Short communicationComparative population genomic analyses of the reconstructed local breed “Nero di Parma” with other commercial and autochthonous Italian pig breeds
Introduction
Over a few decades of the last centuries (from the 1950’ to the 1970’), most rural economies all over Europe experienced a shift from extensive to intensive production systems that relied on few highly productive plant varieties and livestock breeds. In the animal production sector, these changes represented the beginning of the end for many local breeds that were quickly substituted by improved populations. This also happened in Italy for most local pig breeds that were substituted by more productive English breeds (Porter, 1993). At the beginning of the XX century, Italy accounted for more than 30 regional pig breeds, subraces and varieties (Cassella, 1909; Mascheroni, 1927). Conservation programmes that started in the 1980’ with the institution of the first local pig breed herd books, managed by the National Pig Breeder Association (ANAS), prevented the complete extinction of these genetic resources. At present, six Italian autochthonous pig breeds (Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) are officially recognized at the national level and have their own section of the herd book. Another section includes reconstructed local breeds that were completely lost but that were subsequently reconstructed through a specific crossbreeding programme to obtain animals resembling the original extinct population. This is the case of the Nero di Parma breed that was officially recognized as reconstructed breed in 2016.
A black pig population mentioned in old texts (e.g. Toggia, 1820) as Parmense or Parmigiana was spread in the Parma Province, in the North of Italy, over the XIX century and the beginning of the 1900’. The breed was reconstructed starting from the mid of the 1990’ after the identification in mountain farms of three different locations of Parma Province of a few grey and spotted animals resembling, at least in part, the original phenotypic description of the extinct population. Using these animals, crossbreeding and selection programmes were started to obtain a standardized animal with fixed solid grey/black coat colour resembling also some described features, including the robustness in mountain climates, the presence of wattles and the brilliant red color of the meat. The current Nero di Parma population is raised in extensive or semi-extensive production systems in 10 farms and accounts for 103 sows and 12 boars that are registered to its herd book section (ANAS, 2019). Nero di Parma meat products have a positive consumers’ perception of high-quality productions that can assure a premium prize on their niche market, making economically advantageous raising the animals of this breed. However, considering its breeding history and the genetic bottleneck that this population experienced, it is important to monitor the level of genetic diversity compared to that of other local and cosmopolitan pig breed (Sabbioni et al., 2006).
Genome wide analyses using single nucleotide polymorphism (SNP) arrays have been extensively applied to evaluate the level of genetic diversity within and between populations in many livestock species, including the pig (e.g. Bertolini et al., 2018; Mastrangelo et al. 2014; 2018; Muñoz et al., 2019; Strillacci et al., 2018; Yang et al., 2017). Using SNP array data, we recently investigated Italian cosmopolitan pig breeds (Italian Duroc, Italian Landrace and Italian Large White) and Italian autochthonous pig breeds (Apulo-Calabrese, Casertana, Cinta Senese and Nero Siciliano) to identify breed informative SNPs and to analyse the level of autozygosity in comparison with pedigree derived inbreeding level (Schiavo et al., 2020a, 2020b). Thus far, Nero di Parma breed has not been investigated yet.
In this study, using SNPs genotyped with the Illumina PorcineSNP60 BeadChip array we compared, at the genome level, the reconstructed Nero di Parma pig breed with three Italian commercial (Italian Large White, Italian Duroc and Italian Landrace) and four autochthonous (Apulo-Calabrese, Casertana, Cinta Senese and Nero Siciliano) pig breeds. Several population genomic parameters estimated for all these breeds provided a comparative information that could be useful to manage Nero di Parma breed and other local pig breeds.
Access through your organization
Check access to the full text by signing in through your organization.
