SNPGreen : a Database to Navigate Across Plant SNP Arrays

In recent years, the use of genomic information in plant and animal species for genetic improvement, and related fields has become routine. In order to accommodate market requirements (i.e. genotyping cost), manufacturers of single nucleotide polymorphism (SNP) arrays, private companies and international consortia have developed a large number of arrays with different content and different SNP density. The number of currently available SNP arrays differs among species. There is a strong need to standardize and integrate array- specific (e.g. SNP IDs, allele coding) and species-specific (i.e. assemblies) SNP information. After the very positive response to SNPChiMp (bioinformatics.tecnoparco.org/SNPchimp), where we store and provide tools for the 6 major livestock species and more than 20 SNP arrays, we are now extending our family of tools to plant species. SNPGreen ( bioinformatics.tecnoparco.org/SNPgreen) currently includes 3 SNP arrays for Rice and Maize

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

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

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species

Published: 10 April 2015In recent years, the use of genomic information in livestock species for genetic improvement, association studies and many other fields has become routine. In order to accommodate different market requirements in terms of genotyping cost, manufacturers of single nucleotide polymorphism (SNP) arrays, private companies and international consortia have developed a large number of arrays with different content and different SNP density. The number of currently available SNP arrays differs among species: ranging from one for goats to more than ten for cattle, and the number of arrays available is increasing rapidly. However, there is limited or no effort to standardize and integrate array- specific (e.g. SNP IDs, allele coding) and species-specific (i.e. past and current assemblies) SNP information.Here we present SNPchiMp v.3, a solution to these issues for the six major livestock species (cow, pig, horse, sheep, goat and chicken). Original data was collected directly from SNP array producers and specific international genome consortia, and stored in a MySQL database. The database was then linked to an open-access web tool and to public databases. SNPchiMp v.3 ensures fast access to the database (retrieving within/across SNP array data) and the possibility of annotating SNP array data in a user-friendly fashion.This platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines. In recognition of the open-access use of Ensembl resources, SNPchiMp v.3 was officially credited as an Ensembl E!mpowered tool. Availability at http://bioinformatics.tecnoparco.org/SNPchimp.Ezequiel L Nicolazzi, Andrea Caprera, Nelson Nazzicari, Paolo Cozzi, Francesco Strozzi, Cindy Lawley, Ali Pirani, Chandrasen Soans, Fiona Brew, Hossein Jorjani, Gary Evans, Barry Simpson, Gwenola Tosser-Klopp, Rudiger Brauning, John L Williams and Alessandra Stell

Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm

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

An embedded acquisition system for remote monitoring of tire status in F1 race cars through thermal images

L’elaborato di laurea di Michele Nobis ha vinto la selezione italiana del concorso Altran Engineering Academy, voluto da Altran una società di progettazione che collabora con il team Renault F1, che premia ogni anno idee progettuali originali da applicare nel mondo delle competizioni sportive e in particolare in Formula Uno. Il lavoro ha poi partecipato, e ricevuto apprezzamento, a fine giugno, alla selezione mondiale a Enstone in Inghilterra, sede dei laboratori della scuderia Renault F1 insieme agli altri otto vincitori delle selezioni locali, provenienti da tutto il mondo. La tesi ha riguardato il progetto e la realizzazione di un sistema compatto da utilizzare a bordo della vettura per l’acquisizione e l’elaborazione in tempo reale di immagini normali e termografiche da utilizzare in F

An FPGA accelerator for Fingerprint Authentication

Si tratta di un concorso per progetti multidisciplinari nell’ambito dell’ingegneria aperto a laureandi e neo-laureati italiani, nato con lo scopo di aiutare studenti capaci a coltivare il loro interesse verso i sistemi embedded, a migliorare le loro tecniche di progetto e soprattutto a sfruttare creatività e innovazione per ottenere i migliori risultati. Nella primavera di quest’anno, il gruppo di lavoro del laboratorio di Microcalcolatori ha proposto le idee e la documentazione di progetto relativi ad un’attività di tesi di laurea in corso; a metà giugno, ha ricevuto la comunicazione che l’attività era stata giudicata una fra le 40 migliori presentate e dunque idonea per la partecipazione alla selezione finale. A ciò sono seguiti l’invio del progetto completo a fine settembre e la premiazione in occasione della manifestazione annuale “System on a Programmable Chip (SOPC) World Italy 2008” tenutasi a Milano il 5 novembre. Il gruppo era composto da Giulia Matrone, laureata il 13 ottobre 2008, da Mauro Giachero e Nelson Nazzicari, dottorandi di Ricerca, sotto la guida dei professori Giovanni Danese e Francesco Leporati. La proposta riguardava lo studio e la realizzazione di in sistema compatto ed efficiente per il riconoscimento automatico di impronte digitali

An application specific processors for deinterlacing race car images

Il lavoro riguardava lo studio e la realizzazione di in sistema embedde per il deinterlacciamento di immagini provenineti da vetture per la competizione sportiva. In particolare è stato realizzato un dispositivo che permette, attraverso una catena di elaborazione composta da digitalizzazione, deinterlacciamento e formattazione dei dati, di visualizzare, senza una significativa perdita in termini di qualità, i video provenienti dalle telecamere, di dimensioni contenute e a basso costo, montate a bordo delle automobili anche su monitor a scansione progressiva come quelli utilizzati nei comuni computer. Appare chiaro come, in tale prospettiva, servano strumenti adatti: efficienti, embedded, di prezzo limitato e a bassi consumi. Il progetto premiato compie un passo nella direzione giusta: si tratta di un esempio di realizzazione di uno strumento hardware/software in grado di implementare in maniera efficiente gli algoritmi attualmente noti sfruttando componenti comunemente presenti sul mercato e di costo contenuto, dimostrando una volta di più come sia possibile portare un progetto nato ex novo nell'ambito universitario ad un passo da quel processo di industrializzazione che demarca la linea di confine tra ricerca accademica ed applicazioni commerciali