Development of high-density DNA marker and physical map for coconut

For crop species with long generative cycles such as coconut and oil palm, linkage mapping and molecular markers will allow early selection tests in breeding materials. Thus, the time required for bringing new improved varieties to the market can be greatly reduced. Moreover, these technologies will play crucial roles in the identification and isolation of any gene of interest in the future. Although exclusive to coconut and oil palm, the project results can later be extended/applied to other economically important palm species. To build a genome map on coconut, Rodriguez et al (PCA Albay) conducted the research to construct a high-density DNA marker and physical map on coconut. This was implemented from August 2001 to December 2004. Ten international research institutions participated in the project with the Max Planck Institute of Germany as the overall coordinator. Quantitative loci (QTL) and physical mapping were done to identify the most important traits in crop improvement programs. Comparative genome and QTL analysis were performed to share scientific advances between these two crops as well as with other palm species of economic importance. Optional sets of DNA markers (with good genome coverage) were selected for future marker-assisted breeding programs. The consortium generated six individual coconut linkage maps of the Pacific and Indo-Atlantic origin. These were aligned to produce a high-density DNA marker and physical map with 2000 amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers distributed on 16 linkage groups representing the 16 chromosomes of the haploid coconut genome. PCA-ARC made a significant contribution by generating a total of 817 DNA markers. The map has a total genome length of 2,800 cm with 132 markers per linkage group. This represented one of the maps with the highest marker densities in the woody species. QTL locations had been determined for important characters for breeding and has been compared across genotypes. A total of 324 DNA markers was associated with sequenced COS clones. Also, some candidate genes (homeotic gene families, putative resistance genes, and genes for fatty acid biosynthesis) had been mapped and linked to important traits in coconut breeding programs. Out of the various primers used in constructing the high-density map, a subset of primer combinations with good genome coverage was selected for linkage mapping. This was for future applications to other coconut progenies/mapping populations in search for other markers relevant to a particular breeding and selection program. A smaller subset of primers representing the 16 chromosomes was likewise chosen for a comprehensive genetic diversity assessment and characterization of coconut germplasm. The development stage of the molecular marker and genome mapping technologies on coconut, which was labor- and cost-intensive had been done. However, there is still a need to optimize these technologies in terms of saturating further the genetic map, specifically with markers that will provide technological solutions to problems incurred in local breeding programs. This will no longer entail much labor and cost, however, appropriate funding is needed to sustain other applications of the project results such as the development of user-friendly kits for marker-assisted selection (MAS), the identification and isolation of genes of interest, and a comprehensive assessment of genetic variability and characterization of coconut germplasm.