Naturally Occurring Egg Drop Syndrome Infection in Turkeys

A decrease in the egg quality, production, fertility and hatchability without serious clinical signs of illness was recorded in turkey fl ocks in Croatia at the beginning of 2002. It was assumed that the egg drop syndrome virus might be one of the etiological agents responsible for the abnormalities in the egg production. The systematic serological monitoring, using a haemagglutination inhibition test, showed that the antibodies to the egg drop syndrome virus existed in 94.4 and 55.1% of the sera analysed in 2002 and 2003, respectively. The haemagglutination inhibition titres ranged from 16 to 128. The sera samples were randomly collected from 11 - to 46-week-old hens from the affected fl ocks. The serological evidence of the egg drop syndrome virus infection was confirmed by detection of the presence of the virus genome in the turkey sera by the polymerase chain reaction. Vaccination of the 18- and 25-week-old turkey hens against the egg drop syndrome virus started in March 2003. After this period, the presence of antibodies to the egg drop syndrome virus (the haemagglutination inhibition titres between 16 and 256) was found in 96.7% of the analysed sera, while the egg production reached normal or higher values for the Nicholas hybrid line of turkeys

Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness

Alternative polyadenylation (APA) determines mRNA stability, localisation, translation and protein function. Several diseases, including obesity, have been linked to APA. Studies have shown that single nucleotide polymorphisms in polyadenylation signals (PAS-SNPs) can influence APA and affect phenotype and disease susceptibility. However, these studies focussed on associations between single PAS-SNP alleles with very large effects and phenotype. Therefore, we performed a genome-wide screening for PAS-SNPs in the polygenic mouse selection lines for fatness and leanness by whole-genome sequencing. The genetic variants identified in the two lines were overlapped with locations of PAS sites obtained from the PolyASite 2.0 database. Expression data for selected genes were extracted from the microarray expression experiment performed on multiple tissue samples. In total, 682 PAS-SNPs were identified within 583 genes involved in various biological processes, including transport, protein modifications and degradation, cell adhesion and immune response. Moreover, 63 of the 583 orthologous genes in human have been previously associated with human diseases, such as nervous system and physical disorders, and immune, endocrine, and metabolic diseases. In both lines, PAS-SNPs have also been identified in genes broadly involved in APA, such as Polr2c, Eif3e and Ints11. Five PAS-SNPs within 5 genes (Car, Col4a1, Itga7, Lat, Nmnat1) were prioritised as potential functional variants and could contribute to the phenotypic disparity between the two selection lines. The developed PAS-SNPs catalogue presents a key resource for planning functional studies to uncover the role of PAS-SNPs in APA, disease susceptibility and fat deposition. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00335-022-09967-8

Overview of Croatian poultry industry over the period 2003-2004

Peradarska je proizvodnja u Hrvatskoj tijekom 2003. i 2004. godine, unatoč gospodarskim poteškoćama, zadržala razinu iz prethodnih godina. Primje-ćuje se, međutim, restrukturiranje peradarskih proizvođača u smislu okrupnjavanja proizvodnje. Izgrađeno je i dosta novih nastambi za perad koje su opremljene najsuvremenijom opremom, a i dosta je starih nastambi adaptirano i opremljeno novim sustavima. Pojedini proizvođači kasne u primjeni novih tehnoloških rješenja i spoznaja, i to pretežito mali pro-izvođači koji će se vjerojatno izgubiti u tržišnoj utakmici. Analizirane smjese za hranidbu peradi u većini su slučajeva po kemijskom sastavu i higijenskim zahtjevima bile na zadovoljavajućoj razini. Dio smjesa za tov pilića ipak je sadržavao manju količinu proteina i metaboličke energije, pa se u takvim slučajevima ne iskorištavaju u potpunosti potencijali modernih hibrida tovnih pilića i tako gubi profit. Zdravlje se peradi u Hrvatskoj tijekom protekle dvije godine općenito može ocijeniti zadovoljavajućim. Zarazna bolest burze (gumborska bolest), koja je uzrokovala značajne gospodarske gubitke tijekom proteklih desetak godina, sada je u opadanju, no izrazito se povećala učestalost zarazne kržljavosti. S obzirom da se zarazna kržljavost sprečava ponajprije pridržavanjem temeljnih tehnoloških postulata peradarske proizvodnje, smatramo da ovoj bolesti ne bi smjelo biti mjesta u našoj intenzivnoj peradarskoj proizvodnji. Bakterije iz roda Salmonella su u 2004. izdvojene u daleko većem broju negoli u prethodne dvije godine, međutim najveći broj izolata odnosi se na salmonele iz skupine «C1». S. Enteritidis, koji je bio najčešći serovar tijekom proteklih desetak godina, zapravo je u laganom opadanju, dok je serovar S. Typhimurium nešto češće izdvajan. Učestalo izdvajanje salmonela iz skupine «C1» upućuje na njihovu nazočnost u smjesama za hranidbu peradi, čemu treba posvetiti posebnu pozornost.Poultry production in Croatia during 2003 and 2004 remained at the same level as in previous years despite the economical difficulties. However, restructuring of the industry to larger poultry producing companies was noted. Many new poultry farms with modern equipment have been built, and many old farms have been renewed and equipped with new systems. Some of the poultry producers are not up to date with management and husbandry, and these are primarily small producers who will probably disappear due to market competition. Analysed feed for poultry are generally at a satisfactory level regarding chemical composition and hygienic standards. Some broiler feed samples had a lower quantity of protein and energy, therefore genetic potential of the modern broiler hybrids is not fully exploited and profit is lost. Poultry health during the last two years can be generally estimated as satisfactory. Infectious bursal disease (Gumboro disease), which caused significant economic losses in the recent years, has decreased, but incidence of infectious stunting syndrome significantly increases. Infectious stunting syndrome is controlled primarily by basic management principles, so we assume that this disease should not be a problem in our poultry industry. Bacteria from Salmonella genus were isolated in 2004 in a greater number compared to two previous years, but most of the isolates belonged to “C1” group. S. Enteritidis, which was the predominant serovar during the last decade, slightly decreased, whereas S. Typhimurium serovar is increasing. Frequent isolation of “C1” group salmonellas implicates their presence in feed, and particular attention should be paid to this problem

