Genome-wide SSR marker discovery and population genetic analysis in Rhododendron campanulatum: a Himalayan tree line species

Key messageGSS is a rapid and cost-effective technique for identifying de novo SSRs in non-model plant species for their genetic analysis.AbstractRhododendron campanulatum is a tree line tree species occurring in the greater Himalayas at an altitude of 3000-3600 m. The present study aims to generate novel genomic simple sequence repeats (SSRs) markers through a genome survey sequencing approach and investigate population-level genetic processes. A total of 91.18 million reads were generated through the Illumina protocol, and high-quality reads were assembled into 257,413 contigs with 39.60% GC content and contig N50 value 3596 bp. After scanning of genomic assembly, a total of 223,850 perfect SSRs, 10,026 cSSRs, 963,958 iSSRs and 67,332 VNTRs were identified. In perfect SSRs, di-nucleotide repeats were most abundant (43.80%), followed by mono-, tri-, tetra-, penta-, and hexa-nucleotide repeats, respectively. Afterwards, 30,715 primer pairs were designed, and a subset of 50 primers was tested for their amplification through polymerase chain reaction. As a result, 35 SSR loci were successfully amplified and 13 showed polymorphism, which were further utilized to characterize the seven natural populations of R. campanulatum of Uttarakhand Himalayas. Under this study, low genetic diversity (expected heterozygosity, He = 0.28; Allelic richness, Ar = 1.91) was recorded in the analysed populations, which primarily dominated by heterozygotic individuals (FIS = -0.268). Further, AMOVA revealed 83% variation within the populations and the remaining 17% between the populations, indicating a great genetic differentiation (FST = 0.173). Due to high genetic divergence, STRUCTURE and cluster analysis revealed two prominent groups. The marker genetic information generated herein is novel and important for understanding the genetic processes and guiding its conservation programme.