Screening of polymorphic microsatellite markers from the whole-genome sequences of nipa (Nypa fruticans Wurmb.)

Abstract

Nipa (Nypa fruticans Wurmb.), aside from being part of the mangrove forest ecosystem that has been under assault at an alarming rate, lacks information on its genetic variation at the population level for conservation planning purposes. Microsatellites, or simple sequence repeats (SSRs), are molecular markers employed to detect genetic variations in population studies. Here, the primers for this palm were identified through whole-genome sequencing using the Illumina® Sequencing Technology platform. Over half (52.4%) of SSRs consisted of mononucleotide repeats, whereas the remainder mostly consisted of dinucleotide (22.7%) and trinucleotide (22.4%) repeats. The frequencies of longer repeats (tetranucleotides, pentanucleotides and hexanucleotides) were exceptionally rare (2.5%). At least 18 out of 75 genomic loci were polymorphic, based on 37 randomly selected samples assayed for screening. Polymorphic loci (P) reached a mean of 72% across the Indo-West Pacific region. Estimates of genetic diversity showed a lower mean observed heterozygosity (Ho) (0.195) than expected (He) (0.316), suggesting evolutionary forces were acting across nipa populations. The fixation (F) index (0.388) supported this result, which indicates considerable genetic differentiation among populations in the region. An average of 2.111 alleles (Na) was obtained. In conclusion, these microsatellite markers are promising tools for genetic evaluation of nipa populations to facilitate characterization of this species in its distribution range.