175 research outputs found
GENOME-WIDE DETECTION OF QTL AND CNVS IN DAIRY CATTLE POPULATION
No full textThe QTL involved in susceptibility/resistance of infectious diseases and in the productive traits variations, are characterized by genetic heterogeneity and multifactorial inheritance, involving gene polymorphisms from different alternative pathways. With the availavility of single nucleotide polymorphism (SNP) genotyping arrays, the genome-wide association studies (GWAS) have been frequently used to determine the genetic component of complex trait. The Copy Number Variations (CNVs) are another genomic marker that can be possibly used in GWAS and that can be identified from SNP chips themselves.
The aims and related discussions for each of the studies presented in this thesis were grouped into three different chapters.
• Chapter 1 described the QTL mapping analysis to identify the existence of genetic variability associated to the CLA, VA and D9D contents in milk of the Italian Brown Swiss dairy cattle breed. For this study a selective DNA pooling in a daughter design was adopted, using the Illumina Bovine SNP50 Bead Chip to genotype the pools. Milk samples from 60 animals with higher values (after correction for environmental factors) and 60 animals with lower values for each of these traits from each of five half-sib families were pooled separately. Allele frequencies were compared between pools of high and low value at the sire and marker level for each SNPs for which the sires were heterozygous. An R procedure was implemented to perform data analysis. A correction for multiple tests was applied using the proportion of false positives approach. BTA 19 showed the largest number of markers in association with CLA. Associations between SNPs and the VA and D9-desaturase traits were found on several chromosomes. A bioinformatics survey identified genes with an important role in pathways for milk fat and fatty acids metabolism within 1 Mb distance from SNP markers associated with fatty acids contents. This is the first available mapping for fatty acid content in the Brown Swiss population.
• Chapter 2 described a genome-wide association study for somatic cell score (SCS) in the Valdostana Red Pied cattle, with a selective DNA pooling analysis, using the Illumina BovineHD BeadChip. The phenotypes of 275 sires for SCS were expressed as Deregressed Proofs (DP-EBVs) for SCS. The sires were ranked according to DP-EBVs for SCS and the 20% high and 20% low sires included in the pools. The multiple marker test was performed in R software. On BTAs 1, 2, 3, 4, 9, 13, 15, 17, 21 and 22 the largest number of markers in association to the trait was found identifying novel genomic regions related to mastitis (1-Mb SNP windows) and confirming others already mapped. The largest number of significant SNPs exceeding the threshold for genome-wide significant signal was found on BTA 15, located at 50.43-51.63 Mb. The genomic regions identified in this study contribute to a better understanding of the genetic control of the mastitis immune response in cattle and may allow the inclusion of more detailed QTL information in selection programs.
• Chapter 3 described a genome wide CNVs discovery in 651 bulls of the Italian Brown Swiss breed using the Illumina Bovine SNP50 BeadChip data. Hidden Markov Model (HMM) of PennCNV and SVS7 software (Golden Helix) were used for the identification of the CNVs and Copy Number Variation Regions (CNVRs). A total of 5,099 and 1,289 CNVs were identified using PennCNV and SVS7 software, respectively. These were grouped at the population level into 1,101 (220 losses, 774 gains, 107 complex) and 277 (185 losses, 56 gains and 36 complex) CNVRs, covering 682 Mb (27.14%) and 33.7 Mb (1.35%) of the autosome, respectively. Ten of the selected CNVRs were experimentally validated with qPCR and the proportions of confirmed positive samples for each region varied from 50% to 100%. The GO and pathway analyses identified genes (false discovery rate corrected) in the CNVRs related to biological processes, cellular component, molecular function and metabolic pathways. Although there is variability in the CNVRs detection across methods, platforms, this study allowed the identification CNVRs in Italian Brown Swiss, overlapping those already detected in other breeds and finding additional ones
A genome wide association study between CNVs and quantitative traits in Brown Swiss cattle
No full textCopy Number Variations (CNVs) are DNA sequences of 50 bp up to several Mb long, which can vary in number of copies in comparison with a reference genome. CNVs can be used in association studies to disclose genetic basis of quantitative traits phenotypic variation. Up to date, no genome-wide association study (GWAS) with CNVs and quantitative traits in such a large Brown Swiss population (i.e. with 1116 samples) has been described. The purpose of this study was to perform a GWAS using CNVs with functional, health and productive traits and to asses the impact on farming and breeding practices. The CNV – association studies were performed with the Golden Helix SVS 8.4.4 software using a correlation-trend test model. Genes within significant associated CNVs for each trait were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7. A total of 56 CNVs were significantly associated with one or more of the eight evaluated traits. The greatest association signals were given by three CNVs on chromosome 12 for the fat yield trait and on BTA23 for udder traits. The associated CNVs overlap with 23 different genes annotated on the Bos taurus genome assembly (UMD3.1)
