Genome-wide identification of simple sequence repeats and assessment of genetic diversity in Hedychium

Abstract Hedychium is an important industrial crop, which is widely cultivated for its medicinal and horticultural significance. However, the development of simple sequence repeat (SSR) for Hedychium has not yet been reported. In this study, 266,825 SSR markers were identified in H. coronarium ‘ZS’ genome. The relationship between the type, repeat times, content, and content of SSR markers and chromosome length was specifically analyzed. The results revealed that the mononucleotides (59.17 %) were the most abundant repeat motifs, followed by dinucleotides (27.97 %) and trinucleotides (10.85 %). To verify the availability of SSR and its polymorphism among different species, 120 primer pairs were randomly selected. Finally, 22 markers were screened to genotype 44 accessions collected from different geographic locations of China, Thailand, Japan, and USA. A number of 224 alleles were identified, with an average of 10.18 alleles and polymorphism information content ranged from 0.17 to 0.96 with a mean of 0.88. Genetic structure analysis indicated that 44 accessions had strong regional characteristics and a clear distinction between cultivated and wild genotypes. Population structure and PCoA analysis revealed that from 44 accessions, 7 cultivated accession were distinctly grouped into cluster A, whilst other wild accessions belong to cluster B. These new SSR markers will provide important references for genetic diversity analysis, identification of germplasm resources, and breeding of Hedychium.