Research

BIOGEN: Genomics and agrobiodiversity

Research area focuses on animals, plants and microbial genomes to identify potential genetic determinants involved in organism’s adaptation to different environment condition, i.e. natural, modified, or linked to human requirements. Genetic studies are based on the use of wet and in silico molecular approaches, statistical analysis of molecular data and collection and processing of Big Data, applied to biological systems of agricultural interest such as structural and reproductive biology, evolutionary genetics and germplasm conservation. Advanced technologies and bioinformatics tools are also used for the collection and examination of semen for the preservation of genetic resources.

Projects

In progress

FREECLIMB - Fruit Crops Resilience to Climate Change in the Mediterranean Basin
Start date: 01/04/2019   End date: 31/03/2022

Unione Europea

Milano   Sito web

Filippo Biscarini

Project duration:
01/04/2019 - 31/03/2022
Financing Body:
Unione Europea
Project research leader:
Filippo Biscarini
Headquarters:
Milano
Website :
Sito web

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


The FREECLIMB project is built to match topic 1.2.1 of the PRIMA (Sect. 2) framework in developing smart and sustainable farming systems in Mediterranean countries, to preserve natural resources (water and land use) by increasing production efficiency. This will be pursued by advancing knowledge on mechanisms of plant environmental adaptation and biotic/abiotic stress resilience. The project targets major fruit tree species with the aim of improving the availability of breeding and germplasm material adapted to limited external resources (input) and future climatic scenarios predicted for the Mediterranean area, through the characterization and exploitation of local biodiversity. The project will focus on key ideotypes elaborated in collaboration with Fruit Farming Actors (FFAs, breeders, nurseries, growers) with the core objective of providing a toolkit (diverse germplasm, tools and methods) to accelerate exploitation, breeding and selection of resilient varieties in key traditional fruit crops of Mediterranean agriculture (stone fruits such as peach, apricot and almond; Citrus spp.; grape and olive).
AGENZIA VENETA INNOV - BIONET
Start date: 20/07/2018   End date: 19/07/2022

Agenzia Veneta per l’innovazione nel settore primario

Lodi
Flavia Pizzi

Project duration:
20/07/2018 - 19/07/2022
Financing Body:
Agenzia Veneta per l’innovazione nel settore primario
Project research leader:
Flavia Pizzi
Headquarters:
Lodi

AGENZIA VENETA INNOV - BIONET


Collection, evaluation and conservation of genetic material of the Burlina cattle breed as a back-up in the medium and long period in the event of extinction of the breed or the onset of genetic problems in the breed (loss of genetic lines, excessive inbreeding, etc.). The preserved genetic material consists mainly of semen cryopreserved in liquid nitrogen and blood for future DNA extractions.

PARDOM - Parallel Domestications: the Phaseolus replicated experiment to understand genome evolution and adaptation
Start date: 29/04/2020   End date: 28/04/2023

MIUR

Milano, Roma
Francesca Sparvoli

Project duration:
29/04/2020 - 28/04/2023
Financing Body:
MIUR
Project research leader:
Francesca Sparvoli
Headquarters:
Milano, Roma

PARDOM - Parallel Domestications: the Phaseolus replicated experiment to understand genome evolution and adaptation


As similar sets of traits evolved over a wide range of species during domestication (e.g. seed size) the study of wild and domestic forms is a key model to understand convergent phenotypic evolution. Phaseolus is a unique example of multiple parallel domestications in five closely related species. Of these, P. vulgaris (PV), and P. lunatus (PL), were each domesticated independently in Mesoamerica and the Andes, defining at least four independent domestication events. To understand the genomic architecture of domestication, we will set-up a ‘domestication experiment’ with full factorial design for three factors: species, areas and wild/ domestic status. Using cutting-edge population genomics approaches (including machine learning methods) we will compare PV and PL, using high-quality whole-genome sequencing, pan-genome assembly, RNA sequencing, metabolomics, and phenotyping. TILLING-by-sequencing and genome editing will be used for functional validation of candidate domestication genes. Overall, this Project has both fundamental and applied implications: it addresses relevant, but poorly answered, questions related to genomic changes during selection and adaptation, and it will provide crucial knowledge for development of improved crop varieties to meet societal challenges.
ARGENTO
Start date: 29/08/2019   End date: 28/08/2022

MIUR

Milano   Sito web

Incoronata Galasso

Project duration:
29/08/2019 - 28/08/2022
Financing Body:
MIUR
Project research leader:
Incoronata Galasso
Headquarters:
Milano
Website :
Sito web

ARGENTO


ARGENTO project aims at introducing in Italy the new multipurpose oil crop, camelina (Camelina sativa (L.) Crantz), as a valuable source of healthy oil (rich in omega-3) and proteins for animal feeding. Therefore, during this project it will be evaluate the effects of the agronomic management in response to different environments on the final seed quality of newly released camelina lines aiming at optimizing camelina seed qualitative traits for poultry feeding (i.e., quails). In parallel to the optimization of the agronomic management a deep study of the biosynthetic pathway of the glucosinolates (GLSs, antinutritional compound)  and also a reduction in GLS content will be carried out by genome editing technologies that enable precise manipulation at a desired location within the genome.

