Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens.
BACKGROUND
Variations in gene expression, mediated by epigenetic mechanisms, may cause broad phenotypic effects in animals. However, it has been debated to what extent expression variation and epigenetic modifications, such as patterns of DNA methylation, are transferred across generations, and therefore it is uncertain what role epigenetic variation may play in adaptation.


RESULTS
In Red Junglefowl, ancestor of domestic chickens, gene expression and methylation profiles in thalamus/hypothalamus differed substantially from that of a domesticated egg laying breed. Expression as well as methylation differences were largely maintained in the offspring, demonstrating reliable inheritance of epigenetic variation. Some of the inherited methylation differences were tissue-specific, and the differential methylation at specific loci were little changed after eight generations of intercrossing between Red Junglefowl and domesticated laying hens. There was an over-representation of differentially expressed and methylated genes in selective sweep regions associated with chicken domestication.


CONCLUSIONS
Our results show that epigenetic variation is inherited in chickens, and we suggest that selection of favourable epigenomes, either by selection of genotypes affecting epigenetic states, or by selection of methylation states which are inherited independently of sequence differences, may have been an important aspect of chicken domestication.
IFM Biology, Division of Zoology, Avian Behavioural Genomics and Physiology Group, Linköping University, Sweden.
Daniel
D
Nätt
Carl-Johan
CJ
Rubin
Dominic
D
Wright
Martin
M
Johnsson
Johan
J
Beltéky
Leif
L
Andersson
Per
P
Jensen
D000818:Animals; D000835:Animals, Wild / Q000235:genetics*; D002645:Chickens / Q000235:genetics*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D014644:Genetic Variation; D016678:Genome; D005838:Genotype; D007031:Hypothalamus / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic