GENOBU - Water buffalo genome sequencing for the quali-quantitative improvement of agrifood productions

GENOBU is an original, innovative and multidisciplinary project combining genome sequencing of the water buffalo to the healthiness of animals and the improvement of quality and quantity of buffalo food products. The project will develop know-how and innovative process technologies to be provided to breeders and agro-food industry, with the objectives of optimizing the efficiency in milk processing, and to ensure best nutraceutical value to buffalo foods.

Genotyping of the Landolt Duckweed Collection

The project is aimed at the genotyping, through plastid and nuclear molecular markers (TBP), of the whole collection of small aquatic macrophytes (Lemnaceae) known under the name of Landolt Duckweed Collection and currently managed by Dr Lammler in Zurich. This historical collection, the largest in Europe, includes about 500 clones of the 36 known duckweed species, coming from five continents. Accessions have been mostly characterized on a morphological basis, which may cause a high rate of misclassifications in some species, owing to the simplified structure of these tiny plants and the high similarity between some species.

Since long used as environmental bioindicators, duckweeds and renowned for their phytoremediation capacity. Due to their extraordinary fast growth, duckweeds are one of the most promising new crops, under intensive study for energy production and as a source of high quality proteins for animal and human nutrition, already under evaluation as a novel food by EFSA.

Results will be useful to:

• ascertain the classification of all clones, many of which are under study in many laboratories worldwide
• evaluating inter and intraspecific biodiversity
• contribute to duckweed taxonomy
• understanding duckweed evolution.

BRIDGES - Building Reflexivity and response-ability Involving Different narratives of knowledGE and Science

The complexity of the current global socio-ecological crisis highlights the limits of specialist science as the only voice capable of informing decisions. In the contemporary scenario, where the facts are uncertain, the values in contrast and the stakes are high, the social contract between science, society and politics is in a phase of profound transformation. To face this change, the scientific community has to revisit its social role, creating new relationships not only with society but also with ecological systems, to generate responsible research practices capable of producing relevant knowledge. BRIDGES is a social research project that develops trans-disciplinary and participatory research methods to strengthen the relationship between science, society and ecological systems in the Italian context. To do this, it uses as a case study a specific complex socio-ecological issue, very relevant in Italy: soil fertility.

BIO4VERBA - Safeguarding the biodiversity of the local Verzaschese and Bionda dell'Adamello goat breeds: enhancing their production and creating an ex-situ genetic reserve

BIO4VERBA project arises from the need of the breeders of the Verzaschese and Bionda dell’Adamello goat breeds to preserve and enhance their local breeds and the relative products.

BIO4VERBA has the following objectives:

1. to expand the Lombardia Farm Animal Genetic Resources Cryobank – LABank – launched in 2008 with the addition of the Bionda dell’Adamello breed and the increasing of the genetic material of the Verzaschese breed, already present in the LABank;
2. to characterize the milk of the two breeds (fat and protein composition, somatic cells content, fatty acids and terpenes, milk fat globule size, milk-coagulation time and microbiota composition);
3. analyze the “qualitative” contribution made by the milk of the Verzaschese breed in the production of Formaggella del Luinese PDO compared to the other cosmopolitan breeds, evaluating the microbiota and volatilome through an innovative approach (Next Generation Sequencing-Microextraction in Solid Phase Gas Chromatography-Mass Spectrometry);
4. to characterize the Fatulì of the Saviore Valley at microbiome and volatilome levels for its enhancement;

5.     Support breeders who prefer grazing, through a characterization of their products (Formaggella del Luinese PDO and Fatulì of the Saviore Valley) that allow to identify the contribution of grazing to the sensorial cheese properties (characteristics of cheeses).

CASTANEVAL - Chestnut cultivation development in Lombardy: leveraging native genetic resources

The CASTANEVAL project intends to respond to the need for scientific knowledge on Lombardy chestnut genetic resources in order to provide tools for the leverage and conservation of native germplasm and to undertake actions for the management recovery of chestnut groves. The pilot study areas are the chestnut groves in the municipality of Serle (BS) and in the Varese Pre-Alps (VA) The CASTANEVAL project aims also to develop a chestnut micropropagation system in order to offer a concrete, sustainable and economical tool for the conservation and multiplication of native germplasm of high local interest. The project will also study the ecological context and the degree of naturalness of the stands, from wild to coppice and cultivated varieties. A complete characterisation of the chestnut genetic resources in the areas under consideration will result from the integration of genetic, morphological, ecological and production data.

TRANSFER - Characterization and enhancement of historical lombard corn and wheat varieties

The adoption of agronomic practices aimed at maximizing production yields led, during the 20th century, to a drastic change in the characteristics of cultivated varieties toward specific characteristics of the final product and plant architecture.

So-called “old” varieties are sometimes considered capable of providing productions with better quality, organoleptic and health characteristics than those provided by modern varieties bred under intensive agronomic conditions.

The TRANFER project aims at the valorization of historical maize and wheat varieties typical of the Lombardy region through molecular, biochemical and phenotypic approaches. In particular, traits of interest related to resistance to fungal pathogens, characterization of seed morphology and nutraceutical qualities will be studied.

