| EST-SSR is a type of molecular marker developed from the databank of sequence of expression sequence tags (EST) and/or cDNAs. As a new kind of molecular marker, EST-SSR markers have more advantages than the traditional genomic-derived SSRs because they are part of expressed genes. Therefore, EST-SSRs might be involved in gene functioning directly or indirectly. The ability of SSR markers will be greatly enhanced. In this study, we designed primer pairs based on the searching the EST database of wheat, barley, maize, sorghum and rice in GenBank. And we filtered valid EST-SSR markers on wheat and located these EST-SSRs on specific chromosome utilizing Chinese Spring Nulli-tetrasome lines. Then we mapped these EST-SSR markers on the genetic linkage map using a recombinant inbred population of wheat, RIL. Using BLAST, partial EST sequences were related to specific biological functions. The main results were as follows:1. We found 407,663 wheat, maize, barley, sorghum and rice ESTs from the data sets, which contained 10,253 SSRs using the SSRIT Perl script and 2.52 percent over all the data sets tested. There was one SSR in 24.67Kb EST. The frequencies of SSR motif were 3.59% in rice, 1.93% in wheat, 1.99% in maize, 1.30% in barley, 3.21% in sorghum EST collections respectively. While frequency of finding a SSR motif in the EST collection was lowest 40.13Kb in wheat, 34.25Kb in maize, 30.09Kb in barley, 19.65Kb in sorghum, highest 14.59 Kb in rice respectively.2. According to the selected EST-SSR sequences, we designed 1,367 primer pairs. A total of 715 high quality primer pairs were synthesized, of which 500 (69.93%) were successfully amplified PCR products in three varieties of wheat, including 140, 39, 119, 181 and 21developed from wheat, barley, maize, rice and sorghum, respectively.3. The 500 primer pairs which successfully amplified PCR products in wheat were analyzed using a set of Chinese Spring nulli-tetrasomic lines. The results showed that 139 EST-SSR primer pairs with 240 loci were distributed on 21 wheat chromosomes. 86 primer pairs were associated with one chromosome, 33 with two chromosomes, 14 with three chromosomes, 5 with four chromosomes and 1 with six chromosomes. 97 loci were located on the D genome, 81 on the B genome and 64 on the A genome. The number of loci on the A genome was obviously lower than the B and D genomes. The most loci were on group 1 with 58 loci, and the least were on group 5 with 14 loci and group 4 with 16 loci.4. Using the RIL population, 54 EST-SSR polymorphic loci were detected and 47 of them were mapped on 12 chromosomes, 1A, 1B, 1D, 2B, 3B, 4A, 5A, 5B, 5D, 6A, 6D and 7B. Among them, 10 loci were located on chromosomes using nulli-tetrasomic lines, and the other 37 loci mapped on chromosomes based on linkage relationships.5. The ESTs sequences corresponding to EST-SSR markers were analysed by the programs BLAST to get the useful informition. After sequence similarity assignment, 315 ESTs have homologous sequences or proteins, 175 of which had the same results analysed by the programs BLASTN and BLASTX.
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