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.

Genomic Selection in Commercial Perennial Crops: Applicability and Improvement in Oil Palm (Elaeis guineensis Jacq.)

“…For each of the traits, a genome-wide association study (GWAS), using the same method as described in our previous publication 38 , was carried out independently for each iteration during the cross validation step. Markers were ranked according to the association score.…”

Oil Palm Crop Improvement: Role of Biotechnology in the Present Scenario

“…But in oil palm association mapping may offer a valuable technology to identify the genetic loci of important traits. The CK et al [2] performed GWAS for oil-to-dry-mesocarp content on 2045 genotyped tenera palms using 200K SNPs and found that 80 loci were significantly associated with oil-to-dry mesocarp yield (P ≤ 10-4), and three key signals were found. In oil palm, vegetative propagation is made possible only via tissue culture.…”

Review: Omics and Strategic Yield Improvement in Oil Crops

“…GWAS, QTL and association mapping studies have been increasingly reported for oil palm breeding, particularly for oil content [115][116][117][118][119][120]. Bai et al [116] showed that by combining QTLs with beneficial genotypes, the resulting average oil content in fruit bunches was higher.…”

“…Kwong et al [117] developed a SNP array for oil palm using various origins. This platform was particularly useful for developing early trait prediction methods to shorten the oil palm breeding cycle and was used to identify QTL loci for important oil content traits [115]. Informative QTLs linked to oil yield component traits were also mapped in a high-yield population [118].…”

“…Genomic selection, or genome-wide selection, is a markerassisted selection method that uses genome-wide markers to predict the breeding values of selected candidates for improving desired quantitative traits. This same method has been used in oil palm to identify key loci for high mesocarp oil content [115].…”