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.
Highlights
We have focused on several genes encoding key members of the fatty acid biosynthetic pathway, notably stearoyl acyl carrier protein (ACP) desaturases (SAD) and FAT, and on putative R gene candidates involved in disease resistance in oil palm
The analysis showed that 2.9% of the total number of genes used in the model [19] were maintained as single copy genes after divergences. This result is important because such genes can be used as markers for genetic mapping and especially to anchor QTL associated with the traits of interest controlled by the genes
Compared to the other five plant species, there was a high number of conserved protein sequences that was shared between banana and oil palm (10,337), which is consistent with the close evolutionary relationship between their genomes [3]. Another interesting result from gene ontology (GO) annotations was that out of the 2.9% of total oil palm genes that were present as single copies, no fewer than 128 sequences were characterised under ‘cellular aromatic compound metabolic process’ terms of which 39 genes were listed as being involved in ‘aromatic compound biosynthetic process’. This list of genes provides useful candidates to enable us to better understand the biosynthetic pathways of aromatic compounds, and especially shikimic acid, which is an important metabolite in the formation of oil palm phenolics, which are an additional class of useful compounds that are being studies for their potential nutritional and medical applications [43,44]
Summary
We aim to shed light on potential gene-for-gene interactions by the identification of specific R gene classes in order to assist our ongoing efforts to understand and control the molecular mechanisms of Ganoderma infection [21,22]
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