Progetto PRIN 2010-2011

  • PRIN - 2010-2011 - PROGRAMMI DI RICERCA SCIENTIFICA DI RILEVANTE INTERESSE NAZIONALE
  • Biocostruzioni costiere: struttura, funzione, e gestione

UNIPD research team will estimate the degree of genetic connectivity among relevant species using molecular markers. UNIPD will  contribute, together with UNIBO and UNIVPM, to the identification of genetically homogeneous units of selected species by using genetic similarity between nodes as an indirect measure of connectivity functions. To this purpose, UNIPD will perform genetic analyses of species of superficial bioconstructions using mitochondrial markers and Restriction site Associated DNA sequencing, a recently proposed high throughput approach for Single Nucleotide Polimorphism discovery and genotyping. Samples for genetic analyses will be collected by different research units during the general field work of the project. UNIPD focal species will be identified based on the availability of sufficient sampling from relevant areas of the Italian coasts and based on adequate sample size for the downstream genetic analyses. The selection will include species with putatively high potential for dispersal and species with an expected higher degree of isolation.

UNIPD will investigate genetic connectivity with a two-way approach. First, sequencing of informative mitochondrial genes amplified by available or newly developed primers will be performed on about 500 individuals per species representative of different areas. This task will provide a first base of data on genetic connectivity, particularly useful for broad scale comparisons, using a well established molecular and data analysis procedure. Second, we will perform Restriction site Associated DNA sequencing with high throughput Illumina platform on the selected species to perform simultaneous identification and typing of thousand of Single Nucleotide Polimorphisms. In this case, sample size will be probably reduced and approximately one hundred individuals per species will be typed. The Restriction site Associated DNA sequencing approach allows to reduce the complexity of the sequenced genomic fragments by focusing on restriction anchored regions and, thanks to the possibility to tag the DNA of each individual, it allows the simultaneous sequencing of tens of samples followed by individual genotype reconstruction. This activity will produce the most accurate picture of genetic connectivity of the investigated species, enabling  comparisons at the small scale and the identification of footprints of selection at the genomic level.

UNIPD will standardize production and tagging of Restriction site Associated DNA libraries, and will perform the pre-processing of samples, as well as the post-processing of the high throughput sequencing efforts for all the research units involved in the genetic tasks. By assigning each sequence to the individual of origin, clustering sequences in locus-specific stacks, UNIPD will provide individual genotypes to UNIBO and  UNIVPM, ready to be used in data analysis.

National scientific coordinator

  • Prof. Ferdinando Boero, Università degli Studi del Salento

Research local Unit responsible

Keywords

CONNECTIVITY, GENETIC MARKERS, MITOCHONDRIAL DNA AND RAD SEQUENCING