Development of Nuclear DNA Markers for Applications in Genetic Diversity Study of Oil Palm-Pollinating Weevil Populations

Simple Summary The main pollinator for the African oil palm, Elaeis guineensis, in Malaysia and Indonesia is Elaeidobius kamerunicus. The weevil species is not native to these countries, but it was introduced from Cameroon, West Africa, in 1981 to improve pollination efficiency, thus improving bunch formation and yield. Forty years after the 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 the founder effect. Several genetic diversity studies of weevil populations based on morphological and mitochondrial markers have been carried out; however, the studies did not provide sufficient evidence for explaining the genetic variation, particularly at the 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. The marker development lays the foundation for future applications by extending the survey into larger areas where the oil palm is cultivated to obtain a more comprehensive understanding of the genetic diversity and inbreeding occurrence status of E. kamerunicus in these introduced regions. This could facilitate sustainable genetic monitoring and conservation planning of E. kamerunicus, especially in non-native oil palm-growing countries. The 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 as well. This study aims to develop a set of robust E. kamerunicus-specific nuclear DNA markers to directly assess the genetic diversity of the 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. Subsequent filtering steps further reduced these to 1000 SNP and 120 SSR. The selected 220 SNP exhibited a polymorphism information content (PIC) of 0.2387 (+/- 0.1280), and 8 SSR had the PIC of 0.5084 (+/- 0.1928). These markers were found to show sufficient polymorphism, making it possible to assign 180 weevils into three major clusters from Ghana, Cameroon, and Southeast Asia (mainly in Malaysia and Indonesia). These DNA markers successfully confirmed the Cameroon origin of the Southeast Asian cluster. However, the presence of null alleles in the SSR markers, due to limited flexibility of the probe design on the short RAD tags, led to an underestimation of heterozygosity within the populations. Hence, the developed SNP markers turned out to be more efficient than the SSR markers in the genetic diversity assessment of the E. kamerunicus populations. The genetic information provides useful insight into developing guidelines for the genetic monitoring and conservation planning of E. kamerunicus.