New Advances in NGS Technologies

In the next-generation sequencing (NGS) methods, a DNA molecule of an individual is broken down into many small fragments to make up the so-called sequencing library. These small fragments serve as a template for the synthesis of numerous complementary fragments (called reads). Every small piece of the original DNA is copied many times in a variable number of reads. Depending on the desired accuracy level, it is possible to set the system to achieve a certain level of coverage, i.e., a number of reads per fragment. A level of 30X coverage is already sufficient for the routine diagnosis of most of the Mendelian diseases. All the sequences are then transferred into a computer and aligned with a reference sequence available in the international databases. By this way, all sequences of reads can be recomposed as a fine puzzle to obtain the sequence of a single gene or whole genome. The NGS machines, available today, are very flexible devices. In fact, an NGS sequencer can be used for different types of applications: (1) whole-genome sequencing (WGS): analysis of the entire genome of an individual; (2) whole exome sequencing (WES): analysis of the entire coding genes of an individual; (3) targeted sequencing: analysis of a set of genes or a single gene; (4) transcriptome analysis: analysis of all the RNA produced by specific cells

Recent Trends and Economic Aspects in the Rainbow Trout (Oncorhynchus mykiss) Sector

In recent decades, the global aquaculture sector has become more complex and dynamic due to several factors, such as strong demand at the retail level, diversification of farmed species, outsourcing of product processing, and synergies among producers, processors, and retailers. Globally, the fish food sector has become very important to meet the growing human demand for food. In 2020, 89% of fish production was used for direct human consumption (17% of the total protein consumed). Global fish consumption has increased (excluding algae) at an annual rate of 3% since 1960. In 2030, the total fish production is expected to reach 202 million tons (MT) and the aquaculture production 106 MT. The United Nations has estimated that, between now and 2030, the global demand for fish products will increase by at least 40 MT each year. This need cannot be satisfied by fishing alone, given that fishing practices have reached an intensity that is unsustainable, and that climate change and pollution are worsening the problems of marine ecosystems. European and Italian aquaculture is characterised by a diversification scenario in terms of production systems, technologies adopted, and species bred. According to an EU report, Italian aquaculture production has grown by 4% in the last five years (fourth place in Europe). In Italy, rainbow trout is the most widely farmed species. The production of rainbow trout contributes approximately 25.5% of the total value and 69.9% of the volume of farmed fish. Over the past ten years, trout production has increased by 8.5% overall with an average annual growth rate of 2.5%. The purpose of this review is to provide an overview of the economic situation of the rainbow trout production and consumption sectors in Italy using a supply chain approach. In particular, in this brief excursus, the main production trends and the economic and organisational relationships between the various companies and associations in the aquaculture sector are analysed

Canine Genetics and Genomics

In the past fifteen years, tremendous progress has been made in dog genomics. Several genetic aspects of cancer, heart disease, hip dysplasia, vision and hearing problems in dogs have been investigated and studied in detail. Genome-wide associative studies have made it possible to identify several genes associated with diseases, morphological and behavioral traits. The dog genome contains an extraordinary amount of genetic variability that distinguishes the different dog breeds. As a consequence of the selective programs, applied using stringent breed standards, each dog breed represents, today, a population isolated from the others. The availability of modern next generation sequencing (NGS) techniques and the identification of millions of single functional mutations (SNPs) has enabled us to obtain new and unknown detailed genomic data of the different breeds

Applications in Genetics and Animal Biotechnology

The present Special Issue, “Applications in Genetics and Animal Biotechnology”, presents the latest advances in the field of animal genetics [...

Recent Trends and Economic Aspects in the Rainbow Trout (Oncorhynchus mykiss) Sector

In recent decades, the global aquaculture sector has become more complex and dynamic due to several factors, such as strong demand at the retail level, diversification of farmed species, outsourcing of product processing, and synergies among producers, processors, and retailers. Globally, the fish food sector has become very important to meet the growing human demand for food. In 2020, 89% of fish production was used for direct human consumption (17% of the total protein consumed). Global fish consumption has increased (excluding algae) at an annual rate of 3% since 1960. In 2030, the total fish production is expected to reach 202 million tons (MT) and the aquaculture production 106 MT. The United Nations has estimated that, between now and 2030, the global demand for fish products will increase by at least 40 MT each year. This need cannot be satisfied by fishing alone, given that fishing practices have reached an intensity that is unsustainable, and that climate change and pollution are worsening the problems of marine ecosystems. European and Italian aquaculture is characterised by a diversification scenario in terms of production systems, technologies adopted, and species bred. According to an EU report, Italian aquaculture production has grown by 4% in the last five years (fourth place in Europe). In Italy, rainbow trout is the most widely farmed species. The production of rainbow trout contributes approximately 25.5% of the total value and 69.9% of the volume of farmed fish. Over the past ten years, trout production has increased by 8.5% overall with an average annual growth rate of 2.5%. The purpose of this review is to provide an overview of the economic situation of the rainbow trout production and consumption sectors in Italy using a supply chain approach. In particular, in this brief excursus, the main production trends and the economic and organisational relationships between the various companies and associations in the aquaculture sector are analysed

Genetic and Phenotypic Characteristics of the <i>Salmo trutta</i> Complex in Italy

Salmonid fish have become ecological and research models of study in the field of conservation genetics and genomics. Over the last decade, brown trout have received a high level of interest in research and publications. The term Salmo trutta complex is used to indicate the large number of geographic forms present in the species Salmo trutta. In Europe, the S. trutta complex consists (based on mitochondrial DNA control region analysis) of seven major evolutionary lineages: Atlantic (AT), Mediterranean (ME), Adriatic (AD), Danubian (DA), Marmoratus (MA), Duero (DU) and Tigris (TI). In several nations, the difficulty of identifying some lineages derives from their wide phenotypic and geographic plasticity and the presence of mixed lineages (due to introgressive hybridization with domestic AT populations). In Italy, the S. trutta complex populations living in the Tyrrhenian area and on the main islands (Sicily, Sardinia and Corsica) showed high genetic diversity. Currently, on the Italian Red List, the protected (near threatened) populations are the AD and ME lineages. Recent studies based on traditional (mitochondrial and nuclear markers) and NGS (next-generation sequencing) analyses have clarified some genetic differences between the populations of the Tyrrhenian region, Sicily, Sardinia and Corsica. Native populations in Sardinia belong to the AD lineage, while those living in Corsica are mainly characterized by the AD, MA and ME haplotypes. In Sicily, in the area of the Iblei mountains, an AT lineage (North African) exists. According to some authors, the term Salmo macrostigma should only be used for populations in North Africa. The use of genotyping methods based on mtDNA and nuclear markers and the latest generation sequencing techniques can improve the study of populations and evolutionary lineages in areas where there are overlaps and hybridization phenomena