A5070014423- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Cancer-related molecular mechanisms research
- Animal Genetics and Reproduction
- Effects of Environmental Stressors on Livestock
- Vector-Borne Animal Diseases
- melanin and skin pigmentation
- Animal Disease Management and Epidemiology
- Viral Infections and Vectors
- Genomics and Phylogenetic Studies
- Research on Leishmaniasis Studies
- MicroRNA in disease regulation
- Vector-borne infectious diseases
- Reproductive Physiology in Livestock
- Bioinformatics and Genomic Networks
- Extracellular vesicles in disease
- Livestock Farming and Management
- Genetic Associations and Epidemiology
- Molecular Biology Techniques and Applications
- Epigenetics and DNA Methylation
- Genetics and Plant Breeding
- Probiotics and Fermented Foods
- Mycobacterium research and diagnosis
- Gut microbiota and health
Università degli Studi della Tuscia
2021-2025
Università Cattolica del Sacro Cuore
2014-2024
Universidade Estadual Paulista (Unesp)
2016-2023
University of California, Santa Cruz
2015
Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of breeds and these are classified mainly into two types: (i) adaptation different breeding systems and/or purposes (ii) environments. As a result, approximately 600 developed worldwide; they differ considerably from one another in terms phenotypic characteristics adapted wide range climatic conditions. In this work, we analyzed AdaptMap dataset, which is composed data more than 3000 animals...
Abstract Nowadays, molecular data analyses for biodiversity studies often require advanced bioinformatics skills, preventing many life scientists from analyzing their own autonomously. BITE R package provides complete and user-friendly functions to handle SNP third-party software results (i.e. Admixture, TreeMix), facilitating visualization, interpretation use. Furthermore, implements additional useful procedures, such as representative sampling bootstrap TreeMix, filling the gap in existing...
Goat populations that are characterized within the AdaptMap project cover a large part of worldwide distribution this species and provide opportunity to assess their diversity at global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 describe patterns molecular variation, compare them those observed in other livestock species, identify drivers led current goats.A high degree genetic variability exists among goat studied. Our results highlight strong...
Among the European countries, Italy counts largest number of local goat breeds. Thanks to recent availability a medium-density SNP (single nucleotide polymorphism) chip for goat, genetic diversity Italian populations was characterized by genotyping samples from 14 breeds that originate different geographical areas with more than 50 000 SNPs evenly distributed on genome. Analysis data revealed high levels polymorphism and an underlying North–south geographic pattern highlighted both first...
The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. two types of buffalo, i.e. river swamp, display distinct morphological behavioural traits, different karyotypes also have purposes geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil Colombia, swamp China, Thailand, Philippines, Indonesia were genotyped with...
Milk extracellular vesicles (mEVs) seem to be one of the main maternal messages delivery systems. Extracellular (EVs) are micro/nano-sized membrane-bound structures enclosing signaling molecules and thus acting as signal mediators between distant cells and/or tissues, exerting biological effects such immune modulation pro-regenerative activity. is also a unique, scalable, reliable source EVs. Our aim was characterize RNA content cow, donkey, goat mEVs through transcriptomic analysis mRNA...
Abstract Background Nellore cattle ( Bos indicus ) are well-known for their adaptation to warm and humid environments. Hair length coat color may impact heat tolerance. The breed has been strongly selected white coat, but bulls generally exhibit darker hair ranging from light grey black on the head, neck, hump, knees. Given potential contribution of variation populations tropical sub-tropical environments, our aim was map positional functional candidate genetic variants associated with...
Abstract Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well-annotated reference sequence the water an prerequisite studying biology of this species, necessary to manage genetic diversity use modern breeding genomic selection techniques. However, no such genome assembly has been previously reported. There are 2 domestic buffalo, river (2n = 50) swamp 48) buffalo. Here we describe draft quality created from Illumina GA Roche 454 short...
The recent evolution of cattle is marked by fluctuations in body size. Height the Bos taurus lineage was reduced a factor ~1.5 from Neolithic to Middle Ages, and increased again only during Early Modern Ages. Using haplotype analysis, we found evidence that bovine PLAG1 mutation (Q) with major effects on size, weight reproduction >1,000 years old derived allele rapidly frequency Northwestern European B. between 16th 18th centuries. Towards 19th 20th centuries, Q introgressed into...
