Assessing the impact of components of the pan genome on segregation in Vitis vinifera crosses.

Supervisor: Michele Morgante

The analysis of variation in plants has revealed that their genomes are characterised by high levels of structural variation, suggesting that the concept of pan-genome, originally proposed for bacterial species, could be extended to plants. The pan-genome of a species comprises the core genome, shared by all the individuals of that species, and the dispensable genome, a portion of the genome that is present only in some individuals. Structural variants (SVs) are the main components of the dispensable genome and comprise rearrangements (inversions and translocations), copy number variants (CNVs), presence/absence variants (PAVs) as well as insertions of mobile elements (TEs).

PhD project consists in genotyping crosses between several Vitis vinifera varieties (including some self-crosses) and assess the effect of the presence of large CNVs and PAVs comprising genes on segregation. We will specifically focus on epistatic interactions among different SVs that may contain the same genes to evaluate if there are conditionally dispensable portions of the genome, i.e. genomic regions that can individually be absent but that must be present in at least one copy. In addition, we will measure the correlation between presence of various classes of TEs, recombination rate and segregation distortion.

In order to maximize the number of genotyped individuals while minimizing costs we will use Genotyping by Sequencing (GBS) or low-pass sequencing. Single locus as well as two locus combinations will be evaluated for segregation distortion. The availability of an accurate description of the SVs present in the parental genotypes will allow us to putatively link segregation distortion to SVs.

Assessing segregation distortion in Vitis vinifera varieties as a function of CNV and PAV distribution will improve our understanding of the possible effect of several components of the pan genome on segregation. 

Biography and contacts

Alice Fornasiero was born in 1988 in San Daniele del Friuli (Udine - Italy). She graduated in Biological Sciences (110/110 cum laude) in 2010 and in Functional Genomics (110/110 cum laude) in 2012 at the University of Trieste (Italy). She got the Master 2 degree in Génétique at Paris Diderot University. She started the doctoral course at the PhD school “Agriculture Science and Biotechnology” at the University of Udine in 2014.

fornasiero.alice@spes.uniud.it

afornasiero@appliedgenomics.org

[Phone 0432-629783]