Characterization of the biological processes shaping the genetic structure of the Italian population

Abstract

BackgroundThe genetic structure of human populations is the outcome of the combined action of different processes such as demographic dynamics and natural selection. Several efforts toward the characterization of population genetic architectures and the identification of adaptation signatures were recently made. In this study, we provide a genome-wide depiction of the Italian population structure and the analysis of the major determinants of the current existing genetic variation.ResultsWe defined and characterized 210 genomic loci associated with the first Principal Component calculated on the Italian genotypic data and correlated to the North–south genetic gradient. Using a gene-enrichment approach we identified the immune function as primarily involved in the Italian population differentiation and we described a locus on chromosome 13 showing combined evidence of North–south diversification in allele frequencies and signs of recent positive selection. In this region our bioinformatics analysis pinpointed an uncharacterized long intergenic non-coding (lincRNA), whose expression appeared specific for immune-related tissues suggesting its relevance for the immune function.ConclusionsOur study, combining population genetic analyses with biological insights provides a description of the Italian genetic structure that in future could contribute to the evaluation of complex diseases risk in the population context.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0293-x) contains supplementary material, which is available to authorized users.

Impact of demography and population dynamics on the genetic architecture of human longevity

“…To deepen the resolution of our analysis, we restricted the comparison between centenarians and the overall Italian population to a micro-geographical scale. Principal Component Analysis (PCA) showed that centenarians fitted into the previously described patterns of clear differentiation between peninsular Italians and Sardinians described by PC1, as well as of the latitudinal cline of variation pointed out by PC2 [ 13 , 31 ]. However, they seemed to be more homogeneous ( i.e.…”

The mitogenome portrait of Umbria in Central Italy as depicted by contemporary inhabitants and pre-Roman remains

“…Concerning the phylogeography of Italy, it is difficult to identify a clear genetic pattern able to discriminate southern, northern and central populations in spite of several attempts based on autosomal and uniparental markers [19][20][21][22][23][24] . Southern populations were mostly influenced by Greek and Arab colonizations, Northern Italians might reflect admixture with French and German-speaking populations, while Central Italy occupies its own intermediate position creating a continuous cline of variation across the peninsula (with Sardinians as outliers) 13,19,[25][26][27][28][29] .…”

Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula

“…To date, several studies based on the analysis of classical and uniparentally-inherited markers provided evidence of appreciable Italian population structure, especially as concerns Y-chromosome lineages, while a more homogeneous mitochondrial DNA background was described 3 16 17 18 19 . Nevertheless, few autosomal genome-wide datasets have been generated until now to further disentangle this scenario and to explicitly test hypotheses related to occurrence of local adaptive events in diverse Italian subpopulations 20 21 22 . In fact, genome-wide data suggested the existence of potential genetic barriers between Italians and other Europeans 23 and further corroborated evidence for internal differentiation of the overall Italian population 14 22 24 .…”