Transcript Profiling Reveals Abscisic Acid, Salicylic Acid and Jasmonic-Isoleucine Pathways Involved in High Regenerative Capacities of Immature Embryos Compared with Mature Seeds in japonica Rice

doi:10.1016/j.rsci.2018.06.006

Abstract

Abstract:

Induced pluripotent cell mass plays a role in genetic transformation mediated by Agrobacterium. Mature seeds are more recalcitrant to the induction of suitable calli than immature embryos in rice, but the exact molecular mechanisms involved remain elusive. In this study, the morphological structure of calli induced from mature seeds and immature embryos were observed under a scanning electron microscope using a paraffin embedded technique. Meanwhile, a total of 2 173 up- and down-regulated genes were identified in calli induced from mature seeds and immature embryos by RNA-seq technique and furtherly confirmed by quantitative real-time PCR. The results revealed the remarkable morphological differences in calli induced from mature seeds and immature embryos, and plant hormone signal transduction and hormone biosynthesis pathways, such as abscisic acid, salicylic acid and jasmonic-isoleucine, were found to play roles in somatic embryogenesis. This study provided comprehensive gene expression sets for mature seeds and immature embryos that were served as an important platform resource for further functional studies in plant embryogenesis.

Key words: callus, immature embryo, mature seed, japonica rice, RNA sequence, hormone

Kaizhuan Xiao, Xiaohui Mao, Yingheng Wang, Jinlan Wang, Yidong Wei, Qiuhua Cai, Hua’an Xie, Jianfu Zhang. Transcript Profiling Reveals Abscisic Acid, Salicylic Acid and Jasmonic-Isoleucine Pathways Involved in High Regenerative Capacities of Immature Embryos Compared with Mature Seeds in japonica Rice[J]. Rice Science, 2018, 25(4): 227-234.

Figures/Tables 6

Fig. 1. SEM images of callus surface of IMN (A) and MN (B) after the placement of the callus induction medium for 20 d. SEM, Scanning electron microscopy; IMN, Immature Nipponbare embryos; MN, Mature Nipponbare seeds.The asterisks and arrowheads indicate the membrane and fibrillar of the extracellular matrix of the callus respectively. The arrow indicates the membrane structures with holes covering the callus surface.

Fig. 2. Histochemical analysis of the somatic embryogenesis of IMN (A) and MN (B) after placement on callus induction medium for 20 d. IMN, Immature Nipponbare embryos; MN, Mature Nipponbare seeds. The em, nem and white arrows indicate the embryogenic callus units, nonembryogenic callus and large callus domain/protuberances. The va and ep represent the vascellum and epidermis-like tissue on the surface of some protuberances, respectively.

Fig. 3. Global analyze of the mRNA transcriptome data. A, Differentially expressed genes (DEGs) between immature embryos and mature seeds involved in callus induction. B, Kyoto encyclopedia of genes and genomes (KEGG) pathway abundance of DEGs. A total of 20 pathways were identified in each comparison based on 0 < Q value < 1.0, where the abundance of the pathway is more significant if the value is close to zero. Y-axis shows the pathway categories, and X-axis shows the richness factor of each pathway. C, The heat map of genes involved in plant hormone signal transduction pathway.

Table 1 Summary of the fastq file generated by individually sequencing the RNA of all samples.

Sample ID	Total read	GC content (%)	Data with Phred score ≥ 20 (%)	Data with Phred score ≥ 30 (%)	Number of reads aligned to reference genome (%)
MN-1	29 477 712	51.96	96.37	91.27	26 431 504 (89.67)
MN-2	30 345 732	51.95	96.04	90.60	26 884 157 (88.59)
MN-3	31 118 488	52.04	96.08	90.67	27 392 769 (88.03)
IMN-1	33 653 030	51.82	96.29	91.23	30 135 270 (89.55)
IMN-2	37 035 338	53.44	96.03	90.87	32 262 197 (87.11)
IMN-3	29 646 958	51.47	96.14	91.00	26 431 890 (89.16)
IMN, Immature Nipponbare embryos; MN, Mature Nipponbare seeds.

Fig. 4. Relative expression profiles of genes involved in plant hormone signal transduction pathway validated with quantitative real time PCR with the ΔΔCT method. A, Auxin relative genes; B, Abscisic acid relative genes; C, Jasmonic acid relative genes; D, Salicylic acid relative genes.IMN, Immature Nipponbare embryos; MN, Mature Nipponbare seeds.Data represent mean ± SE (n = 5). The significant differences between mean values are indicated by asterisks (*, P < 0.05; **, P < 0.01; ***, P < 0.001) using the Student’s t-test.

Fig. 5. Abscisic acid (ABA, A), salicylic acid (B), jasmonoyl-isoleucine (JA-Ile, C), indole-3-acetic acid (IAA, D), and jasmonic acid (E) contents of immature Nippobare embryos (IMN) and mature Nippobare seeds (MN).Data represent mean ± SE (n = 5).

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