ORCID Profile
0000-0003-4278-2728
Current Organisation
Nanchang University
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Publisher: Oxford University Press (OUP)
Date: 27-05-2014
DOI: 10.1093/GBE/EVU111
Publisher: Informa UK Limited
Date: 05-2012
DOI: 10.4161/PSB.19871
Publisher: Springer Science and Business Media LLC
Date: 31-01-2018
DOI: 10.1038/S41467-018-02839-3
Abstract: Epigenetic variation has been proposed to facilitate adaptation to changing environments, but evidence that natural epialleles contribute to adaptive evolution has been lacking. Here we identify a retrotransposon, named “NMR19” (naturally occurring DNA methylation variation region 19), whose methylation and genomic location vary among Arabidopsis thaliana accessions. We classify NMR19 as NMR19-4 and NMR19-16 based on its location, and uncover NMR19-4 as an epiallele that controls leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE ( PPH ). We find that the DNA methylation status of NMR19-4 is stably inherited and independent of genetic variation. In addition, further analysis indicates that DNA methylation of NMR19-4 correlates with local climates, implying that NMR19-4 is an environmentally associated epiallele. In summary, we discover a novel epiallele, and provide mechanistic insights into its origin and potential function in local climate adaptation.
Publisher: Springer Science and Business Media LLC
Date: 12-05-2018
DOI: 10.1007/S10142-018-0611-2
Abstract: Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important root crops in the world. Initial formation and development of storage roots (SRs) are key factors affecting its yields. In order to study the molecular mechanism and regulatory networks of the SRs development process, we have analyzed root transcriptomes between the high and low starch content sweet potato accessions at three different developmental stages. In this study, we assembled 46,840 unigenes using Illumina paired-end sequencing reads and identified differentially expressed genes (DEGs) between two accessions. The numbers of DEGs were increased with the development of SRs, indicating that the difference between two accessions is enlarging with the maturation. DEGs were mainly enriched in starch biosynthesis, plant hormones regulatory, and genetic information processing pathways. Then, expression patterns of DEGs that are most significant and starch biosynthesis related were validated using qRT-PCR. Our results provide valuable resources to future study on molecular mechanisms of SRs development and candidate genes for starch content improvement in sweet potato.
Publisher: Wiley
Date: 16-08-2019
DOI: 10.1111/PBI.13214
Publisher: Public Library of Science (PLoS)
Date: 28-02-2012
Publisher: Wiley
Date: 09-09-2019
DOI: 10.1111/PBI.13239
Publisher: Proceedings of the National Academy of Sciences
Date: 05-07-2016
Abstract: The epigenome influences gene regulation and genome evolution. The DNA methylomes of Arabidopisis hybrids are distinct from both parents however, how the parental methylomes interact in hybrids is poorly understood. We discovered pervasive, nonadditive DNA methylation changes (“methylation interactions”) throughout the genome in hybrids of Col and C24 Arabidopsis accessions. Methylation interactions correlated with high levels of small interfering RNAs, known components of the RNA-directed DNA methylation (RdDM) pathway. Indeed, abrogation of RdDM activity abolished methylation interactions in filial 1 (F1) hybrids. Methylation interactions have distinct polymorphism frequencies: Regions with increased methylation compared with the parents are highly conserved, whereas regions with decreased methylation are ergent. Our results show that RdDM is required for DNA methylation interactions in hybrids.
Publisher: Springer Science and Business Media LLC
Date: 09-08-2016
Abstract: In plants, hybrid vigor is influenced by genetic and epigenetic mechanisms however, the molecular pathways are poorly understood. We investigated the potential contributions of epigenetic regulators to heterosis in Arabidposis and found that the chromatin remodeler DECREASED DNA METHYLATION 1 (DDM1) affects early seedling growth heterosis in Col/C24 hybrids. ddm1 mutants showed impaired heterosis and increased expression of non-additively expressed genes related to salicylic acid metabolism. Interestingly, our data suggest that salicylic acid is a hormetic regulator of seedling growth heterosis, and that hybrid vigor arises from crosses that produce optimal salicylic acid levels. Although DNA methylation failed to correlate with differential non-additively expressed gene expression, we uncovered DDM1 as an epigenetic link between salicylic acid metabolism and heterosis, and propose that the endogenous salicylic acid levels of parental plants can be used to predict the heterotic outcome. Salicylic acid protects plants from pathogens and abiotic stress. Thus, our findings suggest that stress-induced hormesis, which has been associated with increased longevity in other organisms, may underlie specific hybrid vigor traits.
