Maria Cristina Cozzi

Mitochondrial D-loop sequence variation among Italian horse breeds

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.

Comparison between ultrasound and genetic testing for the early diagnosis of polycystic kidney disease in Persian and Exotic Shorthair cats

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 Cohens 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.

Genome-wide association study for somatic cell score in Valdostana Red Pied cattle breed using pooled DNA

BackgroundMastitis 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.ResultsA 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.ConclusionsThe 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.

Gene Expression of Hepatic Glucocorticoid Receptor NR3C1 and Correlation with Plasmatic Corticosterone in Italian Chickens

This study examined breed-specific stress-related hormonal and gene expression profiles in three Italian chicken breeds (Valdarnese Bianca, Bionda Piemontese, Robusta Maculata) reared in controlled conditions. Glucocorticoids work through the glucocorticoid receptor (GR), which modulates target genes transcription. We investigated breed-specific changes in corticosterone (ELISA) and GR expression. GR mRNA levels were analyzed using one-tube, two-temperature real-time PCR for absolute quantification of the gene expression by the standard curve method. Our results show high expression of GR in hepatic tissue. Significant effect of the breed was recorded for plasma corticosterone concentration: Valdarnese Bianca 3.35 ng/mL, Bionda Piemontese 1.73 ng/mL, Robusta Maculata 2.02 ng/mL. Breed specific gene expression has been recorded with a GR ranging from 1.12E+04 (Robusta Maculata) to 1.00E+05 (Bionda Piemontese) mRNA copy number/100 ng total RNA. Negative correlation was found between gene expression and blood corticosterone level.

Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers

Genomic and genetic variation among six Italian chicken native breeds (Livornese, Mericanel della Brianza, Milanino, Bionda Piemontese, Bianca di Saluzzo and Siciliana) were studied using single nucleotide polymorphism (SNP) and copy number variants (CNV) as markers. A total of 94 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) were used in the analyses. The results showed the genetic and genomic variability occurring among the six Italian chicken breeds. The genetic relationship among animals was established with a principal component analysis. The genetic diversity within breeds was calculated using heterozygosity values (expected and observed) and with Wrights F-statistics. The individual-based CNV calling, based on log R ratio and B-allele frequency values, was done by the Hidden-Markov Model (HMM) of PennCNV software on autosomes. A hierarchical agglomerative clustering was applied in each population according to the absence or presence of definite CNV regions (CNV were grouped by overlapping of at least 1 bp). The CNV map was built on a total of 1003 CNV found in individual samples, after grouping by overlaps, resulting in 564 unique CNV regions (344 gains, 213 losses and 7 complex), for a total of 9.43 Mb of sequence and 1.03% of the chicken assembly autosome. All the approaches using SNP data showed that the Siciliana breed clearly differentiate from other populations, the Livornese breed separates into two distinct groups according to the feather colour (i.e. white and black) and the Bionda Piemontese and Bianca di Saluzzo breeds are closely related. The genetic variability found using SNP is comparable with that found by other authors in the same breeds using microsatellite markers. The CNV markers analysis clearly confirmed the SNP results.

Quantitative trait loci mapping for conjugated linoleic acid, vaccenic acid and ∆9-desaturase in Italian Brown Swiss dairy cattle using selective DNA pooling

A selective DNA pooling approach was applied to identify QTL for conjugated linoleic acid (CLA), vaccenic acid (VA) and Δ(9) -desaturase (D9D) milk content in Italian Brown Swiss dairy cattle. 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. The pools were genotyped using the Illumina BovineSNP50 BeadChip. Sire allele frequencies were compared between high and low tails at the sire and marker level for SNPs for which the sires were heterozygous. An r procedure was implemented to perform data analysis in a selective DNA pooling design. A correction for multiple tests was applied using the proportion of false positives among all test results. BTA 19 showed the largest number of markers in association with CLA. Associations between SNPs and the VA and Δ(9) -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 of SNP markers associated with fatty acids contents.

Italian autochthonous chicken breeds conservation: evaluation of biodiversity in Valdarnese Bianca breed (Callus gallus domesticus).

Three fowl breeds, Valdarnese Bianca, a traditional white feathered breed from Tuscany, Golden Comet® a commercial hybrid and Livornese Bianca, a white leghorn type, were genotyped at eight microsatellite loci. A total of 74 alleles were detected with locus ADL181 recorded the lowest (six alleles) and locus ADL136 the highest (15 alleles) allele frequencies respectively. Heterozygosity values ranged from 0.210 (locus ADL210) to 0.742 (locus ADL176). The Wrights fixation index values were 0.089 (FST), 0.300 (FIs) and 0.363 (FIT). Factorial correspondence analysis and a dendrogram individual tree constructed using individual genetic distances showed genetic differentiation of the three breeds.

Heterozygosity analysis of Bionda Piemontese and Bianca di Saluzzo chicken breeds by microsatellites markers: a preliminary study

Abstract Conservation of genetic variability is one of the main goals in animal production science and the analysis of breeds genetic asset can supply objective basis for effective conservation programs and selection strategies. Bionda Piemontese(PIB) and Bianca di Saluzzo (SAB) chicken breeds originated in Piemonte region. Breeds conservation programmes started in 1999 in Verzuolo (CN) aiming to preserve the breeds and to improve their diffusion being particularly adapted to freerange rearing systems thanks to their resistance. PIB and SAB are both suggested for traditional recipes and production (e.g. Morozzo capon) and are Slow Food presidia. A total of 76 birds were analysed: PIB (n=36), SAB (n=40). Genomic DNA was extracted from blood samples. All birds were genotyped at eight microsatellite loci. Each marker was subjected to PCRand the products were separated by electrophoresis in 4.2% denaturing polyacrylamide gels on ABI Prism 377 DNA Sequencerequipped with Genescan and Genotyper software. The results of this preliminary study highlight the genetic differences occurring between PIB and SAB populations

Mitochondrial DNA control region variation in Sanfratellano horse and two other Sicilian autochthonous breeds

Abstract Mitochondrial D-loop hypervariable region was analysed in 20 Sanfratellano and two other Sicilian autochthonous horse breeds (20 Sicilian Oriental Purebred and 20 Sicilian Indigenous) in order to investigate matrilineal genetic diversity. A total of 20 different haplotypes were identified sequencing a fragment of 397 bp; overall, haplotypes showed 31 polymorphic sites (7.8%). High diversity was detected in Sanfratellano (11 haplotypes) and Sicilian Indigenous (13 haplotypes), whereas only one haplotype was found in Sicilian Oriental Purebred. Sanfratellano sequences were compared with those belonging to the other Sicilian autochthonous horses and 118 sequences selected from the GenBank database in order to calculate the statistics of molecular diversity. Six haplotypes were exclusive of Sanfratellano which shares haplotype C, D, H, and O with the Sicilian Indigenous and haplotype U with the Sicilian Oriental Purebred; not significant differentiation was found between Sanfratellano and Sicilian Indigenous. BLAST search showed Sicilian haplotypes overlap with the database sequences but for three. Phylogenetic analysis did not show monophyletic group for Sanfratellano samples or the other breeds included in this analysis.

Mitochondrial DNA genetic diversity in six Italian donkey breeds (Equus asinus)

Abstract Donkeys 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.