Project description:Purpose: Mechanism of gene expression changes in autotetraploid drought resistance variation Methods: Leaves under control and drought treatment of 6h, 12h and 48h were sampled from diploid and the autotetraploid for RNA-seq. Total RNA was extracted from 100mg sample with RNeasy plant mini kit (Omega Biotech, China) and purified with RNase-Free DNase set. Following, cDNA library was constructed and the library concentration and insert size was respectively assessed on the Qubit2.0 (Invitrogen, USA) and Agilent Bioanalyzer 2100 system, and then the effective concentration of the library was accurately quantified through Q-PCR. Prepared high quality libraries were sequenced on Illumina HiSeq X-ten platform to generate paired-end raw reads. qRT–PCR validation was performed using SYBR Green assays. Results: The study findings showed that the autotetraploid sour jujube exhibited a superior drought tolerance and enhanced regrowth potential after dehydration in comparison with the diploid counterpart. The physiological responses gradually triggered important functions in the autotetraploid sour jujube under extreme drought conditions. Furthermore, a comparative transcriptome analysis showed that more differentially expressed genes (DEGs) were detected in autotetraploid after drought stress. Through GO enrichment analysis, many DEGs between the diploid and autotetraploid sour jujube after drought-stress exposure were respectively annotated to the oxidation–reduction process, photosystem, DNA binding transcription factor activity, oxidoreductase activity. Consistently, six reactive oxygen species scavenging-related genes were specifically differentially expressed, positive changes of the genes involved in glutathione metabolism pathways were greater and the lower O2− level and malonaldehyde (MDA) content and higher antioxidant enzymes activity were detected in the autotetraploid under drought-stress conditions. The higher chlorophyll content and differentially enriched genes during photosynthesis suggest that the photosynthetic system in the autotetraploid, having variations in stomatal and cellular characteristics, was enhanced during drought stress. In addition, DEGs in the autotetraploid after stress exposure were significantly enriched in DNA-replication and plant hormone, including auxin, abscisic acid and gibberellin signal-transduction pathways. Under osmotic stress conditions, genes associated with the synthesis and transport of osmotic regulatory substances including anthocyanin biosynthesis were differentially expressed, and the soluble sugar, soluble protein and proline contents were significantly higher in the autotetraploid. Moreover, several genes encoding transcription factors (TFs) including GRAS, Bhlh, MYB, WRKY and NAC were induced specifically or to higher levels in the autotetraploid under drought-stress conditions, and hub genes, LOC107403632, LOC107422279, LOC107434947, LOC107412673 and LOC107432609, related to up-regulated transcription factors in the autotetraploid compared with the diploid were identified. Conclusions: Owing to the whole-genome doubling, many functional genes in the autotetraploid plants were differentially expressed compared with in the diploid during drought stress, resulting in resistance difference.

Project description:Purpose: Cucumber (Cucumis sativus L.) is an economically important vegetable crop worldwide, and cucumber fruit spine density has an important impact on the commercial value. However, little is known about the regulatory mechanism for the fruit spine formation.In this study, the transcriptome analyses of ovaries and pericarps from numerous-spine parent and few-spine parent were conducted to identify the gene regulatory networks involved in the formation and development of numerous fruit spines in cucumber. Methods: Cucumber mRNA profiles of ovaries and pericarps from numerous-spine parent and few-spine parent were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. Then, clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N sequences and low-quality reads from the raw data. Simultaneously, the Q20, Q30 and GC contents of the clean data were calculated. All of the downstream analyses were based on the high-quality clean data. Clean paired-end reads were mapped to the reference genome using TopHat v2.0.12 (Trapnell et al. 2012). Then, the FPKM (fragments per kilobase of transcript sequence per million base pairs sequenced) value of each gene was calculated to estimate gene expression levels (Trapnell et al. 2010). Genes with an adjusted P-value < 0.05 identified by DESeq were assigned as differentially expressed genes(DEGs). Results: We generated 42.96-57.53 million raw reads from each library, and 39.85-54.02 million clean reads were obtained after the removal of low-quality reads and adapter sequences. Among the clean reads, 79.03-80.94% were mapped to the gene database . Based on the KEGG database, pathway enrichment analysis was performed to identify significantly enriched metabolic pathways or signal transduction pathways in DEGs. Plant hormone signal transduction was significantly enriched in up-regulated genes in both F_6DBF compared with M_6DBF and F_0DAA compared with M_0DAA. Conclusions: Based on the transcriptome analysis, we excavated possible biological regulatory networks involved in the formation and development of numerous fruit spines in cucumber. This work will promote the exploration of molecular mechanisms that regulate cucumber fruit spine density.

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