A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

G3 : Genes - Genomes - Genetics
Jordi Leno-ColoradoM Pérez-Enciso

Abstract

Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig (Sus scrofa) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q-value < 0.05 in Asia and Europe, respectively; five were shared across continents. In Asia, we found six significant pathways related to behavior, which involved essential neurotransmitters like dopamine and serotonin. Several significant pathways were interrelated and shared a variable percentage of genes. There were 12 genes present in >10 ...Continue Reading

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Citations

Jun 27, 2018·Frontiers in Molecular Neuroscience·Anna A IgolkinaMaria G Samsonova
Mar 19, 2020·Frontiers in Genetics·Priyanka BanerjeeHaja N Kadarmideen

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Datasets Mentioned

BETA
SRX2787051
SRX2788443
PRJNA255085

Methods Mentioned

BETA
PCR

Software Mentioned

PLINK
SAMtools rmdup
Ensembl
GATK IndelRealigner
Ensembl Predictor
PCIT
REACTOME
bcftools call
BEDtools
R R Development Core Team

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