Dataset Information

Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.).

ABSTRACT: Present research discovered novel miRNA-SSRs for seed type trait from 761 potential precursor miRNA sequences of pomegranate. SSR mining and BLASTx of the unique sequences identified 69 non-coding pre-miRNA sequences, which were then searched for BLASTn homology against Dabenzi genome. Sixty three true pri-miRNA contigs encoding 213 pre-miRNAs were predicted. Analysis of the resulting sequences enabled discovery of SSRs within pri-miRNA (227) and pre-miRNA sequences (79). A total of 132 miRNA-SSRs were developed for seed type trait from 63 true pri-miRNAs, of which 46 were specific to pre-miRNAs. Through ePCR, 123 primers were validated and mapped on eight Tunisia chromosomes. Further, 80 SSRs producing specific amplicons were ePCR-confirmed on multiple genomes i.e. Dabenzi, Taishanhong, AG2017 and Tunisia, yielding a set of 63 polymorphic SSRs (polymorphism information content ≥0.5). Of these, 32 miRNA-SSRs revealed higher polymorphism level (89.29%) when assayed on six pomegranate genotypes. Furthermore, target prediction and network analysis suggested a possible association of miRNA-SSRs i.e. miRNA_SH_SSR69, miRNA_SH_SSR36, miRNA_SH_SSR103, miRNA_SH_SSR35 and miRNA_SH_SSR53 with seed type trait. These miRNA-SSRs would serve as important genomic resource for rapid and targeted improvement of seed type trait of pomegranate.

SUBMITTER: Patil PG

PROVIDER: S-EPMC9040167 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (<i>Punica granatum</i> L.).

Patil Prakash Goudappa PG Singh Nripendra Vikram NV Bohra Abhishek A Jamma Shivani S N Manjunatha M C Venkatesh S VS Karuppannan Dhinesh Babu DB Sharma Jyotsana J Marathe Rajiv A RA

Frontiers in genetics 20220412

Present research discovered novel miRNA-SSRs for seed type trait from 761 potential precursor miRNA sequences of pomegranate. SSR mining and BLASTx of the unique sequences identified 69 non-coding pre-miRNA sequences, which were then searched for BLASTn homology against Dabenzi genome. Sixty three true pri-miRNA contigs encoding 213 pre-miRNAs were predicted. Analysis of the resulting sequences enabled discovery of SSRs within pri-miRNA (227) and pre-miRNA sequences (79). A total of 132 miRNA-SS ...[more]

PMID: 35495126

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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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Dataset Information

Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.).

Publications

Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (<i>Punica granatum</i> L.).

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