Abstract: 【Objective】The objective of this study was to find the transcriptome differences between ovary tissue in early laying period and egg laying peak period of Shanma ducks, and enrich the laying duck transcriptome data.【Method】Selecting 6 Shanma duck ovarian tissues as a sample (early laying period and peak period 3 samples respectively), then the transcriptome libraries of ovary tissue in the early laying period and the egg laying peak period of Shanma ducks were constructed by using an Illumina HiSeq^TM 2000 sequencing technique, and the bioinformatics methods were analyzed subsequently, such as sequencing assess and gene function annotation. 【Result】 The results showed that the base ratios with quality value higher than 20 in reads (Q20) were more than 93%. 43 489 798 reads and 438 084 706 bp transcriptome data were obtained in the early laying period, and 42 782 676 reads, 4 307 499 083 bp transcriptome data were obtained in the egg laying peak period. Respectively, 70.92% and 72.70% reads could be compared to the duck reference genome sequence. Comparison of the transcriptome of ovary tissue in the early laying period and the egg laying peak period, 26 808 expressed genes were found in the early laying period, 27 013 expressed genes were found in the egg laying peak period. As the early laying period for reference, 1 929 differentially expressed genes were found in the egg laying peak period, including 989 up-regulated genes and 940 down-regulated genes. Annotation analysis indicated that 1 423 genes were annotated in Nr data, including 695 up-regulated genes and 728 down-regulated genes. Through COG analysis, there were 663 functional annotations of these differentially expressed genes, involving 25 functional classifications. With GO function annotation classifications, a total of 1 122 genes were divided into 61 function categories, in which many functional categories were mainly involved, such as molecular binding, catalytic activity, cell process, biological regulation, which including 406 related annotation genes involved development and reproduction biological process. KEGG analysis showed a total of 425 genes were annotated to 160 metabolic pathways, and GnRH signaling pathway, GPI-anchor biosynthesis, TGF-beta signaling pathway, ribosome biosynthesis pathway were significantly enriched. The GnRH and TGF-β signaling pathway played an important role in the ovarian physiology and reproduction activities, but the role of GPI-anchor and ribosome biosynthesis was not clear in ovarian physiology and reproductive activity.【Conclusion】The transcriptome study of the ovary tissue in the early laying period and the egg laying peak period of Shanma ducks by using high-throughput sequencing technology revealed the number of differentially expressed genes under different physiological status of the ovarian tissue in Shanma ducks, obtained the function, classification and metabolic pathway of differentially expressed genes, which enriched the ovary transcriptome information of laying ducks, and laid a foundation for the study on related genes with reproductive traits and molecular mechanisms in laying ducks.

Key words: Shanma duck, ovary, transcriptome, differentially expressed genes, functional classification