Genetic Diversity of Eurycoma longifolia Inferred from Single Nucleotide Polymorphisms,

Abstract

Eurycoma longifolia Jack. is a treelet that grows in the forests of Southeast Asia and is widely used throughout the region because of its reported medicinal properties. Widespread harvesting of wild-grown trees has led to rapid thinning of natural populations, causing a potential decrease in genetic diversity amongE. longifolia. Suitable genetic markers would be very useful for propagation and breeding programs to support conservation of this species, although no such markers currently exist. To meet this need, we have applied a genome complexity reduction strategy to identify a series of single nucleotide polymorphisms (SNPs) within the genomes of several E.longifolia accessions. We have found that the occurrence of these SNPs reflects the geographic origins of individual plants and can distinguish different natural populations. This work demonstrates the rapid development of molecular genetic markers in species for which little or no genomic sequence information is available. The SNP markers that we have developed in this study will also be useful for identifying genetic fingerprints that correlate with other properties of E. longifolia, such as high regenerability or the appearance of bioactive metabolites.

Developing SNP markers and DNA typing using multiplexed single nucleotide primer extension (SNuPE) in Paraserianthes falcataria

“…SNPs provided convictive evidence for human forensic analysis (Brandstatter et al 2003, Vallone et al 2004, for identification and paternity analysis in animals (Heaton et al 2002, Werner et al 2004, Rohrer et al 2007, and for various applications in plants (Jin et al 2003, Batley et al 2003, Jones et al 2007, Osman et al 2003, Varshney et al 2007, Germano and Klein, 1999, Gros-Louis et al 2005. Because of its low information content, however, approximately three times as many SNPs are needed than SSRs for linkage studies, parentage testing and individual identification (Aitken et al 2004, Brumfield et al 2003.…”

Single nucleotide polymorphisms of Gcyc1 (Cycloidea) in Conandron ramondioides (Gesneriaceae) from Southeast China

“…Most recently, SNPs, as the third generation of molecular markers following RFLP and SSR, have gradually become a welcome tool for studying linkage disequilibrium (LD), integrating genetic map and physical maps and elucidating the evolutionary history of populations for model organisms (Brumfield et al 2003, Han and Xue 2003, Rafalski 2002, Tenaillon et al 2001, Zhu et al 2003. Compared with other genetic markers, SNPs are more abundant in the genome and much more stably inherited (Osman et al 2003, Marshall 1997, Weber and Wong 1993. Furthermore, SNPs can be used for association studies because they have a low mutation rate and are amenable to automation (Halushka et al 1999).…”

Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis)

“…The average H E recorded in this analysis was greater than the mean value reported for tongkatali (Eurycoma longifolia, 0.216;Osman et al, 2003), castor bean (Ricinus communis, 0.220; Foster et al, 2010) and maize (Zea mays, 0.319; Hamblin et al, 2007), as revealed by SNP markers. However, the heterozygosity value of selected Angola populations attained from the present work was lower than that reported based on simple sequence repeat (SSR)…”