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Next generation sequencing applied in pigs have recently produced re-sequenced pig genome data from different individuals belonging to a large variety of breeds. The availability of these large datasets is opening new opportunities to mine public nucleotide archives and identify mutations that could putatively affect economic relevant traits. Moreover, resequencing data from pooled pig DNA could provide cost-effective whole genome information from a large number of animals. In this study, we mined 110 individual pig genomes retrieved from the European Nucleotide Archive and from proprietary datasets generated from pigs of 28 different breeds. This dataset was integrated from 8 pooled whole genome resequencing datasets generated from 35 individuals each from 8 distinct commercial or autochthonous breeds (Italian Large White, Italian Duroc, Italian Landrace, Apulo Calabrese, Cinta Senese, Casertana, Mora Romagnola, Nero Siciliano), respectively. Individual and pooled pig genome datasets were searched for polymorphisms in 135 annotated candidate genes, including 25 genes involved in androsterone and skatole biochemical related pathways. Short reads from these genomes were aligned using bowtie to a customized reference sequence generated from the reference pig genome, including sequence of selected genes (with depth ranging from 4 to 40X for each genome). A total of 100k variants were identified (2.3% in coding regions with about 500 missense mutations and a few other potential functional mutations). About 15% of these numbers refers to genes encoding enzymes involved in the androsterone and skatole biochemical pathways. This study provided an overview of the variability in targeted gene regions potentially involved in determining boar taint in pigs. Partially funded by European Union's H2020 RIA program (grant agreement no. 634476). Abstract reflects the authors' view. European Union Agency is not responsible for any use that may be made of the information it contains.

Abstract Monofloral honeys are high-added-value food, a reason for constant cases of fraud. This study investigated Brazilian monofloral honeys from Hovenia dulcis flowering produced by Apis mellifera and Tetragonisca angustula bees. Chemical, physicochemical, rheological, and melissopalynological analysis were assessed. Properties such as moisture, pH, ashes, total acidity, total available carbohydrate, and soluble sugars of all analyzed honey samples agreed with the established by the legislation. All the honey samples were satisfactorily fitted by both Ostwald-de Waele and Casson rheological models revealing homogenous products, mostly presenting pseudoplastic character. The melissopalynology confirmed the presence of H. dulcis pollen in the MH samples; however, some honeys did not show >45% pollen of H. dulcis, thus revealing mislabeling cases. Continuous evaluation of honey is necessary, once this is a valuable food frequently involved in frauds, hence causing problems to consumers.

Stingless bees, important pollinating insects in the tropics, produce honey whose unique quality features differentiate their origin. The feasibility of multivariate data analysis for quality discrimination of stingless bee honey from different genera (Melipona bicolor, quadrifasciata, marginata and Scaptotrigona bipunctata) by mineral content, physicochemical and microbiological properties were investigated. The principal component analysis explained 72.12% of the total variance of the data, and the separation into two main groups in a scatter plot was observed. Group 2 was formed by Scaptotrigona genus, that showed the highest values of pH, ash, and soluble solids. Potassium was the most abundant mineral followed by calcium and sodium for both groups quantified by inductively coupled plasma optical emission spectrometry. This honey has higher acidity and moisture than Apis mellifera honey. Microbiological analyses showed that total aerobic mesophiles ranged between 2.00 and 4.77 log CFU/g. Salmonella spp. was not detected, while the mould and yeast content was above the maximum allowed under the Apis mellifera honey legislation. The evaluated honey samples presented the lactic acid bacteria, which are considered a benefit. The multivariate statistical analysis was efficient in discriminate stingless bee honey, contributing to approaches that can be used for standardization and regulation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13197-019-03939-8) contains supplementary material, which is available to authorized users.

Animal genetic resources are important reservoirs of genetic diversity derived by distinct selection pressures or as result of adaptation to production conditions. The TREASURE project has investigated genetic variability in 20 European autochthonous pig breeds with the aim to describe their singularity, evaluate their adaptation, develop new methodologies for their management and identify DNA markers for breed allocation and meat authentication. Genomic data have been obtained by genotyping candidate gene markers and high density single nucleotide polymorphism arrays in ~48 animals from each breed and by whole genome resequencing. Description of genetic diversity has been obtained using several parameters. Runs of homozygosity and genomic inbreeding measures have been correlated with pedigree inbreeding coefficients. A few breed specific markers have been identified and applied. Genome wide association studies have identified genomic regions affecting unique phenotypes. This project represents one of the few examples of exploitation of genomic information that not only benefits the investigated animal genetic resources but also can provide useful information that could impact commercial populations. Funded by European Union's H2020 RIA program (grant agreement no. 634476).

Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/ breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products. ; This work has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 634476 for the project with acronym TREASURE. The content of this article reflects only the authors' view and the European Union Agency is not responsible for any use that may be made of the information it contains. MŠ and MČP received core-financing by the Slovenian Research Agency (grant number P4-0133). ; info:eu-repo/semantics/publishedVersion

13 Pág. ; Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products. ; This work has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 634476 for the project with acronym TREASURE. The content of this article reflects only the authors' view and the European Union Agency is not responsible for any use that may be made of the information it contains. MŠ and MČP received core-financing by the Slovenian Research Agency (grant number P4-0133). ; Peer reviewed