Genomics of dwarfism in Italian local chicken breeds

The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as “dwarf”, namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.Depto. de Producción AnimalFac. de VeterinariaTRUEMinistry of Agricultural, Food and Forestry Policies (Italy)China Scholarship Councilpu

Genetic Diversity of 17 Autochthonous Italian Chicken Breeds and Their Extinction Risk Status

The preservation of genetic variability of autochthonous poultry breeds is crucial in global biodiversity. A recent report revealed small breed size and potential risk of extinction of all native Italian poultry breeds; therefore, a correct assessment of their genetic diversity is necessary for a suitable management of their preservation. In this work, we provided an overview of the contribution to poultry biodiversity of some Italian autochthonous breeds reared in conservation centers devoted to local biodiversity preservation. The level of genetic diversity, molecular kinship, inbreeding, contribution to overall genetic diversity, and rate of extinction of each breed were analyzed with a set of 14 microsatellite loci in 17 autochthonous chicken breeds. To evaluate genetic variability, total number (Na), and effective number (Ne) of alleles, observed (Ho) and expected (He) heterozygosity, and F (Wright’s inbreeding coefficient) index were surveyed. The contribution of each analyzed breed to genetic diversity of the whole dataset was assessed using MolKin3.0; global genetic diversity and allelic richness contributions were evaluated. All the investigated loci were polymorphic; 209 alleles were identified (94 of which private alleles). The average number of alleles per locus was 3.62, and the effective number of alleles was 2.27. The Ne resulted lower in all breeds due to the presence of low-frequency alleles that can be easily lost by genetic drift, thus reducing the genetic variability of the breeds, and increasing their risk of extinction. The global molecular kinship was 27%, the average breed molecular kinship was 53%, and the mean inbreeding rate 43%, with a self-coancestry of 78%. Wright’s statistical analysis showed a 41% excess of homozygous due to breed genetic differences (34%) and to inbreeding within the breed (9%). Genetic variability analysis showed that 11 breeds were in endangered status. The contribution to Italian poultry genetic diversity, estimated as global genetic diversity, and ranged from 30.2 to 98.5%. In conclusion, the investigated breeds maintain a unique genetic pattern and play an important role in global Italian poultry biodiversity, providing a remarkable contribution to genetic variability

Overview of Native Chicken Breeds in Italy: Conservation Status and Rearing Systems in Use

The ongoing loss of domestic animal breeds around the world is occurring at an alarming rate. Thus, the registration and preservation of native breeds is of great importance. The aim of this study, which forms part of a conservation program, was to provide an overview of the conservation statuses of native Italian poultry breeds being reared by local breeders in Italy. The data collected by means of a census questionnaire demonstrate the low population sizes of these breeds in Italy and highlight the need for campaigns aimed at publicizing and promoting the benefits of native breeds with the goal of increasing population sizes. Identifying strategies to facilitate breeders’ access to pure breed birds is also essential, and would require collaborative efforts of university research centers, public entities, and breeders

Overview of Native Chicken Breeds in Italy: Small Scale Production and Marketing

The intensive use of high-performing strains in poultry production has led to the extinction of several autochthonous chicken breeds and, consequently, loss of genetic variability. Interest in saving biodiversity is growing rapidly and has become a major objective worldwide. The aim of this study was to shed light on the production trends of native Italian poultry breeds and the related market. A questionnaire, which asked about the production cycles, the number of animals and table eggs produced per year and their retail prices was completed by 121 breeders across Italy. The surveyed breeders were divided into two categories: breeders conducting an agrozootechnical farm, referred to as ‘farmers’ (F); and breeders keeping chickens as backyard poultry, referred to as ‘fancy breeders’ (FB). Analysis of the data acquired indicated that animals were mainly slaughtered between 6 and 12 months of age, with F processing more animals per year. The same production trend was observed for table eggs. The recorded retail prices of native chicken products were higher than those for conventional products, but similar to those reported for valuable niche poultry products, such as the Poulet de Bresse in France and organic eggs. Knowledge about these highly valuable markets should be used to encourage the use of local breeds in alternative poultry farming and help protect biodiversity

Egg Quality of Italian Local Chicken Breeds: II. Composition and Predictive Ability of VIS-Near-InfraRed Spectroscopy

