Genome-wide assessment of genetic variation and differentiation for Gastrodia elata germplasm based on SLAF sequencing

Gastrodia elata BI. is an important cultivated medicinal plant in China. To analyze the genetic diversity and evolutionary relationship of the germplasm resources of G. elata, SNP locus and SNP typing of G. elata accessions were identified by specific-locus amplified fragment (SLAF) sequencing. SLAF analysis was used to compare 28 samples of the same G. elata cultivar. Plants of three different varieties from four different populations were collected to explore intraspecific variation and to lay a foundation for resource protection and thus improved variety breeding. In this study, genetic variation and differentiation of G. elata f. glauca, G. elata f. viridis, and G. elata f. elata were analyzed using specific-locus amplified fragment (SLAF) sequencing. A total of 75.95 M reads with an average sequencing depth of 19.32 x and a mean Q30 of 91.71% were obtained. Based on the 19,675 polymorphic SLAF tags, 60,238 SNPs were identified, and a subset of 22,737 SNPs with minor allele frequency > 0.05 and integrity > 0.5 was selected for further analysis. A model-based analysis divided the accessions into two groups, wild-type G. elata f. glauca and G. elata f. viridis groups. Phylogenetic analysis also clustered the samples into the same two major groups. G. elata has high genetic diversity. Population diversity was highest in G. elata f. elata and lowest in G. elata f. viridis. Analysis of molecular variance (AMOVA) revealed significant polymorphism within individuals (92.23%). This study provides new insights into the genetic variation and differentiation of G. elata, which can be exploited to improve existing commercial cultivars.

Automated summary

This study analyzed the genetic diversity and evolutionary relationship of G. elata germplasm resources using SLAF sequencing. The results showed that G. elata has high genetic diversity, with the highest population diversity in G. elata f. elata and the lowest in G. elata f. viridis.