POLYPLOIDBREEDING 4.0: Expanding the toolbox for cereal breeding: high-throughput genomics, 2D-3D phenomics and artificial intelligence for breeding with increasing genome complexity, from barley to durum and bread wheat

The project will focus on technology-driven breeding methods for the genetic improvement of crops (breeding 4.0) in diploid (barley, Hordeum vulgare) and polyploid (durum and bread wheat, Triticum durum, aestivum) species to increase cereal production in a sustainable and climate-smart way. Target technologies are high throughput phenotyping (e.g. drone phenotyping, root scans from rhizotrons) and genotyping (e.g. SNP array, exome sequencing, GBS) for artificial intelligence based breeding. Phenotypes will include yield, morphometric measurements, UAV (unmanned aerial vehicle: drone)-captured image data linked to morphology and production efficiency and rhizotron-based root scans (both 2D and 3D). Machine-learning methods, focussing especially on deep learning methods, will be used for phenomic and whole-genome predictions of target phenotypes.

Sheep-TreeSeq: Analisi scalabile della diversità genetica ovina usando alberi (grafi) di sequenze genomiche

Sheep-TreeSeq will perform scalable analysis of genomic diversity of sheep global populations using the novel tree sequence data format and methodology.

Technological advances in agritech have increased the availability of genomic data, leading to massive datasets (“big data”) which pose challenges for storage, processing and analysis, e.g. the sheer volume of the data, the rapid generation of new data (updating results, expanding training populations, streaming applications), and the heterogeneity of data sources (integration of data from multiple sequencing and genotyping platforms). The tree sequence algorithm offers an excellent way to address such challenges, by providing lossless compression and novel representation of the data. As an example, using tree sequences on the 1000 Bull Genome Project data a 90% lossless compression was obtained, reducing the data size from ~800 GB to 45 GB. For the Sheep TreeSeq project we will use around 3,500 sheep whole genome sequences and over 50,000 genotypes (~10 TB of data).

Our plan is to apply the tree sequence approach to compress the data and obtain a data representation highly suited for population genetics and demographic analysis: (i) principal component and genealogical nearest neighbour clustering; (ii) fixation index measuring genetic differentiation; (iii) deep neural network based clustering methods; iv) detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRR).

This is the first time that this approach is applied to sheep genomics.

FREECLIMB - Fruit Crops Resilience to Climate Change in the Mediterranean Basin

RABoLa - Sustainable strategies to reduce the use of antibiotics in dairy farming

The project, which involves different departments of the University of Milan (DISAA, DIMEVET, VESPA), researchers from the CNR ISPA and CNR IBBA and the DIANA Department of the Catholic University of the Sacred Heart of Piacenza, aims the primary identification of operative practices for reducing the use of antibiotics in the dairy cow herds. During the study, operative protocols already preliminary tested (administration of Aloe arborescens, use of Lactococcus lactis subsp. cremoris in pre and post dipping, molecules to inhibit Prototheca spp) will be validated during the entire lactation cycle of the cows.

This project will allow breeders to take advantages of new nutraceutical strategies and alternatives to the use of antibiotics, to enhance the innate defences and reduce the incidence and severity of mastitis. The validation of an effective protocol for the selective drying of animals would lead to a reduction of the preventive use of antibiotics, in line with what is requested at European level.

FARM-INN Farm-level interventions supporting dairy industry innovation

The project FARM-INN aims to provide farm-level interventions supporting dairy industry enhancing safety and quality of milk and cheese and providing the necessary scientific evidence and new insight regarding their functional properties. The proposed actions will be carried out assessing and improving animal welfare and the environmental sustainability. In particular, two aspects will be tackled and studied in the proposed project: i) the development and use of new feed supplements adsorbing mycotoxins and reducing pathogenic and spoilage clostridia in milk ii) the characterization of cheese making and functional properties of A1 and A2 variants of beta-casein in milk. The evaluation of environmental sustainability of the adsorbent supplementations to the cow rations and the potential effect of cheese making using A1 and A2 beta-casein types in milk analyses through a Life Cycle Assessment approach will be performed.

The project will offer opportunities to the dairy farmers to strengthen their competitiveness, in the context of a better control of safety and quality issues, and will help dairy industry in placing on the market high-quality products adapted to the new expectations of consumers.

USEFUL - Development of techniques and supply chain processes (farms and dairies) to optimize environmental, territorial and managerial factors aimed at obtaining greater production efficiency and qualitative excellence in the production of DOP and typical cheeses

The USEFUL project aims to solve some critical issues in the production of Lombardy PDO cheeses (Grana Padano and Taleggio) in order to guarantee the competitiveness of the agro-industry companies. To this end, supply chain strategies and operational tools will be developed that allow to improve the microbiological and cheese-making quality of the milk and to improve all the cheese-making processes. These objectives will be achieved through the integration of the 3 sub-projects: Coordination, Innovation and Technological Transfer.

The expected results are: 1) to identify new procedures to improve animal health, food safety and the microbiological quality and cheese-making properties of milk; 2) to identify innovative procedures and operational tools to be used in the dairy industry to monitor the cheese-making and maturing phases of the cheese; 3) to define guidelines, technical manuals and fact sheets on the various procedures and techniques.