Genome‐wide detection of copy number variants in European autochthonous and commercial pig breeds by whole‐genome sequencing of DNA pools identified breed‐characterising copy number states

Abstract

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 429. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.

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

“…2018, 2019; Bovo et al . 2020a,b) and can provide additional information that is useful to design conservation plans and mating strategies to maintain the diversity of these pig genetic resources.…”

“…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.…”

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

“…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.…”

“…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.…”

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

“…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 de ne 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.…”