A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice

Abstract

We constructed high-density deletion bin maps of wheat chromosomes 5A, 5B, and 5D, including 2338 loci mapped with 1052 EST probes and 217 previously mapped loci (total 2555 loci). This information was combined to construct a consensus chromosome bin map of group 5 including 24 bins. A relatively higher number of loci were mapped on chromosome 5B (38%) compared to 5A (34%) and 5D (28%). Differences in the levels of polymorphism among the three chromosomes were partially responsible for these differences. A higher number of duplicated loci was found on chromosome 5B (42%). Three times more loci were mapped on the long arms than on the short arms, and a significantly higher number of probes, loci, and duplicated loci were mapped on the distal halves than on the proximal halves of the chromosome arms. Good overall colinearity was observed among the three homoeologous group 5 chromosomes, except for the previously known 5AL/4AL translocation and a putative small pericentric inversion in chromosome 5A. Statistically significant colinearity was observed between low-copy-number ESTs from wheat homoeologous group 5 and rice chromosomes 12 (88 ESTs), 9 (72 ESTs), and 3 (84 ESTs).

Figure 1.—

Consensus physical map of wheat homoeologous group 5 chromosomes. Consensus bin names are shown on the left (the corresponding deletion bin names are in parentheses). Numbers inside bars show the number of EST probes mapped into each consensus interval. Larger bars to the right represent combined consensus bins. Different shadowing patterns within the consensus chromosome indicate colinearity with different rice chromosomes. The 4AL/5AL translocation breakpoint is indicated at the bottom.

Figure 2.—

Southern blot hybridization of probes included in the putative pericentric inversion on chromosome 5A. Hybridization of EcoRI-digested DNAs of wheat-rye translocation lines, nulli-tetrasomic and telosomic lines for homoeologous group 5, and Lophopyrum elongatum and barley telosomic addition lines is shown. (A) Probe BF291333. (B and C) Probe BE403761. (D) Multicolor FISH with pAWRC.1, a rye-specific centromeric probe (labeled with fluorescein-12-dUTP and visualized by yellow-green fluorescence), and pAet6-J9, a grass common centromeric probe (labeled with rhodamine-6-dUTP and visualized by red fluorescence), showing the presence of a complete rye centromere in the T5RS·5AL translocation (indicated with arrows; provided by Dr. Peng Zhang; Francki 2001; Zhang 2002). (E) Schematic of the centromeric location hypothesis. According to this hypothesis these ESTs are located within the functional centromeric region and the arrows indicate different centromeric breakpoints. (F) Schematic of the inversion/deletion hypothesis. ESTs indicated in blue are located within the inversion and ESTs indicated in red are located within a region that is deleted in Dt5AL.