Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Bovo, Samuele; Ribani, Anisa; Muñoz, María; Alves, E.; Araújo, J. P.; Bozzi, Rıccardo; Čandek-Potokar, Marjeta; Charneca, Rui; Palma, Federica Di; Etherington, Graham; Fernández, Ana; García, Fabián; García‐Casco, Juan; Karolyi, Danijel; Gallo, M.; Margeta, Vladimir; Martins, J.M.; Mercat, Marie J.; Moscatelli, Giulia; Núñez, Yolanda; Quintanilla, Raquel; Radović, Čedomir; Razmaitė, Violeta; Riquet, Juliette; Savić, Radomir; Schiavo, Giuseppina; Usai, G.; Utzeri, Valerio Joe; Zimmer, Christoph; Óvilo, Cristina; Fontanesi, Luca

doi:10.1186/s12711-020-00553-7

Cited by 51 publications

(74 citation statements)

References 104 publications

(150 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Collected DNA or samples from previous projects were also re-used in this study. This work took advantage from a study design developed within the Horizon 2020 TREASURE project [65][66][67][68] . Animals included in the study were 30 or 35 from each of the 22 pig breeds that were investigated.…”

Section: Methodsmentioning

confidence: 99%

“…Analysis of variability included a total of 22 European pig breeds and wild boars and two Asian pig populations using next generation sequencing data (NGS). This dataset covered a broad number of pig genetic resources raised in Europe 65,66 in comparison with a few Asian populations. The obtained results could be useful (i) to establish a risk evaluation system in a "One Health" approach, including information on the diversity of pig populations, (ii) to define cross species evolutionary analyses of genes involved in coronavirus infections and (iii) to identify natural genetic variability within the Sus scrofa species that could help to design genetic improvement strategies to increase genetic resistance in commercial and autochthonous pig populations against emerging and re-emerging coronavirus diseases.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Bovo

Schiavo

Ribani

et al. 2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a “One Health” perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a “One Health” perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.

show abstract

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Bovo

Schiavo

Ribani

et al. 2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…2019) and whole genome resequencing data (Bovo et al . 2020a,b). Genome‐wide data indicated that the average persistence and strength of LD between markers and SNP‐based effective population size varied among breeds depending on the genetic structures and history of these breeds that had experienced different genetic events (e.g.…”

Section: Introductionmentioning

confidence: 99%

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Schiavo

Bovo

Muñoz³

et al. 2021

Animal Genetics

Self Cite

View full text Add to dashboard Cite

Summary ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed‐specific ROH islands was obtained via over‐representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo‐Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources.

show abstract

“…DNA markers in the MC1R gene have been already proposed to authenticate pork from domestic pig breeds or wild boars [ 12 , 18 , 19 ]. Additional genes affecting coat colour have been described in pigs and some of them might contribute to determine the classical colour observed in the Mora Romagnola pigs [ 17 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

Redefinition of the Mora Romagnola Pig Breed Herd Book Standard Based on DNA Markers Useful to Authenticate Its “Mono-Breed” Products: An Example of Sustainable Conservation of a Livestock Genetic Resource

Tinarelli

Ribani

Utzeri

et al. 2021

Animals

Self Cite

View full text Add to dashboard Cite

Mora Romagnola is an autochthonous pig breed, raised in the north of Italy. Mono-breed pork products of this breed are part of important niche value chain that is intrinsically linked to the conservation of this local genetic resources that can only survive due to the premium price that these products can obtain on the market. However, the added value attracts fraudsters that unscrupulously sell mis-labelled Mora Romagnola products, causing consumer distrust that, in turn, undermines the conservation strategy of this breed. To monitor and better characterise this local breed, we phenotyped 826 Mora Romagnola pigs for three breed-specific traits. Then, we genotyped almost all living sows and boars registered to the Herd Book (n. = 357 animals) for polymorphisms in the MC1R and NR6A1 genes (affecting coat colour and vertebral number, respectively). The results were used to re-define the breed descriptors of the Mora Romagnala breed that included information on the allowed genotypes at these two genes. A few pigs that did not carry the allowed genotypes were excluded from its Herd Book. Finally, we evaluated the usefulness of these DNA markers to authenticate Mora Romagnola meat against meat derived from other 11 pig breeds and wild boars. To our knowledge, the Mora Romagnola Herd Book is one of the first examples that established a direct link between a genetic standard of a breed with the possibility to authenticate mono-breed products using DNA markers with the specific purpose to combat frauds and, indirectly, support the conservation of a livestock genetic resource.

show abstract

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Cited by 51 publications

References 104 publications

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Redefinition of the Mora Romagnola Pig Breed Herd Book Standard Based on DNA Markers Useful to Authenticate Its “Mono-Breed” Products: An Example of Sustainable Conservation of a Livestock Genetic Resource

Contact Info

Product

Resources

About