RESUMO
Scrapie is a transmissible spongiform encephalopathy affecting sheep and goats. The prion protein-encoding gene (PRNP) plays a crucial role in determining susceptibility and resistance to scrapie. At the European level, surveillance of scrapie is essential to prevent the spread of the disease to livestock. According to the Regulation EU 2020/772 polymorphisms K222, D/S146 could function as resistance alleles in the genetic management of disease prevention. In Italy, a breeding plan for scrapie eradication has not been implemented for goats. However, surveillance plans based on the PRNP genotype have been developed as a preventive measure for scrapie. This research aimed to describe the polymorphisms at 7 positions within the PRNP gene in 956 goats of the Alpine, Saanen and mixed populations farmed in the Lombardy Region in Italy. PRNP polymorphisms were detected using single nucleotide polymorphism markers included in the Neogen GGP Goat 70 k chip. The K222 allele occurred in all populations, with frequencies ranging from 2.1 to 12.7%. No animals carried the S/D146 resistance allele. However, it has been demonstrated that polymorphisms in the other positions analysed could influence resistance or susceptibility to scrapie outbreaks in different ways. Ten potentially distinct haplotypes were found, and the most prevalent of the three populations was H2, which differed from the wild type (H1) in terms of mutation (S vs P) at codon 240. This study provided additional information on the genetic variability of the PRNP gene in these populations in the Lombardy region of Italy, contributing to the development of genetic control measures for disease prevention.
Assuntos
Doenças das Cabras , Cabras , Proteínas Priônicas , Scrapie , Animais , Itália/epidemiologia , Cabras/genética , Doenças das Cabras/genética , Doenças das Cabras/epidemiologia , Proteínas Priônicas/genética , Scrapie/genética , Scrapie/epidemiologia , Códon/genética , Variação Genética , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Copy Number Variants (CNV) are modifications affecting the genome sequence of DNA, for instance, they can be duplications or deletions of a considerable number of base pairs (i.e., greater than 1000 bp and up to millions of bp). Their impact on the variation of the phenotypic traits has been widely demonstrated. In addition, CNVs are a class of markers useful to identify the genetic biodiversity among populations related to adaptation to the environment. The aim of this study was to detect CNVs in more than four thousand Holstein cows, using information derived by a genotyping done with the GGP (GeneSeek Genomic Profiler) bovine 100K SNP chip. To detect CNV the SVS 8.9 software was used, then CNV regions (CNVRs) were detected. A total of 123,814 CNVs (4,150 non redundant) were called and aggregated into 1,397 CNVRs. The PCA results obtained using the CNVs information, showed that there is some variability among animals. For many genes annotated within the CNVRs, the role in immune response is well known, as well as their association with important and economic traits object of selection in Holstein, such as milk production and quality, udder conformation and body morphology. Comparison with reference revealed unique CNVRs of the Holstein breed, and others in common with Jersey and Brown. The information regarding CNVs represents a valuable resource to understand how this class of markers may improve the accuracy in prediction of genomic value, nowadays solely based on SNPs markers.
Assuntos
Variações do Número de Cópias de DNA , Polimorfismo de Nucleotídeo Único , Bovinos/genética , Animais , Itália , Feminino , Cruzamento , Genótipo , FenótipoRESUMO
BACKGROUND: 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.
Assuntos
Búfalos , Variações do Número de Cópias de DNA , Animais , Búfalos/genética , Bovinos , Genoma , Irã (Geográfico) , Fenótipo , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Pedigree 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.
Assuntos
Cruzamento/métodos , Cães/genética , Fertilidade/genética , Animais , Peso ao Nascer , Cesárea/veterinária , Feminino , Endogamia , Masculino , Reprodução/genética , Seleção GenéticaRESUMO
This study aims at investigating genomic diversity of several turkey populations using Copy Number Variants (CNVs). A total of 115 individuals from six Italian breeds (Colle Euganei, Bronzato Comune Italiano, Parma e Piacenza, Brianzolo, Nero d'Italia, and Ermellinato di Rovigo), seven Narragansett, 38 commercial hybrids, and 30 Mexican turkeys, were genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array. The CNV calling was performed with the Hidden Markov Model of PennCNV software and with the Copy Number Analysis Module of SVS 8.4 by Golden Helix®. CNV were summarized into CNV regions (CNVRs) at population level using BEDTools. Variability among populations has been addressed by hierarchical clustering (pvclust R package) and by principal component analysis (PCA). A total of 2,987 CNVs were identified covering 4.65% of the autosomes of the Turkey_5.0/melGal5 assembly. The CNVRs identified in at least two individuals were 362-189 gains, 116 losses, and 57 complexes. Among these regions the 51% contain annotated genes. This study is the first CNV mapping of turkey population using 600K chip. CNVs clustered the individuals according to population and their geographical origin. CNVs are known to be indicators also of adaptation, as some researches in different species are suggesting.
