title: Subgenome-specific markers in allopolyploid cotton Gossypium hirsutum: implications for evolutionary analysis of polyploids.
abstract: We developed a set of genetic markers specific to the A and D genome types of cotton using representational difference analysis (RDA). These markers produce amplification products with genomic DNA from allotetraploid cotton Gossypium hirsutum. One of the markers is a polymorphic amplified restriction fragment (PARF) - a sequence found in both A and D genomes but differently flanked by restriction sites. Results of phylogenetic analysis of the PARF sequences from diploid cottons and from allotetraploid G. hirsutum agree with a previous observation of the interlocus concerted evolution (sequences corresponding to A and D genomes are homogenized to a D genome-type sequence). Our study shows how RDA can be used to develop genome-specific markers that can be used to study molecular evolution of allopolyploids.
authors.affiliation: Department of Biology, Texas Tech University, Lubbock, TX 79409, USA. anton@uchicago.edu
authors.forename: Anton
authors.initials: A
authors.lastname: Nekrutenko
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Baker
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D009693:Nucleic Acid Hybridization / Q000379:methods; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D011123:Polyploidy
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers