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Genome-wide investigation to assess copy number variants in the Italian local chicken population
Full text linkBackground: Copy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock. High-density chips have enabled the detection of CNV with increased resolution, leading to the identification of even small CNV. This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome.
Results: Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV. The majority of CNV in the investigated breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, a high proportion of the length of chromosome 16 was covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the genes identified within CNVR, only those present in at least five animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake.
Conclusions: The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources
Egg Quality of Italian Local Chicken Breeds: I. Yield Performance and Physical Characteristics
Full text linkThe aim of this study was to compare yield performance (from 39 to 50 weeks of age) and egg physical characteristics (at 50 weeks of age) of eight autochthonous chicken breeds of the Veneto region (Italy). Four white eggshell breeds, namely Padovana Camosciata (PA-C, chamois plumage), Padovana Dorata (PA-G, golden plumage), Polverara Bianca (PO-W, white plumage), and Polverara Nera (PO-B, black plumage), and four tinted eggshell breeds, namely Pepoi (PP), Ermellinata di Rovigo (ER), Robusta Maculata (RM), and Robusta Lionata (RL) from a conservation centre were considered in the trial. Significant differences (p < 0.05) among breeds were observed for yield performance and egg quality. From 39 to 50 weeks of age, the hen-day egg production was higher in PA-C and RM than in RL, and PO-W and ER were intermediate; PA-G, PO-B, and PP were the lowest. The hen-day egg production changed according to the age of the hens. From 39 to 42 weeks of age, ER showed the highest hen-day egg production and PA-G the lowest; from 47 to 50 weeks, PA-C, PO-W, and RM were the highest and PP the lowest. The tinted eggshell breeds, with the exception of PP, had higher egg weights than white eggshell breeds. PP egg weight was similar to PO-B. As regards the tinted eggshell breeds, RM eggs had the highest eggshell a* and b*, and PP the lowest. PA-C had the most spherical eggs, and PO-B and ER had the most ovoid eggs. PO-W and RM had the highest eggshell thickness and ER had the lowest. The highest eggshell ratio was observed for PO-W and PO-B, and the lowest for ER. The yolk-to-albumen ratio was higher in the white eggshell breeds than in PP, ER, and RL. ER had the highest Haugh units and PA-G the lowest. PO-W, PO-B, PA-C, PA-G, and ER had the lowest egg inclusions, and RL and RM the highest. Tinted eggshell eggs differed from white eggshell eggs by having higher meat spots. Results indicated that the eggs produced by the eight local chicken breeds differed according to the laying rate and a wide range of physical external and internal characteristics which allow the consumer to distinguish them for their genetic origin by the eggshell shape and colour, and to use them for different purposes to valorise poultry biodiversity
Egg Quality of Italian Local Chicken Breeds: II. Composition and Predictive Ability of VIS-Near-InfraRed Spectroscopy
Full text linkThe aims of the present study were to characterize egg composition and develop VIS-Near-infrared spectroscopy (VIS-NIR) models for its predictions in Italian local chicken breeds, namely Padovana Camosciata, Padovana Dorata, Polverara Bianca, Polverara Nera, Pepoi, Ermellinata di Rovigo, Robusta Maculata and Robusta Lionata. Hens were reared in a single conservation center under the same environmental and management conditions. A total of 200 samples (25 samples per breed, two eggs/sample) were analyzed for the composition of albumen and yolk. Prediction models for these traits were developed on both fresh and freeze-dried samples. Eggs of Polverara Nera and Polverara Bianca differed from eggs of the other breeds (p < 0.05) in terms of the greatest moisture content (90.06 ± 1.23% and 89.57 ± 1.31%, respectively) and the lowest protein content (8.34 ± 1.27% and 8.81 ± 1.27%) in the albumen on wet basis. As regards the yolk, Robusta Maculata and Robusta Lionata differed (p < 0.05) from the other breeds, having lower protein content (15.62 ± 1.13% and 15.21 ± 0.63%, respectively) and greater lipid content (34.11 ± 1.12% and 35.30 ± 0.98%) on wet basis. Eggs of Pepoi had greater cholesterol content (1406.39 ± 82.34 mg/100 g) on wet basis compared with Padovana Camosciata, Polverara Bianca and Robusta Maculata (p < 0.05). Spectral data were collected in reflectance mode in the VIS-NIR range (400 to 2500 nm) using DS2500 (Foss, Hillerød, Denmark) on fresh and freeze-dried samples. Models were developed through partial least-squares regression on untreated and pre-treated spectra independently for yolk and albumen, and using several