RESUMO
Bovine tuberculosis (bTB) is a disease of cattle that represents a risk to public health and causes severe economic losses to the livestock industry. Recently, genetic studies, like genome-wide association studies (GWAS) have greatly improved the investigation of complex diseases identifying thousands of disease-associated genomic variants. Here, we present evidence of genetic variants associated with resistance to TB in Mexican dairy cattle using a case-control approach with a selective DNA pooling experimental design. A total of 154 QTLRs (quantitative trait loci regions) at 10% PFP (proportion of false positives), 42 at 5% PFP and 5 at 1% PFP have been identified, which harbored 172 annotated genes. On BTA13, five new QTLRs were identified in the MACROD2 and KIF16B genes, supporting their involvement in resistance to bTB. Six QTLRs harbor seven annotated genes that have been previously reported as involved in immune response against Mycobacterium spp: BTA (Bos taurus autosome) 1 (CD80), BTA3 (CTSS), BTA 3 (FCGR1A), BTA 23 (HFE), BTA 25 (IL21R), and BTA 29 (ANO9 and SIGIRR). We identified novel QTLRs harboring genes involved in Mycobacterium spp. immune response. This is a first screening for resistance to TB infection on Mexican dairy cattle based on a dense SNP (Single Nucleotide Polymorphism) chip.
RESUMO
BACKGROUND: The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. METHODS: Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. RESULTS: Nucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from -0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.
RESUMO
BACKGROUND: The detection of quantitative trait loci has accelerated with recent developments in genomics. The introduction of genomic selection in combination with sequencing efforts has made a large amount of genotypic data available. Functional traits such as fertility and calving traits have been included in routine genomic estimation of breeding values making large quantities of phenotypic data available for these traits. This data was used to investigate the genetics underlying fertility and calving traits and to identify potentially causative genomic regions and variants. We performed genome-wide association studies for 13 functional traits related to female fertility as well as for direct and maternal calving ease based on imputed whole-genome sequences. Deregressed breeding values from ~1000-5000 bulls per trait were used to test for associations with approximately 10 million imputed sequence SNPs. RESULTS: We identified a QTL on BTA17 associated with non-return rate at 56 days and with interval from first to last insemination. We found two significantly associated non-synonymous SNPs within this QTL region. Two more QTL for fertility traits were identified on BTA25 and 29. A single QTL was identified for maternal calving traits on BTA13 whereas three QTL on BTA19, 21 and 25 were identified for direct calving traits. The QTL on BTA19 co-localizes with the reported BH2 haplotype. The QTL on BTA25 is concordant for fertility and calving traits and co-localizes with a QTL previously reported to influence stature and related traits in Brown Swiss dairy cattle. CONCLUSION: The detection of QTL and their causative variants remains challenging. Combining comprehensive phenotypic data with imputed whole genome sequences seems promising. We present a QTL on BTA17 for female fertility in dairy cattle with two significantly associated non-synonymous SNPs, along with five additional QTL for fertility traits and calving traits. For all of these we fine mapped the regions and suggest candidate genes and candidate variants.
Assuntos
Bovinos/genética , Fertilidade/genética , Locos de Características Quantitativas , Animais , Feminino , Variação Genética , Estudo de Associação Genômica Ampla , Genômica , Masculino , Gravidez , Natimorto/genéticaRESUMO
The aim of this study was to evaluate the variations of protein, casein, saturated (SFA), unsaturated (UFA), monounsaturated (MUFA), polyunsaturated (PUFA) fatty acids contents and cheese yield in the milk of two groups of Italian Brown cows conventionally reared in indoor period of housing or consuming pasture during the summer months in 2008 and 2013. Milk components were obtained from samples collected during the national routine (conventionally reared) and 'extraordinary' (pasture period) milk recording scheme in herds located near Sondrio (Lombardia, Italy). Milk samples were processed with the MilkoScanTM FT6000 for the identification of milk casein, SFA, UFA, MUFA and PUFA composition. The groups were analysed separately per year and the environmental factors affecting milk protein, casein, and fatty acids contents (pasture/indoor, parity, data of sampling, days in milk, days from collection to analysis) were included in the MIXED procedure of SAS 9.3. A total of 778 milk samples were available, including 234 records from indoor and 544 observations from pasture feeding. Pasture intake affected the content of casein (%) and the proportion of fat in milk (g/100 g), enhancing milk casein levels (from 2.90 to 3) and reducing the concentration of milk SFA in milk from grazing cows (from 2.29 to 1.92). Additionally, the cheese yield was calculated as 'kg of cheese per 100 kg of milk' and resulted to be 10.4 and 12 in 2008 from milk of cows reared indoor and with pasture based diet, respectively. The dairy industry should take advantage of the milk production during grazing periods from which high quality products may be obtained.
