Genetic Diversity and Phylogeography of cultivated and wild Ophipogon japonicus based on chloroplast DNA exploration for origin and sustainable cultivation

Abstract Background Ophipogon japonicus , planted in Sichuan (CMD) and Zhejiang (ZMD) Province in China, has a long cultivation history that can trace back to Ming dynasty (500 years ago) and Song dynasty (600 years ago) respectively. During the long period of domestication, the genetic diversity of cultivated O. japonicus has decreased a lot so that this species is facing with plant degradation. Therefore, it is urgent to clarify the genetic diversity and origin of cultivated O. japonicus to establish a theoretical basis for the utilization and conservation of the genetic resources of O. japonicus . Result We analyzed the genetic diversity and population structure of 266 O. japonicus individuals from 23 sampling sites based on 4 chloroplast DNA sequences ( atpB-rbcL 、 rpl16 、 psbA-trnH and rpl20-5’rps12 ), identified the effects of domestication on genetic diversity of cultivars and determined the geographic origins of cultivars. The results showed that cultivated O. japonicus and wild O. japonicus had 4 haplotypes and 15 haplotypes respectively. The genetic diversity of two cultivars ( H d = 0.35700, π = 0.06667) was much lower than the wild populations ( H d = 0.76200, π = 0.20378), and the level of genetic diversity in CMD ( H d = 0.01900, π = 0.00125) was lower than that in ZMD ( H d = 0.06900, π = 0.01096). Genetic differentiation between the cultivated and the wild ( F ST = 0.82044) was significant, especially between the two cultivars ( F ST = 0.98254). This species showed a more pronounced phylogeographical structure ( N ST > G ST , P < 0.05). The result of phylogenetic tree showed that demonstrated with the outgroup O. amblyphyllus Wang et Dai, the genetic difference between CMD and ZMD is not enough to distinguish the cultivars from two producing area. Besides, both CMD and ZMD have a closer relationship with wild populations in Sichuan than that in Zhejiang. In addition, according to the TCS network and MaxEnt suggested that the wild population TQ located in Sichuan Province should be served as the ancestor of cultivated O. japonicus , which is supported by RASP analysis. Conclusion These results suggest that cultivated O. japonicus has experienced dramatic loss of genetic diversity under anthropogenic influence. The genetic differentiation between CMD and ZMD was likely to be influenced by founder effect and strong artificial selection for plant traits. It appears that wild populations in Sichuan area were involved in the origin of not only CMD but also ZMD. Furthermore, some scientific strategies are suggested for resource conservation of O. japonicus based on its genetic diversity and population structure in this study.