Unlimited molecular marker resource to breed for value-added coconut varieties: the application of whole genome sequencing

Coconut is a major agricultural crop and export product in the Philippines. Being the second top producer next to Indonesia, the country has a total production of 14.7 million metric contributing to 24% of the world's production. Here, the author present the whole genome sequencing (WGS) of CATD coconut variety, chosen for its genome simplicity and low heterozygosity. PacBio SMRT sequencing was generated at 11x coverage and corrected with assembled 40x Illumina pair-end MiSeq reads. Through a hybrid assembly approach, the improved draft assembly of coconut genome sequence has now a 25-fold increase in N50 (120 kb) and genome coverage of 73%. BUSCO identified the completeness of 88.2% based on 1440 genes in the plant-specific gene database. A total of approximately 1.4 gB was identified as interspersed repeat sequences which represent to about 78% of the total assembled genome. As expected, retro elements were the most common mobile elements found in the coconut genome and highly represented by LTR elements (60%). SSRs constitute 0.79% of the assembly which is higher to what is observed in Medicago truncatula (0.203%), Glycine max (0.328%) and Cicer arietinum (0.329%). Gene models were identified using the MAKER annotation pipeline. Through global sequence-homology search by BLAST, gene models for economically important traits were characterized. Markers targeting these traits were developed using Primer 3 and validated by in silico PCR. Neutral markers (i.e SSR) for population genetics studies were also designed using the GMATA toolkit. As the genome sequence assembly and gene/trait annotation is advanced towards completeness into organized chromosomal elements, the power to mine and design marker-tags would be unlimited, and to any target gene network. The gene-maker resource that will be established through this advancement in genomics should facilitate the development of climate change-resilient and pest/disease resistant coconut varieties with high copra yield and quality.