Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing

Abstract

Background: Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos isone of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified. Results: Here, 99 individuals of C. macranthos from north and northeastChina were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gbhigh-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11 C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant “Isolation by Distance” between populations. Conclusions: Our study demonstrates that the present genetic diversity andgenetic structure of C. macranthos populations weremainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.

Effects of human activities on the genetic characteristics of Phaius flavus populations

“…Phaius avus (Pi = 1.439 × 10 − 4 , Ho = 0.788, He = 0.707) from the BM population exhibited a higher level of genetic diversity. This is in contrast to other orchids such as Cypripedium macranthos (Pi = 0.154, Ho = 0.134, He = 0.153) [13], Geodorum eulophioides (Pi = 0.158, Ho = 0.012, He = 0.025) [18], and D. catenatum (Pi = 0.158, Ho = 0.099, He = 0.158) [29]. Similarly, P. avus from the BM population showed signi cant genetic diversity compared to congeneric Phaius such as P. australis and P. bernaysii [20].…”

“…Roads have played a crucial role in human activities throughout the agricultural development and urbanization process, negatively impacting the genetic diversity and differentiation of wild plant populations [9], by reducing plant diversity and limiting certain species [10]. Orchids, one of the most sensitive plants in nature, suffer from habitat fragmentation due to indiscriminate mining and overexploitation [11][12][13], resulting in changes in their genetic structure and reduced genetic diversity. An evaluation of 653 orchid species in China revealed that 65% of these species face challenges related to habitat fragmentation [14].…”