Development Of Genomic-SSR Markers And Genetic Diversity Analysis Of Gracilariopsis Lemaneiformis(Rhodophyta)

Gracilariopsis lemaneiformis, belonging to Rhodophyta, is an importanteconomic alga that produce agar. It also shows bioremediation potential to eliminatecoastal eutrophication. It is crucial to establish genetic breeding system of this speciesand SSR markers is often used for genetic breeding research. In order to obtainenough SSR markers for further construction of genetic linkage map and localizationof QTLs, genome survey sequencing was adopted in this study to develop SSRs in thewhole genome of Gp.lemaneiformis. Polymorphic SSR markers identified bypolyacrylamide gel electrophoresis were used to analyze the genetic diversity ofdifferent geographical populations. Hopefully, the wild idioplasm resource conditionof Gp. lemaneiformis can be understood and the theoretical basis for genetic breedingcan be provided. Meanwhile, genome survey acts as a preliminary assessment ofgenomic information, providing sequence data for subsequent research.18.69G clean data was generated by genome survey sequencing. The K-meranalysis suggested a genome size of97.02M. After de novo assembly, a GC contentof48%was calculated and repeat sequences accounted for55%of the genome. Fromthe assembled sequences,7737SSR loci were identified and primers were designedfor4498of them. Trinucleotide repeat type was the most abundant with a frequencyof73.20%, followed by dinucleotide (17.41%), tetranucleotide (5.49%),hexanucleotide (2.90%) and pentanucleotide (1.00%).120pairs of SSR primers were detected in12samples, among which115(95.83%) were successfully amplified and31(25.83%) were identified aspolymorphic primers. Subsequently, the polymorphic primers were used to screen82samples from three geographical populations: Qingdao Sculpture Garden, QingdaoZhanshan Bay and Weihai Stone Island. The related parameters such as Na (~2.0500), Ne (~1.0783), H (~0.0729), I (~0.1539) and PIC (~0.0676) reflected the lowgenetic diversity level of the overall wild population. Analysis of differentgeographical populations revealed that the genetic diversity level of Weihai StoneIsland was the highest while Qingdao Sculpture Garden was the lowest. Based onNei’s genetic diversity index and Shannon’s diversity index, genetic diversity withinpopulation and genetic differentiation among populations were estimated and theresults showed that the genetic variation within population contributed the most to thetotal genetic variation, as the analysis of molecular variance (AMOVA) reflected(97.07%). In addition, the genetic differentiation coefficient (Gst) betweenpopulations was below0.05, revealing that the degree of differentiation betweenpopulations was very low. UPGMA cluster analysis showed that individuals weremixed among different populations and there were no obvious regional features,further indicating that the degree of genetic differentiation among geographicalpopulations was low.The genetic diversity analysis of Gp.lemaneiformis reflected a scarcity of itsidioplasm resources, which was related to its special living environment andreproduction mode. The over-exploitation of coastal areas was also an importantfactor for the low genetic diversity of wild population.