Utility of single nucleotide polymorphism markers in clonal profiling of Hevea brasiliensis

The Para rubber tree, Hevea brasiliensis, is the main source of commercially cultivated natural rubber. It is estimated that by 2024, 4.3-8.5 million ha of land will be required for new rubber plantations to meet the projected growth in demand. This poses a threat of deforestation to protected biodiversity conservation areas and calls for improvement of planting materials and crop management. Misidentification of clones, or cultivars, is an issue for many tree crops and rubber is no exception. Without proper classification, plantations cannot reach optimal efficiency and plantation owners may inadvertently continue to misuse their time, land and resources on low yielding crops. To demonstrate their usefulness as an effective system for clonal verification, SNP markers were used for profiling of rubber genotypes. High-throughput fingerprinting was performed on 900 trees spanning over 300 clones from the germplasm collection of the Rubber Research Institute of Malaysia. In the absence of established clonal references, SNP profiles were compared with other samples within a supposed clonal line; these comparisons unambiguously identified a number of outliers. For materials without clonal replicates, parentage analysis was applied. This study concludes that a small set of SNP markers can be used as a robust and accurate rubber clone identification tool.