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

• Published in: Scientific reports Vol. 7; no. 1; pp. 2872 - 9
• Main Authors: Kwong, Qi Bin, Ong, Ai Ling, Teh, Chee Keng, Chew, Fook Tim, Tammi, Martti, Mayes, Sean, Kulaveerasingam, Harikrishna, Yeoh, Suat Hui, Harikrishna, Jennifer Ann, Appleton, David Ross
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06.06.2017; Nature Publishing Group; Nature Portfolio
• Subjects: 45/43; 631/114; 631/208/721; Accuracy; Bayes Theorem; Bayesian analysis; Crops; Crops, Agricultural - genetics; Elaeis guineensis; Fruits; Genetic Markers; Genetics, Population; Genome, Plant; Genomes; Genomics; Heritability; Humanities and Social Sciences; Inheritance Patterns; Linkage Disequilibrium; Methods; multidisciplinary; Plant Breeding; Population; Science; Science (multidisciplinary); Selection, Genetic; Vegetable oils
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-017-02602-6

Genomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included: shell-to-fruit ratio (S/F, %), mesocarp-to-fruit ratio (M/F, %), kernel-to-fruit ratio (K/F, %), fruit per bunch (F/B, %), oil per bunch (O/B, %) and oil per palm (O/P, kg/palm/year). Genomic heritabilities of these traits were estimated to be in the range of 0.40 to 0.80. GS methods assessed were RR-BLUP, Bayes A (BA), Cπ (BC), Lasso (BL) and Ridge Regression (BRR). All methods resulted in almost equal prediction accuracy. The accuracy achieved ranged from 0.40 to 0.70, correlating with the heritability of traits. By selecting the most important markers, RR-BLUP B has the potential to outperform other methods. The marker density for certain traits can be further reduced based on the linkage disequilibrium (LD). Together with in silico breeding, GS is now being used in oil palm breeding programs to hasten parental palm selection.