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Thursday, 6 October 2016

Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm

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Scientific Reports 6, Article number: 19075 (2016)
  • doi:10.1038/srep19075



    GWAS in out-crossing perennial crops is typically limited by insufficient marker density to account for population diversity and effects of population structure resulting in high false positive rates. The perennial crop oil palm is the most productive oil crop. We performed GWAS for oil-to-dry-mesocarp content (O/DM) on 2,045 genotyped tenera palms using 200K SNPs that were selected based on the short-range linkage disequilibrium distance, which is inherent with long breeding cycles and heterogeneous breeding populations. Eighty loci were significantly associated with O/DM (p ≤ 10−4) and three key signals were found. We then evaluated the progeny of a Deli x AVROS breeding trial and a 4% higher O/DM was observed amongst those having the beneficial genotypes at two of the three key loci (p < 0.05). We have initiated MAS and large-scale planting of elite dura and pisifera parents to generate the new commercial tenera palms with higher O/DM potential.


    Genome-wide association study (GWAS) has emerged as a powerful method and commonly adopted, particularly in human populations to identify a broad range of complex diseases1. The method was then wide implemented in annual plants, including rice2,3,4, foxtail millet5, maize6 and Arabidopsis7 when their reference genomes were successfully sequenced. As for perennial crops, GWAS progress is often hindered due to insufficient marker density and population structure effects8,9. We carried out GWAS on oil palms (Elaeis guineensis Jacq.) as a model to address these limiting factors and to illustrate the potential of marker-assisted selection (MAS) in out-crossing breeding programmes. The oil palm with the highest yield per hectare of all oil crops, it accounts for a quarter of vegetable oil traded worldwide annually, despite occupying only 5% of the global oil planting acreage10. Only five to six generations of selection and breeding have been completed since plantations were established in the 1920s and 1930s11, primarily due to long phenotyping cycles (typically twelve years per cycle).
    In recent decades, molecular markers have been employed to identify quantitative trait loci (QTL) for traits of importance in oil palm. By determining the allelic variation present, palms that possess particular combinations of desired QTL can be selected at the nursery stage. Markers could significantly reduce the conventional phenotyping cycles and also enrich the best combinations of alleles in palms planted from each cross. Most marker discovery programmes in oil palm are still mainly based on controlled cross-based linkages using various marker systems with modest density, including restriction fragment length polymorphisms (RFLPs)12,13, amplified fragment length polymorphisms (AFLPs)14 and simple sequence repeats (SSRs)15. To further increase marker density, single nucleotide polymorphisms (SNPs) that distribute abundantly throughout a genome, were developed for oil palm16. Nevertheless, the application of SNPs was still mainly deployed for linkage map construction16 and followed by localisation of fruit form trait with Mendelian inheritance10 and stem height trait17. While the family-based mapping approach and high-density markers are reasonably powerful for detecting the major QTLs, the mapping resolution, particularly for complex traits, like oil yield is always constrained by small population size. Typically, seed numbers from a single breeding cross exceeds 1,000, but currently only 16–96 palms are randomly selected for assessment.

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