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Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness.

ABSTRACT: The breeding of new soft-seeded pomegranate cultivars provides new products for the market and increases farmers' incomes, yet the genetic architecture mediating seed hardness is largely unknown. Here, the seed hardness and hundred-seed weights of 26 cultivars were determined in 2 successive years. We conducted miRNA and mRNA sequencing to analyse the seeds of two varieties of Punica granatum: soft-seeded Tunisia and hard-seeded Sanbai, at 60 and 120 d after flowering. Seed hardness was strongly positively correlated with hundred-seed weight. We detected 25 and 12 differentially expressed miRNA-mRNA pairs with negative regulatory relationships between the two genotypes at 60 and 120 d after flowering, respectively. These miRNA-mRNA pairs mainly regulated seed hardness by altering cell wall structure. Transcription factors including NAC1, WRKY and MYC, which are involved in seed hardness, were targeted by differentially expressed mdm-miR164e and mdm-miR172b. Thus, seed hardness is the result of a complex biological process regulated by a miRNA-mRNA network in pomegranate. These results will help us understand the complexity of seed hardness and help to elucidate the miRNA-mediated molecular mechanisms that contribute to seed hardness in pomegranate.

SUBMITTER: Luo X

PROVIDER: S-EPMC6006261 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness.

Luo Xiang X Cao Da D Zhang Jianfeng J Chen Li L Xia Xiaocong X Li Haoxian H Zhao Diguang D Zhang Fuhong F Xue Hui H Chen Lina L Li Yongzhou Y Cao Shangyin S

Scientific reports 20180618 1

The breeding of new soft-seeded pomegranate cultivars provides new products for the market and increases farmers' incomes, yet the genetic architecture mediating seed hardness is largely unknown. Here, the seed hardness and hundred-seed weights of 26 cultivars were determined in 2 successive years. We conducted miRNA and mRNA sequencing to analyse the seeds of two varieties of Punica granatum: soft-seeded Tunisia and hard-seeded Sanbai, at 60 and 120 d after flowering. Seed hardness was strongly ...[more]

PMID: 29915181

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Project description:BackgroundParaquat, (PQ), an herbicide that can induce Parkinsonian-like symptoms in rodents and humans. The consumption of phytochemical-rich plants can reduce the risk of chronic illnesses such as inflammation and neurodegenerative diseases. The present study aimed to investigate the protective effects of pomegranate seed extract (PSE) and juice (PJ) against PQ-induced neurotoxicity in mice.MethodsMice were assigned into 4 groups; three groups received PQ (10 mg/kg, i.p.) twice a week for 3 weeks. Two of the PQ-induced groups pretreated with either PSE or PJ. Detection of phytochemicals, total phenolics, and total flavonoids in PSE and PJ was performed. Tyrosine hydroxylase (TH) level was measured in the substantia nigra (SN) by Western blotting technique. Striatal dopamine (DA) and 3,4-dihydroxyphenylacetic acid (DOPAC) were detected using high-performance liquid chromatography (HPLC). The levels of adenosine triphosphate (ATP), malondialdehyde (MDA), and the activity of the antioxidant enzymes were estimated in the striatum by colorimetric analysis. Striatal pro-inflammatory and anti-inflammatory markers using enzyme-linked immunosorbent assay (ELISA) as well as DNA fragmentation degree by qualitative DNA fragmentation assay, were evaluated. Real-time polymerase chain reaction (qPCR) assay was performed for the detection of nuclear factor kappa B (NF-кB) gene expression. Moreover, Western blotting analysis was used for the estimation of the cluster of differentiation 11b (CD11b), transforming growth factor β (TGF-β), and glial cell-derived neurotrophic factor (GDNF) levels in the striatum.ResultsPretreatment with PSE or PJ increased the levels of TH in the SN as well as DA and its metabolite in the striatum that were reduced by PQ injection. PSE and PJ preadministration improved the PQ-induced oxidative stress via a significant reduction of the MDA level and the augmentation of antioxidant enzyme activities. PSE and PJ also significantly downregulated the striatal NF-кB gene expression, reduced the PQ-enhanced apoptosis, decreased the levels of; pro-inflammatory cytokines, CD11b, and TGF-β coupled with a significant increase of; interleukin-10 (IL-10), GDNF, and ATP levels as compared with PQ-treated mice.ConclusionsThe current study indicated that PSE and PJ consumption may exhibit protective effects against PQ-induced neurotoxicity in mice.

Project description:Background: MicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression posttranscriptionally, play multiple key roles in plant growth and development and the stress response. Knowledge of and the roles of miRNAs in pomegranate fruit development have not been explored. Results: Pomegranate, which accumulates a large amount of anthocyanins in skin and arils, is valuable to human health, mainly because of antioxidant properties. In this study, we developed a small RNA library from pooled RNA samples from young seedling to matured fruits and identified both conserved and pomegranate-specific miRNA from 29,948,480 high-quality reads. For the pool of 15- to 30-nt small RNAs, ~50% were 24 nt. The miR157 family was the most abundant, followed by miR156, miR160, and miR159, with many variants within each family. The base bias at the first position from the 5’ end has a strong preference for U for most 18- to 26-nt miRNAs but a preference for A for 18-nt miRNAs. In addition, for all 24-nt miRNAs, the nucleotide U is preferred (97%) in the first position. RT-qPCR was used to validate the expression of the predominant miRNA families in leaves, male and female flowers, and multiple fruit developmental stages; miR156, miR156-v1, miR159, miR159-v1, and miR319 were upregulated during the later stages of fruit development. Gene ontology and KEGG pathway analyses revealed predominant metabolic processes and catalytic activities, important for fruit development. In addition, KEGG pathway analyses revealed the involvement of miRNAs in ascorbate and linolenic acid, starch and sucrose metabolism; RNA transport; plant hormone signaling pathways; and circadian clock. Conclusion: Pomegranate largely contains anthocyanin, flavonoids, and antioxidants, which play critical roles in treating cancer, Alzheimer disease, and preventing heart attacks. Our first and preliminary report of novel miRNAs provides information on the biochemical compounds of pomegranate for future research. The functions of the targets of these novel miRNAs need further investigation.

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Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness.

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Integrated microRNA and mRNA expression profiling reveals a complex network regulating pomegranate (Punica granatum L.) seed hardness.

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