Marker discovery for Elaeidobius kamerunicus to study genetic diversity. Marker discovery for oil palm pollinating weevil, Elaeidobius kamerunicus

The native oil palm-pollinating weevil (Elaeidobius kamerunicus Faust) was introduced from Cameroon, West Africa to Malaysia in 1981 and subsequently to other oil palm-growing countries to improve pollination efficiency, thus improving bunch formation and yield. After 40 years of weevil introduction, recent reductions in bunch yield reported in Malaysia caused by poor bunch formation could be associated with a decrease in pollination efficiency due to founder effect. To validate this, several genetic diversity studies of weevil populations based on morphological and mitochondrial markers were carried out. These marker systems, however, do not provide sufficient resolution for explaining the genetic variation, particularly at intra-species level. This study aims to develop a set of robust E. kamerunicus-specific nuclear DNA markers to directly assess the genetic diversity of weevil populations. A total of 19,148 SNP and 223,200 SSR were discovered from 48 weevils representing three origins (Peninsular Malaysia, Sabah and Riau) using RAD tag sequencing method, and subsequent filtering steps further reduced them to 1,000 SNP and 120 SSR. Selected 8 SSR and 220 SNP markers with sufficient polymorphism information (0.2411 ±0.1268 and 0.5103 ±0.1896) were able to assign 180 weevils into three major clusters including Ghana, Cameroon and Southeast Asia (mainly in Malaysia and Indonesia). Also, these DNA markers successfully confirmed the Cameroon origin of the Southeast Asian cluster. However, presence of null alleles in SSR markers due to limited flexibility of probe design on short RAD tags have led to an underestimation of heterozygosity within populations. Hence, the developed SNP markers turned out to be superior in genetic diversity assessment of E. kamerunicus populations to provide a useful guideline for monitoring and conservation purposes in non- and native oil palm-growing countries. In general, RAD tag sequencing method is a robust and cost effective solution for DNA marker development, especially for non-model species.