title: Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm.
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.
authors.affiliation: Biotechnology &Breeding Department, Sime Darby Plantation R&D Centre, Malaysia.
authors.forename: Chee-Keng
authors.initials: CK
authors.lastname: Teh
authors.affiliation: Biotechnology &Breeding Department, Sime Darby Plantation R&D Centre, Malaysia.
authors.forename: Ai-Ling
authors.initials: AL
authors.lastname: Ong
authors.affiliation: Biotechnology &Breeding Department, Sime Darby Plantation R&D Centre, Malaysia.
authors.forename: Qi-Bin
authors.initials: QB
authors.lastname: Kwong
authors.affiliation: Biotechnology &Breeding Department, Sime Darby Plantation R&D Centre, Malaysia.
authors.forename: Sukganah
authors.initials: S
authors.lastname: Apparow
authors.affiliation: Department of Biological Sciences, National University of Singapore, Singapore.
authors.forename: Fook-Tim
authors.initials: FT
authors.lastname: Chew
authors.affiliation: School of Biosciences, University of Nottingham, UK.
authors.forename: Sean
authors.initials: S
authors.lastname: Mayes
authors.affiliation: Biotechnology &Breeding Department, Sime Darby Plantation R&D Centre, Malaysia.
authors.forename: Mohaimi
authors.initials: M
authors.lastname: Mohamed
authors.affiliation: Biotechnology &Breeding Department, Sime Darby Plantation R&D Centre, Malaysia.
authors.forename: David
authors.initials: D
authors.lastname: Appleton
authors.affiliation: Biotechnology &Breeding Department, Sime Darby Plantation R&D Centre, Malaysia.
authors.forename: Harikrishna
authors.initials: H
authors.lastname: Kulaveerasingam
mesh_terms: D028023:Arecaceae / Q000235:genetics* / Q000378:metabolism; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D056426:Genetic Loci; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D000073878:Palm Oil; D000069600:Plant Breeding; D010938:Plant Oils / Q000302:isolation & purification / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable
chemical_list: D010938:Plant Oils; D000073878:Palm Oil