Identification, expression, and artificial selection of silkworm epigenetic modification enzymes.
BACKGROUND
Understanding the genetic basis of phenotype variations during domestication and breeding is of great interest. Epigenetics and epigenetic modification enzymes (EMEs) may play a role in phenotypic variations; however, no comprehensive study has been performed to date. Domesticated silkworm (Bombyx mori) may be utilized as a model in determining how EMEs influence domestication traits.


RESULTS
We identified 44 EMEs in the genome of silkworm (Bombyx mori) using homology searching. Phylogenetic analysis showed that genes in a subfamily among different animals were well clustered, and the expression pattern of EMEs is constant among Bombyx mori, Drosophila melanogaster, and Mus musculus. These are most highly expressed in brain, early embryo, and internal genitalia. By gene-related selective sweeping, we identified five BmEMEs under artificial selection during the domestication and breeding of silkworm. Among these selected genes, BmSuv4-20 and BmDNMT2 harbor selective mutations in their upstream regions that alter transcription factor-binding sites. Furthermore, these two genes are expressed higher in the testis and ovary of domesticated silkworm compared to wild silkworms, and correlations between their expression pattern and meiosis of the sperm and ova were observed.


CONCLUSIONS
The domestication of silkworm has induced artificial selection on epigenetic modification markers that may have led to phenotypic changes during domestication. We present a novel perspective to understand the genetic basis underlying animal domestication and breeding.
['Gao|Rui|R|', 'Li|Chun-Lin|CL|', 'Tong|Xiao-Ling|XL|', 'Han|Min-Jin|MJ|', 'Lu|Kun-Peng|KP|', 'Liang|Shu-Bo|SB|', 'Hu|Hai|H|', 'Luan|Yue|Y|', 'Zhang|Bi-Li|BL|', 'Liu|Yan-Yu|YY|', 'Dai|Fang-Yin|FY|http://orcid.org/0000-0002-0215-2177']
D000818:Animals D012831:Bombyx D000071278:Domestication D004331:Drosophila melanogaster D044127:Epigenesis, Genetic D005260:Female D008297:Male D051379:Mice D010802:Phylogeny
Silkworm Domesticated traits Selective sweeping BmDNMT2 BmSuv4–20 Epigenetic modifying enzymes Reproduction