Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates

Abstract

Loci detected by Southern blot hybridization of 3,977 expressed sequence tag unigenes were mapped into 159 chromosome bins delineated by breakpoints of a series of overlapping deletions. These data were used to assess synteny levels along homoeologous chromosomes of the wheat A, B, and D genomes, in relation to both bin position on the centromere-telomere axis and the gradient of recombination rates along chromosome arms. Synteny level decreased with the distance of a chromosome region from the centromere. It also decreased with an increase in recombination rates along the average chromosome arm. There were twice as many unique loci in the B genome than in the A and D genomes, and synteny levels between the B genome chromosomes and the A and D genome homoeologues were lower than those between the A and D genome homoeologues. These differences among the wheat genomes were attributed to differences in the mating systems of wheat diploid ancestors. Synteny perturbations were characterized in 31 paralogous sets of loci with perturbed synteny. Both insertions and deletions of loci were detected and both preferentially occurred in high recombination regions of chromosomes.

Fig. 1.

Synteny (S) along the average chromosome arm. The distance of an interval from the centromere is expressed as a fraction of the average chromosome arm length. The centromere of the average chromosome arm is at 0.00, and the telomere is at 1.00.

Fig. 2.

Southern blot hybridization of cDNA clone WHE0825–0828_L16_L16 with EcoRI-digested genomic DNA of Chinese Spring (CS), L. elongatum (E genome) disomic substitution lines in Chinese Spring, disomic addition lines of barley (H genome) chromosomes in Chinese Spring and lines of T. urartu (lanes 1–9), Ae. tauschii (lanes 10–16), and Ae. speltoides (lanes 17–25). In the designations of disomic substitution lines, the wheat chromosome replaced by its L. elongatum homoeologue is indicated in parentheses. The chromosomal locations of the restriction fragments are shown on the left. The four A-genome loci found in wheat were found in the T. urartu genome, whereas only one locus each was found in the genomes of Ae. tauschii and Ae. speltoides. Restriction fragments shared by Chinese Spring D and B genomes and Ae. tauschii and Ae. speltoides, respectively, are marked by arrows.