Avian leukosis virus subgroup E (ALVE) as a kind of endogenous retroviruses extensively exists in chicken genome. The insertion of ALVE has some effects on chicken production traits and appearance. Most of the work on ALVEs has been done with commercial breeds. We present here an investigation of ALVE elements in seven Chinese domestic breeds and four standard breeds. Firstly, we established an ALVE insertion site dataset by using the obsERVer pipeline to identify ALVEs from whole-genome sequence data of eleven chicken breeds, seven Chinese domestic breeds, including Beijing You (BY), Dongxiang (DX), Luxi Game (LX), Shouguang (SG), Silkie (SK), Tibetan (TB) and Wenchang (WC), four standard breeds, including White Leghorn (WL), White Plymouth Rock (WR), Cornish (CS), and Rhode Island Red (RIR). A total of 37 ALVE insertion sites were identified and 23 of them were novel. Most of these insertion sites were distributed in intergenic regions and introns. We then used locus-specific PCR to validate the insertion sites in an expanded population with 18~60 individuals in each breed. The results showed that all predicted integration sites in 11 breeds were verified by PCR. Some ALVE insertion sites were breeds specific, and 16 out of 23 novel ALVEs were found in only one Chinese domestic chicken breed. We randomly selected three ALVE insertions including ALVE_CAU005, ALVE_ros127, and ALVE_ros276, and obtained their insertion sequences by long-range PCR and Sanger sequencing. The insertion sequences were all 7525 bp, which were full-length ALVE insertion and all of them were highly homologous to ALVE1 with similarity of 99%. Our study identified the distribution of ALVE in 11 chicken breeds, which expands the current research on ALVE in Chinese domestic breeds.
Keywords: Avian leukosis virus subgroup E; Chinese domestic breeds; chicken.
Avian leukemia virus subgroup E (ALVE) is an endogenous retrovirus, which is extensively integrated with the chicken genome, and has some effects on chicken production traits and appearance. Most of the current studies on ALVE insertion sites were conducted in standard breeds. In this study, we performed a comprehensive analysis of ALVE insertion sites in seven Chinese domestic breeds and four standard breeds using whole genome sequencing data. A total of 37 ALVE insertion sites were identified and all of them were verified by PCR. Twenty-three of the insertion sites were novel. Some ALVE insertion sites were breeds specific, and 16 out of 23 novel ALVEs were found in only one Chinese domestic chicken breed. In addition, the whole sequences of three ALVE insertions were collected by long-range PCR and Sanger sequencing. We found all the insertion sequences were 7525 bp, which were full-length ALVE insertions and all of them were highly homologous to ALVE1 with similarity of 99%. These results provide a theoretical basis for further studies on the effects of ALVE on production traits and disease resistance traits in chickens. Distribution of ALVE insertions in the genome of 11 chicken breeds.
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