Section snippets
Animals
A total of 240 pigs belonging to eight Italian breeds were included in this study. Three of them (Italian Large White: n. 50; Italian Duroc: n. 50; Italian Landrace: n. 44) were commercial breeds. These breeds can be considered cosmopolitan-derived breeds due to their specific heavy pig selection objectives different from those of all other pig breeds (ANAS 2019), which have contributed to shape their genome over the last three decades (Schiavo et al., 2016). All pigs of these breeds were from
Results and discussion
Fig. 1 shows the multidimensional scaling (MDS) plots obtained with the analysed pigs, including Nero di Parma animals. Pigs from the same breed were, in general, grouped together, as it might be expected considering their genetic closeness. Italian Duroc pigs were clearly separated from the pigs of all other breeds, confirming the larger distance of this commercial breed to all other breeds, as already reported (Schiavo et al., 2020a). The other two commercial breeds (Italian Landrace and
Conclusion
In this work we investigated, for the first time, variability at the genome wise level in the reconstructed Nero di Parma pig breed. This breed might constitute and interesting case study to explore the effect of genetic bottleneck, genetic drift and recurred admixture on the genetic structure of a pig population. The comparative analysis against several other Italian pig breeds made it possible to evaluate the obtained information that could be helpful to define potential future conservation
Declaration of Competing Interest
The authors declare that there is no conflict of interest regarding the publication of this paper.
Acknowledgements
The authors thank CONSDABI for the collaboration in this study. This study was supported by the PSRN (Progetto di Sviluppo Rurale Nazionale) SUIS project (co-funded by the European Agricultural Fund for Rural Development of the European Union and by the Italian Ministry of Agriculture, Food, Forestry and Tourism - MiPAAFT), received funding from the Italian Ministry of Agriculture, Food and Forestry (MiPAAF) under the project INNOVAGEN and from the University of Bologna RFO 2018 and 2019
References (24)
- et al.
Second-generation PLINK: rising to the challenge of larger and richer datasets
Gigascience
(2015) - et al.
A machine learning approach for the identification of population-informative markers from high-throughput genotyping data: application to several pig breeds
Animal
(2020) - et al.
Looking at genetic structure and selection signatures of the Mexican chicken population using single nucleotide polymorphism markers
Poultry Sci.
(2018) - et al.
Genomic inbreeding and relationships among Holsteins, Jerseys, and Brown Swiss
J. Dairy Sci.
(2011) - et al.
GCTA: a tool for genome-wide complex trait analysis
Am. J. Hum. Genet.
(2011) - ANAS, 2019. Libro Genealogico. Retrieved on the 12 th of October 2019,...
- et al.
SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data
Front. Genet.
(2015) - et al.
Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats
Genet. Sel. Evol.
(2018) Il Maiale
(1909)- et al.
Structure Harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method
Conserv. Genet. Res.
(2012)
A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes
BMC Genomics
(2012)
Scatterplot3d – an R package for visualizing multivariate data
J. Stat. Softw.
(2003)
Cited by (3)
Genomic inbreeding estimated through runs of homozygosity in Moura pigs and four commercial swine breeds
2024, Livestock ScienceCitation Excerpt :Few scientific studies are available on locally adapted Brazilian breeds, although low values were observed in a locally adapted Chinese breed by Wu et al. (2020), similar to those reported herein. The Duroc breed presented the highest FROH values (from 0.107 to 0.001, considering the different ROH classes), similar to the results reported by Schiavo et al. (2020a). The inbreeding coefficient estimates differed according to the calculation method (FGRM and FROH), and mean FGRM values were considerably higher than FROH values, indicating considerable variations between breeds.
Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India
2021, Livestock ScienceCitation Excerpt :However, mtDNA based studies are less suited to resolve the phylogeny due to a limited number of loci involved (Frantz et al., 2013). Recent studies (Schiavo et al., 2020) have shown the utility of the PorcineSNP60K BeadChip for characterization and comparison of small local pig breeds. In this study we characterize the Indian Ghurrah pig breed using a genome wide panel of markers.
Genetic characterisation of the Nero d’Aspromonte pig population in Southern Italy
2024, Italian Journal of Animal Science
© 2020 Elsevier B.V. All rights reserved.
