Differential leaf transcriptomes for somatic embryogenesis of Elaeis guineensis

Identification of differentially expressed genes from RNA-seq data of non-embryogenic and embryogenic ortets. Selected ortets were previously cloned, thereby somatic embryogenesis rates are known for these ortets. Ortets fitting the study criteria were supplied by two agencies, namely L1 and L2. Principal Component Analysis indicated that variance between agencies were higher than the variance between embryogenesis groups within the agency. Therefore, differential analysis was conducted separately for each agency. Differential expression analysis using DESeq2 package suggested the L2 transcriptomes of zero and low embryogenesis groups were more similar compared to the high embryogenesis group. The L1 transcriptomes consisting of zero and low embryogenesis groups similarly showed overlapping clusters. Differential expression analysis was conducted on the L1 samples (low vs. zero embryogenesis) using DESeq2 R package and the identified differentially expressed genes (DEGs) was used for clustering analysis of the L2 samples. The clustering profiles suggested that expression of these DEGs in L2 samples were able to differentiate high embryogenesis from zero-low embryogenesis L2 groups. Spear leaf (frond F0) was sampled from ortets, supplied by two agencies, L1 (n=32) and L2 (n=20). From the previous somatic embryo production records, ortets were categorized into 3 groups, zero, low and high embryogenesis, with production rates of 0, 1-89 and ≥90 embryoid lines per ortet, respectively. Based on the embryogenesis data, samples from the L2 agency could be categorized into the 3 embryogenesis groups but samples from L1 were categorized into the zero and low groups only. Differential expression analysis was conducted separately for each agency. For the analysis, the zero-low group was designated as reference group for L2 while the zero group was designated as reference group for L1.