In silico screening of oil palm early and continuously flowering gene candidates for faster breeding program

Abstract

Oil palm (Elaeis guineensis Jacq.) is a vegetable oil-producing crop used for consumption and biodiesel production. Fastrack breeding is one of breeding techniques to reduce plant vegetative phase significantly by a combination of conventional and transgene technologies. However, the lack information of flowering genes in oil palm become a gap for developing this technology. This paper aimed to discover the candidate genes from oil palm for developing early flowering oil palm lines. Screening potential florigen protein by comparing rice OsHd3a protein sequence in the NCBI database successfully discovered 13 florigen protein candidates with more than 53% similarity and up to 90% query cover. All protein candidates were analyzed by protein structure homology modeling (SWISS-MODEL) based on several parameters, including GMQE score and QMEAN Z-score. The modeling discovered that at least eight proteins predicted a similar structure to AtFT1 and four proteins are related to AtTFL1, which repress flowering process. Based on GMQE, QMEAN Z-score, and phylogenetic tree, we suggested three proteins (XP_010911427, XP_010925712, and XP_019705101) as the strong candidates for florigen protein. However, to verify their functions, all selected proteins should be inserted to the model plant and evaluate them as morphologically and physiologically.