Vlatka Cubric-Curik

Presence of Torque teno sus virus in porcine circovirus type 2-associated disease in Croatia

Torque teno virus (TTV) is ubiquitous and species-specific, and two different TTV species, Torque teno sus virus 1 (TTSuV1) and Torque teno sus virus 2 (TTSuV2), have been described in domestic pigs and wild boars. Whether these two species are involved in clinical cases of porcine circovirus type 2-associated disease (PCVDs) remains unknown. This study investigates the presence of TTSuV in 85 fetuses, pigs and wild boars infected by PCV2 and affected by PCVDs other than postweaning multisystemic wasting syndrome (PMWS) and porcine dermatitis and nephropathy syndrome. It also explores the genetic diversity of identified strains using phylogenetic analysis. The presence or absence of TTSuV was determined in 85 samples of PCV2-containing organs from 85 infected animals using a specific, one-step PCR method. A nucleotide distance matrix between sequences was computed to infer phylogeny based on a median-joining (MJ) network. TTSuV2 showed high prevalence in animals affected by nephropathy and proliferative and necrotising pneumonia (PNP), and both TTSuV1 and TTSuV2 showed high prevalence in wild boars affected by PMWS. TTSuV1 showed low prevalence in animals affected by nephropathy and PNP, and both TTSuV1 and TTSuV2 showed low prevalence in animals with reproductive disorders. MJ network analysis revealed significant genetic diversity among Croatian isolates.

The Effect of Sex and Dgat1 Gene Polymorphism on Fat Deposition Traits in Simmental Beef Cattle

This study investigated diacylglycerol O-acyltransferase 1 (DGAT1) gene K232A mutation in Simmental cattle and its effects on fat deposition traits. The sample (n=26) consisted of yearling bulls and beef heifers from an intensive rearing system in Croatia. Carcass fatness was assessed by total dissection method, whereas intramuscular fat (m. longissimus dorsi) content was determined using Soxhlet extraction with hydrolysis. Intramuscular fatty acid composition was determined by gas liquid chromatography using in situ transesterification. The muscle DNA was extracted and Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCRRFLP) analysis of the 411 bp fragment of DGAT1 gene was applied. The DGAT1 K allele was less frequent in heifers than in bulls, with the overall allelic frequency of 17% K allele. Only KA and AA genotypes were obtained, without deviation from the Hardy-Weinberg equilibrium. Heifers showed a higher degree of carcass and muscle fattening with more unsaturated intramuscular fat than bulls; however, there was no interaction between sex and DGAT1 gene. Generally, no significant difference between DGAT1 AA and KA animals was observed for any of the examined traits, except the slightly higher carcass share of the fattest beef category and higher intramuscular C14:0 desaturation index in KA heterozygous.

Are the dinaric mountains a boundary between continental and mediterranean wild boar populations in Croatia

Wild boar is the most important large game species in Croatia, with populations subjected to hunting/management programs. There are indications from previous analyses of morphological variation and reproductive performance that population structure of wild boar in Croatia is strongly influenced by the Dinaric mountain range that separates Croatia in two biogeographic regions: Continental and Mediterranean. Of the two main wild boar haplogroups found in Europe, the most widespread is the E1 clade (present from Portugal to Russia), while the E2 clade is found within the Italian peninsula and on Sardinia. Outside Italy, the E2 clade has to date been found only in archaeological samples from the Mediterranean region of Croatia. The aims of this study were to investigate the hypotheses that (i) the Dinaric Mountains act as a natural boundary separating the Continental and Mediterranean wild boar subpopulations in Croatia; and (ii) the mtDNA E2 clade is present in Croatian wild boar. A total of 14 unlinked microsatellite loci were examined in 264 geo-referenced individuals, and the 486-bp fragment of the mtDNA control region sequence was examined in 69 individuals. The results suggest that the region of the Dinaric Mountains. represents a weak boundary between the Continental and Mediterranean subpopulations, and that the predominant factor causing the observed genetic structuring is isolation by distance. Based on these results, it can be proposed that the Croatian wild boar population in the mainland should be managed as a whole. Three variable sites and four haplotypes were obtained from the mtDNA sequences, all of which belonged to the major European clade (E1).

Sequence Analysis of Bitter Taste Receptor Gene Repertoires in Different Ruminant Species.

