Abstract：Blue shell trait is not only a protective coloration that can avoid predation, but also is one of the important economic traits of poultry. Due to the differences of evolutionary and genetic backgrounds, the formation mechanism of blue shell egg are divergent in different poultries. By using the high-throughput sequencing, the oviduct shell gland of blue egg shell ducks and white egg shell ducks were studied to enrich and analyze microRNAs (miRNAs) and its target genes involved in formation of blue shell egg traits. The analysis result of sequencing data quality showed the GC content of each sample was not less than 42.60%, and the proportion of clean reads that was ≥ 30 bases (Q30) was not less than 89.02%. Compared with the chicken (Gallus gallus) genome sequence (Gallus_gallus-4.0, GCF_000002315.3) using the miRDeep2 software, all 269 miRNAs were screened in the shell gland of blue shelled ducks and white shelled ducks, including known 245 miRNAs and new 24 miRNAs. Based on the expression of miRNAs in each sample, the correlation analysis was performed between the all of each samples. The result showed that the correlation coefficient were higher between all of the shell gland samples in blue and white shelled ducks (r＞0.99), which suggested that miRNAs expression profiles might be similar in the shelled gland of blue and white shelled ducks. Compared with white shelled ducks, the shell gland of blue shelled ducks had 169 differently expressed miRNAs, including 85 up-regulated and 84 down-regulated, and total 4 872 target genes were obtained, but the miRNAs were not significant difference (P＞0.05). The Top Gene Ontology (TopGO) analysis of target genes showed that molecules function including heme binding (count=23, P=0.008) were existed, and most of them were accompanied by function of electron and Fe2+ transport. In addition, the analysis of differently expressed miRNAs found that biliverdin synthetic gene — heme oxygenase 1 (HMOX1) and a large number of organic matter transport and metabolism genes were predicted by gga-miR-133b, gga-miR-193b-3p and gga-miR-449a (log2 (fold change (FC))＞1, P＞0.05). These results suggested that some miRNAs might participate in the formation of blue shell egg traits, but miRNAs might not be an important role in the formation of blue shell egg traits in duck. The study provides a theoretical basis for revealing the molecular mechanism of the formation of the blue shelled eggs in poultry, and basic information for the poultry cultivation of blue shelled eggs which based on gene manipulation technology.
