Development of novel microsatellite markers using RAD sequencing technology for diversity assessment of rambutan (Nephelium lappaceum L.) germplasm

Abstract

The trend of microsatellite marker discovery and development revolved as a result of the advancement of next generation sequencing (NGS) technology as it has developed numerous microsatellites within a short period of time at a low cost. This study generated microsatellite markers using RAD sequencing technologies for the understudied Nephelium lappaceum . A total of 1403 microsatellite markers were successfully designed, which consisted of 853 di-, 525 tri-, 17 tetra-, 5 penta-, and 3 hexanucleotide microsatellite markers. Subsequently, selection of 39 microsatellites was made for the evaluation of genetic diversity of the selected 22 rambutan varieties. Twelve microsatellites, which exhibited high call rates across the samples, were used to assess the diversity of the aforementioned rambutan varieties. The analysis of 12 microsatellites revealed the presence of 72 alleles and six alleles per locus in average. Furthermore, the polymorphic information content (PIC) value ranged from 0.326 (NlaSSR20) to 0.832 (NlaSSR32), which included an average of 0.629 per locus, while the generated Neighbour Joining dendrogram showed two major clusters. The pairwise genetic distance of shared alleles exhibited a range of values from 0.046 (R134↔R170) to 0.818 (R5↔R170), which suggested highest dissimilarity detected between R5 and R170. Notably, these research findings would useful for varietal identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.

RAD sequencing for the development of microsatellite markers for identification of Malaysian taro cultivars

“…Furthermore, despite the expanding ubiquity of various SNP genetic studies, microsatellites remain one of the most informative and flexible markers accessible to various genetic domains. High throughput microsatellite markers are extensively used in plant genomic research given their exceptionally polymorphic, multi-allelic nature, simple logical system and transferability over genotypes [7,28]. As a result, microsatellite markers are seen as a valued tool for the identification of taro cultivars, providing crucial, if not essential data for sustaining future biodiversit y preser vation and gene bank management.…”

“…Despite the more recent and remarkable marker system, namely single nucleotide polymorphism (SNP), microsatellites are still preferred in conducting various research including cultivar identification and authentication, population structure analyses, genetic drift and gene flow and pedigree or breeding estimation [6]. Likewise, the advancement in next-generation sequencing (NGS) has evolved into a mainstream approach in dealing with high-throughput in identifying and discovering a thousand microsatellites at reduced costs, even in non-model species [7,8].…”