1) Identification and analysis of mutations in candidate genes
for meat quality and production traits in pigs.
2) Gene expression analysis for the identification of genes
affecting meat quality traits: study of the post mortem
skeletal muscle gene expression in pigs.
3) Identification and analysis of QTL and QTG for milk
production and quality traits in Italian Dairy cattle breeds.
4) Identification and study of genes affecting coat and feather
color in livestock and game species.
5) Development of new systems for animal products authentication
and traceability.
6) Studies of animal models for human complex genetic
pathologies (pig and rabbit).
7) Application of genomics in the rabbit.
8) New sex determination DNA based methods in animals.
9) Analysis of Copy Number Variations in livestock genomes.
10) Next Generation Sequencing
11) Metabolomics in livestock
12) Genome Wide Association Studies in livestock
13) Sequencing and ri-sequencing of genomes in livestock and
game-species
14) Selection signature in livestock
15) Biodiversity in livestock
16) Genomic Selection in livestock
17) Analysis of microbiota
18) Study of domestication processes in farm animals
19) Environmental DNA analyses.
20) Pig male castration
21) Apiculture genomics
1) Identification and analysis of mutations in candidate
genes for meat quality and production traits in pigs. These
research activities have as main objectives the study of candidate
genes for meat quality and production traits in Italian heavy pigs
in order to identify DNA markers useful for marker assisted
selection plans. The considered traits are the following:
glycolytic potential, cathepsin activity, backfat thickness,
intermuscular fat, lean meat percentage, and average daily gain.
Identification of mutations is carried out in silico mining DNA
databases (in collaboration with the Biocomputing Group, University
of Bologna) and by sequencing. High throughput genotyping platforms
are used to analyse these polymorphisms in different pig
populations. Association studies are carried out with appropriate
statistical models, including genome wide association approaches.
This activity is carried out in collaboration with Associazione
Nazionale Allevatori Suini (ANAS).
2) Gene expression analysis for the identification of genes
affecting meat quality traits: study of the post mortem
skeletal muscle gene expression in pigs. To evaluate the
possibility to use porcine post mortem skeletal muscle gene
expression or gene stability as potential indicator of meat quality
traits, several post mortem times are investigated using
Affymetrix microarray chips.
3) Identification and analysis of QTL and QTG for milk
production and quality traits in Italian Dairy cattle breeds.
This research line is towards the identification of QTL
(Quantitative Trait Loci) and QTG (Quantitative Trait Genes) for
milk composition (protein and fat percentage), milk somatic cell
count and milk yield in the Italian Holstein Friesian breed. The
study is based on the use of the daughter design and the milk
selective DNA pooling strategy in order to reduce the cost of
genotyping. Identified QTL and QTG are also investigated in other
dairy and dual purpose Italian cattle breeds.
4) Identification and study of genes affecting coat and
feather color in livestock. The species included in this
research program are farm animals such as cattle, pig, sheep, goat,
rabbit and avian species as well as wild species. The basic biology of
coat colour determination is of interest as well as the application
of the results for breed traceability.
5) Development of new systems for food product characterizations,
authentication and traceability. This research activity includes: i) the application of genomics, metagenomics and transcriptomics for the characterization of food products; ii) the use of metabarcoding approaches for the authentication of animal and plant products and honey; iii) the use of tracers of plant, animal or
microbial origin are used to label in appropriate way animal
products. DNA of the tracers can be used to trace and authenticate
the products (patented); iv) the identification of DNA markers for breed traceability of mono-breed products.
6) Studies of animal models for human complex genetic
pathologies. Two animal models are included in this research activity: the
pig as a model for human obesity and the rabbit as a model for
enteric neuromuscular dysfunction.
7) Application of genomics in the rabbit. The study includes: i) candidate genes are selected mainly on the basis of
their putative effects on muscle mass, growth rate, reproduction parameters and disease resistance; ii) genome wide association studies for several production traits; iii) analysis of the rabbit genome for structural mutations and NUMTS integration. The studies are carried out in collaboration with Martini Group.
8) New sex determination DNA based methods in animals.
Genes on sex chromosomes are studied and new DNA based based for
sex determination are developed.
9) Analysis of Copy Number Variation in the livestock
genomes. Copy Number Variations (CNVs) at the
genome wide level are identified using array comparative genome
hybridization (aCGH) and high throughput SNP genotyping using
Illumina platform. CNVs are confirmed using other techniques and
using for association analysis with phenotypic traits and in
population genetic studies.
10) Next Generation Sequencing. Application of Next
Generation Sequencing technologies at different levels:
developments of new protocols and approaches to study microbial and
livestock genomes; applications in different biomedical fields.
11) Metabolomics in livestock. Development of methods to
analyse metabolites and metabolome characterization of
livestock using several targeted and untargeted approaches.
12) Genome Wide Association Studies in livestock. Use of
high density SNP chips in pig and cattle to identify chromosome
regions and genes associated with production traits.
13) Sequencing and ri-sequencing of genomes in livestock and
game-species. Use of Next Generation Sequencing technologies to
obtain information about the variability of the genomes within
species. Production and analysis of RNA-Seq and microRNA-seq
data.
14) Selection signature in livestock and genomic inbreeding. Identification of
genomic regions under selection in farm animals. Methodological aspects to calculate genomic inbreeding coefficients.
15) Biodiversity in livestock. Characterization of breeds
and populations with next generation sequencing data.
16) Genomic Selection in livestock. Implementation of new
methods and strategies for the application of genomic selection
approaches in pigs.
17) Microbiota analysis in livestock. Characterization of microbiota in
animals by using next generation sequencing approaches. Association with genetic variability of the host.
18) Study of domestication processes in farm animals.
Analysis of evolutionary processes that have contributed to the
domestication of farm animals starting from wild
counterparts.
19) Environmental DNA (eDNA) studies. Application of metagenomic approaches for the characterization of environmental signatures, including the analysis of plant-sucking insects in agricultural and forest lanscapes.
20) Pig male castration. All aspects related to pig castration, including alternatives to the surgical castration and related problems including husbandry and genetics aspects.
21) Apiculture genomics. Honey metagenomic analysis to identify environmental DNA markers. Genomics of parasites and pathogens of the honey bees. Authentication of honey based on DNA markers of botanical, entomological and geographic origin.
