Genome-wide Development And Identification Of SSRs In Potato

Potato (Solanum tuberosum L.) is one of the most important crops worldwide, and essential to global food security. Cultivated potato is clonally reproduction, with autotetraploid and highly heterozygous genetic composition; it suffers with acute inbreeding depression, and complex separation within hybrids. Hence, genetic and breeding researches of potato are far behind the level of other major cultivated crops. SSR has been proved to be an indispensable tool in crop genetics and breeding. With the progress of genome sequencing, the traditional SSR markers development method by library-screening has been replaced by genome-wide search and identification using bioinformatics technology. In this paper, MISA program was adapted to search and analyze SSR loci within reference genome of potato, and the SSR markers developed were identified. The main results and conclusions are as follows:1. A new method for potato SSRs development, different from all methods reported, were proposed:Searching and screening unique SSR loci genome-wide first, and then taking potato EST sequences as templates to identify polymorphic SSRs, which means taking the advantage of redundancy and polymorphism of the EST data. Our method can improve the efficiency of SSRs development greatly, and also prevent eliminating the potentially valuable SSR markers by mistake, as identified by the genome data, or genotypes of potato in the laboratory.2. A relatively higher overall and unique SSR loci number and density were revealed on reference genome of potato, which is much higher than the number and density revealed by traditional methods, and also higher than the results obtained based on partial genome searching.3. SSRs of potato locate mainly in the intergenic region, but the density of unique SSR loci in the intron region is higher than unique SSR loci located in the intergenic region. That gives the feasibility of development SSR markers closely associated with genes.4. The average GC rate of SSR loci in potato is 13.81%; and the most frequency motif of MNRs, DNRs and TNRs are A/T, AT/TA and AAT-type respectively. This means the traditional library-screening method for SSR markers development may not be a reliable choice for potato.5. EST sequences were employed as templates to screen and analysis polymorphic SSR loci.2104 SSRs with e-PCR products were revealed, and 611 of them were proved to be polymorphic, while 357 of them gave products with no less than 3bp in length difference.6. Primers of 34 SSRs on different chromosome were designed by Primer (software) and 20 potato lines were employed to identify the polymorphism of them.28 SSR primers amplified clear bands,25 of them proved to be polymorphic primers. Polymorphic information contents (PICs) of 5 primers are no less than 0.55, and the highest PIC reaches 0.823.7. Further application of newly developed SSR markers and bioinformatics methods for development of polymorphic SSRs located in intron and promoter region were discussed.