Genetic diversity analysis of Rhododendron arboreum in western Himalaya indicates altitudinal population differentiation and mid-elevation enrichment of heterozygotes

Abstract

Genetic diversity of Rhododendron arboreum, a keystone tree species in the Himalaya facing threats from habitat-loss, limited regeneration, overexploitation, and climate-change, was assessed. We sampled trees of the species across nine populations occupying different altitudes in Uttarakhand's Garhwal region. The species' genome was sequenced by using next-generation sequencing to identify SSR markers. The genomic data produced ~ 72 million reads, leading to the assembly of 265,673 scaffolds, with 66,742 unique microsatellite loci identified. Out of 140 SSR primer pairs designed, 102 were successfully amplified, with 55 being polymorphic. Genetic diversity metrics, population structure, and genetic variation were evaluated using GenAlEx, STRUCTURE, PCoA, NJ tree, and AMOVA. The diversity indices revealed that genetic diversity was low in populations at the higher and lower elevations, whilst those located at the mid-elevations were more diverse. Observed heterozygosity was higher than expected for all the populations considered. Population genetic structure analysis identified four genetic clusters that aligned with geographical proximity and altitudes. Pairwise FST values indicated a significant genetic differentiation among the populations. AMOVA revealed that genetic variation was largely attributed to heterozygosity within the trees. These results highlight the substantial genetic diversity and differentiation in R. arboreum populations, influenced by geographic and elevational factors. These findings emphasize the need to preserve their germplasm. Importantly, this diversity is also essential for tree breeding programs, conservation efforts, and gaining insights into the species' evolutionary dynamics. With the availability of new and reliable markers, their applicability may also be tested in related species.