Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

Abstract

Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops.

PalmXplore: oil palm gene database

“…Apart from that, the information in PalmXplore provides fundamental and important information needed to expedite biological research pertaining to oil palm. The information in this database further aids in identification of new genes and gene families that will be responsible for traits of interest such as the height, FAB and disease resistance genes ( 35 ). The database is continuously updated with new features, improvements to the oil palm genome and gene models, as they become available, along with the associated data mining and updated versions of bioinformatics analysis tools.…”

Pengembangan Biomarka Untuk Seleksi Tanaman Tahan Penyakit Busuk Pangkal Batang Pada Kelapa Sawit

“…Liu et al, 2020). Penelitian sebelumnya telah mengembangkan marka SNAP (Single Nucleotide Amplified Polymorphism) berdasarkan sekuens transkriptomik pada lobak (Raphanus sativus L.) Wang et al, 2017), namun informasi SNP dari transkriptomik pada tanaman kelapa sawit untuk marka molekuler ketahanan GD belum dimanfaatkan secara optimal (Rosli et al, 2018).…”

“…Saat ini, bioteknologi dengan memanfaatkan data RNA sekuensing atau transkriptomik berkembang sangat cepat (C.-L. Ho et al, 2018;Isaac et al, 2018;Rosli et al, 2018). Genomik komparatif dan hasil transkriptomik telah dianalisis pada 2 kelompok gen besar yang berperan pada regulasi kualitas minyak dan gen resisten terhadap penyakit (gen R) (Rosli et al, 2018).…”

Multiplex CRISPR/Cas9 gene-editing platform in oil palm targeting mutations in EgFAD2 and EgPAT genes

“…The EgFATB-1 gene is highly expressed in 15WAA kernels and in 10WAA mesocarp tissues, whereas EgFATB-2 is expressed mainly in the mesocarp and early stages of kernel development at 15WAA. While EgFATB-4 is not expressed in either tissue, the EgFATB-3 gene is expressed in all transcriptome libraries [ 11 ]. With the availability of the complete oil palm genome sequence data released in 2013 [ 12 ], genome-editing technology such as clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) has opened the possibility of targeted modification of the oil palm genome for future trait improvement.…”