Transcriptome analysis and identification of genes associated with ω-3 fatty acid biosynthesis in Perilla frutescens (L.) var. frutescens

Abstract

BackgroundPerilla (Perilla frutescens (L.) var frutescens) produces high levels of α-linolenic acid (ALA), a ω-3 fatty acid important to health and development. To uncover key genes involved in fatty acid (FA) and triacylglycerol (TAG) synthesis in perilla, we conducted deep sequencing of cDNAs from developing seeds and leaves for understanding the mechanism underlying ALA and seed TAG biosynthesis.ResultsPerilla cultivar Dayudeulkkae contains 66.0 and 56.2 % ALA in seeds and leaves, respectively. Using Illumina HiSeq 2000, we have generated a total of 392 megabases of raw sequences from four mRNA samples of seeds at different developmental stages and one mature leaf sample of Dayudeulkkae. De novo assembly of these sequences revealed 54,079 unique transcripts, of which 32,237 belong to previously annotated genes. Among the annotated genes, 66.5 % (21,429 out of 32,237) showed highest sequences homology with the genes from Mimulus guttatus, a species placed under the same Lamiales order as perilla. Using Arabidopsis acyl-lipid genes as queries, we searched the transcriptome and identified 540 unique perilla genes involved in all known pathways of acyl-lipid metabolism. We characterized the expression profiles of 43 genes involved in FA and TAG synthesis using quantitative PCR. Key genes were identified through sequence and gene expression analyses.ConclusionsThis work is the first report on building transcriptomes from perilla seeds. The work also provides the first comprehensive expression profiles for genes involved in seed oil biosynthesis. Bioinformatic analysis indicated that our sequence collection represented a major transcriptomic resource for perilla that added valuable genetic information in order Lamiales. Our results provide critical information not only for studies of the mechanisms involved in ALA synthesis, but also for biotechnological production of ALA in other oilseeds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2805-0) contains supplementary material, which is available to authorized users.

Alpha-linolenic acid content and expression of KASII and FAD3 in perilla seed associated with altitude of cultivation areas

“…These finding were also in good-agreement with the high expression of fad3 gene in perilla. The increase of ALA to LA ratio during perilla seed development indicated that the n-3 desaturase was very active in the middle stage of the developing seed and then sharply declined in the late stage before seed maturation 9 . It was also found that the content of ALA reached a steady state and remained constant throughout the late stage of seed development until the end of seed maturation.…”

“…In terms of genetic factors, several genes encoding enzymes involving lipid biosynthesis are expressed differently during seed development of oilproducing plants 9,19 . In particular, a number of genes contributing to the production and accumulation of lipids are up-regulated.…”

“…While the expression of fad3 has a seedspecific expression 12 . There were also reports showing that the expression of fad3 was higher in developing seeds than in leaves 9,13 . Indeed, at a certain time, gene expression would not be a sole indicator representing ALA production.…”

“…In this study, we determined whether ALA contents in mature perilla dry seeds from 3 locations, Maehongson, Chiang Rai and Nan, are different in relation to the altitudes of each cultivation area, particularly in the aspect of gene expression. In general, many genes encoding enzymes in lipid biosynthesis are temporally up-regulated during oilseed development 9,10 . The key genes involved in n-3 fatty acid biosynthesis, β-ketoacyl-acyl carrier protein synthase II (kasII) and fatty acid desaturase-3 (fad3), were selected as candidates for surrogate markers in this study.…”

Identification of Key Genes Involved in Embryo Development and Differential Oil Accumulation in Two Contrasting Maize Genotypes

“…Transcriptome approaches such as RNA sequencing (RNA-seq) and micro-array have the potential to greatly accelerate the rate of genes' mining for desired phenotypes [3,26]. Several transcriptome studies on important oil seed crops have identified key candidate genes and molecular pathways related to seed oil biosynthesis [27][28][29][30]. However, transcriptome studies focused on identifying important regulators and processes required for embryo development and/or seed oil biosynthesis in maize based on a genome-wide transcriptional profile are scarce [3,31].…”