Giorgio Chessari

Biodiversity is the key-word of his research topic, which consists in the application of omics approaches to investigate the genetic diversity in livestock species, with a focus on Sicilian local breeds as an important part of the genetic heritage. Several omics techniques are used to determine the within- and between breeds variability, their genomic structure and ultimately to be able to enhance their products. In this context, three different approaches are involved: (1) analysis of the biodiversity using the genomic characterization via medium- and/or high-density SNP (single nucleotide polymorphism) arrays, (2) implementation of imputation technique on SNP panels to WGS (whole genome sequencing) data, (3) characterization of sheep and goat milk microbiota as an important index for food quality and animal health.

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PROJECTS

Biodiversity analyses of local livestock breeds

• Italy counts several local livestock populations, some of which do not have a recognized genetic structure. They are an important part of the species biodiversity. Most of these populations are kept by smallholders under extensive or semi-extensive production systems, and are well adapted to local environments, representing an important economic source in marginal areas. In this context, a genetic characterization is necessary to provide information in establishing proper management plans. The availability of genome assemblies for several domestic animals allows the identification of thousands of single nucleotide polymorphisms (SNPs) distributed along the entire genome, which permit to retrieve background information concerning genomic structure and admixture events. The publications well explain not only the genetic identity of a breed, but also its importance due to resistance or productive traits. 

Imputation analysis and implementation of innovative methodologies

• Genotype imputation has become a common method to augment the information obtained from low- and medium-density SNP panels. This approach provides a wider view of the genome by predicting those gaps not assayed during the genetic characterization through SNP arrays. Thus, imputation technique can be used to boost the number of markers that can be tested for association studies or population analyses, reducing the cost of genotyping. The aim of this part of the project is to perform biodiversity analyses on horse species in order to evaluate the genetic diversity that occurs within each breed, as well as the relationships among them. On the other hand, there is a more methodological approach that wants to prove if and how imputation technique can affect the results, by comparing the same analyses before and after imputation. SVs are a relevant source of genomic variation that can be associated to several types of alterations on the genome (e.g. deletion, insertion, duplication) and are still not commonly used in association and speciation studies because of their challenging identification.

Milk microbiota characterization in sheep and goat local breeds

• In livestock science, nutrigenomics aims to improve the knowledge in animal production by integrating genomic approaches into nutrition research, and thus studies the genotype-diet interaction in order to obtain a better-quality product. The investigation of milk microbiota is considered the latest frontier of milk quality research and the recent omics technologies have been applied to clarify how different breeds and diets might affect it. Milk microbiota composition is rather dynamic and linked to several host-related and environmental-related factors. Although only a few studies have been carried out on locally-adapted breeds, they seem to be more capable of preventing infections than cosmopolite breeds thanks to their microbial communities in mammary gland. The aim of the project is to investigate, for the first time, the milk microbiota composition in two Sicilian autochthonous breeds: Valle del Belice sheep and Girgentana goat. Moreover, Valle del Belice’s milk microbiota will be also analysed as part of a nutritional trial which includes a supplementation of carob pulp to the ordinary diet, to evaluate how diet could influence it. The species-level characterization of milk microbiota is still a new topic, especially in small ruminants. Only few studies are available and they will be used as references, but some differences are expected due to the breed and diet factors. Moreover, a correlation between milk microbiota and udder health will be investigated. A recent study evidenced how the supplementation of carob pulp influences the milk composition. Thus, a significant difference in Valle del Belice’s milk microbiota is expected due to the diet.

KEY WORDS

Genomics - Genetics - Livestock biodiversity - Milk microbiota - Omics technologies - Bioinformatics - Genomic tools - SNP - WGS - Imputation - SVs