Integration of genomic and transcriptomic data of inbred mouse models for polygenic obesity and leanness revealed “obese” and “lean” candidate alleles in polyadenylation signals

Most mammalian genes have multiple polyadenylation (PA) sites, and alternative polyadenylation (APA) has been linked to diseases such as obesity. Studies have shown that changes in the polyadenylation signal (PAS) can influence the efficiency of cleavage and affect disease susceptibility and phenotype. In our recent study we used inbred mouse models of polygenic obesity and leanness and identified single-nucleotide polymorphisms in PAS (PAS-SNPs) within several obesity candidate genes, including five with differential expression. Nevertheless, to date, there has been no systematic, whole-genome-level approach aiming to prioritise PAS-SNPs potentially affecting APA. Therefore, in this study, we build upon our previous work by integrating existing genomics data with transcriptomics. DEGs were identified in nine tissues by Affymetrix GeneChip. PA and PAS sites were from the PolyASite 2.0 portal. Prioritisation of candidate PAS-SNPs was performed based on whether they were located in DEG, the type of PAS changes they caused, locations of PA sites relative to PAS, and location(s) and expression(s) of Affymetrix probes within a given gene in various tissues. For the candidates, potential consequences due to the alteration in APA events were investigated using bioinformatics databases and tools. The analysis found 127 PAS-SNPs in 101 DEGs across different tissues and identified 12 high-priority and 7 moderate-priority PAS-SNP candidates in 10 and 7 DEGs, respectively. Candidate PAS-SNPs were in 3′ UTR of 12 protein-coding genes (Lean line: Edil3, Eif2s1, Fbxl3, Hlf, Hsf2bp, Knop1, Lair1, Nmrk1Fat line: Ehd1, Rpl14, Spon1, Txndc9), introns of four protein-coding genes (Lean line: Abi3bp, Prr16Fat line: Agmo, Itga7) and intron of one lncRNA (Lean line: 1700086O06Rik). The integration of whole-genome sequencing and transcriptome analyses in this study has identified potential genome-wide candidate SNPs that could affect APA by altering/disrupting PAS motifs and be related to obesity in mice. The data provides a foundation for further research into these PAS-SNPs, their genes, and their contribution to the obesity/leanness phenotype, and contributes a part in explaining missing heritability commonly observed in complex traits

Whole genome sequencing of mouse lines divergently selected for fatness (FLI) and leanness (FHI) revealed several genetic variants as candidates for novel obesity genes

Background Analysing genomes of animal model organisms is widely used for understanding the genetic basis of complex traits and diseases, such as obesity, for which only a few mouse models exist, however, without their lean counterparts. Objective To analyse genetic differences in the unique mouse models of polygenic obesity (Fat line) and leanness (Lean line) originating from the same base population and established by divergent selection over more than 60 generations. Methods Genetic variability was analysed using WGS. Variants were identified with GATK and annotated with Ensembl VEP. g.Profiler, WebGestalt, and KEGG were used for GO and pathway enrichment analysis. miRNA seed regions were obtained with miRPathDB 2.0, LncRRIsearch was used to predict targets of identified lncRNAs, and genes influencing adipose tissue amount were searched using the IMPC database. Results WGS analysis revealed 6.3 million SNPs, 1.3 million were new. Thousands of potentially impactful SNPs were identified, including within 24 genes related to adipose tissue amount. SNP density was highest in pseudogenes and regulatory RNAs. The Lean line carries SNP rs248726381 in the seed region of mmu-miR-3086-3p, which may affect fatty acid metabolism. KEGG analysis showed deleterious missense variants in immune response and diabetes genes, with food perception pathways being most enriched. Gene prioritisation considering SNP GERP scores, variant consequences, and allele comparison with other mouse lines identified seven novel obesity candidate genes: 4930441H08Rik, Aff3, Fam237b, Gm36633, Pced1a, Tecrl, and Zfp536. Conclusion WGS revealed many genetic differences between the lines that accumulated over the selection period, including variants with potential negative impacts on gene function. Given the increasing availability of mouse strains and genetic polymorphism catalogues, the study is a valuable resource for researchers to study obesity