RNA interference as a key to knockdown overexpressed cycloxygenase 2 gene in tumour cells
No full textSilencing those genes that are overexpressed in cancer and contribute to the survival and progression of tumour cells is the aim of several researches. Cyclooxygenase-2 (COX-2) is one of the most intensively studied genes since it is overexpressed in most tumours, mainly in colon cancer. The use of specific COX-2 inhibitors to treat colon cancer has generated great enthusiasm. Yet, the side effects of some inhibitors emerging during long-term treatment have caused much concern. Genes silencing by RNA interference (RNAi) has led to new directions in the field of experimental oncology. In this study, we detected sequences directed against COX-2 mRNA, that potently downregulate COX-2 gene expression and inhibit phorbol 12-myristate 13-acetate-induced angiogenesis in vitro in a specific, nontoxic manner. Moreover, we found that the insertion of a specific cassette carrying anti-COX-2 short hairpin RNA sequence into a viral vector (pSUPER.retro) greatly increased silencing potency in a colon cancer cell line (HT29) without activating any interferon response. Phenotypically, COX-2 deficient HT29 cells showed a significant impairment of their in vitro malignant behaviour. Thus, the retroviral approach enhancing COX-2 knockdown, mediated by RNAi, proved to be an useful tool to better understand the role of COX-2 in colon cancer. Furthermore, the higher infection efficiency we observed in tumour cells, if compared to normal endothelial cells, may disclose the possibility to specifically treat tumour cells without impairing endothelial COX-2 activit
Canine fertility : the consequences of selection for special traits
No full textPedigree dogs and cats are bred aiming to conform breed standards with very poor consideration for breeding stock fertility. At the same time, the genetic asset underlining reproductive traits could be effectively analysed like in other species under selection. The definition of selection targets is very important in breeding protocols determination. The aim of the present work is to present an overview of the different correlations between reproduction and genetics, starting from selection procedure and inbreeding coefficient moving to genomic and the application of SNPs and GWAS on population study and identification of genes involved in phenotypical variation of reproductive traits in dogs. Particular relevance has been given to the concept of inbreeding which effects on canine reproduction have been presented. The use of genomic information in inbreeding coefficient calculation can be considered an improved effective procedure in the evaluation of the genetic variability loss in canine population and its negative effects on reproductive traits
Genetic variability in a Holstein population using SNP markers and their use for monitoring mating strategies
No full textAs genotyping costs continue to decrease, the demand for genotyping has increased among farmers. In most livestock herds, an important issue is controlling the increase in inbreeding coefficient. While this remains a large motive to genotype, producers are often unaware of the other benefits that genotyping could bring. The aim of this study was to demonstrate that SNP chips could be used as an effective herd management tool by utilizing a population of Italian Holstein-Friesian cattle. After filtering, the total number of animals and SNPs retained for analyses were 44 and 27,365, respectively. The principal component analyses (PCA) were able to identify a sire and origin-of-sire effect within the herd, while determining that sires do not influence individual genomic selection index values. The inbreeding coefficients calculated from genotypes (FIS) provided a glimpse into the herd’s heterozygosity and determined that the genetic variability is being well maintained. On the other hand, inbreeding coefficients on the genomic level were deduced from runs of homozygosity (FROH) and were compared to the inbreeding coefficients based on pedigree (FPED). Furthermore, 1,950 runs of homozygosity (ROH) were identified with the average length of ROH being 4.66 Mb. Genes and QTL within the genomic regions most commonly associated (top 1% and top 5% of SNP) with ROH were characterized. These results indicate that genotyping small herds, albeit at low-density, provides insights to the genetic variability within the herd and thus allows producers the ability to manage their stock from a genetic standpoint
Mitochondrial DNA genetic diversity in six Italian donkey breeds (Equus asinus)
No full textDonkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered
Genomic approach to manage genetic variability in dairy farms
