An assessment of European pig diversity using molecular markers: Partitioning of diversity among breeds

Abstract

Genetic diversity within and between breeds (and lines) of pigs was investigated. The sample comprised 68 European domestic breeds (and lines), including 29 local breeds, 18 varieties of major international breeds, namely Duroc, Hampshire, Landrace, Large White and Pie´train, and 21 commercial lines either purebred or synthetic, to which the Chinese Meishan and a sample of European wild pig were added. On average 46 animals per breed were sampled (range 12-68). The genetic markers were microsatellites (50 loci) and AFLP (amplified fragment length polymorphism, 148 loci). The analysis of diversity showed that the local breeds accounted for 56% of the total European between-breed microsatellite diversity, and slightly less for AFLP, followed by commercial lines and international breeds. Conversely, the group of international breeds contributed most to within-breed diversity, followed by commercial lines and local breeds. Individual breed contributions to the overall European between-and within-breed diversity were estimated. The range in between-breed diversity contributions among the 68 breeds was 0.04-3.94% for microsatellites and 0.24-2.94% for AFLP. The within-breed diversity contributions varied very little for both types of markers, but microsatellite contributions were negatively correlated with the between-breed contributions, so care is needed in balancing the two types of contribution when making conservation decisions. By taking into account the risks of extinction of the 29 local breeds, a cryopreservation potential (priority) was estimated for each of them.

Genetic diversity and population structure in Portuguese goat breeds

“…The results presented here can be useful in outlining conservation strategies, even though it remains a subject of discussion what are the optimum weights to be given to the between-and within-breed components of genetic diversity in defining conservation priorities (Ollivier et al, 2005, Toro et al, 2006. In any case, it is very clear from our results that the PM breed, which has a very small breeding population, presents high levels of inbreeding, and the resulting inbreeding depression could put at risk its survival for the future.…”

Genetic differentiation between Cinta Senese and commercial pig breeds using microsatellite

“…The analysis of the SSRs polymorphism observed in the European pig breeds showed that the allelic diversity pattern among breeds is quasi-independent from that evaluated based on allele frequency and local breeds do not generally cluster with international breeds, confirming the uniqueness of the European local breeds compared to main international breeds (Ollivier et al 2005;Ollivier, 2009). The European pig industry relies on a limited number of breeds, and is mainly focused on the LW genotype asset.…”

Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

“…The lack of compliance with the Hardy-Weinberg equilibrium that was observed for at least one locus in most breeds is probably related to the overall deficit in heterozygosity in most of the breeds. This deficit could be a consequence of inbreeding or breed substructure, which are common features in local breeds of small census size [13,15], which is the case for nearly all the breeds included here. Moreover, deviations from the Hardy-Weinberg equilibrium due to sampling error are expected given the number of breed-loci combinations and, as expected, these were more often observed in loci with a larger number of alleles [See Additional file 1: Table S2].…”

“…In pigs, this approach has been applied to analyze the genetic diversity of several Spanish and Portuguese breeds both at the local level [2,5,8-12], and at a broader level including many European breeds [13,14]. Notwithstanding, some of the more isolated breeds from the Iberian Peninsula were absent from these studies, and it is known that local breeds, many of which are in danger of extinction, contribute significantly to the genetic variability of the species [15]. Today, new statistical tools are available which refine our ability to detect, e.g., how admixture among populations or fragmentation of some of the breeds may have affected their variability and genetic structure.…”