Genetic erosion and population decline in four threatened rattan species of India: insights from genome-wide microsatellite analysis

Rattans are climbing palms, known for their strong flexible canes and are important Non-Timber Forest Products (NTFPs) in south and southeast Asian countries. Of the five palm genera known as rattans, Calamus holds a pivotal position owing to huge local and global market demand. A substantial part of the NTFPs is harvested from the natural populations, thus many of the economically exploited rattan species are on the verge of extinction. The present work intended to study the consequences of population decline on the genetic structure and diversity parameters of four economically exploited threatened Calamus species ( C. brandisii, C. acanthospathus, C. nambariensis and C. andamanicus ) distributed in the three geographical zones of India ( viz . Western Ghats, northeast and Andaman-Nicobar Islands). The study generated a 848.89 Mb length draft assembly of C. brandisii genome and genome-wide microsatellite (SSR) markers were mined out. The microsatellite markers standardized in C. brandisii were cross-amplified in other Calamus species used in the study. Population genetic analysis revealed deviations from the Hardy-Weinberg equilibrium, heterozygosity excess in the populations, unique/private alleles, and genetic distinctiveness of populations in the species’. This has been inferred as the result of small reproductive population size and obligatory outcrossing in the species. Genetic structure analysis revealed high genetic divergence and evidence for genetic bottleneck events which can severely impact their long-term evolution and survival. Conservation and management actions should focus on the augmentation of population size, improving genetic connectivity and assisted migration with unique alleles to enhance the adaptive potential and survival of these threatened rattan resources.