CASTADIVA-Biodiversity and multifunctionality of the chestnut tree. Valorization of genetic resources for the development of Lombardy sub mountain areas
Start date: 11/06/2021   End date: 10/06/2023

Regione Lombardia

Milano
Eleonora Cominelli

Project duration:
11/06/2021 - 10/06/2023
Financing Body:
Regione Lombardia
Project research leader:
Eleonora Cominelli
Headquarters:
Milano

CASTADIVA-Biodiversity and multifunctionality of the chestnut tree. Valorization of genetic resources for the development of Lombardy sub mountain areas


Over the centuries, the chestnut tree, cultivated for its fruits and timber, has become an essential element of subsistence for many societies in mountain and sub-mountainous areas, revealing its potential as a multifunctional species. However, today a large part of chestnut forests is in a state of degradation and abandonment, mainly due to the depopulation of rural areas, global climate change and recent outbreaks of exotic pests. With a view to the recovery and enhancement of chestnut genetic resources, the CASTADIVA project mainly aims to:

  • map the chestnut areas of pilot areas in the Lombardy Region (chestnut groves in the Municipality of Serle, BS and in the Varese Prealps, VA);
  • evaluate the genetic diversity of chestnut woods, genetically characterize local varieties
  • to characterize the fruits from a morphological, pomological, qualitative and nutritional point of view
  • integrate data obtained from genetic and morphometric analysis with ecological, silvicultural, phytosanitary and possibly socio-economic data;
  • identify the best practices and management criteria for the conservation and enhancement of chestnut genetic resources to be applied in the areas of greatest interest; transfer information to local administrations and the agricultural world.
Genotyping of the Landolt Duckweed Collectionn
Start date: 01/08/2021   End date: 31/07/2024

Landolt Duckweed Collection

Milano
Laura Morello

Project duration:
01/08/2021 - 31/07/2024
Financing Body:
Landolt Duckweed Collection
Project research leader:
Laura Morello
Headquarters:
Milano

Genotyping of the Landolt Duckweed Collectionn


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.

Completed

COVES - Development and validation of a rapid method for the detection of SARSCoV-2 on environmental surfaces
Start date: 21/04/2020   End date: 20/10/2020

Regione Lombardia

Lodi
Paola Cremonesi

Project duration:
21/04/2020 - 20/10/2020
Financing Body:
Regione Lombardia
Project research leader:
Paola Cremonesi
Headquarters:
Lodi

COVES - Development and validation of a rapid method for the detection of SARSCoV-2 on environmental surfaces


The COVES project will develop and validate a simplified sampling and analysis procedure on a portable device for the specific and sensitive detection of the SARS-CoV-2 virus in the environment. This procedure will ensure greater safety in the work areas, thus reducing the negative impact that the COVID-19 emergency has on the local and national economy and decreasing the gap between the information and the suggested solutions. The main result of the project will be the development of a method for the rapid analysis of the SARS-CoV-2 in the environment, suitable for a field-use also by non-expert users. The project involves Hyris Ltd, leader of the project, which develops the technology, IBBA CNR which will take charge of the method validations and IZSLER (section of Pavia) which will validate “in-situ” the efficacy of this method on various contaminated surfaces using SARS-CoV-2 positive samples with known concentration.

BILLBOARDADVERTISING PLATE POSTER

DNA analysis using a low-cost portable device for food safety
Start date: 13/02/2019   End date: 12/06/2019

Hyris Ltd

Lodi   Sito web

Bianca Castiglioni

Project duration:
13/02/2019 - 12/06/2019
Financing Body:
Hyris Ltd
Project research leader:
Bianca Castiglioni
Headquarters:
Lodi
Website :
Sito web

DNA analysis using a low-cost portable device for food safety


The objective of this project is the development of new specific molecular methods for pathogen detection along the dairy supply chain, in order to overcome the critical issues related to field sample analysis. In particular, within this project Hyris Ltd intends to implement on its platform new Real-Time PCR protocols for analyzing dairy products, in order to detect the presence of pathogens responsible for toxic infections along the production chain.
InterOmics – Sottoprogetto Tecnologie omiche per la valorizzazione del germoplasma di frumento duro
Start date: 29/07/2014   End date: 31/12/2018

