Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm.
High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineensis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of >3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r(2) = 0.43 to 146 kb at r(2) = 0.50) when compared with the semi-wild populations (19.5 kb at r(2) = 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thickness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r = 0.65) with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia. Electronic address: kwong.qi.bin@simedarby.com.
Qi Bin
QB
Kwong
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
Chee Keng
CK
Teh
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
Ai Ling
AL
Ong
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
Huey Ying
HY
Heng
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
Heng Leng
HL
Lee
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
Mohaimi
M
Mohamed
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
Joel Zi-Bin
JZ
Low
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
Sukganah
S
Apparow
Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
Fook Tim
FT
Chew
School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough LE12 5RD, UK.
Sean
S
Mayes
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
Harikrishna
H
Kulaveerasingam
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
Martti
M
Tammi
Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
David Ross
DR
Appleton
D028023:Arecaceae / Q000235:genetics*; D002874:Chromosome Mapping; D018745:Genome, Plant / Q000235:genetics; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*
genetic fixation; genome-wide association study; genome-wide linkage disequilibrium; genomic selection; oil palm; whole-genome SNP array