Bitter taste has been extensively studied in mammalian species and is associated with sensitivity to toxins and with food choices that avoid dangerous substances in the diet. At the molecular level, bitter compounds are sensed by bitter taste receptor proteins (T2R) present at the surface of taste receptor cells in the gustatory papillae. Our work aims at exploring the phylogenetic relationships of T2R gene sequences within different ruminant species. To accomplish this goal, we gathered a collection of ruminant species with different feeding behaviors and for which no genome data is available: American bison, chamois, elk, European bison, fallow deer, goat, moose, mouflon, muskox, red deer, reindeer and white tailed deer. The herbivores chosen for this study belong to different taxonomic families and habitats, and hence, exhibit distinct foraging behaviors and diet preferences. We describe the first partial repertoires of T2R gene sequences for these species obtained by direct sequencing. We then consider the homology and evolutionary history of these receptors within this ruminant group, and whether it relates to feeding type classification, using MEGA software. Our results suggest that phylogenetic proximity of T2R genes corresponds more to the traditional taxonomic groups of the species rather than reflecting a categorization by feeding strategy.

Origin of porcine circovirus type 2 (PCV2) from swine affected by PCV2-associated diseases in Croatia

Porcine circovirus type 2 (PCV2) causes some of the most significant economic losses in pig production. Several multisystemic syndromes have been attributed to PCV2 infection, which are known as PCV2-associated diseases (PCVDs). This study investigated the origin and evolution of PCV2 sequences in domestic pigs and wild boars affected by PCVDs in Croatia. Viral sequences were recovered from three wild boars diagnosed with PCV2-systemic disease (PCV2-SD), 63 fetuses positive for PCV2 DNA as determined by PCR, 14 domestic pigs affected with PCV2-SD (displaying severe interstitial nephritis) and five domestic pigs with proliferative and necrotising pneumonia. Seventeen complete PCV2 genomes were recovered. Phylogenetic and evolutionary analyses based on median-joining phylogenetic networks, amino acid alignments and principal coordinate analysis were performed using complete genomes, as well as complete and partial ORF sequences for ORF1 and ORF2. Two of the 17 PCV2 sequences belonged to PCV2a, 14 to PCV2b and one was unclustered. PCV2b was the predominant genotype in Croatia and has been linked to international trade as a route of introduction. Correlation between particular viral strains with PCVDs is lacking.

Sequence polymorphism of PrP exon 3 gene in Istrian and crossbred sheep

Abstract Polymorphisms in sheep PrP (prion protein) gene are known for scrapie susceptibility. We sequenced part of PrP exon 3 gene in 92 autochthonous Istrian (IS) and 38 crossbred sheep (CBS). ARQ, ARR and AHQ alleles were predominant with frequency of 0.674 (0.526), 0.228 (0.132) and 0.082 (0.263) in IS (CBS), respectively, while VRQ (0.011 in IS) and ARH (0.005 in IS and 0.079 in CBS) alleles were rare. We also found non-synonymous mutations at codons 112 (M→T), 127 (G→S) and 143 (H→R), and synonymous mutations at codons 231 (R) and 237 (L). Additional mutations were associated only with AHQ, ARH and ARQ alleles. The polymorphism of PrP gene in IS was not critical with respect to scrapie susceptibility and with some efforts number of “favourable” genotypes can be increased.

MaGelLAn 1.0: a software to facilitate quantitative and population genetic analysis of maternal inheritance by combination of molecular and pedigree information.

BackgroundIdentification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis. Current research in our group focuses on acquiring the necessary mitochondria sequence information and analysing its influence on the phenotype of a quantitative trait. To facilitate these tasks we have produced software for processing pedigrees that is optimised for maternal lineage analysis.ResultsWe present MaGelLAn 1.0 (maternal genealogy lineage analyser), a suite of four Python scripts (modules) that is designed to facilitate the analysis of the impact of mitogenome polymorphism on quantitative trait variation by combining molecular and pedigree information. MaGelLAn 1.0 is primarily used to: (1) optimise the sampling strategy for molecular analyses; (2) identify and correct pedigree inconsistencies; and (3) identify maternal lineages and assign the corresponding mitogenome sequences to all individuals in the pedigree, this information being used as input to any of the standard software for quantitative genetic (association) analysis. In addition, MaGelLAn 1.0 allows computing the mitogenome (maternal) effective population sizes and probability of mitogenome (maternal) identity that are useful for conservation management of small populations.ConclusionsMaGelLAn is the first tool for pedigree analysis that focuses on quantitative genetic analyses of mitogenome data. It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source code, along with the manual and the example files can be downloaded at http://lissp.irb.hr/software/magellan-1-0/ and https://github.com/sristov/magellan.