Assessment of Genetic Diversity of the Medicinal and Aromatic Crop, <i>Amomum tsao-ko</i>, Using PAAP and CDDP Markers

<i>Amomum tsao-ko</i> (Zingiberaceae) is a well-known medicinal and aromatic crop with a long history of cultivation in China. Food and pharmaceutical industries widely use its dried ripe fruit. In this study, 12 promoter anchored amplified polymorphism (PAAP) primer pairs and 12 conserved DNA-derived polymorphism (CDDP) primers were used to assess the genetic diversity and population structure of 96 <i>A. tsao-ko</i> accessions from eight cultivated populations. A total of 98 polymorphic loci were detected by 12 PAAP primers with 8.167 polymorphic loci per primer, and 203 polymorphic loci were observed using 12 CDDP primers with 16.92 alleles per primer. Nei’s gene diversity (PAAP, <i>H =</i> 0.207; CDDP, <i>H</i> = 0.188) and Shannon’s information index (PAAP, <i>I =</i> 0.329; CDDP, <i>I</i> = 0.305) revealed the relatively high level of genetic diversity in these populations of <i>A. tsao-ko</i>. The genetic differentiation coefficient (<i>Gst</i>) for the populations was 0.151 (PAAP) and 0.128 (CDDP), which indicated that 84.9% and 87.2%, respectively, of the genetic variation was within populations. Analysis of molecular variance (AMOVA) also revealed that genetic differentiation of the <i>A. tsao-ko</i> populations mainly occurred within populations (91% variation within populations for both PAAP and CDDP). Genetic identity among the investigated populations was high for PAAP (0.957) and CDDP (0.967). Cluster and principal coordinate analysis (PCoA) grouped the 96 <i>A. tsao-ko</i> accessions into two major groups. Accession classification was consistent with population structure analysis. Overall, these results will be useful for <i>A. tsao-ko</i> germplasm resource characterization, conservation, and utilization.