Publisher: Elsevier BV
Date: 2013
DOI: 10.1016/J.CUB.2012.11.038
Abstract: DNA transfer between host cells and their endosymbionts has had a profound effect on the evolution of eukaryotic cells. A new sequencing study suggests that other forces may be equally important.
Publisher: MDPI AG
Date: 16-01-2023
Abstract: Non-coding RNAs play vital roles in the erse biological processes of plants, and they are becoming key topics in horticulture research. In particular, miRNAs and long non-coding RNAs (lncRNAs) are receiving increased attention in fruit crops. Recent studies in horticulture research provide both genetic and molecular evidence that miRNAs and lncRNAs regulate biological function and stress responses during fruit development. Here, we summarize multiple regulatory modules of miRNAs and lncRNAs and their biological roles in fruit sets and stress responses, which would guide the development of molecular breeding techniques on horticultural crops.
Publisher: Oxford University Press (OUP)
Date: 10-05-2023
DOI: 10.1093/HR/UHAD096
Publisher: Oxford University Press (OUP)
Date: 24-01-2012
Abstract: DNA of plastid (chloroplast) origin comprises between 1% and 10% of the mitochondrial genomes of higher plants, but functions are currently considered to be limited to rare instances where plastid tRNA genes have replaced their mitochondrial counterparts, where short patches of mitochondrial genes evolved using their homologous plastidic copies by gene conversion or where a new promoter region is created. Here, we show that, in some angiosperms, plastid-derived DNA in mitochondrial genomes (also called mtpt for mitochondrial plastid DNA) contributes codons to unrelated mitochondrial protein-coding sequences and may also have a role in posttranscriptional RNA processing. We determined that these transfers of plastid DNA occurred a few to 150 Ma and that mtpts can sometimes remain dormant many millions of years before contributing to the mitochondrial proteome.
Publisher: Oxford University Press (OUP)
Date: 23-12-2022
DOI: 10.1093/JXB/ERAC482
Abstract: Long non-coding RNAs (lncRNAs) are a group of RNAs greater than 200 nucleotides in length exhibiting low or no coding potential that are involved in erse biological functions through their molecular interaction with proteins, DNA, or other RNAs. With the emergence of advanced high-throughput RNA sequencing technologies, tens of thousands of novel long non-coding RNAs have been identified in plant transcriptomes in the last decade. More importantly, functional studies revealed that several lncRNAs play key regulatory roles in plant development and stress responses. In this review, we focus on summarizing recent progress uncovering regulatory roles and mechanisms of lncRNAs during the plant life cycle, and briefly discuss the possible biotechnological applications of lncRNAs for plant breeding.
Publisher: Elsevier BV
Date: 08-2023
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.MOLP.2019.04.009
Abstract: In plants, microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs have been well explored. However, the mechanisms regulating the accumulation of miRNAs remain poorly understood. Here, we report that distinct mechanisms regulate accumulation of a monocot-specific miRNA, rice (Oryza sativa) miR528. At the transcriptional level, miR528 accumulated to higher levels in older plants than in young seedlings and exhibited aging-modulated gradual accumulation and diurnal rhythms in leaves at the post-transcriptional level, aging also modulated miR528 levels by enhancing pri-miR528 alternative splicing. We found that miR528 promotes rice flowering under long-day conditions by targeting RED AND FAR-RED INSENSITIVE 2 (OsRFI2). Moreover, natural variations in the MIR528 promoter region caused differences in miR528 expression among rice varieties, which are correlated with their different binding affinities with the transcription factor OsSPL9 that activates the expression of miR528. Taken together, our findings reveal rice plants have evolved sophisticated modes fine-tuning miR528 levels and provide insight into the mechanisms that regulate MIRNA expression in plants.
