Exploring Triacylglycerol Biosynthetic Pathway in Developing Seeds of Chia (Salvia hispanica L.): A Transcriptomic Approach

Chia (Salvia hispanica L.), a member of the mint family (Lamiaceae), is a rediscovered crop
with great importance in health and nutrition and is also the highest known terrestrial plant
source of heart-healthy omega-3 fatty acid, alpha linolenic acid (ALA). At present, there is
no public genomic information or database available for this crop, hindering research on its
genetic improvement through genomics-assisted breeding programs. The first comprehensive
analysis of the global transcriptome profile of developing Salvia hispanica L. seeds,
with special reference to lipid biosynthesis is presented in this study. RNA from five different
stages of seed development was extracted and sequenced separately using the Illumina
GAIIx platform. De novo assembly of processed reads in the pooled transcriptome using
Trinity yielded 76,014 transcripts. The total transcript length was 66,944,462 bases (66.9
Mb), with an average length of approximately 880 bases. In the molecular functions category
of Gene Ontology (GO) terms, ATP binding and nucleotide binding were found to be the
most abundant and in the biological processes category, the metabolic process and the regulation
of transcription-DNA-dependent and oxidation-reduction process were abundant.
From the EuKaryotic Orthologous Groups of proteins (KOG) classification, the major category
was “Metabolism” (31.97%), of which the most prominent class was ‘carbohydrate
metabolism and transport’ (5.81% of total KOG classifications) followed by ‘secondary metabolite
biosynthesis transport and catabolism’ (5.34%) and ‘lipid metabolism’ (4.57%). A
majority of the candidate genes involved in lipid biosynthesis and oil accumulation were
identified. Furthermore, 5596 simple sequence repeats (SSRs) were identified. The transcriptome
data was further validated through confirmative PCR and qRT-PCR for select
lipid genes. Our study provides insight into the complex transcriptome and will contribute to
further genome-wide research and understanding of chia. The identified novel UniGenes
will facilitate gene discovery and creation of genomic resource for this crop.