High-resolution radiation hybrid map of wheat chromosome 1D

Abstract

Physical mapping methods that do not rely on meiotic recombination are necessary for complex polyploid genomes such as wheat (Triticum aestivum L.). This need is due to the uneven distribution of recombination and significant variation in genetic to physical distance ratios. One method that has proven valuable in a number of nonplant and plant systems is radiation hybrid (RH) mapping. This work presents, for the first time, a high-resolution radiation hybrid map of wheat chromosome 1D (D genome) in a tetraploid durum wheat (T. turgidum L., AB genomes) background. An RH panel of 87 lines was used to map 378 molecular markers, which detected 2312 chromosome breaks. The total map distance ranged from approximately 3,341 cR(35,000) for five major linkage groups to 11,773 cR(35,000) for a comprehensive map. The mapping resolution was estimated to be approximately 199 kb/break and provided the starting point for BAC contig alignment. To date, this is the highest resolution that has been obtained by plant RH mapping and serves as a first step for the development of RH resources in wheat.

Figure 1.

Wheat chromosome 1D RH map (right) as compared with the genetic (left) and the deletion map (middle). The boxed markers on the deletion map refer to sequences assigned to a specific region on chromosome 1D. The nonboxed set of markers (seven total on 1DS) are assigned to a region covered by the two deletion breakpoints. Regions with high density (red), medium density (blue), and low density (teal) of mapped ESTs are identified on the deletion map (Peng et al. 2004). The RH map has an estimated total length of 11,737 cR_35,000 covered by 378 AFLP (marked in blue), EST, RFLP, and SSR (all marked in red) markers. The locations of major linkage groups (A–E) and minor linkage groups are indicated by lines on the right of the RH map with the major marker classes of that linkage group identified by blue (AFLP) and red (EST, RFLP, and SSR).

Figure 2.

The ability to order previously deletion-binned but unordered ESTs by RH mapping approach. (A) Comparison of maps generated by the recombination-based linkage, chromosome deletion bin, and radiation hybrid approach. EST loci placed in deletion bin 1DL2 (0.41–1.00 FL distance coverage of chromosome, middle) are part of linkage group A presented in centiray distances (right). Markers in this region cover the majority of the long arm recombination-based linkage map (left, centimorgan distances). The two-point LOD scores are shown in parentheses after the name of the EST in the RH map. Two ESTs indicated by asterisks were placed in bins other than 1DL2-0.41–1.00, but were placed within this linkage group in the RH analysis and represent possible multiple-copy ESTs or simply deletion mapping errors. (B) Actual marker retention data for this region identifying the critical lines used to determine the distance between various markers. The + sign indicates the presence of a marker in the line and the − sign (shaded boxes) indicates absence of that marker. Where marker information was not available the cell is left blank. Markers are organized according to their position on the RH map and critical breaks (shaded boxes) are clearly evident. Two individuals among the population were missing all of the markers within this linkage group (e.g., line 186-29-3 genotype) and 60 individuals had all of the markers within this linkage group (e.g., line 185-31-2 genotype). The total number of unique obligate breaks for each individual is indicated in the right column and totals to 36 unique breaks for this entire region.

Figure 2.

The ability to order previously deletion-binned but unordered ESTs by RH mapping approach. (A) Comparison of maps generated by the recombination-based linkage, chromosome deletion bin, and radiation hybrid approach. EST loci placed in deletion bin 1DL2 (0.41–1.00 FL distance coverage of chromosome, middle) are part of linkage group A presented in centiray distances (right). Markers in this region cover the majority of the long arm recombination-based linkage map (left, centimorgan distances). The two-point LOD scores are shown in parentheses after the name of the EST in the RH map. Two ESTs indicated by asterisks were placed in bins other than 1DL2-0.41–1.00, but were placed within this linkage group in the RH analysis and represent possible multiple-copy ESTs or simply deletion mapping errors. (B) Actual marker retention data for this region identifying the critical lines used to determine the distance between various markers. The + sign indicates the presence of a marker in the line and the − sign (shaded boxes) indicates absence of that marker. Where marker information was not available the cell is left blank. Markers are organized according to their position on the RH map and critical breaks (shaded boxes) are clearly evident. Two individuals among the population were missing all of the markers within this linkage group (e.g., line 186-29-3 genotype) and 60 individuals had all of the markers within this linkage group (e.g., line 185-31-2 genotype). The total number of unique obligate breaks for each individual is indicated in the right column and totals to 36 unique breaks for this entire region.