[Truncated abstract] Lophopyrum elongatum, a wild relative of wheat, can be used as a source of novel genes for improving the salt tolerance of bread wheat. Na+ `exclusion? is a major physiological mechanism for salt tolerance in the wheat L. elongatum amphiploid, and a large proportion (~50%) of the improved Na+ `exclusion? is contributed by a gene(s) on chromosome 3E. This study integrated physiological analysis with comparative genomics to identify gene orthologues that may regulate Na+ transport, and designed and implemented molecular markers for developing wheat L. elongatum recombinant lines with reduced portions of L. elongatum chromatin retaining the Na+ `exclusion? trait. Physiological analysis of leaf Na+ accumulation in wheat L. elongatum substitution lines confirmed that the 3E chromosome contributes a major effect on reduced leaf Na+ accumulation in wheat when grown at 200 mM NaCl. Candidate genes from the model plant, Arabidopsis thaliana, controlling Na+ transport into and from cells (SOS1, HKT1) or compartmentalisation within vacuoles (NHX1, NHX5, AVP1, AVP2) were targeted for comparative analysis in wheat. Wheat gene orthologues were identified by BLAST searching to identify either FL-cDNAs or ESTs, which were subsequently used to amplify genomic DNA, and orthologues confirmed by similar intron-exon structure between Arabidopsis and rice. Intron-exon comparisons showed the majority of exons were conserved between Arabidopsis, rice and wheat, but also indicated exon shuffling events since divergence from a common ancestor. Gene orthologues were assigned to homoeologous chromosomes and non-syntenic regions between wheat and L. elongatum, with the SOS1 orthologue located on group 3 chromosomes in wheat and L. elongatum. ... The recombinant line 524-568 contains a small introgression on the distal end of the long arm of wheat chromosome 3A and represents the most desirable line presently available for further germplasm development. The main outcomes of this thesis have been an increased understanding of the physiology and evolution of orthologues for Na+ transport in wheat and L. elongatum, improved methodologies for designing alien-specific PCR markers, and the development of overlapping recombinant lines that provide a source of novel genes for pyramiding into wheat and improving its tolerance to salt stress.