1,721,013 research outputs found
Authentication of a food product based on DNA analysis of an added natural biological tracer: Testing the application to dry cured hams
Full text linkFood authenticity is crucial for all value chains, including many meat products. Various methods have been developed to authenticate meat products based on the intrinsic DNA information of the animals from which the products originated. In this study, we propose an alternative method of authentication based on DNA analysis of a biological tracer added to the product. To demonstrate its effectiveness, we conducted a pilot study focused on dry-cured hams that were authenticated using genetically characterised wheat flours, obtained from different accessions. The study consisted of three main steps: first, we analysed 23 wheat accessions using random amplified polymorphic DNA assays and seven wheat microsatellites to assess the accession homogeneity/homozygosity and establish accession specific microsatellite fingerprinting; next, we tested, as a proof-of-concept, the feasibility of using genetically characterised wheat flours as natural tracers when mixed with lard (used to cover the skin-free part of the legs) and ink (used to label the legs), which are routinely applied in ham production; finally, we tested the possibility of authenticating hams by retrieving DNA information from the applied matrices (lard and ink mixed with flour) on the legs that were cured and ripened for 16 months. The DNA fingerprinting was consistent throughout all evaluation stages enabling the authentication of the marked hams. One advantage of this system is that the tracer (and its DNA profile) is known only to the authentication system managers. This approach can be adapted to authenticate many other food products
Authentication of honey based on a DNA method to differentiate Apis mellifera subspecies: Application to Sicilian honey bee (A. m. siciliana) and Iberian honey bee (A. m. iberiensis) honeys
No full textHoney contains intrinsic markers that can be used to identify its origin. In this study, we used the honey as source of honey bee DNA and developed a test to detect the entomological origin of the honey by identifying the Apis mellifera subspecies using an informative mitochondrial DNA region. We then applied this method for the authentication of A. m. siciliana and A. m. iberiensis honeys. DNA was extracted from 60 honey samples produced in several Italian regions (including Sicily and close minor islands), Portugal, Spain and other countries. PCR primers were designed to amplify a fragment of 85 bp (A. mellifera C lineage; highly frequent in A. m. ligustica, the Italian honey bee that is frequently implicated in human introductions worldwide), or 138 bp (M lineage; characteristic of A. m. mellifera) or 152 bp (A lineage; of the honey bee subspecies of African origin). All sampled Sicilian honeys (that were from A. m. siciliana) showed only the fragment of 152 bp, confirming its expected origin. All honeys from A. m. iberiensis showed only the fragment of 152 bp or only the fragment of 138 bp or both, in agreement with the hybrid origin of Iberian honey bee populations. All other analyzed honeys showed the fragments of 85 bp or 85 + 138 bp, suggesting that they were produced from other subspecies. This authentication system could be a useful tool to support conservation genetic programs that rely on marketing links between honey bee genetic resources and the honey they produce
Honey Environmental DNA Can Be Used to Detect and Monitor Honey Bee Pests: Development of Methods Useful to Identify Aethina tumida and Galleria mellonella Infestations
Full text linkEnvironmental DNA (eDNA) contained in honey derives from the organisms that directly and indirectly have been involved in the production process of this matrix and that have played a role in the hive ecosystems where the honey has been produced. In this study we set up PCR-based assays to detect the presence of DNA traces left in the honey by two damaging honey bee pests: the small hive beetle (Aethina tumida) and the greater wax moth (Galleria mellonella). DNA was extracted from 82 honey samples produced in Italy and amplified using two specific primer pairs that target the mitochondrial gene cytochrome oxidase I (COI) of A. tumida and two specific primer pairs that target the same gene in G. mellonella. The limit of detection was tested using sequential dilutions of the pest DNA. Only one honey sample produced in Calabria was positive for A. tumida whereas about 66% of all samples were positively amplified for G. mellonella. The use of honey eDNA could be important to establish early and effective measures to contain at the local (e.g., apiary) or regional scales these two damaging pests and, particularly for the small hive beetle, to prevent its widespread diffusion
Sustainable animal breeding in a local cattle breed: a genomic strategy to redefine Reggiana HerdBook standards and breeding goals.
