Genomics approach to mine genes and search for genetic material towards insect resistance breeding in coconut

The coconut (Cocos nucifera) is an important economic crop largely grown for its 'Tree of Life' industrial uses. In the Philippines, 26% of total agricultural land is devoted to coconut farming. However, due to outbreak infestation of coconut scale insect (CSI), millions of palms were devastated posing a serious threat to the coconut industry. As among the R and D approaches towards insect resistance breeding, the Institute of Plant Breeding, UPLB and the Philippine Coconut Authority (PCA) jointly implements a genomics pre-breeding program in coconut. A draft genome assembly of Catigan Green Dwarf coconut was generated using combined platforms of 50X Illumina Miseg and 15X SMRT-PacBio sequencing. The genome assembly and gene models generated from preliminary annotation are currently deposited in an in-house genome database prototype with pre-installed bioinformatics tools i.e. BLAST, in silico PCR and JBrowse genome browser. The genome database is now utilized to mine and develop DNA markers that target putative genes for CSI resistance such as genes encoding proteins and metabolites in coconut glandular trichome. Trichome characters associated to insect resistance are also investigated in coconut such as leaf density, ultra-structural imaging through scanning electron microscopy, and their genetic and biochemical variability among different coconut genotypes. To associate trichome traits to CSI-resistance, controlled and natural host-plant resistance (HPR) screening as well as open-field natural infestation are being conducted on different coconut varieties obtained from the PCA germplasm collection. To identify a potential CSI-resistant genotypes, the coconut varieties/accessions will also be mined for the desired gene-variant that putative confers HPR. Ultimate outcome from this genomics research is to uncover the mechanism of coconut HPR against CSI, identify resistant coconut variety/ies for recommendation in CSI affected areas, develop markers for routine marker-assisted breeding, and construct a database repository of genomic and phenotypic information for coconut breeders and scientist.