No full textIn this study we investigated the genetic variability, the inbreeding and allele frequencies of
monogenic traits in seven herds of Holstein breed and provided insight to farmers on the value
of genomic management of reproduction in their herds. A total of 3,953 Holstein cows were
sampled and genotyped with the Neogen GGP Bovine 100K SNP chip within the activities of
the Regione Lombardia funded GO-PEI project ‘GENOmic tool for the management of reproduc-
tion in dairy cattle and for the control of inbreeding – GENORIP’. Principal component analysis
was applied for analysing the genetic variability within and among farms using the SVS software
of Golden Helix. Run of Homozygosity (ROH) and the genomic inbreeding were obtained with
the detectRUNS package of the R software. Genotype frequencies for mendelian disease, fertility
and production traits were also obtained. A total of 458,267 ROH were identified and ROH were
distributed on all autosomes with an average length of 2,703,811 bp covering 12.7% of the gen-
ome. Several genomic regions appear under selection, while a specific region on BTA4 was iden-
tified in one herd, harbouring genes mainly related to the specific selection strategy of the
farmer. The FROH values obtained considering ROH greater than 16 Mb, varied from 0.004 to
0.325, with the highest FROH average value of 0.136. Among mendelian heritable diseases, the
Haplotype Cholesterol Deficiency was the one with the largest proportion of carrier animals, i.e.
5.6%. A herd-tailored process to assist farmers in genomic management of reproduction was
released. The ROH distribution within herd, together with the genotype frequencies for disease,
fertility and production mendelian traits, suggest that similar directional selection is occurring
across herds. This study released to each farmer the genomic make-up of their herd used jointly
with the gEBV estimated by their national breeders’ association (ANAFIBJ) for herd reproductive
management
Caveolae and caveolae constituents in mechanosensing: effect of modelled microgravity on cultured human endothelial cells.
No full textStudies in modeled microgravity or during orbital space flights have clearly demonstrated that endothelial cell physiology is strongly affected by the reduction of gravity. Nevertheless, the molecular mechanisms by which endothelial cells may sense gravity force remain unclear. We previously hypothesized that endothelial cell caveolae could be a mechanosensing system involved in hypergravity adaptation of human endothelial cells. In this study, we analyzed the effect on the physiology of human umbilical vein endothelial cell monolayers of short exposure to modeled microgravity (24-48 h) obtained by clinorotation. For this purpose, we evaluated the levels of compounds, such as nitric oxide and prostacyclin, involved in vascular tone regulation and synthesized starting from caveolae-related enzymes. Furthermore, we examined posttranslational modifications of Caveolin (Cav)-1 induced by simulated microgravity. The results we collected clearly indicated that short microgravity exposure strongly affected endothelial nitric oxide synthase activity associated with Cav-1 (Tyr 14) phosphorylation, without modifying the angiogenic response of human umbilical vein endothelial cells. We propose here that one of the early molecular mechanisms responsible for gravity sensing of endothelium involves endothelial cell caveolae and Cav-1 phosphorylation
The genomic variation in the Aosta cattle breeds raised in an extensive alpine farming system
No full textThe Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler®(GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were −0.003, −0.01 and −0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed
A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes
No full textBackground: In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming across the Country and to convert low-quality feed into valuable milk. The genetic variability in Iranian buffalo breeds have been recently studied using SNPs genotyping data, but a whole genome Copy Number Variants (CNVs) mapping was not available. The aim of this study was to perform a genome wide CNV scan in 361 buffaloes of the three Iranian river breeds (Azeri, Khuzestani and Mazandarani) through the analysis of data obtained using the Axiom® Buffalo Genotyping Array 90 K. Results: CNVs detection resulted in a total of 9550 CNVs and 302 CNVRs identified in at least 5% of samples within breed, covering around 1.97% of the buffalo genome. and A total of 22 CNVRs were identified in all breeds and a different proportion of regions were in common among the three populations. Within the more represented CNVRs (n = 302) mapped a total of 409 buffalo genes, some of which resulted associated with morphological, healthy, milk, meat and reproductive traits, according to Animal Genome Cattle database. Conclusions: This work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo’s natural adaptive history together to a recent selection for milk used as primary food source from this species
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