No full textReggiana is an Italian autochthonous cattle breed, mainly reared in the Emilia Romagna region. At present, a total of about 2800 Reggiana cows, distributed in about 100 farms, are registered to its breed Herd Book. Nowadays, almost all the milk produced by the Reggiana breed is processed into mono-breed Protected Designation of Origin (PDO) Parmigiano-Reggiano cheese that is labelled with the brand name ‘Vacche Rosse’ (according to the typical red coat colour – fromentino – of the breed). This cheese is marketed at a higher price than those of undifferentiated origin. Phenotypic selection in the Reggiana breed has been applied over the last decades to maintain the breed standard defined in the Herd Book (e.g. solid fromentino coat colour, pink or pale muzzle, medium-tall stature, dual-purpose conformation, absence of morphological defects), but a few Reggiana animals do not completely match the breed standard phenotypes. In this study, we defined a strategy to design a sustainable breeding and conservation programme of the Reggiana population, by considering both phenotypic and genetic data. About 70% of the whole Reggiana breed population was genotyped with the GeneSeek GGP Bovine 150k SNP chip. The allele and genotype frequencies and distribution of single nucleotide polymorphism (SNP) markers involved or associated with phenotypic exterior (coat colour and muzzle), morphological traits (e.g. stature and morphological defects), and the presence of deleterious alleles derived from other cattle breeds were analysed. Based on obtained results, information on the genotype at the Extension locus/melanocortin 1 receptor (MC1R) gene has been included in the Reggiana Herd Book as part of the breed standard. Other DNA markers could be included or could be used to cull some animals carrying unwanted alleles/defects or to design appropriate strategies for their effective eradication from the population. These strategies might be integrated in optimum contribution selection plans that would also carefully evaluate the potential loss of genetic variability and effective population size of the breed. This strategy can be useful to design further refine a genomic-driven sustainable breeding and conservation program of Reggiana cattle that is also linked to the genetic authentication of its mono-breed Parmigiano Reggiano cheese.
Acknowledgements
The research was funded by the PSRN Dual Breeding and Dual Breeding 2
Entomological signatures in honey: an environmental DNA metabarcoding approach can disclose information on plant-sucking insects in agricultural and forest landscapes
Full text linkHoneydew produced from the excretion of plant-sucking insects (order Hemiptera) is a carbohydrate-rich material that is foraged by honey bees to integrate their diets. In this study, we used DNA extracted from honey as a source of environmental DNA to disclose its entomological signature determined by honeydew producing Hemiptera that was recovered not only from honeydew honey but also from blossom honey. We designed PCR primers that amplified a fragment of mitochondrial cytochrome c oxidase subunit 1(COI) gene of Hemiptera species using DNA isolated from unifloral, polyfloral and honeydew honeys. Ion Torrent next generation sequencing metabarcoding data analysis assigned Hemiptera species using a customized bioinformatic pipeline. The forest honeydew honeys reported the presence of high abundance of Cinara pectinatae DNA, confirming their silver fir forest origin. In all other honeys, most of the sequenced reads were from the planthopper Metcalfa pruinosa for which it was possible to evaluate the frequency of different mitotypes. Aphids of other species were identified from honeys of different geographical and botanical origins. This unique entomological signature derived by environmental DNA contained in honey opens new applications for honey authentication and to disclose and monitor the ecology of plant-sucking insects in agricultural and forest landscapes
Investigating genetic factors affecting a production disease in meat rabbits: a genome-wide association study on susceptibility to diarrhea before weaning
No full textEnsuring animal welfare and reducing antimicrobial agents are becoming key aspects in the development of sustainable livestock production systems. The implementation and adoption of novel breeding and selection strategies that align with these aspects can enhance both production efficiency and farmers' profitability. As a result, sustainability and economic returns in livestock farming can be simultaneously improved, especially in the rabbit production system, where diseases like diarrhea in newborn rabbits represent a major source of economic losses. In this study, we aimed to genetically dissect the resistance against diarrhea by designing a case-control genome-wide association study (GWAS) to identify genetic markers affecting the sensitivity to this disease in a commercial meat rabbit population. The study included rabbits from 133 litters produced by crossing 7 bucks and 45 does. A total of 332 suckling rabbits were selected from 45 different litters, with 151 rabbits with severe symptoms of diarrhea, 42 with mild symptoms and 129 without any symptoms until