Functional Genomics Research in Aquaculture: Principles and General Approaches

Shikai Liu, Yu Zhang, Fanyue Sun, Yanliang Jiang, Ruijia Wang, Chao Li, Jiaren Zhang, Zhanjiang John Liu

Research output: Chapter in Book/Entry/PoemChapter

2 Scopus citations


Functional analysis has always been more difficult, but it is nothing compared with structural analysis. This is especially true when the number of genes under study is increased to cover various systems and pathways on a genome scale. In this chapter, we provide an overview of functional genomics focusing on general approaches for functional genomics to include (1) Functional inference based on expression profiling such as analysis of expressed sequence tag (EST) analysis, microarray analysis, and RNA-Seq; (2) Functional inference of gene functions based on positional analysis such as genome-wide association studies (GWAS), quantitative trait loci (QTL) mapping, and expression quantitative trait loci (eQTL) mapping; (3) Functional inference of gene functions by comparative genome analysis; (4) Gene pathway analysis; and (5) Experimental determination of gene functions using novel technologies, such as the zinc finger nuclease (ZFN) technology.Wealso provide a section on epigenetics and analysis of protein-DNA interactions. At the end of the chapter, we offer our assessment of the potential of various technologies for functional genomics in aquaculture.

Original languageEnglish (US)
Title of host publicationFunctional Genomics in Aquaculture
PublisherWiley Blackwell
Number of pages40
ISBN (Print)9780470960080
StatePublished - Jun 11 2012
Externally publishedYes


  • Comparative genome pathway, epigenetic using ChIP, and gene expression
  • Data generation, management and data set mining
  • Functional genomics research in aquaculture, and general approaches
  • Functional genomics, genome-wide using structural genomics
  • Functional inference on expression profiling, EST, BLAST and ORF
  • Gene function determination with ZFN
  • Gene function on positional analysis, GWAS, QTL, eQTL
  • Genome mapping, sequencing "structural genomics" and "functional genomics"
  • RNA-Seq in aquaculture, DNA, mRNA, microarray and RNASeq complementary
  • Vertebrates and conserved synteny and orthology

ASJC Scopus subject areas

  • General Agricultural and Biological Sciences


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