Transcriptomics,Genomics

Dataset Information

160

RNA-seq of breast in 3-week and 6-week age native Pekin and Cherry Valley Pekin ducks


ABSTRACT: Muscle development and lipid deposition are complex processes regulated by a coordinated expression profile of genes. Pekin ducks displayed a significant difference from Cherry Valley duck in muscle fiber development and IMF contents. Genetic comparisons between these two breeds would contribute to the exploration of mechanisms underlying the phenotypic differences. In the present study, breast tissues of Pekin (BD) and Cherry Valley (CD) ducks were used for RNA-seq in two different time points (3 and 6-week) to investigate the transcriptome basis. A total of 16705 genes from duck breast muscle were detected as positively expressed genes (RPKM>0.1) and 2273 genes were regarded as novel genes. Differentially expressed genes (DEGs) in BD3 VS CD3 were regarded as muscle development-related genes as CD3 grown faster than BD3 in muscle fibers. DEGs in BD6 VS CD6 were regarded as lipid-related genes as a much higher IMF contents in BD6 than CD6 while no differences observed in 3-week. DEGs obtained from BD3 VS BD6 and CD3 VS CD6 were also analyzed as relative genes here. In all, 9 genes (MAT1A, KAZALD1, SHROOM3, KLHL6, MYH13, ALDOA, TNNT2, PDLIM3 and PFKM) were validated as muscle development correlated candidate genes, and another 11 genes (DHCR24, CNTFR, ANGPTL4, BCL6, HIP1, TRIB1, ADORA1, C1QTNF2, CD36, PRKAG2 and ACSL1) were regarded as lipid correlated genes in duck. What’s more, functional analysis confirmed that the immune reaction, ECM and energy metabolism also correlated with muscle development and lipid deposition closely. The present study not only enlarged the duck genetic information pool but also provided a dozen of candidate genes related to muscle development and lipid deposition, which laid a firm foundation for the further studies on molecular mechanisms in duck. Overall design: RNA-deep sequencing of breast muscle in 3-week and 6-week age native Pekin duck and Cherry Valley Pekin duck under Hi-seq 2000

INSTRUMENT(S): Illumina HiSeq 2000 (Anas platyrhynchos)

SUBMITTER: Liyuan Wang  

PROVIDER: GSE92920 | GEO | 2016-12-27

SECONDARY ACCESSION(S): PRJNA358835

REPOSITORIES: GEO

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