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Research article - Peer-reviewed, 2012

Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens

Daniel Nätt, Carl-Johan Rubin, Dominic Wright, Martin Johnsson, Johan Beltéky, Leif Andersson and Per Jensen


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. Keywords:

Domestication; gene expression; tiling array; behaviour; methylation

Published in

BMC Genomics
2012, Volume: 13:59, pages: 1-12

    SLU Authors

      • Andersson, Leif

        • Uppsala University
        • Jensen, Per

          • Linköping University

        Associated SLU-program

        Centre of Excellence in Animal Welfare Science

        UKÄ Subject classification

        Genetics and Breeding

        Publication Identifiers


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