Analysis of expressed sequence tag loci on wheat chromosome group 4

Abstract

A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes (ESTs) from 26 Triticeae cDNA libraries, were mapped to wheat (Triticum aestivum L.) homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes, while 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions, previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoeologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology (only 26 of the 119 consensus ESTs) was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases.

Figure 1.—

C-banding ideograms of the three wheat homoeologous group 4 chromosomes and the group 4 consensus map. For the three ideograms, the number of EST loci mapped to the corresponding bins is given on the left and the deletion bin designation is on the right of each chromosome. For the consensus map, the consensus bin breakpoints are identified on the left and given on the right are the number of consensus ESTs in the bin (boldface), the density of that bin (in parentheses), and the bin designation. More detailed information on the identity of the consensus ESTs and their distribution on the three group 4 chromosomes can be found in the supplemental online material at http://wheat.pw.usda.gov/pubs/2004/Genetics/. Note that as the text and Figure 2 show, it is the long arm of 4A that is homoeologous to the short arms of 4B and 4D and the short arm of 4A that is homoeologous to the long arms of 4B and 4D. Therefore the ideogram for chromosome 4A is presented here with the long arm at the top to emphasize that homoeology.

Figure 2.—

Translocations involving chromosome arms 4AL, 5BL, and 7AS and inversions within chromosome 4A detected by EST mapping. In the rightmost ideogram, where >10 ESTs mapped in the corresponding segments, the total number of ESTs rather than their accession numbers are noted. The “+” sign between these numbers differentiates ESTs mapped to opposite sides of a deletion breakpoint when the segment covers more than one mapping bin.

Figure 3.—

Wheat-rice colinear relationships for the wheat ESTs composing the group 4 consensus chromosome. The consensus bin designations and bin breakpoints are given on the left of the wheat consensus chromosome. The colors on the wheat consensus chromosome represent specific rice chromosomes that had genomic sequences homologous to ESTs in those wheat consensus bins. The colors used correspond to the rice chromosome color designations used by Sorrells et al. (2003). The order of the colors along the consensus wheat chromosome within a bin does not imply any order of ESTs within a bin with respect to rice homologs.

Figure 4.—

Functional classification of wheat ESTs mapped on group 4 chromosomes based on the Arabidopsis gene classification.