CRISPR/Cas mediated base editing: a practical approach for genome editing in oil palm

Abstract

The improvement of the yield and quality of oil palm via precise genome editing has been indispensable goal for oil palm breeders. Genome editing via the CRISPR/Cas9 (CRISPR-associated protein 9) system, ZFN (zinc finger nucleases) and TALEN (transcription activator-like effector nucleases) has flourished as an efficient technology for precise target modifications in the genomes of various crops. Among the genome editing technologies, base editing approach has emerged as novel technology that could generate single base changes i.e. irreversible conversion of one target base in to other in a programmable manner. A base editor (adenine or cytosine) is a fusion of catalytically inactive CRISPR-Cas9 domain (Cas9 variants) and cytosine or adenosine deaminase domain that introduces desired point mutations. However, till date no such genetic modifications have ever been developed in oil palm via base editing technology. Precise genome editing via base editing approach can be a challenging task in oil palm due to its complex genome as well as difficulties in tissue culture and genetic transformation methods. However, availability of whole genome sequencing data in oil palm provides a platform for developing the base editing technology. Here, we briefly review the potential application and future implications of base editing technology for the genetic improvement of oil palm Keywords CRISPR/Cas • Base editors • Oil palm

OIL PALM ECONOMIC PERFORMANCE IN MALAYSIA AND R&D PROGRESS IN 2020

“…The updated physical genome coverage of 79% from the earlier 43%, has successfully placed 1968 unassigned scaffolds onto the genome which extended the 16 pseudochromosomes thus, enhancing its overall quality (Ong et al, 2020). Leveraging the available oil palm genome databases as well as next generation sequencing technologies, Zhou et al (2020) and identified candidate genes, potential pathways as well as transcription factors likely to be involved in drought tolerance in the oil palm. Aside from drought, EgMYB transcription factors (Zhou et al, 2020) were also found to be differentially expressed when exposed to other stresses such as cold and salinity.…”

“…Leveraging the available oil palm genome databases as well as next generation sequencing technologies, Zhou et al (2020) and identified candidate genes, potential pathways as well as transcription factors likely to be involved in drought tolerance in the oil palm. Aside from drought, EgMYB transcription factors (Zhou et al, 2020) were also found to be differentially expressed when exposed to other stresses such as cold and salinity.…”

“…As the oil palm industry continues to embrace technology in its research pursuit, genome editing has begun to gain traction due to its precision and less invasive nature supported by available whole genome information (Yarra et al, 2020). This revolutionary technology also known as the CRISPR/Cas9 system is pioneered by Jennifer Doudna and Emmanuelle Charpentier, which won the 2020 Nobel Prize in Chemistry, touted as a gamechanger for crop agriculture (Carpenter, 2019) and more so if coupled with speed breeding (Haroon et al, 2019).…”

Oil Palm in the 2020s and Beyond: Challenges and Solutions

“…The available gene pool has now been greatly (123). Recent breeding-related reviews include genomics (124,125), genomic selection (126), transgenics (6), genome editing (127), and marker-assisted selection (128,129). Following the publication of the OP genome sequence in 2013 (130), several detailed linkage maps have now become available for the use of breeders (131,132).…”

“…An alternative to transgenic crop manipulation is the used of so-called cisgenic approaches such as genome editing. Specific applications of genome editing to OP breeding via CRISPR have been reviewed recently by Yarra et al (127). Modern crop breeding is also able to profit from a host of advanced technologies such as association genetics (141), molecular mutagenesis including TILLING (TargetIng Local Lesions IN Genomes) and marker-assisted selection (142).…”