Differentially expressed genes associated with resistance to red palm weevil (Rhynchophorus ferrugineus) infestation in coconut (Cocos nucifera L.) and identification of rSNP markers in disease resistance genes

BACKGROUND Red palm weevil ( Rhynchophorus ferrugineus ) is a major pest threatening coconut ( Cocos nucifera ) production worldwide. The hidden nature of larval feeding in the tree trunk hinders early detection. When visible symptoms appear, often it is already too late to save infested trees. Despite its economic importance, the molecular basis of host resistance to this invasive pest remains unclear. This study aimed to identify differentially expressed genes (DEGs) associated with resistance to red palm weevil (RPW) and develop gene-based single nucleotide polymorphic markers for coconut improvement. RESULTS Comprehensive assessment of internal and external damages of coconut trees in a heavily infested field identified Malayan Yellow Dwarf (MYD) as a resistant while Pandan and Malayan Tall (MT) as the susceptible coconut varieties. Illumina NovaSeq platform generated 150 bp paired ends reads from 18 cDNA libraries constructed using RNA from the leaves of these three coconut varieties from infested fields and non-infested fields (control). Differential expressed genes analysis by DESeq2 showed MYD had the greatest number of DEGs (4,314 upregulated and 4,469 downregulated), while Pandan had 1,999 upregulated and 1,660 downregulated and MT had 1,988 upregulated and 2,185 downregulated DEGs. Disease-resistance genes, including the RGA1 , RGA3 and RPS2 were significantly upregulated in MYD. Genes encoding transcription factors (NAC, WRKY, MYB, ERF and CAMTA) as well as phytohormone signalling (jasmonic acid, salicylic acid and ethylene) and stress responsive (heat shock protein and hypersensitive response) genes exhibited highest expression levels in MYD and lower or undetectable in the Pandan and MT. Alignment of 3.0 kb of sequences upstream of the transcriptional start site in the DEGs encoding disease resistance genes from the different varieties identified SNP variants associated with differential response to RPW. Three significant SNP variants were identified in RGA3 promoter region of the Pandan variety. These variants were found in the MYB-binding motif, TATA-box and CAAT-box. COCLUSION Collectively, our findings provide an integrated view of transcriptional and genetic variations linked to coconut resistance against RPW. The identified DEGs and variants within the RGA3 promoter represent valuable markers to be used in marker assisted selection in breeding programs for developing RPW-resistant coconut varieties.