Development of genome-wide microsatellites from Primula denticulata and their utility in different species of the genus

Abstract

The genus Primula (Primulaceae) harbours habitat-sensitive species. It is a valuable tool for monitoring and assessing the overall state of the ecosystem as it can serve as a reliable indicator of ecological health. Primula denticulata Sm. is one of the most prevalent Primrose species found in the Indian Himalayan region with a wide extent of distribution from 1500 m to 3500 m altitude. Considering the ecological importance of Primulas, it is imperative to develop microsatellite markers to study genetic variability which can offer valuable insights into the adaptive strategies of the plants in response to changing environmental conditions. In this study, we sequenced the P. denticulata genome by utilizing Illumina paired-end sequencing technology at ∼15X coverage. 27,196 sequences harbouring 31,584 microsatellite loci were identified. 100 primer pairs were synthesized and tested for amplification. Impressively, 84 of these primers exhibited robust amplification, and 64 of these displayed polymorphism. Primer pairs from trinucleotide motifs were identified as more polymorphic. To assess the broader applicability of these primers, we also tested cross-species transferability on 14 different Primula species representing different sections of the genus that were collected from different parts of Himalaya. Notably, one SSR locus, Next Generation Sequencing Primula_5 (NGSPr_5) was able to produce bands in all the species showing 100 % transferability. Primula atrodentata showed a maximum (88.23 %) while P. glabra exhibited minimum (19.60 %) cross-transferability. The UPGMA dendrogram clustered different sections of sub-genus Aleuritia, and species from subgenera Sphondylia and Auganthus separately into two major groups. The groupings are in accordance with the known relationship between the different species from the genus.