weaning. Genotyping of these animals was done using the Affymetrix Axiom OrcunSNP Array, which interrogates a total of 199,692 single nucleotide polymorphisms (SNPs). The data obtained were quality checked and filtered using PLINK v.1.9 software. Genomic heritability (h2G) estimation of the trait was carried out with GEMMA v.0.98 software with linear mixed models. Genomic heritability estimates ranged from 0.19 to 0.21 (with standard error that ranged from 0.09 to 0.10). Three main peaks of SNPs were identified on rabbit chromosome 12 (OCU12), OCU13 and OCU16, with annotation of these genomic regions indicating genes involved in the innate immune system as potential candidates for this pathogenic condition. Results were validated by genotyping associated SNPs in additional cases and control animals from a different rabbit cohort of the same population. Fine mapping of these genomic regions was conducted by mining whole genome resequencing data obtained from several susceptible and resistant rabbits within the same litters, identifying a few candidate causative mutations. Overall, the results obtained in this genomic study demonstrate that resistance to enteropathy occurring in suckling rabbits is partially genetically determined and can be dissected at the genomic level. This information will be useful for implementing a marker assisted selection program aimed at improving resistance against pre-weaning diarrhea, animal welfare and the overall sustainability of the rabbit production system
A genotyping by sequencing approach can disclose Apis mellifera population genomic information contained in honey environmental DNA
Full text linkAwareness has been raised over the last years on the genetic integrity of autochthonous honey bee subspecies. Genomic tools available in Apis mellifera can make it possible to measure this information by targeting individual honey bee DNA. Honey contains DNA traces from all organisms that contributed or were involved in its production steps, including the honey bees of the colony. In this study, we designed and tested a genotyping by sequencing (GBS) assay to analyse single nucleotide polymorphisms (SNPs) of A. mellifera nuclear genome using environmental DNA extracted from honey. A total of 121 SNPs (97 SNPs informative for honey bee subspecies identification and 24 SNPs associated with relevant traits of the colonies) were used in the assay to genotype honey DNA, which derives from thousands of honey bees. Results were integrated with information derived from previous studies and whole genome resequencing datasets. This GBS method is highly reliable in estimating honey bee SNP allele frequencies of the whole colony from which the honey derived. This assay can be used to identify the honey bee subspecies of the colony that produced the honey and, in turn, to authenticate the entomological origin of the honey
Genotyping-by-sequencing of honey derived environmental DNA can retrieve information on the Apis mellifera subspecie.
No full textHoney contains environmental DNA (eDNA) traces derived from all organisms that directly or indirectly contributed to its production or that have been part of the production niche and environment from which this matrix is obtained. We recently demonstrated that honey constitutes an easily accessible source of Apis mellifera DNA useful to retrieve population genetic information. We also recently demonstrated that honey bee mitochondrial DNA (mtDNA) specific lineages detected in the honey can be used to authenticate the entomological origin of the honey. In this study we analysed honey DNA and integrated honey bee mtDNA information with nuclear genome polymorphisms to set up an improved tool that can detect the honey bee subspecies using these two genome levels. To this aim, we designed and tested a genotyping by sequencing (GBS) assay to analyse 121 single nucleotide polymorphisms (SNPs) of A. mellifera nuclear genome using eDNA extracted from honey. Results were integrated with information derived from previous studies and whole genome resequencing datasets. Genomic analyses were obtained for 61 specimens (honey samples and honey bees) collected in a few Italian regions (Emilia-Romagna, Liguria and Sicily) and that included: (i) individual honey bees of the subspecies A. m. ligustica, A. m. mellifera and A. m. siciliana; (ii) groups of pooled DNA samples from more than 30 A. m. ligustica workers belonging to the same colonies from which honey samples (see below) have been collected; (iii) honey samples obtained from 32 single hives; (iv) undifferentiated honey samples produced from A. m. ligustica and A. m. siciliana. The GBS runs produced more than 53 million reads that were used to obtain genotype information of the selected bi-allelic SNPs. Allele frequency estimation combined with several multidimensional scaling approaches were able to 25th Congress of Animal Science and Production Associationcorrectly assign the honey to the honey bee subspecies that produced it with high correlations between samples and runs. Overall, results obtained from GBS demonstrated the possibility to use A. mellifera nuclear genome variability to authenticate the entomological origin of the honey by detecting the honey bee subspecies.