In recent years, the involvement of gut microbiota in disease and health has been investigated by sequencing 16S gene from fecal samples. Dysbiotic was also observed Autism Spectrum Disorder (ASD), a neurodevelopmental disorder characterized gastrointestinal symptoms. However, despite relevant number studies, it is still difficult to identify typical dysbiotic profile ASD patients. The discrepancies among these studies are due technical factors (i.e., experimental procedures) external...
Recently, much interest has been raised for the characterization of signaling molecules carried by extracellular vesicles (EVs), which are particularly enriched in milk (mEVs). Such is linked to capability EVs cross biological barriers, resist acidification gastric environment, and exert modulation immune system, mainly through their microRNA (miRNA) content. We characterized small-RNA cargo colostrum (colosEVs) mEVs from Italian Mediterranean buffalo next generation sequencing. Colostrum...
The domestication of the aurochs took place approximately 10,000 years ago giving rise to two main types domestic cattle known today, taurine (Bos taurus) domesticated somewhere on or near Fertile Crescent, and indicine (B. indicus) in Indus Valley. However, although have historically played a prominent role human society exact origin many extant breeds is not well known. Here we used combination medium high-density Illumina Bovine SNP arrays (i.e. ~54,000 ~770,000 SNPs respectively),...
Heat stress has a detrimental impact on cattle health, welfare and productivity by affecting gene expression, metabolism immune response, but little is known the epigenetic mechanisms mediating effect of temperature at cellular organism level. In this study, we investigated genome-wide DNA methylation in blood samples collected from 5 bulls heat resilient Nellore breed Angus that are more susceptible, exposed to sun high temperature-high humidity during summer season Brazilian South-East...
A number of methods are available to scan a genome for selection signatures by evaluating patterns diversity within and between breeds. Among these, "extended haplotype homozygosity" (EHH) is reliable approach detect regions under recent selective pressure. The objective this study was use identify that positive shared the most representative Italian dairy beef cattle total 3220 animals from Holstein (2179), Brown (775), Simmental (493), Marchigiana (485) Piedmontese (379) breeds were...
East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease transmitted by the tick Rhipicephalus appendiculatus, caused protozoan Theileria parva parva, which invades host lymphocytes promotes their clonal expansion. Importantly, indigenous show tolerance to infection in ECF-endemically stable areas. Here, putative genetic bases underlying ECF-tolerance were investigated using molecular data epidemiological information from...
Abstract The GHap R package was designed to call haplotypes from phased marker data. Given user-defined haplotype blocks (HapBlock), the identifies different alleles (HapAllele) present in data and scores sample allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). output is not only useful for analyses that can handle multi-allelic markers, but also conveniently formatted existing pipelines intended bi-allelic markers. Availability implementation:...
Sperm motility is directly related to the ability of sperm move through female reproductive tract reach ovum. a complex trait that influenced by environmental and genetic factors associated with male fertility, oocyte penetration rate, success cattle. In this study we carried out GWAS in Italian Holstein bulls identify candidate regions genes variations progressive total (PM TM, respectively). After quality control, final data set consisted 5,960 records from 949 having semen collected 10...
Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be detected unexpected behavior marker linkage disequilibrium (LD) decay. We developed heuristic process to identify misassembly applied it bovine reference genome assembly (UMDv3.1) and presented consequences misassemblies in two case studies. identified 2,906 single nucleotide polymorphism (SNP) markers presenting LD decay 626 putative misassembled contigs, which comprised less than 1 % whole...
Nelore and Gir are the two most important indicine cattle breeds for production of beef milk in Brazil. Historical records state that these were introduced Brazil from Indian subcontinent, crossed to local taurine order quickly increase population size, then backcrossed original recover adaptive productive traits. Previous investigations based on sparse DNA markers detected admixture breeds. High-density genome-wide analyses can provide high-resolution information genetic composition current...
Two complementary methods, namely Multi-Trait Meta-Analysis and Versatile Gene-Based Test for Genome-wide Association Studies (VEGAS), were used to identify putative pleiotropic genes affecting carcass traits in Bos indicus (Nellore) cattle. The genotypic data comprised over 777,000 single-nucleotide polymorphism markers scored 995 bulls, the phenotypic included deregressed breeding values (dEBV) weight measurements at birth, weaning yearling, as well visual scores taken yearling finishing...
Abstract Background During the last decade, with aim to solve challenge of post-genomic and transcriptomic data mining, a plethora tools have been developed create, edit analyze metabolic pathways. In particular, when complex phenomenon is considered, creation network multiple interconnected pathways interest could be useful investigate underlying biology ultimately identify functional candidate genes affecting trait under investigation. Results PANEV (PAthway NEtwork Visualizer) an R...