Lophopyrum elongatum (tall wheatgrass), a wild relative of wheat, can be used as a source of novel genes for improving salt tolerance of bread wheat. Sodium ‘exclusion’ is a major physiological mechanism for salt tolerance in a wheat–tall wheatgrass amphiploid, and a large proportion (~50%) of reduced Na+ accumulation in the flag leaf as compared with wheat, was earlier shown to be contributed by chromosome 3E from tall wheatgrass substituted for wheat chromosomes 3A and 3D. Homoeologous recombination between 3E and wheat chromosomes 3A and 3D was induced using the Ph1 mutant and putative recombinants were identified using SSR markers specific for tall wheatgrass loci. Fourteen recombinants with relatively small segments of tall wheatgrass chromatin were identified. A finer resolution of wheat–tall wheatgrass chromosomal breakpoints in selected recombinants was achieved using genetic and bin-mapped wheat SSR markers. Seven recombinants were identified to have leaf Na+ concentrations similar to those in 3E3A and 3E3D substitution lines, when grown in 200 mM NaCl in nutrient solution. The combined analysis of chromosomal breakpoints and phenotyping identified the region controlling leaf Na+ concentration on the telomeric region where tall wheatgrass 3E recombined with the long arm of wheat chromosome 3A. Genomic in-situ hybridization of the recombinant line having the smallest tall wheatgrass segment, 524-568, contained a small introgression of tall wheatgrass chromatin on the distal end of the long arm of wheat chromosome 3A; this line is desirable for further germplasm development.
