Comparative Genome-Wide Association Studies (GWAS), Genomic Selection (GS), And Heterosis Analysis For Trait Improvement In African Oil Palm (Elaeis Guineensis Jacq.)

Aini, Kirana Syarifa (2026) Comparative Genome-Wide Association Studies (GWAS), Genomic Selection (GS), And Heterosis Analysis For Trait Improvement In African Oil Palm (Elaeis Guineensis Jacq.). Other thesis, Institut Teknologi Sepuluh Nopember.

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Abstract

African oil palm (Elaeis guineensis Jacq.), despite the controversies surrounding its cultivation, served as Indonesia’s most economically important perennial crop. Especially because Indonesia is a major producer and exporter of crude palm oil, which is widely used as a raw material for both consumer and industrial products. However, oil palm improvement remains constrained by its long breeding cycle, extensive progeny-testing requirements, incomplete crossing designs, and the relatively limited density of available molecular markers. This study aimed to compare genome-wide association studies (GWAS) and genomic selection (GS) models, identify significant marker-trait associations, and determine promising parental lines and hybrid combinations through heterosis and combining ability analyses. A dataset comprising 6,878 single-nucleotide polymorphism markers and 24 phenotypic traits was analysed. Several GWAS models were compared based on false discovery rate and Type I error, while genomic selection was evaluated using GAPIT-based models, rrBLUP, BGLR, and a reproducing kernel Hilbert space additive-dominance model, followed by estimation of general and specific combining ability, mid-parent and better-parent heterosis. MLMM, FarmCPU, and BLINK showed the most suitable overall GWAS performance, and significant marker–trait associations were detected for 10 of the 24 traits. Among the identified markers, SNP_6203 and SNP_2808 were repeatedly associated with multiple traits or detected by multiple models. The additive GS models generally produced similar low-to-moderate prediction accuracies, whereas the additive-dominance model improved predictive performance for 14 traits, achieving the lowest RMSE (2.158) for fruit weight. Combining-ability analysis identified D.02 and P.06 as promising parental lines, while D.02 × P.06 yielded the highest predicted hybrid value. Overall, these findings demonstrate that integrating GWAS, genomic selection, and heterosis analysis provides complementary information for identifying candidate genomic regions, predicting genetic merit, and selecting promising parents and hybrid combinations to accelerate oil-palm breeding.

Item Type:	Thesis (Other)
Uncontrolled Keywords:	African oil palm, Genome-wide association study, Genomic selection, Heterosis
Subjects:	Q Science > QA Mathematics > QA401 Mathematical models. Q Science > QH Biology > QH301 Biology
Divisions:	Faculty of Science and Data Analytics (SCIENTICS) > Statistics > 49201-(S1) Undergraduate Thesis
Depositing User:	Kirana Syarifa Aini
Date Deposited:	04 Aug 2026 03:19
Last Modified:	04 Aug 2026 03:19
URI:	http://repository.its.ac.id/id/eprint/143029

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