68 research outputs found
Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep
No full textSupplementary data for publication: Rosalia Di Gerlando, Anna Maria Sutera, Salvatore Mastrangelo, Marco Tolone, Baldassare Portolano, Alessandro Bagnato, Maria Giuseppina Strillacci, Maria Teresa Sardina. (2018). Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep. PLoS ONE 14(4): e0215204
Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep
No full textSupplementary data for publication: Rosalia Di Gerlando, Anna Maria Sutera, Salvatore Mastrangelo, Marco Tolone, Baldassare Portolano, Alessandro Bagnato, Maria Giuseppina Strillacci, Maria Teresa Sardina. (2018). Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep. PLoS ONE 14(4): e0215204
Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep
No full textSupplementary data for publication: Rosalia Di Gerlando, Anna Maria Sutera, Salvatore Mastrangelo, Marco Tolone, Baldassare Portolano, Alessandro Bagnato, Maria Giuseppina Strillacci, Maria Teresa Sardina. (2018). Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep. PLoS ONE 14(4): e0215204
Antibiotic treatments and somatic cell count as phenotype to map QTL for mastitis susceptibility in Holstein cattle breed
No full textMastitis is one of the most significant diseases affecting dairy cattle profitability. A genome wide association study (GWAS) was performed using the selective genotyping approach to identify Quantitative Trait Loci (QTL) associated with mastitis susceptibility. According to the received antibiotic treatments in all their productive life, 52 lactating cows have been classified in resistant (no therapy and low SCC) and susceptible (more than one treatment and high SCC) to mastitis. Genotyping of animals was performed using the NEOGEN’s GGP Bovine 100K SNP chip and QTL were identified comparing the SNPs allelic frequencies between the two groups. 26 SNPs related to mastitis susceptibility were identified in 9 chromosomes. The use of treatment data, coupled with SCC from milk recording, improved cow’s classification accuracy in resistant and susceptible individuals. For this reason, the mandatory recording of treatments active from January 2022, could be a new source of information to improve the genetic selection for mastitis resistance
Genetic and Phenotypic Characteristics of Belted Pig Breeds: A Review
No full textBelted pig breeds have unique, distinguishing phenotypic characteristics. This review
summarises the current knowledge on pig breeds displaying a belted coat pattern. Belts of different
widths and positions around the animal’s trunk characterise specific pig breeds from all around the
world. All the breeds included in the present paper have been searched through the FAO domestic
animal diversity information system (DAD-IS), Every country was checked to identify all breeds
described as having black or red piebald coat pattern variations. Advances in genomic technologies
have made it possible to identify the specific genes and genetic markers associated with the belted
phenotype and explore the genetic relationships between different local breeds. Thus, the origin,
history, and production traits of these breeds, together with all the genomic information related
to the mechanism of skin pigmentation, are discussed. By increasing our understanding of these
breeds, we can appreciate the richness of our biological and cultural heritage and work to preserve
the biodiversity of the world’s animals
Breeders management and reproductive traits in three heritage rabbit (Oryctolagus cuniculus) breeds: a preliminary study
No full textThe aim of the present research is to investigate breeders’ management strategies and their effects on reproductive performances in heritage breeds. A total of 468 litters were analysed: Belgian Hare (N = 151), Burgundy Fawn (N = 105), Californian (N = 212). Litter size (born alive), percentage of weaned kits and percentage of selected kits were analysed using a model that included the effects of breed, year of birth, litter’s origin (with three levels: both internal parents = 0, one outside parent = 1 both outside parents = 2) and their interactions (breed*year of birth, breed*litter’s origin, year of birth*litter’s origin, breed*year of birth*litter’s origin). Besides, number of litters per buck and number of litters per doe were analysed using a model with only effect of breed. All these analyses were carried out with SPSS software. No effects of breeds on litter size, percentage of weaned and percentage of selected kits were found. Year of birth presented significant effects on litter size and percentage of weaned kits (p ≤ 0.05). The inclusion of external breeders didn’t significantly influence analysed reproductive data. The number of litters per buck and per doe were not influenced by breed. The frequency of external breeders’ inclusion is breed specific. Data recording is a basic step in phenotypical characterization, our results supply some information about breeders’ management strategies and their effects on some reproductive parameters. Our results show breed specific frequencies of inclusions of external breeders and a positive effect of management procedures (genetic plus environment) on percentage of weaned kits according to the year of birth.HIGHLIGHTS Breeders management and reproductive parameters have been described The most frequent combination is a home bred doe mated to an external male A mean of 2 litters per doe and per buck have calculated in all the breeds The frequency of use of external breeders is breed specifi
The genomic comparison between autochthonous and cosmopolitan cows reveals structural variants involved in environmental adaptation
