Genome-wide mapping reveals conservation of promoter DNA methylation following chicken domestication.
It is well-known that environment influences DNA methylation, however, the extent of heritable DNA methylation variation following animal domestication remains largely unknown. Using meDIP-chip we mapped the promoter methylomes for 23,316 genes in muscle tissues of ancestral and domestic chickens. We systematically examined the variation of promoter DNA methylation in terms of different breeds, differentially expressed genes, SNPs and genes undergo genetic selection sweeps. While considerable changes in DNA sequence and gene expression programs were prevalent, we found that the inter-strain DNA methylation patterns were highly conserved in promoter region between the wild and domestic chicken breeds. Our data suggests a global preservation of DNA methylation between the wild and domestic chicken breeds in either a genome-wide or locus-specific scale in chick muscle tissues.
1] Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China [2] State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing 100193, China [3] National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China.
Qinghe
Q
Li
1] Department of Biological Sciences, Bengbu Medical College, Bengbu 233030, China [2] State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing 100193, China [3] National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China.
Yuanyuan
Y
Wang
1] State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing 100193, China [2] National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China.
Xiaoxiang
X
Hu
1] State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing 100193, China [2] National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China.
Yaofeng
Y
Zhao
1] State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing 100193, China [2] National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China.
Ning
N
Li
D000818:Animals; D000829:Animals, Domestic; D000835:Animals, Wild; D030161:Avian Proteins / Q000235:genetics; D002645:Chickens / Q000235:genetics*; D002874:Chromosome Mapping; D019175:DNA Methylation; D019143:Evolution, Molecular; D005260:Female; D020869:Gene Expression Profiling; D063990:Gene Ontology; D016678:Genome / Q000235:genetics*; D009132:Muscles / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
D030161:Avian Proteins