Identification and Development of New Polymorphic Microsatellite Markers for Main Causal Agent of Oil Palm Basal Stem Rot Disease using Ganoderma boninense Genome Assembly

Ganoderma boninense is a telluric lignicolous basidiomycete and the main causal agent of the basal stem rot (BSR), one of the most devastating diseases of oil palm (Elaeis guinensis). While the fight against G. boninense should be a priority in South-East Asia, only scarce information is available about the diversity level of this fungus, and almost nothing is known about its genetic structure and history. In this context, the development of an informative molecular marker set to characterize G. boninense diversity is the key step to understand the biology of this pathogen. A G. boninense draft genome sequence assembly of 61.5 Mb combining 454 and Illumina sequencing technologies has been used to identify and develop a set of microsatellite markers (Simple Sequence Repeat). A total of 2487 SSR were identified, for which 145 SSR primer pairs were developed. These SSR are characterized by di- to hexa motifs with 5 to 34 repetitions. Subsequently, a total of 97 SSR were successfully amplified on a first small set of G .boninense isolates from Indonesia. Then a population of 107 isolates from several locations in South-East Asia was screened to characterize each locus for allele number, heterozygosity and the absence of null allele. These results allow us to propose an efficient set of 17 SSR to study G boninensediversity.

Keywords: Ganoderma boninense, oil palm, basal stem rot, microsatellite, genome sequence