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

Chee-Keng Teh,Sukganah Apparow,David Appleton,Ai-Ling Ong,Mohaimi Mohamed,Harikrishna Kulaveerasingam,Sean Mayes,Qi-Bin Kwong,Fook-Tim Chew

doi:10.1038/srep19075

Abstract

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.

Highlights

Genome-wide association study (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
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]
The publication of the oil palm genome consisting of 1.535 gigabase (Gb) of assembled sequence[10], the independent assembly of Sime Darby’s oil palm genome and development of high throughput single nucleotide polymorphisms (SNPs) genotyping technologies has enabled us to produce a pipeline for marker-assisted breeding in oil palm, from discovery to the planting of marker-selected breeding materials in the field

Summary

Result and Discussion

The Deli dura palms are a breeding population of restricted origin (BPRO) derived from the four original palms planted at Bogor Botanical Garden in 184818. We adopted a compressed mixed linear model (MLM) with population parameters previously determined (P3D) to address the problem of genomic inflation that was based on a principle component analysis and a group kinship matrix[29] This method greatly reduced false positives in Deli x AVROS (GIF = 1.1) and Nigerian x AVROS (GIF = 1.9) as illustrated in Quantile-Quantile plots (Fig. 2a,b). We report the most comprehensive use of high density SNP genotyping in oil palm to date, the use of a GWAS approach to identify SNP variants associated with differences in the key oil-to-dry mesocarp yield trait, and confirmation of their action in an independent cross Based on these results, we have implemented a MAS programme to breed new parental lines for commercial oil palm hybrid production. The reported study lays the foundations for a genomic selection model for oil palm and will act as a model for other perennial tree crops

Methods

Author Contributions

Findings

Additional Information