Transcriptome analysis of developing castor bean seeds and identification of ricinoleic acid biosynthesis genes

Ricinoleic acid is a kind of unsaturated fatty acids in oil of castor bean (Ricinus communis) seeds with wide application value. However, there is little transcriptomic information on genes related to ricinoleic acid biosynthesis in castor beans. To better understand the regulation mechanism of ricinoleic acid biosynthesis, immature seeds at three developmental stages (S1, S2, and S3 corresponding to 15, 30, and 45 d after pollination) were collected. The results indicated that the accumulation of castor bean oil and ricinoleic acid increased gradually during seed development, and reached the maximum value at the late stages of seed development (45 d after pollination). Furthermore, RNA sequencing was conducted to analyze the transcriptome of the developing seeds at three developmental stages. Totals of 9 875 differentially expressed genes (DEGs) were identified among the three time points. Based on the annotation information, 49 DEGs related to lipid biosynthesis were screened among all DEGs. Through cluster analysis of the 49 DEGs, ten genes with increasing FPKM values from seed development stages S1 to S3 were selected as candidate key enzymes, since they showed similar patterns of increase with castor bean oil accumulation and ricinoleic acid biosynthesis during seed development. The transcriptomic data of the 10 candidate key enzyme genes was further validated by RT-qPCR. Ultimately, a putative model of key genes correlated with ricinoleic acid accumulation was built. Our study identified a series of key genes and revealed the proposed molecular mechanism of ricinoleic acid accumulation in castor bean seeds through the transcriptional analysis. It broadens our knowledge of ricinoleic acid biosynthesis and castor bean oil accumulation and also provides a theoretical foundation for the genetic engineering key genes that can improve the ricinoleic acid production in castor beans as well as in other plants.