Development of EST-SSR markers and their application in an analysis of the genetic diversity of the endangered species Magnolia sinostellata.

Abstract

Magnolia sinostellata is an endemic species of Magnoliaceae that is narrowly distributed in the south of Zhejiang Province, China. To explore the genetic diversity and population structure of this endangered species, this study developed sequence tag-simple sequence repeat (EST-SSR) markers based on transcriptome data of M. sinostellata. In total, 25472 SSRs were identified among 110644 unique assembled sequences with a total of 90.83Mb and an average frequency of 23.02%. The mononucleotide (33.53%) and dinucleotide (42.08%) motifs appeared to be the most abundant. In total, 150 potential loci were randomly selected to validate the quality of the developed SSR markers; an effective PCR rate of 32.00% and a polymorphism rate of 15.33% were obtained for these loci. After performing sequencing and cloning for validation, 23 pairs of SSR primers were retained and used to characterize the genetic diversity and population structure of M. sinostellata. Overall, 204 alleles were amplified. The results of Shannon's information index (I), heterozygosity (Ho), heterozygosity (He) and Nei's expected heterozygosity (H) indicated rich genetic diversity in M. sinostellata. However, the high inbreeding coefficient and differential coefficient suggest that serious genetic drift occurred within populations, and genetic differentiation is apparent among the populations. Consequently, although M. sinostellata has high genetic diversity among populations, it is still in a serious and dangerous condition. Habitat destruction caused by human activities is the main threat to this species, and enhancing the species abundance by adopting some conservation measures should be favourable for saving the species.