Acknowledgements
This study was supported by Regione Emilia Romagna – BEE-RER3
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Comparative analysis of heterozygosity-enriched regions in Reggiana and Modenese genomes providesinformation on local cattle breed specific variabilit.
No full textReggiana and Modenese are dual-purpose cattle breeds mainly reared in the North of Italy and linked to the production of monobreed branded Parmigiano-Reggiano cheese, which provides the economic income to the farmers that is needed for the sustainable conservation of these autochthonous breeds. The population size of these breeds experienced a drastic reduction in the 1980’ and a subsequent slow recovery. Inbreeding is an important parameter that should be monitored to define appropriate conservation programs of local genetic resources. We therefore already evaluated inbreeding in these breeds using pedigree and genomic information based on runs of homozygosity (ROH). Hotspot regions of heterozygosity may be useful to define other relevant population genomic information. Runs of Heterozygosity (ROHet) are regions of continuous single nucleotide polymorphisms (SNPs) with heterozygous genotype. In this study, we obtained a genomic landscape picture of ROHet in Reggiana and Modenese cattle breeds and identified ROHet islands. A total of 2730 Reggiana cows and 564 Modenese cattle (almost two thirds of the actual population for both breeds) were genotyped with the GGP Bovine 150K SNPchip. Quality filters were applied with PLINK1.9. ROHet were identified with detectRuns R package. In total, 38942 and 7289 ROHet were identified in Reggiana and Modenese cattle populations, respectively. The average number of ROHet per animal in Reggiana was 14.24±3.8, with a minimum of 1 ROHet and a maximum of 30. In Modenese breed, the average number of ROHet per animal was 12.91±3.3, with a minimum of 1 and a maximum of 23. For Reggiana, the longest ROHet was on chromosome BTA10, with a length of 1029 kb, while for Modenese the longest ROHet was on BTA21 and measured 1228 kb. The total average size of the genome covered by ROHet for each animal was 2532.38±858 and 2291.26±781 kb in Reggiana and Modenese, respectively. These regions included many genes involved in fecundity, survival, and fitness-related traits that might be involved in defining breed genetic features.
Acknowledgements
The research was funded by the PSRN (Programma di Sviluppo Rurale Nazionale) Dual Breeding 2 (co-funded by the European Agricultural Fund for Rural Development of the European Union and by the MASAF)
The Agouti locus and coat colour in cattle: evaluating ASIP gene variability in local andcosmopolitan cattle breeds.
No full textCoat colour in mammals depends on the relative amount of two types of pigments, eumelanin (black/brown) and phaeomelanin (yellow/red), which are in turn controlled by the Extension (E) and Agouti (A) loci. While E locus encodes the melanocortin-1 receptor (MC1R) gene which is involved in both melanins production, A locus encodes the agouti signaling protein (ASIP) gene that downregulates MC1R activity, resulting in phaeomelanin synthesis. According to the classical epistatic interaction between the E and A loci, wild type alleles at the MC1R gene would allow to express mutated alleles at the A locus. Cattle breeds have a large variability in coat colour. In this study we focused on two autochthonous breeds (Reggiana and Modenese) and a cosmopolitan breed (Holstein) with different coat colour: Reggiana has a classical red coat colour derived by the recessive mutated allele at the MC1R gene; Modenese is characterized by a white-pale grey solid coat colour; and Holstein usually has a spotted white and black coat colour with black derived by a dominant mutated MC1R allele. In this study we characterized the cattle ASIP gene region variability starting from whole genome sequencing (WGS) data obtained from Reggiana (n.50), Modenese (n. 10) and Holstein breeds (n. 50). We identified four insertion/deletions (indels) which might putatively affect ASIP gene regulatory regions. The indels have been also genotyped by end-point PCR and Sanger sequencing in a larger population of the same three breeds and other 10 breeds. The results revealed that the Reggiana and the Italian Holstein breeds were almost completely fixed for alleles that were almost absent in Modenese breed. Variability in the ASIP gene in this breed might be involved in determining its white coat colour. These results provide some first evidence on the elusive role of the ASIP gene in affecting coat colour also in cattle, similarly to what already reported in sheep and goat, where variants in this gene are associated with white coat colours.
Acknowledgements
The research was funded by the PSRN (Programma di Sviluppo Rurale
Nazionale) Dual Breeding 2 (co-funded by the European Agricultural
Fund for Rural Development of the European Union and by the MASAF)
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