Genetic Diversity And Population Structure Of Cultivated Dendrobium Huoshanense (Cz Tang Et Sj Cheng) Using Snp Markers Generated From Gbs Analysis

Dendrobium huoshanense C.Z. Tang et S.J. Cheng, plants have been declared as geographical indicators (GI) of different ecoregions of China, and wild D. huoshanense has been listed as one of the rare and endangered medicinal herbs of China, owing to overexploitation, habitat deteriorationand, et al., Therefore, D. huoshanense plants have been cultivated on a large scale for protecting the endangered species and meeting the great market demands. However, the genetic diversity and population structure of cultivated D. huoshanense are still unknown. Therefore, genetic diversity and population structure of 72 cultivated D. huoshanense samples were investigated in the study, using single nucleotide polymorphism (SNP) markers generated from genotyping-by-sequencing (GBS) analysis. A total of 100,098,874 clean read pairs were generated, with 1,390,262 clean read pairs per sample on average, and the ratio of mapped reads to total clean reads was 96.45%. A total of 108,557,703 SNPs were detected which included 94,382,323 (87%) homozygous and 14,175,380 (13%) heterozygous loci. Transition SNPs were more frequent than transversed SNPs, and the ratio of transition SNPs to transversion SNPs was 1.47. An unrooted neighbor-joining phylogenetic tree based on 359,521 filtered SNPs classified 72 cultivated D. huoshanense samples into two major clusters. According to ADMIXTURE analysis, these samples collection could be divided into two groups, which was in agreement with the NJ tree. According to AMOVA analysis, 96.68% variance was due to variation within populations, and 3.32% among populations, indicating a high gene exchange (or low genetic differentiation) among these populations.These results provided a valuable resource for understanding genetic diversity of cultivated D. huoshanense.