TRANFER will provide information on the diversity that exists in Lombardy’s germplasm collections for its valorisation and use in local production

ANASB BIG: Italian Mediterranean Buffalo - Innovative Technologies for Genetic Improvement

The project aims at the genetic improvement of innovative traits related to resistance/resilience to diseases (brucellosis, tuberculosis, paratuberculosis, transverse hemimelia), environmental sustainability (food efficiency, atmospheric emissions ), quality of productions (cheese making), enhancement of meat production as a secondary product (for example muscularity and Body Condition Score) as well as the maintenance of genetic variability of the Italian Mediterranean buffalo breed through inbreeding control and the creatio of a biobank of both male semen and embryos.

ANACLI I-BEEF 2 Italian Biodiversity Environment Efficiency and Fitness 2

The I-BEEF project aims not only to improve the breeding plan of the Italian Limousine and Charolaise breeds by adapting it to the new sustainability and environmental selection criteria, but also to speed up the genomic characterization of 6 autochthonous beef genetic types (TGA), namely: Calvana, Mucca Pisana, Pontremolese, Sarda, Sardo Bruna, Sardo Modicana. The main objectives are biodiversity conservation and inbreeding control

ASSONAPA SHEEP&GOAT - Sustainability Health Environment Economy Profitability & Genomic Organisation Animal (pheno)Typing

The SHEEP&GOAT project aims to introduce a series of actions related to the collection and use of phenotypic and molecular data in the Italian sheep and goat farming industry, with the goal of making the breeding sustainable and competitive, and contributing to the preservation and management of its rich biodiversity.

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SUS-MIRRI.IT - Strengthening the MIRRI Italian Research Infrastructure for Sustainable Bioscience and Bioeconomy

The Microbial Resource Research Infrastructure (MIRRI) is the pan-European infrastructure in charge of preservation, analysis, supply and exploitation of microbial resources and biodiversity. The project SUS-MIRRI.IT aims to develop research, services and training within the Italian network of culture collections MIRRI-IT, which will preserve biological diversity, collect and store data associated with microorganisms, carry on research and provide external users with support and services related to microbial resources. The optimised management of the bioresources at the MIRRI-IT Research Infrastructure, coupled with the digital platform and data handling/sharing strategy will allow the exploitation of microbial biodiversity and provide innovative solutions and products of biotechnological interest, stimulating the bio- and circular economy.

The IBBA Pisa unit participates with the microbial culture collection MLIP (Microbiology Lab IBBA Pisa), including microorganisms originated from different environmental and food sources.

DISCOVER THE MICROBIAL CULTURE COLLECTION CNR-MLIP

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.

IN-FACT One Health Basic and Translational Actions Addressing Unmet Needs on Emerging Infectious Diseases

The INF-ACT research program addresses pressing unmet needs of human emerging infectious diseases in both fundamental as well as in translational aspects, taking into consideration human health in a wider context including domestic and wild animals as potential disease reservoirs and environmental factors enhancing the possibility for spillover (One Health approach).

The project is focused on three “vertical” research nodes

• Emerging and re-emerging viral diseases (respiratory viruses and zoonotic viruses);
• Arthropod vectors and vector-borne pathogens (with a focus on VBDs most at risk of expand or emerge in Italy, such as arboviruses);
• Diseases sustained by bacteria and fungi resistant to multiple antibiotics (AMR and molecular mechanisms of MDR).

and two “transversal” research nodes to interact with the basic and translational activities

• Integrated “One Health” epidemiology (man, animal and man-animal), monitoring and mathematical models;
• Development of new therapeutic treatment strategies (identification of molecular targets, generation of small molecule libraries for drug discovery, testing of lead compounds and their optimization).

The INF-ACT consortium is composed of 25 research Institutions from the public and the private sector from all over Italy; the CNR is involved in Node 1, 3, 4 and 5.

SCALA-MEDI Improving sustainability and quality of Sheep and Chicken production by leveraging the Adaptation potential of LocAl breeds in the MEDIterranean area

The SCALA-MEDI project will optimise the sustainable use and conservation of local breeds of chicken and sheep from the Mediterranean region, focusing on adaptation to climatic conditions and consumer preferences .

The expertise and data from previous EU projects will be extended to the genetic and epigenetic characterisation of local resources and their adaptation to different production environments in three North African countries, Tunisia, Algeria and Morocco.

Tools and strategies will be developed to improve local breeds for sustainable production. Application of these tools will be demonstrated to farmers in diverse Mediterranean production systems.

AGRITECH SPOKE 1 Plant, animal and microbial genetic resources and adaptation to climatic changes

Resilience of agricultural and forest ecosystems under stressful conditions generated by climate change (CC) requires valorization and exploitation of genetic resources through cutting-edge conservation strategies, combined with deep characterization of genomes and high-throughput phenotyping.

Activities will include massive sequencing of accession/breeds/strains, extensive marker-based description of genomes, (pan)genome elucidation, deep phenotyping and multi-omics characterization.

Resulting information, processed through advanced methods for complex data analysis/interpretation/storage/management, will highlight superior alleles/haplotypes, identify beneficial interactions under a variety of conditions, and define conservation units.