Published
- 2018
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180. PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data.
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Cirilli M, Flati T, Gioiosa S, Tagliaferri I, Ciacciulli A, Gao Z, Gattolin S, Geuna F, Maggi F, Bottoni P, Rossini L, Bassi D, Castrignanò T, and Chillemi G
- Subjects
- Data Mining methods, Databases, Genetic, High-Throughput Nucleotide Sequencing methods, Internet, Phylogeny, Polymorphism, Single Nucleotide, Prunus persica classification, Rosaceae classification, Rosaceae genetics, Computational Biology methods, Genetic Variation, Genome, Plant genetics, Prunus persica genetics
- Abstract
Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalog of genetic variants present in peach (Prunus persica L. Batsch) and wild-related species of Prunus genera, annotated from 146 samples publicly released on the Sequence Read Archive (SRA). We designed a user-friendly web-based interface of the database, providing search tools to retrieve single nucleotide polymorphism (SNP) and InDel variants, along with useful statistics and information. PeachVar-DB results are linked to the Genome Database for Rosaceae (GDR) and the Phytozome database to allow easy access to other external useful plant-oriented resources. In order to extend the genetic diversity covered by the PeachVar-DB further, and to allow increasingly powerful comparative analysis, we will progressively integrate newly released data., (© The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
- Published
- 2018
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181. Seizure activity per se does not induce tissue damage markers in human neocortical focal epilepsy.
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Rossini L, Garbelli R, Gnatkovsky V, Didato G, Villani F, Spreafico R, Deleo F, Lo Russo G, Tringali G, Gozzo F, Tassi L, and de Curtis M
- Subjects
- Adolescent, Adult, Brain pathology, Child, Child, Preschool, Epilepsies, Partial pathology, Epilepsy pathology, Female, Humans, Infant, Male, Malformations of Cortical Development, Group I pathology, Neuroglia metabolism, Neuroglia pathology, Neurons metabolism, Neurons pathology, Seizures pathology, Young Adult, Brain metabolism, Epilepsies, Partial metabolism, Epilepsy metabolism, Malformations of Cortical Development, Group I metabolism, Seizures metabolism
- Abstract
Objective: The contribution of recurring seizures to the progression of epileptogenesis is debated. Seizure-induced brain damage is not conclusively demonstrated either in humans or in animal models of epilepsy. We evaluated the expression of brain injury biomarkers on postsurgical brain tissue obtained from 20 patients with frequent seizures and a long history of drug-resistant focal epilepsy., Methods: The expression patterns of specific glial, neuronal, and inflammatory molecules were evaluated by immunohistochemistry in the core of type II focal cortical dysplasias (FCD-II), at the FCD boundary (perilesion), and in the adjacent normal-appearing area included in the epileptogenic region. We also analyzed surgical specimens from cryptogenic patients not presenting structural alterations at imaging., Results: Astroglial and microglial activation, reduced neuronal density, perivascular CD3-positive T-lymphocyte clustering, and fibrinogen extravasation were demonstrated in the core of FCD-II lesions. No pathological immunoreactivity was observed outside the FCD-II or in cryptogenetic specimens, where the occurrence of interictal and ictal epileptiform activity was confirmed by either stereo-electroencephalography or intraoperative electrocorticography., Interpretation: Recurrent seizures do not induce the expression of brain damage markers in nonlesional epileptogenic cortex studied in postsurgical tissue from cryptogenic and FCD patients. This evidence argues against the hypothesis that epileptiform activity per se contributes to focal brain injury, at least in the neocortical epilepsies considered here. Ann Neurol 2017;82:331-341., (© 2017 American Neurological Association.)
- Published
- 2017
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182. FCD Type II and mTOR pathway: Evidence for different mechanisms involved in the pathogenesis of dysmorphic neurons.
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Rossini L, Villani F, Granata T, Tassi L, Tringali G, Cardinale F, Aronica E, Spreafico R, and Garbelli R
- Subjects
- Adolescent, Adult, Brain Neoplasms metabolism, Brain Neoplasms pathology, Brain Neoplasms surgery, Cerebral Cortex pathology, Cerebral Cortex surgery, Child, Child, Preschool, Drug Resistant Epilepsy metabolism, Drug Resistant Epilepsy pathology, Drug Resistant Epilepsy surgery, Epilepsy pathology, Epilepsy surgery, Humans, Immunohistochemistry, Infant, Malformations of Cortical Development, Group I pathology, Malformations of Cortical Development, Group I surgery, Middle Aged, Phosphatidylinositol 3-Kinases metabolism, Proto-Oncogene Proteins c-akt metabolism, Ribosomal Protein S6 Kinases metabolism, Signal Transduction, Young Adult, Cerebral Cortex metabolism, Epilepsy metabolism, Malformations of Cortical Development, Group I metabolism, Neurons metabolism, TOR Serine-Threonine Kinases metabolism
- Abstract
Type II focal cortical dysplasia (FCD II) is a malformation of cortical development, frequently associated with intractable epilepsy, characterised by cortical dyslamination, dysmorphic neurons (DNs) and balloon cells (BCs). We investigated the expression of pS6 (downstream target) and pPDK1-pAkt (upstream targets) as evidence for mTOR pathway activation and their co-expression with Interleukin-1β in FCD II surgical specimens and compared the findings with control non-epileptic tissue, non-malformed epileptic tissue or acquired epilepsy-Rasmussen's Encephalitis (RE) occasionally presenting pS6 and Interleukin-1β positive abnormal neurons. Downstream mTOR activation was demonstrated in almost all abnormal cells in both FCD II and RE. Conversely, upstream activation in FCD II was observed in the majority of BCs, in a proportion of DNs, not presenting Interleukin-1β expression, but not at all in RE scattered abnormal neurons. Based on these findings we suggest that the presence of BCs and DNs in FCD II could be due to a first upstream mTOR pathway PI3K-Akt-mediate event occurring very early during cortical development in the large proportion of abnormal cells; followed by the appearance of additional pS6 positive DNs promoted by the presence of a later inflammatory processes., (Copyright © 2016 Elsevier B.V. All rights reserved.)
