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Genomics technologies and applications

Image by Stijn te Strake

Coordinator : Prof. Paolo Ajmone Marsan


Members :

Sara Albarella, Mario Barbato, Francesca Bertolini, Stefano Biffani, Stefano Capomaccio, Martino Cassandro, Alessio Cecchinato, Elena Ciani, Licia Colli, Paola Crepaldi, Andrea Criscione, Edo D'Agaro, Nicolò Pietro Paolo Macciotta, Salvatore Mastrangelo, Paolo Zambonelli. Alessandra Crisà, Cinzia Marchitelli, Marco Milanesi, Riccardo Moretti.


Goals:

The objectives are to promote:

  1. Updating knowledge on genomics technologies and applications and on methods of integration with other -omics technologies;

  2. Integration of the knowledge of the national scientific community;

  3. Involvement of young people and research/creation of training opportunities for their education;

  4. Interactions with other commissions (e.g. statistics, welfare);

State of the art and reasons justifying the activation of the Study Commission:

 

Given the decreasing costs of sequencing, the development of new methods for capturing specific regions of the genome and new T2T technologies, it is possible that in the near future SNP arrays will be progressively joined or even replaced by targeted or complete genome sequencing. T2T sequencing will allow the reliable detection of polymorphisms not captured by SNP arrays, such as CNVs, inversions, indels. The latter are often not in LD with adjacent SNPs, due to their different evolution dynamics. It is necessary that the transition from the use of arrays to that of sequences and new polymorphisms is accompanied by a critical evaluation of the quality of the data and the ability to manage big data. Even with complete genome sequencing, it remains extremely difficult to identify the gene and even more so the causative mutation of a marker-trait association signal. 

 

The integration of genomic information with that produced by other biological sciences, including -omics sciences, appears to be promising, but multi-omics models are still in their infancy. Identification of the true genetic architecture of phenotypic differences associated with genomic signals is important to increase knowledge of the biology of livestock species and the effectiveness of genetic improvement. The study of epigenetic variants, their effect and their possible passage through generations is currently a topic that deserves attention to understand if and how epigenetics can be included in breeding programs. The genetics of biodiversity, conservation and adaptation to the environment (landscape genomics) is poorly integrated with selection. How is it possible to validate the selection signatures identified in many works? Can they be integrated into breeding? AI models for genome analysis must be compared with "classic" big data analysis methods, in order to understand any added value.

 

Activities of the Study Commission:

 

The Select Commission, made up of the coordinator and the four supporting proponents, will meet for the first time electronically to define the possible sub-commissions and the objectives to propose. In general, and following preliminary contacts, there will be three sub-commissions under discussion, focused on:

 

  1. management and use of WGS data in breeding.

  2. interactions between genomics-other -omics sciences for the identification of causative genes/variants.

  3. biodiversity and breeding.

Once the support has been collected from the ASPA scientific community, a second telematic meeting will be organized to discuss the proposed scheme, activate the sub commissions with at least four participants and possibly discuss new proposals. A roadmap of activities will also be defined until the next ASPA Congress.

 

The invitation to participate will be extended to young researchers and doctoral students as auditors. It will be proposed that the sub-commissions decide the calendars of their meetings, while a global telematic meeting will be organized every quarter. Two global meetings will be organized in person or mixed, one on the occasion of the ASPA Congress and the second 6 months after the first.

 

Deliverables of the Study Commission:

 

Type and number of deliverables will depend on the number and interests of participants. In the first year the minimum objective is the drafting of a review to be published in the Italian Journal of Animal Science and the definition of a training program for young researchers.

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