Publisher: Springer Science and Business Media LLC
Date: 12-08-2021
Publisher: Proceedings of the National Academy of Sciences
Date: 30-01-2012
Abstract: Mitochondria and chloroplasts (photosynthetic members of the plastid family of cytoplasmic organelles) in eukaryotic cells originated more than a billion years ago when an ancestor of the nucleated cell engulfed two different prokaryotes in separate sequential events. Extant cytoplasmic organellar genomes contain very few genes compared with their candidate free-living ancestors, as most have functionally relocated to the nucleus. The first step in functional relocation involves the integration of inactive DNA fragments into nuclear chromosomes, and this process continues at high frequency with attendant genetic, genomic, and evolutionary consequences. Using two different transplastomic tobacco lines, we show that DNA migration from chloroplasts to the nucleus is markedly increased by mild heat stress. In addition, we show that insertion of mitochondrial DNA fragments during the repair of induced double-strand breaks is increased by heat stress. The experiments demonstrate that the nuclear influx of organellar DNA is a potentially a source of mutation for nuclear genomes that is highly susceptible to temperature fluctuations that are well within the range experienced naturally.
Publisher: No publisher found
Date: 2009
DOI: 10.1134/S0006297909010167
Abstract: The trypsin inhibitor SOTI was isolated from Spinacia oleracea L. seeds through ammonium sulfate precipitation, Sepharose 4B-trypsin affinity chromatography, and Sephadex G-75 chromatography. This typical Kunitz inhibitor showed remarkable stability to heat, pH, and denaturant. It retained 80% of its activity against trypsin after boiling for 20 min, and more than 90% activity when treated with 6 M guanidine hydrochloride. The formation of stable SOTI-trypsin complex (K(i) = 2.3x10(-6) M) is consistent with significant inhibitory activity of SOTI against trypsin-like proteinases present in the larval midgut of Pieris rapae. Sequences of SOTI fragments showed homology with other inhibitors.
Publisher: Wiley
Date: 16-12-2017
DOI: 10.1111/TPJ.13769
Abstract: The mitochondria and plastids of eukaryotic cells evolved from endosymbiotic prokaryotes. DNA from the endosymbionts has bombarded nuclei since the ancestral prokaryotes were engulfed by a precursor of the nucleated eukaryotic host. An experimental confirmation regarding the molecular mechanisms responsible for organelle DNA incorporation into nuclei has not been performed until the present analysis. Here we introduced double-stranded DNA breaks into the nuclear genome of tobacco through inducible expression of I-SceI, and showed experimentally that tobacco chloroplast DNAs insert into nuclear genomes through double-stranded DNA break repair. Microhomology-mediated linking of disparate segments of chloroplast DNA occurs frequently during healing of induced nuclear double-stranded breaks (DSB) but the resulting nuclear integrants are often immediately unstable. Non-Mendelian inheritance of a selectable marker (neo), used to identify plastid DNA transfer, was observed in the progeny of about 50% of lines emerging from the screen. The instability of these de novo nuclear insertions of plastid DNA (nupts) was shown to be associated with deletion not only of the nupt itself but also of flanking nuclear DNA within one generation of transfer. This deletion of pre-existing nuclear DNA suggests that the genetic impact of organellar DNA transfer to the nucleus is potentially far greater than previously thought.
