Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B

• Published in: The Plant journal : for cell and molecular biology Vol. 48; no. 3; pp. 463 - 474
• Main Authors: Paux, Etienne, Roger, Delphine, Badaeva, Ekatherina, Gay, Georges, Bernard, Michel, Sourdille, Pierre, Feuillet, Catherine
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01-11-2006; Blackwell Publishing Ltd; Blackwell Science; Wiley
• Subjects: Aegilops tauschii; BAC‐end sequencing; Base Sequence; B‐genome; Chromosomes; Chromosomes, Artificial, Bacterial; Chromosomes, Plant; Cloning; DNA, Plant; Evolution, Molecular; Genetics; genome composition; Genome, Plant; Genomics; homoeologous genome evolution; In Situ Hybridization, Fluorescence; Karyotyping; Life Sciences; Molecular biology; molecular markers; Molecular Sequence Data; Plants genetics; Polyploidy; Triticum - genetics; Triticum aestivum; Wheat; HOMOEOLOGOUS GENOME EVOLUTION; GENOME COMPOSITION; MOLECULAR MARKERS; STRUCTURE DU GENOME; WHEAT; BAC-END SEQUENCING; B-GENOME
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313x.2006.02891.x

Bread wheat (Triticum aestivum) is one of the most important crops worldwide. However, because of its large, hexaploid, highly repetitive genome it is a challenge to develop efficient means for molecular analysis and genetic improvement in wheat. To better understand the composition and molecular evolution of the hexaploid wheat homoeologous genomes and to evaluate the potential of BAC-end sequences (BES) for marker development, we have followed a chromosome-specific strategy and generated 11 Mb of random BES from chromosome 3B, the largest chromosome of bread wheat. The sequence consisted of about 86% of repetitive elements, 1.2% of coding regions, and 13% remained unknown. With 1.2% of the sequence length corresponding to coding sequences, 6000 genes were estimated for chromosome 3B. New repetitive sequences were identified, including a Triticineae-specific tandem repeat (Fat) that represents 0.6% of the B-genome and has been differentially amplified in the homoeologous genomes before polyploidization. About 10% of the BES contained junctions between nested transposable elements that were used to develop chromosome-specific markers for physical and genetic mapping. Finally, sequence comparison with 2.9 Mb of random sequences from the D-genome of Aegilops tauschii suggested that the larger size of the B-genome is due to a higher content in repetitive elements. It also indicated which families of transposable elements are mostly responsible for differential expansion of the homoeologous wheat genomes during evolution. Our data demonstrate that BAC-end sequencing from flow-sorted chromosomes is a powerful tool for analysing the structure and evolution of polyploid and highly repetitive genomes.