MIUR

Milano, Lodi   Sito web

Aldo Ceriotti

Project duration:
29/07/2014 - 31/12/2018
Financing Body:
MIUR
Project research leader:
Aldo Ceriotti
Headquarters:
Milano, Lodi
Website :
Sito web

InterOmics – Sottoprogetto Tecnologie omiche per la valorizzazione del germoplasma di frumento duro


Il progetto si articola in tre step:

1) L’avvio di un’iniziativa volta al sequenziamento del genoma di frumento duro; l’obiettivo sarà perseguito attraverso strategie complementari che, nel loro complesso, permetteranno di affrontare le due principali problematiche associate al sequenziamento del complesso genoma di questa specie (presenza di due genomi altamente simili e alta percentuale di sequenze ripetute).

2) La caratterizzazione a livello proteomico e metabolomico delle varietà utilizzate per gli studi di genomica. I risultati di questa analisi saranno integrati con quelli prodotti dall’analisi genomica, evidenziando la presenza di eventi post-trascrizionali e post-traduzionali nella biosintesi delle proteine e fornendo indicazioni sulla attivazione di specifici percorsi metabolici.

3) La fenotipizzazione di 150 accessioni già genotipizzate (profili SNP) e derivate tramite Single Seed Descent da landraces/ecotipi. Questa collezione è conservata presso la sede di Bari dell’Istituto di Bioscienze e Biorisorse del Consiglio Nazionale delle Ricerche. Questi materiali consentiranno la realizzazione di una analisi di mappatura per associazione tra gli SNPs e le caratteristiche morfo-fisiologiche delle piante, fornendo quindi le basi per l’utilizzazione di queste risorse genetiche nella costituzione di nuove varietà di frumento duro.

FilAgro – Innovative and sustainable strategies for the agri-food chain
Start date: 05/08/2013   End date: 31/10/2015

Regione Lombardia

Milano, Lodi
Diego Breviario

Project duration:
05/08/2013 - 31/10/2015
Financing Body:
Regione Lombardia
Project research leader:
Diego Breviario
Headquarters:
Milano, Lodi

FilAgro – Innovative and sustainable strategies for the agri-food chain


The FILAGRO project aims to provide solutions to several issues that are emerging in the field of modern agriculture. They concern: production sustainability, biodiversity and environment preservation; improvement in food quality, safety and healthy and nutritional aspects; technology development in favor of industry; new knowledge dissemination. These issues are highlighted as of high importance in the EXPO 2015 and Horizon 2020 programs as well as in the 2013-2015 plan of the Agriculture Directorate of the Lombardy Region.

GENOBU - Water buffalo genome sequencing for the quali-quantitative improvement of agrifood productions
Start date: 01/01/2019   End date: 31/12/2021

MIUR

Lodi
Bianca Castiglioni

Project duration:
01/01/2019 - 31/12/2021
Financing Body:
MIUR
Project research leader:
Bianca Castiglioni
Headquarters:
Lodi

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.

ASSONAPA - Creation of the criobank of local Italian sheep and goat breeds
Start date: 30/05/2018   End date: 29/05/2020

Associazione Nazionale della Pastorizia (ASSONAPA)

Lodi
Flavia Pizzi

Project duration:
30/05/2018 - 29/05/2020
Financing Body:
Associazione Nazionale della Pastorizia (ASSONAPA)
Project research leader:
Flavia Pizzi
Headquarters:
Lodi

ASSONAPA - Creation of the criobank of local Italian sheep and goat breeds


The aim of the project was the management of the genetic variability of the local Italian sheep and goat breeds through the choice of donors to be stored in the Cryobank and therefore the collection and conservation of their genetic material. For this purpose, the donors of genetic material to be stored in the Criobank have been identified in the Massese sheep, Langhe sheep, Gentile sheep of Puglia, Garganica goat and Nicastrese goat breeds. The seminal material was then collected using reproductive biotechnologies, such as the extraction of epididymal spermatozoa procedures, that had previously been developed in the IBBA laboratories in Lodi. The material collected in the project can be distributed to breeders for the insemination of the females for proper management of the genetic variability of their herds and more generally of the whole breed.

NewPearl - Combining new phenotyping approaches and next generation sequencing to accelerate breeding in pearl millet, an orphan cereal from arid regions
Start date: 01/05/2013   End date: 30/09/2018

Fondazione Cariplo

Milano
Francesca Sparvoli

Project duration:
01/05/2013 - 30/09/2018
Financing Body:
Fondazione Cariplo
Project research leader:
Francesca Sparvoli
Headquarters:
Milano

NewPearl - Combining new phenotyping approaches and next generation sequencing to accelerate breeding in pearl millet, an orphan cereal from arid regions


Pearl millet is a major crop contributing to food security for poor farmers in arid and semi arid regions of the world. The project aims at providing tools and knowledge to accelerate the breeding of new pearl millet varieties with increased nutritional qualities as well as better adaptation to environmental stresses. New phenotyping methods will be used to characterize a collection of 100 pearl millet inbred lines for 1) root system development and interaction with the rhizosphere microbiota and 2) nutritionally important seed compounds: phytic acid and C-glucosylflavones (goitrogen). The impact of certain root phenotypes on agronomical performances will also be assessed in field trials. In parallel, thousands of high quality DNA markers will be produced on the inbred lines for phenotype/genotype association purpose using next generation sequencing technologies. Together, these approaches should lead to the identification of QTLs/genes involved in agronomically relevant root and seed quality traits.

FASTBIOS
Start date: 01/06/2018   End date: 31/12/2019

Blumen Group SpA, Molino Zanone

Milano
Francesca Sparvoli

Project duration:
01/06/2018 - 31/12/2019
Financing Body:
Blumen Group SpA, Molino Zanone
Project research leader:
Francesca Sparvoli
Headquarters:
Milano

FASTBIOS


Aim of the project is the development of common bean lines/varieties with an improved nutritional profile (biofortified and low anutinutrients) resulting from a breeding program in which the biofortified and low antinutrients parents have been provided by IBBA-CNR. These lines will be used for the production of innovative products, such as bakery products, pasta or snacks, destined to specific target consumers, such as diabetics, celiac or individuals with iron requirements. To this purpose bean flours will be prepared from genotypes with different compositions in nutrients and bioactive compounds.

CERSAA17 - Identification of sequential polymorphisms, exclusive to Citrus x myrtifolia Savona ecotype or Chinotto di Savona
Start date: 28/08/2017   End date: 27/02/2018

Centro Di Sperimentazione e Assistenza Agricola (CERSAA)

Milano
Luca Braglia

Project duration:
28/08/2017 - 27/02/2018
Financing Body:
Centro Di Sperimentazione e Assistenza Agricola (CERSAA)
Project research leader:
Luca Braglia
Headquarters:
Milano

CERSAA17 - Identification of sequential polymorphisms, exclusive to Citrus x myrtifolia Savona ecotype or Chinotto di Savona


The project aims to identify unique DNA polymorphisms charactering Citrus × myrtifolia, Savona ecotype (Chinotto di Savona) with particular attention to intronic sequences. The goal is to identify single nucleotide polymorphisms specific for the investigated ecotype, in order to genetically characterize it from other ecotypes spread throughout the country, encouraging cultivation and production.

ANAFI - Analysis of genetic variability and haplotype at protein milks loci aimed at protecting biodiversity and producing diversified milks
Start date: 06/12/2017   End date: 05/12/2019

Associazione Nazionale Allevatori di bovini della razza Frisona Italiana (ANAFI)

Lodi   Sito web

Paola Cremonesi

Project duration:
06/12/2017 - 05/12/2019
Financing Body:
Associazione Nazionale Allevatori di bovini della razza Frisona Italiana (ANAFI)
Project research leader:
Paola Cremonesi
Headquarters:
Lodi
Website :
Sito web

ANAFI - Analysis of genetic variability and haplotype at protein milks loci aimed at protecting biodiversity and producing diversified milks


The objective of this project was to analyse how the frequencies of the main casein variants and haplotypes changed in the Italian Holstein breed, and the possible effects on milk technological properties (milks more suitable for dairy processing, with potential greater digestibility). The results obtained by the genotyping (Illumina beadchip) of all the historical data available (over 220,000 Italian Holstein Friesian individuals and over 600 Italian Jersey individuals) were analysed in order to verify how the allele frequencies to the casein genes have been changing in recent years. The results indicate that the increase of the B allele, favourable for cheese-making, and the decrease of the unfavourable E allele at the k-casein are compensating the increase of the A 2 allele at the β-casein, generally maintaining a good proportion of haplotypes associated with good cheese-making properties.

RABoLa - Sustainable strategies to reduce the use of antibiotics in dairy farming
Start date: 28/12/2018   End date: 27/12/2021

Regione Lombardia

Milano, Lodi   Sito web

Paola Cremonesi, Laura Morello

Project duration:
28/12/2018 - 27/12/2021
Financing Body:
Regione Lombardia
Project research leader:
Paola Cremonesi, Laura Morello
Headquarters:
Milano, Lodi
Website :
Sito web

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.

Istituto

Search website