Development of nuclear DNA markers for genetic diversity study of oil palm pollinating weevil, Elaeidobius kamerunicus faust (Coleoptera: Curculionidae)

Abstract

Elaeidobius kamerunicus Faust, a native oil palm pollinating weevil species of West and Central Africa, was introduced to Southeast Asia in the 1980s, enhancing oil palm pollination rates in commercial estates. Concerns have emerged regarding potential genetic heterozygosity loss due to suspected inbreeding over the past four decades, attributed to inconsistent pollination efficiency and susceptibility to nematode parasitism. However, the absence of species-specific genetic markers hindered in-depth investigations of the weevil genetic diversity. To address this gap, this study aimed (i) to identify specific Single Nucleotide Polymorphisms (SNP) and Simple Sequence Repeats (SSR) markers for E. kamerunicus, (ii) to validate polymorphisms of putative SNP and SSR markers, and (iii) to evaluate the application of SNP and SSR markers for genetic diversity analysis and population clustering of E. kamerunicus in introduced and native populations. GBS-RAD sequencing was performed in 48 individual weevils from Peninsular Malaysia (n=40), Sabah (n=5), and Riau (n=3), resulted to identification of 19 148 SNP and 223 200 SSR. The markers were filtered to 1000 SNP and 120 SSR. Validation by genotyping experiments in 180 individual samples has confirmed that 220 SNP and eight SSR are with sufficient polymorphism information content (PIC) of 0.2411 (±0.1268) for SNP and 0.5103 (±0.1896) for SSR. These marker sets clustered 180 weevil individuals into one major Southeast Asian cluster (Malaysia and Indonesia) and two lineages (Cameroon and Ghana). SSR markers developed in this study exhibited null alleles. This study evaluated that the developed SNP markers able to provide estimation of genetic diversity. It is suggested to improve on the SSR marker set to include highly polymorphic markers without the presence of null alleles before proceeding to the genetic diversity analysis and inbreeding index assessment using SSR. The inbreeding coefficients calculated using SNP-based data showed negative values, indicating that inbreeding is not currently observed in the introduced E. kamerunicus populations. Future studies should consider expanding the survey to larger population sets to gain additional insights into the genetic diversity status of E. kamerunicus. This information will be useful in conservation planning and sustainability monitoring of this oil palm pollinating weevil species from the estate up to the national level.