Sequencing and Genotyping

Technological Platform (DGBPF S) - Development of new methods of experimental investigation.

The Sequencing and Genotyping Platform takes part in the research and development activity of the CRI by offering support at the researchers activity and with the development of new methods of experimental investigation. The first purpose of the Platform is the development of new investigative methods, with the acquisition of new knowledge in the green biotechnology field and the continuous improvement of present and future instruments.

 

Platform facilities & Application fields: Three FREEDOM EVO TECAN workstations can automate a diverse range of applications including primary and secondary screening, DNA extraction, amplification set-up, sample dilution, normalization and assay development. Thanks to the 96-capillary 3730xl DNA analyzer and the 16-capillary 3130xl DNA analyzer a wide variety of sequencing and fragment analysis applications including resequencing, microsatellite analysis, AFLP, LOH, SSCP, SNP screening and SNP validation are available to allowing researchers to save time, reduce costs and increase productivity.  The Roche Genome Sequencer FLX and the Illumina HiScanSQ system integrates the power and resolution of next-generation sequencing with the high-throughput capacity of genotyping and gene expression arrays, delivering unprecedented flexibility for experimental design.

Liquid Handling and Robotics - Three FREEDOM EVO TECAN workstations are combined in a robotics platform with various liquid handling and manipulative robotic arms. Each platform is combined with a wide choice of robotic arms, liquid handling tools (8, 96 or 384 multichannel arms) and application options powered by straightforward software to meet individual needs. Freedom EVO workstations can automate a diverse range of applications including primary and secondary screening, DNA extraction, amplification set-up, sample dilution, normalization and assay development.

Sequencing and Genotyping platform - Thanks to two 96-capillary 3730xl DNA analyzer and three 16-capillary 3130xl DNA analyzer a wide variety of sequencing and fragment analysis applications including resequencing, microsatellite analysis, AFLP, LOH, SSCP, SNP screening and SNP validation are available to allowing researchers to save time, reduce costs and increase productivity.  The Roche Genome Sequencer FLX and the Illumina HiScanSQ system integrates the power and resolution of next-generation sequencing with the high-throughput capacity of genotyping and gene expression arrays, delivering unprecedented flexibility for experimental design.

Labs instrumentation - Inside the Sequencing Platform, there are many instruments of the latest generation, both available for quantitative and qualitative analysis. The Platform management of these resources allows their maintenance in a complete efficiency, their correct use and the possibility of exploiting the technologic potentials of C.R.I. by the researcher staff above all, by a service of on-line reservation.

Platform services

The activity of direct support of the Platform allows the extension and the achievement of the purposes, which were appointed in the C.R.I staff research projects. This support directly involves the Platform staff, whose highly qualificated vocational training, allows the achievement of the expected results and, where asked, the result analysis too.

Sample Preparation

  • Nucleic Acid extraction, purification and quantification (DNA, RNA, plasmid)
  • BAC pooling strategy
  • NGS Library preparation and quantification

Sequencing Support

  • SANGER Sequencing (PCR, Plasmid, BAC sequencing)
  • Next Generation Sequencing (genomic DNA, cDNA, Amplicons, Paired End)

Genotyping Support

  • SSR Genotyping
  • SNP Genotyping

Main publications

  • Chagné D., Krieger C., Rassam M., Sullivan M., Fraser J., André C., Pindo M., Troggio M., Gardiner S.E., Henry R.A., Allan A.C., McGhie T.K., Laing W.A. (2012) QTL and candidate gene mapping for polyphenolic composition in apple fruit. BMC Plant Biology 12(12), 1-16.
  • Illa E., Sargent D.J., Lopez Girona E., Bushakra J, Cestaro A., Crowhurst R., Pindo M., Cabrera A., van der Knaap E., Iezzoni A., Gardiner S., Velasco R., Arús P., Chagné D., Troggio M. (2011). Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family. BMC Evolutionary Biology 11(9), 1-13.
  • Scalabrin S., Troggio M., Moroldo M., Pindo M., Felice N., Coppola G., Prete G., Malacarne G., Marconi R., Faes G., Jurman I., Grando M.S., Jesse T., Segala C., Valle G., Policriti A., Fontana P., Morgante M., Velasco R. (2010). Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar. BMC Genomics 11(204), 1-14.
  • Velasco R. et al. (2010). The genome of the domesticated apple (Malus x domestica Borkh.). Nature Genetics 42, 833-839.
  • Carra A., Mica E., Gambino G., Pindo M., Moser C., Pè M.E., Schubert A. (2009). Cloning and characterization of small non-coding RNAs from grape. The Plant Journal 59(5), 750-763.
  • Pindo M., Vezzulli S., Coppola G., Cartwright D.A., Zharkikh A., Velasco R., Troggio M. (2008). SNP high-throughput screening in grapevine using the SNPplex ™ genotyping system. BMC Plant Biology 8(12), 1-6.
  • Troggio M., Vezzulli S., Pindo M., Malacarne G., Fontana P., Moreira Maia F., Costantini L., Grando M.S., Viola R., Velasco R. (2008). Beyond the genome opportunities for a modern viticulture: a research overview. American Journal of Enology and Viticulture 59(2), 117-127.
  • Vezzulli S., Micheletti D., Riaz S., Pindo M., Viola R., This P., Walker M.A., Troggio M., Velasco R. (2008). A SNP transferability survey within the genus Vitis. BMC Plant Biology 8(128), 1-10.
  • Velasco R. et al. (2007). A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PloSONE 2(12), 1326.
  • Troggio M., Malacarne G., Coppola G., Segala C., Cartwright D.A., Pindo M., Stefanini M., Mank R., Moroldo M., Morgante M., Grando M.S., Velasco R. (2007). A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot noir bacterial artificial chromosome contigs. Genetics 176(4), 2637-2650.

platform services

online booking - The activity of direct support of the Platform allows the extension and the achievement of the purposes, which were appointed in the C.R.I staff research projects. This support directly involves the Platform staff, whose highly qualificated vocational...

platform equipments

online booking - Inside the Sequencing Platform, there are many instruments of the latest generation, both available for quantitative and qualitative analysis. The Platform management of these resources allows their maintenance in a complete efficiency, their correct use and the...

platform facilities & application fields

Three FREEDOM EVO TECAN workstations can automate a diverse range of applications including primary and secondary screening, DNA extraction, amplification set-up, sample dilution, normalization and assay development. Thanks to the 96-capillary 3730xl DNA analyzer and the 16-capillary 3130xl DNA analyzer a wide variety of sequencing and fragment analysis applications including resequencing,...