The 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

Morphological and genetic characterization of 13 Italian local chicken breeds

Submitted 2020-07-02 | Accepted 2020-09-03 | Available 2020-12-01https://doi.org/10.15414/afz.2020.23.mi-fpap.137-143According to census accomplished in 2001, only 9% of Italian poultry breeds are still widespread. This project aims to describe morphological variability and genetic background among 13 Italian autochthonous chicken breeds, 10 from Northern Italy and 3 from Central Italy. An updated biometrical measurement protocol was established starting from phenotypic characterization guidelines released by FAO. Six traits were registered on each animal: live body weight (LBW), body length (BL), shank length (SL), shank width (SW), breast width (BW), and wingspan (WS). Moreover, all breeds were genotyped using the Affymetrix 600 K Chicken SNP Array, in order to evaluate genetic variability and population structure. Means of BL and BW showed low variability among breeds, with the lowest value in Pepoi (BL = 32.29 ± 1.57 cm and BW = 28.92 ± 1.93 cm), and maximum in Robusta Lionata for BL (46.79 ± 1.66 cm) and in Robusta Maculata for BW (42.33 ± 3.60 cm). On the contrary, average LBW varied notably among breeds, with the highest value for Robusta Maculata (♂ 4,221.7 ± 450.6 g; ♀ 2,831.7 ± 253.2 g) and the lowest values for Modenese males (1,695.0 ± 128.1 g) and Pepoi females (1,293.3 ± 219.2 g). The lowest observed heterozygosity (Ho) and expected heterozygosity (He) were obtained for Padovana Argentata (Ho: 0.151 ± 0.198; He: 0.146 ± 0.185) and the highest for Millefiori di Lonigo (Ho: 0.293 ± 0.199; He: 0.291 ± 0.178). Furthermore, multidimensional scaling plot showed clear genetic identity for each breed, with clusters formed according to geographical and historical origin of the breeds, which were confirmed in neighbor networks. In conclusion, local breeds have conserved authentic genetic patterns and these results can help improve conservation strategies.Keywords: safeguard, SNP, genomic, morphological trait, poultry, ItalyReferencesBianchi, M. et al. (2011). A microsatellites-based survey on the genetic structure of two Italian local chicken breeds. Italian Journal of Animal Science, 10(3), e39. https://doi.org/10.4081/ijas.2011.e39Bortoluzzi, C. et al. (2018). The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity. Heredity, 121, 564–578. https://doi.org/10.1038/s41437-018-0072-3Cassandro, M. et al. (2015). Carcass characteristics and meat quality traits of the Padovana chicken breed, a commercial line, and their cross. Italian Journal of Animal Science, 14, 304–309. https://doi.org/10.4081/ijas.2015.3848Cerolini, S. et al. (2010). Breeding performance in the Italian chicken breed Mericanel della Brianza. Italian Journal of Animal Science, 9(4), e72. https://doi.org/10.4081/ijas.2010.e72Chang, C. et al. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 4(1), s13742-015. https://doi.org/10.1186/s13742-015-0047-8De Marchi, M. et al. (2003). Genetic traceability of chicken breeds. Agriculturae Conspectus Scientificus, 68(4), 255-259.De Marchi, M. et al. (2005a). Assessing genetic variability in two ancient chicken breeds of Padova area. Italian Journal of Animal Science, 4(Suppl. 3), 151-153. https://doi.org/10.4081/ijas.2005.3s.151De Marchi, M. et al. (2005b). Conservation of poultry genetic resource in the Veneto region of Italy. Animal Genetics, 37, 63-74. https://doi.org/10.1017/S1014233900001978FAO. (2012). Phenotypic characterization of animal genetic resources. FAO Animal Production and Health Guidelines No. 11. Rome.FAO. (2018). The future of food and agriculture – Alternative pathways to 2050. Rome. pp. 224.FAO DAD-IS. Available online: http://www.fao.org/dad-is/browse-by-country-and-species/en/ (accessed on 20 August 2020).Franzoni, A. et al. (2018). Phenotypic characterisation of Italian local chicken populations. In 6th Mediterranean Poultry Summit, 74, p. 37.Fulton, J. E. (2006). Avian genetic stock preservation: an industry perspective. Poultry Science, 85(2), 227-231. https://doi.org/10.1093/ps/85.2.227Huson, D. H. and Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23(2), 254-267. https://doi.org/10.1093/molbev/msj030Malomane, D. K. et al. (2019). The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution. BMC Genomics, 20, 345. https://doi.org/10.1186/s12864-019-5727-9Mazzon, I. (1932). Pollicoltura Padovana, Padova, 11, 10-26.Mugnai, C. et al. (2009). Effect of rearing system and season on the performance and egg characteristics of Ancona laying hens. Italian Journal of Animal Science, 8(2), 175-188. https://doi.org/10.4081/ijas.2009.175Muir, W. M. et al. (2008). Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proceedings of the National Academy of Sciences, 105(45), 17312-17317. https://doi.org/10.1073/pnas.0806569105Paradis, E. et al. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289–290. https://doi.org/10.1093/bioinformatics/btg412R Development Core Team. (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.Sabbioni, A. et al. (2006). Carcass yield and meat quality parameters of two Italian autochthonous chicken breeds reared outdoor: Modenese and Romagnolo. Proc. XII European Poultry Conference, Verona, Italy, 10-14 September, paper no. 10565.Spalona, A. et al. (2007). Population size in conservation of local chicken breeds in chosen European countries. Archiv fur Geflugelkunde, 71(2), 49-55.Strillacci, M. G. et al. (2017). Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers. Animal, 11(5), 737-745. https://doi.org/10.1017/S1751731116002135Warren, W. C. et al. (2017). A new chicken genome assembly provides insight into avian genome structure. G3: Genes, Genomes, Genetics, 7(1), 109-117. https://doi.org/10.1534/g3.116.035923Zanetti, E. et al. (2010). Genetic characterization of local Italian breeds of chickens undergoing in situ conservation. Poultry Science, 89(3), 420-427. https://doi.org/10.3382/ps.2009-00324Zanon, A. et al. (2006). Physico-chemical characteristics of eggs from two Italian autochthonous chicken breeds: Modenese and Romagnolo. World's Poultry Science Journal, 62, 203. 

Egg Quality of Italian Local Chicken Breeds: I. Yield Performance and Physical Characteristics

The 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