ISOLATION AND CHARACTERISATION OF SSR MARKERS IN TONGKAT ALI (<em>EURYCOMA</em> <em>LONGIFOLIA</em>) USING NEXT-GENERATION SEQUENCING APPROACH

Abstract

Eurycoma longifolia is an important medicinal plant in Malaysia. Due to the high demand for E. longifolia roots, the natural populations are under tremendous harvesting pressure. Hence, attention should be given to conserve the genetic resources as well as to produce elite planting materials for cultivation. As simple sequence repeats (SSRs) are the most versatile markers to be used in genetic diversity assessment and molecular breeding, the study was aimed to develop SSR markers based on transcriptome sequences of E. longifolia root. Root transcriptome of a 10-year-old E. longifolia was sequenced via Illumina paired-end sequencing. From the 39,100,208 trimmed sequencing reads, a total of 51,551 contigs were generated with an average length of 672 bp. The assembled contigs were annotated and functionally classified. Based on these transcriptome sequences, we have successfully developed and validated 46 polymorphic SSR markers applicable across 102 E. longifolia samples from five natural forest reserves in Peninsular Malaysia. A total of 232 alleles were observed among the five populations, with an average of 5.0 alelles per locus. The SSR markers developed are valuable genetic tools for a wide spectrum of genetic analyses for E. longifolia, be it for conservation or breeding-related applications.