Genomic selection in commercial perennial crops: applicability and improvement in oil palm (Elaeis guineensis Jacq.)

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

Abstract

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: shellto- 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.

Citation

Kwong, Q. B., Ong, A. L., Teh, C. K., Chew, F. T., Tammi, M., Mayes, S., …Appleton, D. R. (in press). Genomic selection in commercial perennial crops: applicability and improvement in oil palm (Elaeis guineensis Jacq.). Scientific Reports, 7, Article 2872. https://doi.org/10.1038/s41598-017-02602-6

• Journal Article Type: Article
• Acceptance Date: Apr 13, 2017
• Online Publication Date: Jun 6, 2017
• Deposit Date: Jun 13, 2017
• Publicly Available Date: Jun 13, 2017
• Journal: Scientific Reports
• Electronic ISSN: 2045-2322
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 7
• Article Number: 2872
• DOI: https://doi.org/10.1038/s41598-017-02602-6
• Public URL: https://nottingham-repository.worktribe.com/output/864803
• Publisher URL: http://www.nature.com/articles/s41598-017-02602-6
• Contract Date: Jun 13, 2017