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Novel variation in plant breeding and the plant pan-genomes

Objective

"The analysis of variation in plants has revealed that their genomes are characterised by high levels of structural variation, consisting of both smaller insertion/deletions, mostly due to recent insertions of transposable elements, and of larger insertion/deletion similar to those termed in humans Copy Number Variants (CNVs). These observations indicate that a single genome sequence might not reflect the entire genomic complement of a species, and prompted us to introduce the concept of the plant pan-genome, including core genomic features common to all individuals and a Dispensable Genome (DG) composed of partially shared and/or non shared DNA sequence elements. The very active transposable element systems present in many plant genomes may account for a large fraction of the DG. The mechanisms by which the CNV-like variants are generated and the direction of the mutational events are still unknown. Uncovering the intriguing nature of the DG, i.e. its composition, origin and function, represents a step forward towards an understanding of the processes generating genetic diversity and phenotypic variation. Additionally, since the DG clearly appears to be for the most part the youngest and most dynamic component of the pan genome, it is of great interest to understand whether it is a major contributor to the creation of new genetic variation in plant evolution and more specifically in the breeding process. We thus aim at:
i) defining extent and composition of the pan genome in two plant species, maize and grapevine;
ii) identifying the different mechanisms that generate and maintain the dispensable portion in these 2 species;
iii) identifying the phenotypic effects of the DG;
iv) estimating the rates and modes of creation of new genetic variation due to DG components and whether this could represent an important factor in the breeding process;
v) extending our findings to other plant species for which the genome sequence in the meantime may have become available."

Call for proposal

ERC-2011-ADG_20110310
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Host institution

UNIVERSITA DEGLI STUDI DI UDINE
Address
Via Palladio 8
33100 Udine
Italy

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Activity type
Higher or Secondary Education Establishments
Administrative Contact
Paolo Ceccon (Prof.)
Principal investigator
Michele Morgante (Prof.)
EU contribution
€ 2 252 055

Beneficiaries (2)

UNIVERSITA DEGLI STUDI DI UDINE
Italy
EU contribution
€ 2 252 055
Address
Via Palladio 8
33100 Udine

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Activity type
Higher or Secondary Education Establishments
Administrative Contact
Paolo Ceccon (Prof.)
Principal investigator
Michele Morgante (Prof.)
ASSOCIAZIONE ISTITUTO DI GENOMICA APPLICATA
Italy
EU contribution
€ 221 445
Address
Via J. Linussio
33100 Udine

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Activity type
Research Organisations
Administrative Contact
Erica Ietri (Ms.)