No full textCopy Number Variants (CNVs) are structural variants affecting genetic diversity and phenotypic variability of populations. Different authors underlined the relevance of CNV in relation to the adaptation to environmental conditions (e.g., altitude, harsh farming environment). Aosta cattle (Aosta Red Pied - ARP; Aosta Black Pied/Chestnut - ABC and Mixed Chestnut-Héren - ACH) farmed in the Aosta Valley, and the Oropa Red Pied (ORO), farmed in the Piedmont region, are autochthonous dual-purpose breeds well adapted to the natural Alpine environment. In contrast, the Holstein (HOL) breed is a specialized dairy breed raised in intensive farming systems, representing an artificial environment. The aim of this study is to use CNVs to characterize these breeds and explore the relationship between structural genomic variability and adaptation to mountain farming systems (natural environment) vs. intensive farming systems (artificial environment). Using the GeneSeek Genomic Profiler Bovine 100K data, a total of 160,798 CNVs were identified across 5,610 individuals. Principal Component Analysis (PCA) using CNV Regions (CNVRs) revealed that Aosta breeds clustered into two separate groups, with one smaller cluster including part of ORO cows, while the Holstein formed a distinct cluster. These results suggest that CNVs may act as markers of adaptive selection, influencing both Aosta and ORO breeds, though to a different extent compared to the intensively farmed HOL breed. A total of 526 CNVRs were identified in at least 2% of the samples. Annotated genes and overlapping QTL were functionally associated with production, functional traits, and health-related characteristics. VST analysis revealed candidate genes linked to environmental adaptation, reproduction, and metabolic efficiency in Aosta, ORO, and HOL cattle. Key findings include TCF12 and SRGAP1 deletions in Aosta, suggesting trade-offs between muscle growth and endurance, while ELF2 and ARID5B gains in Holstein indicate aptitude for milk protein synthesis and feed efficiency. Additionally, reproductive genes (RGS3, GSE1, MARCH10) showed distinct selection pressures between Dual-purpose and Holstein breeds, reflecting adaptation to different production systems
Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep
No full textCopy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits
A copy number variant scan in the autochthonous Valdostana Red Pied cattle breed and comparison with specialized dairy populations
No full textCopy number variants (CNVs) are an important source of genomic structural variation, recognized to influence phenotypic variation in many species. Many studies have focused on identifying CNVs within and between human and livestock populations alike, but only few have explored population-genetic properties in cattle based on CNVs derived from a high-density SNP array. We report a high-resolution CNV scan using Illumina's 777k BovineHD Beadchip for Valdostana Red Pied (VRP), an autochthonous Italian dual-purpose cattle population reared in the Alps that did not undergo strong selection for production traits. After stringent quality control and filtering, CNVs were called across 108 bulls using the PennCNV software. A total of 6,784 CNVs were identified, summarized to 1,723 CNV regions (CNVRs) on 29 autosomes covering a total of ~59 Mb of the UMD3.1 assembly. Among the mapped CNVRs, there were 812 losses, 832 gains and 79 complexes. We subsequently performed a comparison of CNVs detected in the VRP and those available from published studies in the Italian Brown Swiss (IBS) and Mexican Holstein (HOL). A total of 171 CNVRs were common to all three breeds. Between VRP and IBS, 474 regions overlapped, while only 313 overlapped between VRP and HOL, indicating a more similar genetic background among populations with common origins, i.e. the Alps. The principal component, clustering and admixture analyses showed a clear separation of the three breeds into three distinct clusters. In order to describe the distribution of CNVs within and among breeds we used the pair VST statistic, considering only the CNVRs shared to more than 5 individuals (within breed). We identified unique and highly differentiated CNVs (n = 33), some of which could be due to specific breed selection and adaptation. Genes and QTL within these regions were characterized
Mitochondrial D-loop sequence variation among Italian horse breeds
No full textAbstract The genetic variability of the mitochondrial D-loop DNA sequence in seven horse breeds bred in Italy (Giara, Haflinger, Italian trotter, Lipizzan, Maremmano, Thoroughbred and Sarcidano) was analysed. Five unrelated horses were chosen in each breed and twenty-two haplotypes were identified. The sequences obtained were aligned and compared with a reference sequence and with 27 mtDNA D-loop sequences selected in the GenBank database, representing Spanish, Portuguese, North African, wild horses and an Equus asinus sequence as the outgroup. Kimura two-parameter distances were calculated and a cluster analysis using the Neighbour-joining method was performed to obtain phylogenetic trees among breeds bred in Italy and among Italian and foreign breeds. The cluster analysis indicates that all the breeds but Giara are divided in the two trees, and no clear relationships were revealed between Italian populations and the other breeds. These results could be interpreted as showing the mixed origin of breeds bred in Italy and probably indicate the presence of many ancient maternal lineages with high diversity in mtDNA sequences.</p
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