Abstract: Although the duck genome sequence has been released， its genomic structure， especially its transcriptome characterization needs to be further studied. This study characterized the transcriptome of abdominal fat in ducks by using RNAseq. In total， 203 200 984 clean reads were obtained， and 18 464 genes were identified to be expressed in abdominal fat， among which 96.9% genes RPKM values were lower than 1 000. 15 070 genes had alternative splicing （AS）， and the splicing times were 35 913. Intron retention was found to be the rarest AS type， while alternative first exons， alternative last exons and skipped exon were the three major types， with the proportions of 45.92%， 43.67% and 6.23%， respectively. Using these transcriptome data， 229 276 SNPs were called， among which transitions were the main type， accounting for 73.28% of all the SNPs. Gene ontology(GO) annotation analysis revealed that genes including these SNPs took part in numerous functions belonging to the three categories of cellular component， molecular function， and biological process， and further kyoto encyclopedia of genes and genomes(KEGG) pathway analysis showed that most of these genes were related to cancer， immune system， and endocrine system， suggesting that the adipose tissue was an important immune and endocrine tissue， as well as an energy store tissue. These data could enlarge the genetic information of ducks. The numerous SNPs identified in this study would contribute to the molecular breeding and help in mapping the genes associated with important economic traits. The SNPs related with cancers and immune systems would serve as useful markers in related studies.

Key words: gene expression, alternative splicing, single nucleotide polymorphism, adipose tissue