Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags

Abstract

To localize wheat (Triticum aestivum L.) ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions (bins) flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs, 2043 (loci) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin.

Figure 1.—

Deletion maps of wheat chromosomes 6A, 6B, and 6D. The chromosomes are drawn to scale. Each centromere is marked by a constriction and the C-bands are shown as solid boxes. The deletion breakpoints along with fraction length (FL) are marked by arrows on the left of the chromosomes and the number of EST loci in each bin is on the right.

Figure 2.—

Distribution of 2043 homoeologous group 6-specific EST loci by genome. The actual number of loci is shown at the top of each bar.

Figure 3.—

Comparison of observed and expected numbers of homoeologous group 6-specific EST loci. The shaded and solid bars represent the short and long arms, respectively. The actual numbers are given at the top of the bars; not counted are the 22 loci that mapped to centromere bins.

Figure 4.—

Comparison of the frequency of the bands (fragments) detected by ESTs mapping on group 6 with that of those mapping on other wheat homoeologous groups. The percentage of ESTs detecting the number of fragments is given at the top of the bars.

Figure 5.—

A consensus physical map of homoeologous group 6 chromosomes. The physical map on the left was generated on the basis of the actual number of ESTs per bin, whereas the map on the right was based on EST density. Deletion breakpoints are indicated by lines and FL values on the left. The numbers in the boxes and color scheme for the left side of the consensus physical chromosome represent the number of ESTs present in that region and the right side represents the gene density based on the percentage of the chromosome arm.

Figure 6.—

Comparative analysis of wheat group 6 ESTs with rice BAC/PAC sequences. The wheat consensus chromosome 6 is shown with deletion breakpoints and FL values on the left. Each deletion bin is color coded according to the rice chromosome with matching ESTs mapped to that bin. Each bin is spanned by red and blue bar charts on the right of the chromosome. The bar charts are drawn to scale using actual number of ESTs. The width of the red bar chart shows the number of wheat ESTs with homology to the rice chromosomes and the blue bar chart shows the number of ESTs on the consensus wheat group 6 map.