Physical Mapping of Wheat and Rye Expressed Sequence Tag–Simple Sequence Repeats on Wheat Chromosomes

Six hundred and seventy two loci belonging to 275 expressed sequence tag–simple sequence repeats [EST–SSRs, including 93 wheat ( Triticum aestivum L.) and 182 rye ( Secale cereale L.) EST–SSRs] were physically mapped on 21 wheat chromosomes. The mapping involved two approaches, the wet‐lab approach involving use of deletion stocks and the in silico approach involving matching with ESTs that were previously mapped. The number of loci per EST–SSR mapped using the in silico approach was almost double the number of loci mapped using the wet‐lab approach (using deletion stocks). The distribution of loci on the three subgenomes, on the seven homoeologous groups and on the 21 individual chromosomes was nonrandom ( P ≪ 0.01). Long arms had disproportionately (relative to the difference in DNA content) higher number of loci, with more loci mapped to the distal regions of chromosome arms. A fairly high proportion of EST–SSRs had multiple loci, which were largely (81%) homoeoloci. Rye EST–SSRs showed a high level of transferability (≈77%) to the wheat genome. Putative functions were assigned to 216 SSR‐containing ESTs through homology searches against the protein database. As many as 104 SSR‐containing ESTs (a subset of the above ESTs) were also mapped to the 12 rice chromosomes, which corresponded with the known homology between wheat and rice chromosomes. These physical maps of EST–SSRs should prove useful for comparative genomics, gene tagging, fine mapping, and cloning of genes and QTLs.