Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

Abstract

BackgroundA major concern in conservation genetics is to maintain the genetic diversity of populations. Genetic variation in livestock species is threatened by the progressive marginalisation of local breeds in benefit of high-output pigs worldwide. We used high-density SNP and re-sequencing data to assess genetic diversity of local pig breeds from Europe. In addition, we re-sequenced pigs from commercial breeds to identify potential candidate mutations responsible for phenotypic divergence among these groups of breeds.ResultsOur results point out some local breeds with low genetic diversity, whose genome shows a high proportion of regions of homozygosis (>50%) and that harbour a large number of potentially damaging mutations. We also observed a high correlation between genetic diversity estimates using high-density SNP data and Next Generation Sequencing data (r = 0.96 at individual level). The study of non-synonymous SNPs that were fixed in commercial breeds and also in any local breed, but with different allele, revealed 99 non-synonymous SNPs affecting 65 genes. Candidate mutations that may underlie differences in the adaptation to the environment were exemplified by the genes AZGP1 and TAS2R40. We also observed that highly productive breeds may have lost advantageous genotypes within genes involve in immune response – e.g. IL12RB2 and STAB1–, probably as a result of strong artificial in the intensive production systems in pig.ConclusionsThe high correlation between genetic diversity computed with the 60K SNP and whole genome re-sequence data indicates that the Porcine 60K SNP Beadchip provides reliable estimates of genomic diversity in European pig populations despite the expected bias. Moreover, this analysis gave insights for strategies to the genetic characterization of local breeds. The comparison between re-sequenced local pigs and re-sequenced commercial pigs made it possible to report candidate mutations to be responsible for phenotypic divergence among those groups of breeds. This study highlights the importance of low input breeds as a valuable genetic reservoir for the pig production industry. However, the high levels of ROHs, inbreeding and potentially damaging mutations emphasize the importance of the genetic characterization of local breeds to preserve their genomic variability.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-601) contains supplementary material, which is available to authorized users.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information

“…Their use is also becoming feasible because of the lower genotyping costs, for example, of the Porcine SNP60 Bead-array (Ramos et al, 2009) that has recently been used for comparative studies between European pig breeds (Manunza et al, 2013;BurgosPaz et al, 2013;Herrero-Medrano et al, 2014). However, there is a well-known ascertainment bias implicit when SNP chips are used in cattle and other livestock species (Albrechtsen et al, 2010;Lachance and Tishkoff, 2013).…”

Deleterious alleles in the context of domestication, inbreeding, and selection

“…Herrero‐Medrano et al. () suggested that European local pig breeds have exceptionally high levels of both ROHs and potentially damaging mutations, probably a combination of their European heritage and current low effective population size.…”

“…A popular approach to identify harmful mutations that are (almost) lethal is to screen populations for the absence of specific variants in homozygous state. If populations contain heterozygous carriers of such variants, homozygotes would be expected based on allele frequencies and carrier-carrier matings (Derks et al, 2017;Pausch et al, 2015;VanRaden, Olson, Null, & Hutchison, 2011). This method relies on the biological implications of the lethality of a variant-resulting in an absence of the allele in F I G U R E 1 Genomic consequences of inbreeding.…”

“…Position on chromosome homozygous state. Depending on the frequency of the lethal allele in the population, large sample size is often required to identify such alleles (Derks et al, 2017). Therefore, most of the studies implementing this depletion of homozygotes approach use large panels of genotyped animals.…”

Research Article Study of genetic variability in pigs after the traditional breeding program.

“…Every day the need for the use of molecular markers is becoming more evident, whether it is to help in assisted breeding programs or genetic analyses and the determination of population inbreeding (Herrero-Medrano et al, 2014;Schiavo et al, 2016;Peripolli et al, 2017).…”