title: Methods for genome-wide analysis of gene expression changes in polyploids.
abstract: Polyploidy is an evolutionary innovation, providing extra sets of genetic material for phenotypic variation and adaptation. It is predicted that changes of gene expression by genetic and epigenetic mechanisms are responsible for novel variation in nascent and established polyploids (Liu and Wendel, 2002; Osborn et al., 2003; Pikaard, 2001). Studying gene expression changes in allopolyploids is more complicated than in autopolyploids, because allopolyploids contain more than two sets of genomes originating from divergent, but related, species. Here we describe two methods that are applicable to the genome-wide analysis of gene expression differences resulting from genome duplication in autopolyploids or interactions between homoeologous genomes in allopolyploids. First, we describe an amplified fragment length polymorphism (AFLP)--complementary DNA (cDNA) display method that allows the discrimination of homoeologous loci based on restriction polymorphisms between the progenitors. Second, we describe microarray analyses that can be used to compare gene expression differences between the allopolyploids and respective progenitors using appropriate experimental design and statistical analysis. We demonstrate the utility of these two complementary methods and discuss the pros and cons of using the methods to analyze gene expression changes in autopolyploids and allopolyploids. Furthermore, we describe these methods in general terms to be of wider applicability for comparative gene expression in a variety of evolutionary, genetic, biological, and physiological contexts.
authors.affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843-2474, USA.
authors.forename: Jianlin
authors.initials: J
authors.lastname: Wang
authors.forename: Jinsuk J
authors.initials: JJ
authors.lastname: Lee
authors.forename: Lu
authors.initials: L
authors.lastname: Tian
authors.forename: Hyeon-Se
authors.initials: HS
authors.lastname: Lee
authors.forename: Meng
authors.initials: M
authors.lastname: Chen
authors.forename: Sheetal
authors.initials: S
authors.lastname: Rao
authors.forename: Edward N
authors.initials: EN
authors.lastname: Wei
authors.forename: R W
authors.initials: RW
authors.lastname: Doerge
authors.forename: Luca
authors.initials: L
authors.lastname: Comai
authors.forename: Z Jeffrey
authors.initials: ZJ
authors.lastname: Chen
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D018745:Genome, Plant; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D011123:Polyploidy; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification; D018749:RNA, Plant / Q000235:genetics / Q000302:isolation & purification
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant; D012333:RNA, Messenger; D018749:RNA, Plant