BACKGROUND: In 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. RESULTS: A 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. CONCLUSIONS: This 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.
@article{esteve-codina_dissecting_2013,
Author = {Esteve-Codina, Anna and Paudel, Yogesh and Ferretti,
Luca and Raineri, Emanuele and Megens, Hendrik-Jan and
Silió, Luis and Rodríguez, María C. and Groenen,
Martein A. M. and Ramos-Onsins, Sebastian E. and
Pérez-Enciso, Miguel},
Title = {Dissecting structural and nucleotide genome-wide
variation in inbred {Iberian} pigs},
Journal = {BMC genomics},
Volume = {14},
Pages = {148},
abstract = {BACKGROUND: In 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. RESULTS: A 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.
CONCLUSIONS: This 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.},
doi = {10.1186/1471-2164-14-148},
issn = {1471-2164},
language = {eng},
pmcid = {PMC3601988},
pmid = {23497037},
year = 2013
}
