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. Dna-based molecular markers, particularly SSRs, have been developed and mapped on chromosomes in a variety of crop plants. In bread wheat, genetic and physical mapping of SSRs has been an ongoing exercise, and, to date, ≈2450 SSRs (1 SSR 1.63 cM-1) have been genetically mapped (for details see Torada et al., 2006) and ≈1320 SSRs (62 SSRs chromosome-1) have been physically mapped (for details see Goyal et al., 2005). With a genome size of ≈16 000 Mbp, it is evident that despite concerted efforts, the density of mapped SSRs in bread wheat remains relatively low and continued efforts are needed to increase the density of these SSRs on available genetic and physical maps. In recent years, emphasis has also shifted from genomic SSRs to EST-SSRs due to the availability of very large databases of ESTs from all of the cereals including bread wheat. Consequently, the number of EST-SSRs in cereals now includes 43 598 from bread wheat (Peng and Lapitan, 2005), 16 917 from rice and 184 from rye (La Rota et al., 2005; Hackauf and Wehling, 2002). The genetic mapping of these EST-SSRs is difficult due to a low level of polymorphism, as a result of their conserved nature. Physical mapping of these EST-SSRs in wheat is equally difficult due to the occurrence of homoeoloci exhibiting no polymorphism. This has discouraged wheat researchers from undertaking a large-scale project to genetically or physically map wheat EST-SSRs although genetic mapping of 325 EST-SSRs (Gao et al., 2004; Nicot et al., 2004; Yu et al., 2004) and physical mapping of 305 EST-SSRs was recently undertaken (Yu et al., 2004; Zhang et al., 2005; Peng and Lapitan, 2005). We previously reported genetic mapping of 58 and physical mapping of 270 genomic SSRs (Gupta et al., 2002; Goyal et al., 2005). The present study is an extension of our earlier studies on physical mapping of SSRs and involved both wet-lab and in silico approaches, leading to the successful mapping of as many as 672 loci. The in silico approach allowed mapping of twice the number of loci (per EST-SSR) mapped using wet-lab analysis.