A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat

Abstract

Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.

Figure 1.—

An example of localization of EST loci to individual bins of three chromosomes in a homoeologous group. (A) An autoradiograph of Southern hybridization of genomic DNA of standard Chinese Spring (CS) and aneuploid and deletion stocks for group 3 chromosomes. Chromosome ideograms indicate the specific chromosome constitution in the corresponding genetic stocks. The dashed line means the chromosome, chromosome arm, or segment is missing. The genomic DNA of nullisomic-tetrasomic (NT), ditelosomic (DT), and deletion (del) lines was digested with EcoRI and hybridized with BE406607. The first and second fragments from the top detected by this EST were missing in all deletion lines of 3DS and 3AS arms, as well as corresponding NT and DT lines, and were mapped to the bins of 3DS6-0.55-1.00 and 3AS3-0.45-1.00, respectively. The third fragment was absent in N3BT3D, Dt3BL, del3BS-1, and del3BS-9, but present in del3BS-8, and was assigned to the bin 3BS9-0.57-0.78. (B) Depiction of chromosome bins and mapping information. Ideogram of C-banded chromosomes of group 3 is after B. S. Gill et al. (1991). The deletion names and breakpoints (indicated as fraction length from the centromere) are on the left and the bin assignments are on the right of each chromosome. The EST mapped to bins is in italics on the right of each chromosome.

Figure 2.—

Number of observed and expected EST loci for the A, B, and D genomes of wheat.

Figure 3.—

Gene density in the 42 chromosome arms of wheat. Gene density was calculated by the ratio of observed to expected loci (on the basis of chromosome length).

Figure 4.—

Gene densities (ratio of observed to expected loci) in individual chromosome bins of common wheat. Values <1 (gray and light blue) indicate low gene density and >1 denote high gene density (yellow, blue, and red). Note gene-dense regions are located toward the distal ends of chromosomes. The numbers on the left of a chromosome indicate the individual deletion lines and the numbers in parentheses are the FL values of each deletion. The number in boldface type in parentheses at the bottom of each chromosome is the total number of EST loci mapped in that chromosome. Previously mapped agronomic traits (indicated on the right in italics) were assigned to chromosome bins on the basis of the bin allocation of linked markers. Note that most traits colocalized to regions of high EST density.