- Published
- 2017
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183. Crossability of Triticum urartu and Triticum monococcum wheats, homoeologous recombination, and description of a panel of interspecific introgression lines.
- Author
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Fricano A, Brandolini A, Rossini L, Sourdille P, Wunder J, Effgen S, Hidalgo A, Erba D, Piffanelli P, and Salamini F
- Subjects
- Breeding, Chromosome Mapping, Diploidy, Genetic Linkage, Genetic Variation, Microsatellite Repeats, Principal Component Analysis, Recombination, Genetic, Genome, Plant, Triticum genetics
- Abstract
Triticum monococcum (genome A(m)) and T. urartu (genome A(u)) are diploid wheats, with the first having been domesticated in the Neolithic Era and the second being a wild species. In a germplasm collection, rare wild T. urartu lines with the presence of T. monococcum alleles were found. This stimulated our interest to develop interspecific introgression lines of T. urartu in T. monococcum, a breeding tool currently implemented in several crop species. Moreover, the experiments reported were designed to reveal the existence in nature of A(m)/A(u) intermediate forms and to clarify whether the two species are at least marginally sexually compatible. From hand-made interspecific crosses, almost-sterile F1 plants were obtained when the seed-bearing parent was T. monococcum. A high degree of fertility was, however, evident in some advanced generations, particularly when T. urartu donors were molecularly more related to T. monococcum. Analysis of the marker populations demonstrated chromosome pairing and recombination in F1 hybrid plants. Forty-six introgression lines were developed using a line of T. monococcum with several positive agronomic traits as a recurrent parent. Microsatellite markers were tested on A(u) and A(m) genomes, ordered in a T. monococcum molecular map, and used to characterize the exotic DNA fragments present in each introgression line. In a test based on 28 interspecific introgression lines, the existence of genetic variation associated with T. urartu chromosome fragments was proven for the seed content of carotenoids, lutein, β-cryptoxanthin, and zinc. The molecular state of available introgression lines is summarized., (Copyright © 2014 Fricano et al.)
- Published
- 2014
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184. Heterotopic reelin in human nodular heterotopia: a neuropathological study.
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Rossini L, Tassi L, Spreafico R, and Garbelli R
- Subjects
- Adult, Cell Adhesion Molecules, Neuronal physiology, Cerebral Cortex cytology, Cerebral Cortex embryology, Cerebral Cortex metabolism, Epilepsies, Partial surgery, Extracellular Matrix Proteins physiology, Female, Humans, Immunohistochemistry, Male, Nerve Tissue Proteins physiology, Neurons cytology, Neurons metabolism, Periventricular Nodular Heterotopia complications, Reelin Protein, Serine Endopeptidases physiology, Young Adult, Cell Adhesion Molecules, Neuronal metabolism, Cell Movement physiology, Epilepsies, Partial etiology, Extracellular Matrix Proteins metabolism, Nerve Tissue Proteins metabolism, Periventricular Nodular Heterotopia metabolism, Serine Endopeptidases metabolism
- Abstract
Aim: The extracellular matrix glycoprotein reelin plays a crucial role in the control of neuronal migration and during development is expressed by Cajal-Retzius cells in the marginal zone. The purpose of this study was to investigate the possible involvement of reelin in the pathogenesis of human nodular heterotopia, a malformation of cortical development frequently associated with focal drug-resistant epilepsy., Methods: Five patients presenting with subcortical nodular heterotopia and referred for epilepsy surgery, after a comprehensive presurgical investigation, were considered. The surgical specimens were studied by combining immunohistochemistry, double immunofluorescence, and in situ hybridisation procedures., Results: The selected cases were characterised by the presence of multiple nodules presenting in the core cell-free zones, reminiscent of the cortical molecular layer. In all cases, small reelin-positive cells, without typical Cajal-Retzius cell features, were distributed inside the nodules and localised in these cell body-sparse regions., Conclusion: The presented data corroborate the hypothesis that reelin might be involved in human heterotopic nodular formation.
- Published
- 2012
- Full Text
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