Temporal transcriptome profiling of developing seeds reveals a concerted gene regulation in relation to oil accumulation in Pongamia (Millettia pinnata)

Abstract

BackgroundPongamia (Millettia pinnata syn. Pongamia pinnata), an oilseed legume species, is emerging as potential feedstock for sustainable biodiesel production. Breeding Pongamia for favorable traits in commercial application will rely on a comprehensive understanding of molecular mechanism regulating oil accumulation during its seed development. To date, only limited genomic or transcript sequences are available for Pongamia, while a temporal transcriptome profiling of developing seeds is still lacking in this species.ResultsIn this work, we conducted a time-series analysis of morphological and physiological characters, oil contents and compositions, as well as global gene expression profiles in developing Pongamia seeds. Firstly, three major developmental phases were characterized based on the combined evidences from embryonic shape, seed weight, seed moisture content, and seed color. Then, the gene expression levels at these three phases were quantified by RNA-Seq analyses with three biological replicates from each phase. Nearly 94% of unigenes were expressed at all three phases, whereas only less than 2% of unigenes were exclusively expressed at one of these phases. A total of 8881 differentially expressed genes (DEGs) were identified between phases. Furthermore, the qRT-PCR analyses for 10 DEGs involved in lipid metabolism demonstrated a good reliability of our RNA-Seq data in temporal gene expression profiling. We observed a dramatic increase in seed oil content from the embryogenesis phase to the early seed-filling phase, followed by a steady and moderate increase towards the maximum at the desiccation phase. We proposed that a highly active expression of most genes related to fatty acid (FA) and triacylglycerol (TAG) biosynthesis at the embryogenesis phase might trigger both the substantial oil accumulation and the membrane lipid synthesis for rapid cell proliferation at this phase, while a concerted reactivation of TAG synthesis-related genes at the desiccation phase might further promote storage lipid synthesis to achieve the maximum content of seed oils.ConclusionsThis study not only built a bridge between gene expression profiles and oil accumulation in developing seeds, but also laid a foundation for future attempts on genetic engineering of Pongamia varieties to acquire higher oil yield or improved oil properties for biofuel applications.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1356-8) contains supplementary material, which is available to authorized users.

Transcriptome Analysis of Jojoba (Simmondsia chinensis) during Seed Development and Liquid Wax Ester Biosynthesis

“…The high expression level of this group is consistent with previously reported data [27,43]. In the Millettia pinnata transcriptome, MCAAT, KAR, and EAR had two unigenes, whereas KASI and HAD had one detected unigene [24]. Fatty acid biosynthesis genes were also detected in the Camelina sativa seed transcriptome [22].…”

“…The expression of the same four subunits was reported in similar studies on Arbidopsis [40] and B. napus [41]. Fourteen unigenes were detected for ACCase and its subunits in the transcriptome of Millettia pinnata developing seeds [24]. Two types of ACCase were reported in C. merolae algae; the multifunctional type is encoded by nuclear genes and is located in the cytosol, whereas the multisubunit type is encoded by nuclear and plastid genes and is located in the plastid [36].…”

“…In this study, FATB (AAT) was highly expressed with an FPKM value of 21.47 (Table 2), whereas FATA was not detected. FATB was detected in the transcriptome of developing seeds of B. napus (four unigenes) [43], Millettia pinnata (two unigenes) [24], B. napus (two uingenes) [43], Millettia pinnata (two unigenes) [24], Pongamia pinnata [20], and Camelina sativa [22]. However, FATB was not detected in the transcriptome of developing seeds in Perilla frutescens [27].…”

“…In the B. napus transcriptome, ten unigenes were detected, three of which were upregulated and six were downregulated [43]. A family of six LACS genes was detected in the Millettia pinnata transcriptome with different levels of expression [24]. Also, LACS kept a high level of expression during the seed development of Pongamia pinnata [20], Perilla frutescence [27], and Camelina sativa [22].…”

“…Transcriptome sequencing (de novo or resequencing) is a powerful approach to investigate changes in global gene expression during plant growth and development. It has been employed to study gene expression during seed germination in Phelipanche aegyptiaca [19], floral initiation in Pongamia pinnata [20], seed development in pecan trees (Carya illinoinensis) [21], seed development in Camelina sativa [22], seed development in Euryale ferox [23], and seed development in Millettia pinnata [24]. Transcriptome analysis has also been employed to study oil biosynthesis in Pongamia pinnata [20], oil content and fatty acid composition in Camellia oleifera [25], lipid metabolism in pecan trees seeds (Carya illinoinensis) seeds (21), alpha-linolenic acid synthesis in tree peony seeds [26], triacylglycerol biosynthesis in Camelina sativa [22], oil accumulation in Millettia pinnata [24], and the biosynthesis of unsaturated fatty acids in Perilla frutescens [27].…”