A pathway-centered analysis of pig domestication and breeding in eurasia

Leno-Colorado, Jordi, Hudson, Nick J., Reverter, Antonio and Pérez-Enciso, Miguel (2017) A pathway-centered analysis of pig domestication and breeding in eurasia. G3: Genes, Genomes, Genetics, 7 7: 2171-2184. doi:10.1534/g3.117.042671


Author Leno-Colorado, Jordi
Hudson, Nick J.
Reverter, Antonio
Pérez-Enciso, Miguel
Title A pathway-centered analysis of pig domestication and breeding in eurasia
Journal name G3: Genes, Genomes, Genetics   Check publisher's open access policy
ISSN 2160-1836
Publication date 2017-07-01
Year available 2017
Sub-type Article (original research)
DOI 10.1534/g3.117.042671
Open Access Status DOI
Volume 7
Issue 7
Start page 2171
End page 2184
Total pages 14
Place of publication Bethesda, MD United States
Publisher Genetics Society of America
Language eng
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. 9,000 years 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 more than 10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), an important target trait as well during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding processes. Purifying selection was, nevertheless, stronger in significantly differentiated pathways than in random pathways, mainly in Europe. We conclude that pathway analysis facilitates the biological interpretation of genome-wide studies. Notably in the case of pig, behavior played an important role, among other physiological and developmental processes.
Keyword Behavior
Domestication
Pathway analysis
Pig
Genome
Sequence data
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID AGL2013-41834-R
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Agriculture and Food Sciences
 
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Created: Mon, 03 Jul 2017, 15:30:13 EST by Nick Hudson on behalf of School of Agriculture and Food Sciences