Identification, expression, and artificial selection of silkworm epigenetic modification enzymes
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RESEARCH ARTICLE
Open Access
Identification, expression, and artificial selection of silkworm epigenetic modification enzymes Rui Gao, Chun-Lin Li, Xiao-Ling Tong, Min-Jin Han, Kun-Peng Lu, Shu-Bo Liang, Hai Hu, Yue Luan, Bi-Li Zhang, Yan-Yu Liu and Fang-Yin Dai*
Abstract 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 factorbinding 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. Keywords: Domesticated traits, Epigenetic modifying enzymes, Selective sweeping, BmSuv4–20, BmDNMT2, Reproduction, Silkworm
Background Domestication of plants and animals is a milestone in the history of human civilization that involves the long-term artificial selection of advantageous natural variations. The history and genetic basis of rapid phenotypic evolution in domestication and breeding * Correspondence: [email protected] State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing 400715, China
remains a topic of research interest. Epigenetics is usually defined as stably heritable phenotypes resulting from several types of changes on chromosomes such as DNA methylation, histone post-translational modifications (PTMs), non-coding RNA regulation, and chromatin remodeling, but not on the DNA sequence [1]. Epigenetic modifications can alter the structure of chromatin and play a critical role in maintaining genomic integrity, gene expression, cellular memory, cell reprogramming [2, 3], and individual
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