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Duck egg quality improvement is an essential target for Asian poultry breeding. In total, 15 RNA-Seq libraries (magnum, isthmus, and uterus at two different physiological states) were sequenced from 48 weeks old Pekin ducks. De novo assembly and annotation methods were utilized to generate new reference transcripts. Our results revealed that 1264 and 2517 genes were differentially expressed in magnum and uterus in the presence versus absence of an egg, respectively. We identified 1089 genes that were differentially expressed in isthmus compared to uterus (in both presence and absence of a calcifying egg). We observed that 11 common DEGs were detected in the egg white proteomes of 6 different bird species including domestic Chicken, Duck, Goose, Turkey, Quail, and Pigeon. On the other hand, only one of the top five most highly expressed genes in duck isthmus was in this category for the chicken isthmus (SPINK7). Among the large number of DEGs during eggshell formation in ducks, only 41 genes showed a similar differential expression pattern in both duck and chicken. By combining chicken QTL database, chicken oviduct transcriptome and egg proteome data for five bird species, we have obtained high-quality gene lists for egg formation. This is the first study to elucidate the transcriptomic changes in different duck oviduct segments during egg formation, and to integrate QTL, proteome and transcriptome data to probe the functional genes associated with albumen secretion and eggshell mineralization., Competing Interests: Declaration of Competing Interest The authors declare that they have no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)