Publisher: Springer Science and Business Media LLC
Date: 27-08-2020
DOI: 10.1007/S10142-019-00702-2
Abstract: Soybean is an economically important leguminous crop, and pod dehiscence of soybean could cause huge yield loss. In this study, we measured fruit-cracking forces and percentages of dehisced pods for ten soybean accessions, then separated them into two groups as shattering-sensitive (SS) and shattering-resistant (SR) soybeans. Pod transcriptomes from these two groups were analyzed, and 225 differentially expressed genes (DEGs) were identified between SS and SR soybeans. Some of these DEGs have been previously reported to be associated with pod dehiscence in soybean. The expression patterns of selected DEGs were validated by real-time quantitative reverse transcription PCR, which confirmed the expression changes found in RNA-seq analysis. We also de novo identified 246 soybean pod-long intergenic ncRNAs (lincRNAs), 401 intronic lncRNAs, and 23 antisense lncRNAs from these transcriptomes. Furthermore, genes and lincRNAs co-expression network analysis showed that there are distinct expression patterns between SS and SR soybeans in some co-expression modules. In conclusion, we systematically investigated potential genes and molecular pathways as candidates for differences in soybean pod dehiscence and will provide a useful resource for molecular breeding of soybeans.
Publisher: Oxford University Press (OUP)
Date: 08-05-2013
DOI: 10.1093/GBE/EVT070
Publisher: Springer Science and Business Media LLC
Date: 26-06-2017
DOI: 10.1007/S00299-017-2165-5
Abstract: Our study systematically explored potential genes and molecular pathways as candidates for differences in seed weight resulting from soybean domestication. In addition, potential contributions of lncRNAs to seed weight were also investigated. Soybeans have a long history of domestication in China, and there are several significant phenotypic differences between cultivated and wild soybeans, for ex le, seeds of cultivars are generally larger and heavier than those from wild accessions. We analyzed seed transcriptomes from thirteen soybean s les, including six landraces and seven wild accessions using strand-specific RNA sequencing. Differentially expressed genes related to seed weight were identified, and some of their homologs were associated with seed development in Arabidopsis. We also identified 1251 long intergenic noncoding RNAs (lincRNAs), 243 intronic RNAs and 81 antisense lncRNAs de novo from these soybean transcriptomes. We then profiled the expression patterns of lncRNAs in cultivated and wild soybean seeds, and found that transcript levels of a number of lncRNAs were s le-specific. Moreover, gene transcript and lincRNA co-expression network analysis showed that some soybean lincRNAs might have functional roles as they were hubs of co-expression modules. In conclusion, this study systematically explored potential genes and molecular pathways as candidates for differences in seed weight resulting from soybean domestication, and will provide a useful future resource for molecular breeding of soybeans.
Publisher: Proceedings of the National Academy of Sciences
Date: 27-08-2021
Abstract: In plants, several DNA methylation pathways help maintain DNA methylation patterns to ensure that transposons remain in a silenced state and cell-specific DNA methylation is preserved after cell ision. Here, we demonstrate that loss of function of the chromatin remodeler DDM1 induces a pathway conversion from CMT2- to RdDM-dependency to ensure the maintenance of CHH methylation. In plants defective in both DDM1 and RdDM, there is strong reactivation of TEs and a burst of TE transposition. Thus, our work not only identifies a variant of the RdDM pathway, but also shows that DNA methylation maintenance at a given locus is an adaptable process, revealing the existence of a double-insurance mechanism for the regulation of DNA methylation to guarantee genome integrity.
Publisher: Springer Science and Business Media LLC
Date: 16-08-2021
Publisher: Springer Science and Business Media LLC
Date: 09-03-2016
Publisher: Springer Science and Business Media LLC
Date: 25-06-2021
Publisher: Public Library of Science (PLoS)
Date: 19-03-2021
DOI: 10.1371/JOURNAL.PGEN.1009461
Abstract: Long noncoding RNAs (lncRNAs) are emerging as important regulators in plant development, but few of them have been functionally characterized in fruit ripening. Here, we have identified 25,613 lncRNAs from strawberry ripening fruits based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries, most of which exhibited distinct temporal expression patterns. A novel lncRNA, FRILAIR harbours the miR397 binding site that is highly conserved in erse strawberry species. FRILAIR overexpression promoted fruit maturation in the Falandi strawberry, which was consistent with the finding from knocking down miR397, which can guide the mRNA cleavage of both FRILAIR and LAC11a (encoding a putative laccase-11-like protein). Moreover, LAC11a mRNA levels were increased in both FRILAIR overexpressing and miR397 knockdown fruits, and accelerated fruit maturation was also found in LAC11a overexpressing fruits. Overall, our study demonstrates that FRILAIR can act as a noncanonical target mimic of miR397 to modulate the expression of LAC11a in the strawberry fruit ripening process.