Assuntos
Caseínas/química , Bovinos/genética , Bovinos/fisiologia , Ácidos Graxos/química , Leite/química , Proteínas/química , Animais , Queijo/análise , Estações do AnoRESUMO
BACKGROUND: Mastitis is a major disease of dairy cattle occurring in response to environmental exposure to infective agents with a great economic impact on dairy industry. Somatic cell count (SCC) and its log transformation in somatic cell score (SCS) are traits that have been used as indirect measures of resistance to mastitis for decades in selective breeding. A selective DNA pooling (SDP) approach was applied to identify Quantitative Trait Loci (QTL) for SCS in Valdostana Red Pied cattle using the Illumina Bovine HD BeadChip. RESULTS: A total of 171 SNPs reached the genome-wide significance for association with SCS. Fifty-two SNPs were annotated within genes, some of those involved in the immune response to mastitis. 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. These regions identified novel genomic regions related to mastitis (1-Mb SNP windows) and confirmed those 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. CONCLUSIONS: 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.
Assuntos
Bovinos/genética , Mapeamento Cromossômico/veterinária , Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Animais , Feminino , Genótipo , Masculino , Mastite Bovina/genéticaRESUMO
Autosomal-dominant polycystic kidney disease (AD-PKD) is common in Persians and Persians-related breeds. The aims of this study were to evaluate the sensitivity and specificity of early ultrasound examination and to compare ultrasound and genetic testing for early diagnosis. Sixty-three Persians and seven Exotic Shorthairs were considered. All underwent ultrasonographic and genetic testing (polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) assay) between 2.5 and 3.5 months of age (10-14 weeks). With ultrasound, 41.4% showed renal cysts, while 37.1% were PKD positive by genetic testing and DNA sequencing. Six cats with at least one renal cyst were negative by genetic testing, while only one cat negative at ultrasound resulted positive at genetic test. DNA sequencing of three polycystic cats, negative by genetic test, revealed they were heterozygous for the mutation. Agreement was described by Cohen's kappa that resulted 0.85, considering genetic test and DNA sequencing. Sensitivity and specificity of ultrasound were 96.2% and 91%, respectively. Sensitivity was higher and specificity lower than reported previously. The higher sensitivity could be due to improved technical capabilities of ultrasound machines and transducers. Other causes of PKD could explain the lower specificity. In conclusion, ultrasound resulted in a reliable diagnostic method for feline AD-PKD1 at early age and it should always be used with genetic testing, in order to reach a complete screening programme and eventually to identify other genetic mutations.
Assuntos
Doenças do Gato/diagnóstico por imagem , Doenças do Gato/genética , Doenças Renais Policísticas/veterinária , Polimorfismo de Nucleotídeo Único/genética , Animais , Doenças do Gato/diagnóstico , Gatos , Diagnóstico Precoce , Feminino , Genótipo , Doenças Renais Policísticas/diagnóstico por imagem , Doenças Renais Policísticas/genética , Polimorfismo de Fragmento de Restrição , Sensibilidade e Especificidade , UltrassonografiaRESUMO
Ichthyosis is a heterogeneous group of keratinization disorders reported both in human and animals. Two rare, inherited forms have been reported in cattle, both characterized by autosomal recessive transmission. Because mutations of transglutaminase 1 (TGM1) gene are associated with autosomal recessive ichthyosis in people, this gene was investigated as a candidate for the diseases in cattle. Three different polymorphisms were identified in 5' end region of cattle TGM1. Marker homozygosity was not found among affected calves. Linkage analysis excluded (logarithmic odds [LOD] score -2.0) TGM1 as the cause for ichthyosis phenotype in the analyzed Chianina cases.