| Gracilaria lemaneiformis is an important Gracilaria species. As a main agarophyte, G. lemaneiformis shows not only important theoretic study but also economic values. However, the study on its molecular breeding system of this species is limited. In this study, Simple sequence repeats (SSRs) were isoloated directly from the genome of G. lemaneiformis, and applied on the genetic diversity analysis of different G. lemaneiformis geographical groups and different G. lemaneiformis individuals that have different agar contents. The study will provide data for further related studies of this species, and lay the foundation for genetic analysis, genetic linkage mapping, molecular markers- assistant breeding, species identification, gene localization and QTL studies of G. lemaneiformis. AFLP technique was further applied on this species for genetic diversity analysis of G. lemaneiformis.Two approaches were adapted to enrich SSR containing clones directly from wild G. lemaneiformis material, one of which was screening via hybridizing on membrane-affinity probe (HMAP). Two kind of probe with (CA)n and (GA)n sequences,respectively were used. The positive clones containing SSR DNA were obtained by clonal in-situ hybridization and PCR amplification, respectively. Totally 24 SSR containing clones were obtained, which including 77 SSR DNA after sequencing. On the other hand, SSR DNA containing clones were enriched by a magic beed adsorbent process (MBAP). PCR amplification was operated to screen positive clones. Fifty-one positive clones containing SSR DNA were obtained, with 82 SSR DNA sites involved.Thirty-seven pair of SSR primers were designed from the isolated SSR containing fragements. However, only 16 of them will give expected products. Fourty G. lemaneiformis individules from four different geographical groups, Zanshan Bay, Huiquan Bay, Taiwan Road of Qingdao and Shidao of Weihai, 10 of each were analyzed of their gengtic diversity by the 16 primers. However, no diversity was detected. Thirty G. lemaneiformis individuals that have different agar contents were analyzed for their genetic diversity by 4 primers of the sixteen. No genetic diversity was detected, either. In addition, the universal of the primer in other closely related species was studied. Twelve of 16 primers were applicable in 981 G. lemaneiformis, while only one can give positive amplifications in Gracilaria verrucosa and Gracilaria txetorii.AFLP technique was further applied after EcoRâ… and Mseâ… double endonuclease digestion of the algal genome. Eight from 16 primer pair were selected to analysis the fourty G. lemaneiformis invididuals from four different geographical groups. A total of 347 reproducible bands were amplified with 8 AFLP primer pairs on the tested material. The percentage of polymorphic loci ranged from 9.8% to 20.4% within the four groups, and the overall polymorphic loci percentage was 51%. The effective number of alleles(Ne) of the four groups ranged from 1.0477 to 1.1130. The overall effective number of alleles was 1.3779; the Neis gene diversity (H) were from 0.0292 to 0.0715; the Shannon diversity indices (I) were from 0.0457 to 0.1151; the Genetic similarity coefficient were from 0.6797 to 0.9388; the Genetic distance were from 0.0632 to 0.3861. All of the AFLP results suggested that the genetic diversity of wild G. lemaneiformis populations be very poor. They were close related in genetic relationship and the idioplasm resources were poor. This is maybe the reason that produces the low level genetic diversity status of different G. lemaneiformis geographical groups.
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