Publisher: Wiley
Date: 03-01-2008
DOI: 10.1111/J.1399-3054.2007.01027.X
Abstract: Leaf carbon isotope discrimination (delta13C) was widely considered to directly reflect the rainfall environment in which the leaf developed, but recent observations have queried this. The relationship between delta13C and rainfall was explored in Eucalyptus species growing along a rainfall gradient in Australia. The leaves of 43 species of Eucalyptus and the closely related Corymbia species produced in 2003 were s led in September 2004 at 50 sites and grouped into 15 locations along a rainfall gradient in southwest Western Australia. At 24 sites, the same species and same trees were s led as in a study in September 2003 when leaves produced in 2002 were s led. The rainfall in 2004 was on average 190 mm (range 135-270 mm) higher at all locations than in 2003. In the leaves s led in 2004, the mean carbon isotope discrimination (delta13C) across the 15 locations decreased 2.9 per thousand per 1000 mm of rainfall, the specific leaf area (SLA) increased by 2.9 m2 kg(-1) per 1000 mm of rainfall and the nitrogen (N) content decreased by 1.56 g m(-2) per 1000 mm of rainfall. In contrast, a comparison between the leaves produced in the drier 2002 year compared with the wetter 2003 year showed that there was a strong correlation (r2= 0.85) between the SLA values between years and a trend for higher values with increasing SLA, but the values of delta(13)C were on average only 0.38 per thousand lower (more negative) at all locations in the wetter year, equivalent to a decrease of 2.0 per thousand per 1000 mm of rainfall. The results suggest that while there may be constitutive differences in leaf morphology, SLA and N content per unit area, increasing rainfall or cloudiness associated with higher rainfall increases SLA and decreases N content per unit area. We conclude that rainfall does not directly influence delta13C, but induces leaf morphological and physiological changes that affect the resultant delta13C.
Publisher: Elsevier BV
Date: 04-2018
Publisher: Elsevier BV
Date: 07-2023
Publisher: Springer Science and Business Media LLC
Date: 16-01-2019
DOI: 10.1007/S11103-018-0806-X
Abstract: We reported that knockdown of OsDCL3b decreased grain yield but increased grain quality in rice, which is helpful for molecular breeding in crops. Multiple DICER-LIKE (DCL) genes usually exist and show erse biochemical and phenotypic functions in land plants. In rice, the biochemical function of OsDCL3b is known to process 24-nucleotide panicle phased small RNAs, however, its phenotypic functions are unclear. Here we reported that knockdown of OsDCL3b led to reduced pollen fertility, seed setting rate, and decreased grain yield but increased grain quality in rice. To reveal the molecular mechanism of the above phenomena, extracted RNAs from rice panicles of the wild type (WT) and OsDCL3b-RNAi line S6-1 were analyzed by deep sequencing. It showed that knockdown of OsDCL3b affected the biogenesis of both 21- and 24-nucleotide small RNAs including miRNAs and phased small RNAs. Using RNA-seq, 644 up- and 530 down-regulated mRNA genes were identified in panicles of line S6-1, and 550 and 273 differentially spliced genes with various alternative splicing (AS) events were observed in panicles of line S6-1 and WT, respectively, suggesting that OsDCL3b involved in influencing the transcript levels of mRNA genes and the AS events in rice panicles. Thus, our results show that knockdown of OsDCL3b will affect the biogenesis of small RNAs, which is involved in regulating the transcription of mRNA genes, and consequently influence the grain yield and quality in rice.
Start Date: 2014
End Date: 2017
Funder: National Natural Science Foundation of China
View Funded ActivityStart Date: 2021
End Date: 2024
Funder: National Natural Science Foundation of China
View Funded Activity