combinations of scattering corrections and mathematical treatments. The predictive ability of the models developed for each compound was evaluated through the coefficient of determination (R2cv), standard error of prediction (SEcv) and the ratio of performance to deviation (RPDcv) in cross-validation. Prediction models performed better for freeze-dried than fresh albumen and yolk. In particular, for the albumen the performance of models using freeze-dried eggs was excellent (R2cv ≥ 0.91), and for yolk it was suitable for the prediction of protein content and dry matter. Good performances of prediction were observed in yolk for dry matter (R2cv = 0.85), lipids and cholesterol (R2cv = 0.74). Overall, the results support the potential of infrared technology to predict the composition of eggs from local hens. Prediction models for proteins, dry matter and lipids of freeze-dried yolk could be used for labelling purposes to promote local breeds through the valorization of nutritional aspects
Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review
Full text linkChicken products are the most consumed animal-sourced foods at a global level across greatly diverse cultures, traditions, and religions. The consumption of chicken meat has increased rapidly in the past few decades and chicken meat is the main animal protein source in developing countries. Heat stress is one of the environmental factors which decreases the productive performance of poultry and meat quality. Heat stress produces the over-expression of heat shock factors and heat shock proteins in chicken tissues. Heat shock proteins regulate several molecular pathways in cells in response to stress conditions, changing the homeostasis of cells and tissues. These changes can affect the physiology of the tissue and hence the production ability of chickens. Indeed, commercial chicken strains can reach a high production level, but their body metabolism, being comparatively accelerated, has poor thermoregulation. In contrast, native backyard chickens are more adapted to the environments in which they live, with a robustness that allows them to survive and reproduce constantly. In the past few years, new molecular tools have been developed, such as RNA-Seq, Single Nucleotide Polymorphisms (SNPs), and bioinformatics approaches such as Genome-Wide Association Study (GWAS). Based on these genetic tools, many studies have detected the main pathways involved in cellular response mechanisms. In this context, it is necessary to clarify all the genetic and molecular mechanisms involved in heat stress response. Hence, this paper aims to review the ability of the new generation of genetic tools to clarify the molecular pathways associated with heat stress in chickens, offering new perspectives for the use of these findings in the animal breeding field
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Italian local chicken breeds: a comparative analysis of biodiversity on a global scale
Full text linkBackground: Chickens, domesticated around 3500 years ago, are crucial in global agriculture, resulting in hundreds of breeds worldwide. In Europe, intensive breeding has led to the creation of numerous distinct commercial lines at the expense of local breeds. As a result, local breeds, which are not subject to rigorous selective practices, face higher risks of genetic problems due to a narrower genetic base. Modern genotyping and bioinformatic approaches allow detailed genetic analysis. This study offers a comprehensive genetic overview of Italian chicken biodiversity compared to global breeds, emphasizing the importance of preserving local genetic diversity. Results: Hundred and ninety-two chicken breeds from various countries were analyzed, with Italian breeds being highly represented. Genetic relationships showed that Italian breeds clustered with some European, African, and Asian breeds. The ADMIXTURE analysis identified 25 distinct populations and highlighted genetic similarities of certain Italian breeds with German, French, and Swiss ones. Genetic diversity was high in African and some Asian and European breeds, with Italian breeds exhibiting moderate diversity and variability. The TreeMix analysis revealed significant migration events and evolutionary clustering. The Italian breeds had close genetic ties and some highlighted evidence of genetic introgression from common ancestors. Conclusions: Italian chicken breeds have significant genetic relationships with European, Asian, and African breeds, reflecting historical trade and breeding exchanges. Southern Italian breeds form a distinct genetic group, highlighting regional uniqueness. Overall, the research points out the need for conservation strategies to preserve genetic diversity and account for historical and contemporary gene flows, ensuring the sustainability of Italian chicken biodiversity in the face of environmental and agricultural challenges
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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