Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

Abstract

BackgroundIn contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besides, Iberian pigs exhibit high meat quality as well as appetite and propensity to obesity. Here we provide a genome wide analysis of nucleotide and structural diversity in a reduced representation library from a pool (n=9 sows) and shotgun genomic sequence from a single sow of the highly inbred Guadyerbas strain. In the pool, we applied newly developed tools to account for the peculiarities of these data.ResultsA total of 254,106 SNPs in the pool (79.6 Mb covered) and 643,783 in the Guadyerbas sow (1.47 Gb covered) were called. The nucleotide diversity (1.31x10-3 per bp in autosomes) is very similar to that reported in wild boar. A much lower than expected diversity in the X chromosome was confirmed (1.79x10-4 per bp in the individual and 5.83x10-4 per bp in the pool). A strong (0.70) correlation between recombination and variability was observed, but not with gene density or GC content. Multicopy regions affected about 4% of annotated pig genes in their entirety, and 2% of the genes partially. Genes within the lowest variability windows comprised interferon genes and, in chromosome X, genes involved in behavior like HTR2C or MCEP2. A modified Hudson-Kreitman-Aguadé test for pools also indicated an accelerated evolution in genes involved in behavior, as well as in spermatogenesis and in lipid metabolism.ConclusionsThis work illustrates the strength of current sequencing technologies to picture a comprehensive landscape of variability in livestock species, and to pinpoint regions containing genes potentially under selection. Among those genes, we report genes involved in behavior, including feeding behavior, and lipid metabolism. The pig X chromosome is an outlier in terms of nucleotide diversity, which suggests selective constraints. Our data further confirm the importance of structural variation in the species, including Iberian pigs, and allowed us to identify new paralogs for known gene families.

Copy number variants in a highly inbred Iberian porcine strain

“…However, their analysis involved mainly Chinese pig breeds, which also are very distant from the Iberian breed. The reliability of the CNVRs detected in Guadyerbas also is supported by recent results describing genome variability of a single Guadyerbas female using whole-genome sequencing (Esteve-Codina et al 2013). Note that the most overlap was found with the study of Chen et al (2012), who applied similar analysis criteria.…”

The use of genomic coancestry matrices in the optimisation of contributions to maintain genetic diversity at specific regions of the genome

“…This added flexibility has great value since genomic data shows that nucleotide diversity varies greatly across the genome (e.g., [12, 13]), probably as a result of evolutionary forces such as genetic drift and selection. In practical conservation programmes, regions that display a greater loss of diversity should be prioritized to better avoid further loss of diversity in those regions.…”

Mining the pig genome to investigate the domestication process

“…In addition, historical admixture with wild boars may have also had a role until a few hundred years ago (White, 2011;Goedbloed et al, 2013;Manunza et al, 2013). Amaral et al (2011) observed a positive correlation between the level of variability and recombination (also observed in Badke et al, 2012;Bosse et al, 2012 andEsteve-Codina et al, 2013), suggesting that selection (positive or negative) has an active role in shaping the variability of Sus scrofa and that interference among genomic positions has an impact on variability. The significant presence of candidate mutations that are functionally harmful suggests that many of the variants that have been artificially selected were new variants with strong effects (as indicated in Rubin et al, 2012).…”