The miR164-dependent regulatory pathway in developing maize seed

Zheng, Lanjie; Zhang, Xiangge; Zhang, Haojun; Gu, Yong; Huang, Xinrong; Huang, Huanhuan; Liu, Hanmei; Zhang, Junjie; Hu, Yu‐Feng; Li, Yangping; Yu, Guowu; Liu, Yanping; Lawson, Shaneka S.; Huang, Yubi

doi:10.1007/s00438-018-1524-4

Cited by 25 publications

(10 citation statements)

References 65 publications

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“…The protein-coding transcripts were downloaded from BRAD (see text footnote 1). Together with previously reported degradome data and the results of the 5 RNA ligase-mediated rapid amplification of cDNA ends (Lu et al, 2008;Vaucheret, 2009;Chen et al, 2011;Ng et al, 2011;Kinoshita et al, 2012;Bari et al, 2013;Song et al, 2013;Zhang et al, 2013Zhang et al, , 2015Liu H. et al, 2014;Park et al, 2014;Windels et al, 2014;Xian et al, 2014;Ma et al, 2015Ma et al, , 2017Ai et al, 2016;Ouyang et al, 2016;Leng et al, 2017;He F. et al, 2018;Kuo et al, 2018;Tang et al, 2018;Zheng et al, 2019), we identified 1,644 high-confidence target site sequences (Supplementary Table 8). After being generated from stem-loop precursors by the DCL1 complex, the mature miRNAs are loaded into an AGO1-dominant RNA-induced silencing complex (RISC) and repress the target transcripts mainly in two ways: cleavage and translational repression (Brodersen et al, 2008).…”

Section: Prediction Of Mirna Target Sites In Rapeseed Transcriptssupporting

confidence: 72%

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

Zhu

Zhang

et al. 2021

Front. Genet.

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MicroRNAs (miRNAs) and their target genes play vital roles in crops. However, the genetic variations in miRNA-targeted sites that affect miRNA cleavage efficiency and their correlations with agronomic traits in crops remain unexplored. On the basis of a genome-wide DNA re-sequencing of 210 elite rapeseed (Brassica napus) accessions, we identified the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in miRNA-targeted sites complementary to miRNAs. Variant calling revealed 7.14 million SNPs and 2.89 million INDELs throughout the genomes of 210 rapeseed accessions. Furthermore, we detected 330 SNPs and 79 INDELs in 357 miRNA target sites, of which 33.50% were rare variants. We also analyzed the correlation between the genetic variations in miRNA target sites and 12 rapeseed agronomic traits. Eleven SNPs in miRNA target sites were significantly correlated with phenotypes in three consecutive years. More specifically, three correlated SNPs within the miRNA-binding regions of BnSPL9-3, BnSPL13-2, and BnCUC1-2 were in the loci associated with the branch angle, seed weight, and silique number, respectively; expression profiling suggested that the variation at these 3 miRNA target sites significantly affected the expression level of the corresponding target genes. Taken together, the results of this study provide researchers and breeders with a global view of the genetic variations in miRNA-targeted sites in rapeseed and reveal the potential effects of these genetic variations on elite agronomic traits.

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Section: Prediction Of Mirna Target Sites In Rapeseed Transcriptssupporting

confidence: 72%

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

Zhu

Zhang

et al. 2021

Front. Genet.

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“…10). In plants, miR164 targeted genes participate in various physiological and biochemical processes during plant development and in response to biotic/abiotic stress [31, 32]. For example, miR164 is involved in age-dependent cell death in Arabidopsis leaves by cleaving ORE (A NAM transcription factor) [33].…”

Section: Discussionmentioning

confidence: 99%

Genomic identification and characterization of MYC family genes in wheat (Triticum aestivum L.)

et al. 2019

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BackgroundMYC transcriptional factors are members of the bHLH (basic helix-loop-helix) superfamily, and play important roles in plant growth and development. Recent studies have revealed that some MYCs are involved in the crosstalk between Jasmonic acid regulatory pathway and light signaling in Arabidopsis, but such kinds of studies are rare in wheat, especially in photo-thermo-sensitive genic male sterile (PTGMS) wheat line.Results27 non-redundant MYC gene copies, which belonged to 11 TaMYC genes, were identified in the whole genome of wheat (Chinese Spring). These gene copies were distributed on 13 different chromosomes, respectively. Based on the results of phylogenetic analysis, 27 TaMYC gene copies were clustered into group I, group III, and group IV. The identified TaMYC genes copies contained different numbers of light, stress, and hormone-responsive regulatory elements in their 1500 base pair promoter regions. Besides, we found that TaMYC3 was expressed highly in stem, TaMYC5 and TaMYC9 were expressed specially in glume, and the rest of TaMYC genes were expressed in all tissues (root, stem, leaf, pistil, stamen, and glume) of the PTGMS line BS366. Moreover, we found that TaMYC3, TaMYC7, TaMYC9, and TaMYC10 were highly sensitive to methyl jasmonate (MeJA), and other TaMYC genes responded at different levels. Furthermore, we confirmed the expression profiles of TaMYC family members under different light quality and plant hormone stimuli, and abiotic stresses. Finally, we predicted the wheat microRNAs that could interact with TaMYC family members, and built up a network to show their integrative relationships.ConclusionsThis study analyzed the size and composition of the MYC gene family in wheat, and investigated stress-responsive and light quality induced expression profiles of each TaMYC gene in the PTGMS wheat line BS366. In conclusion, we obtained lots of important information of TaMYC family, and the results of this study was supposed to contribute novel insights and gene and microRNA resources for wheat breeding, especially for the improvement of PTGMS wheat lines.

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“…miR156, miR396, miR393, miR393 target SPL , GRF , TIR1 , LAC , respectively, and may play a crucial role in the regulation of grain filling by governing growth and development ( Jin et al, 2015 ). miR164 plays a regulatory role during seed development ( Zheng et al, 2019 ). The development of the maize kernel is regulated by nine miRNAs belonging to the conserved zma-miR169 family ( Xing et al, 2017 ).…”

Section: Effect Of Epigenetics On Agronomic Traits In Various Cropsmentioning

confidence: 99%

Epigenetics and its role in effecting agronomical traits

Gupta

Salgotra

2022

Front. Plant Sci.

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Climate-resilient crops with improved adaptation to the changing climate are urgently needed to feed the growing population. Hence, developing high-yielding crop varieties with better agronomic traits is one of the most critical issues in agricultural research. These are vital to enhancing yield as well as resistance to harsh conditions, both of which help farmers over time. The majority of agronomic traits are quantitative and are subject to intricate genetic control, thereby obstructing crop improvement. Plant epibreeding is the utilisation of epigenetic variation for crop development, and has a wide range of applications in the field of crop improvement. Epigenetics refers to changes in gene expression that are heritable and induced by methylation of DNA, post-translational modifications of histones or RNA interference rather than an alteration in the underlying sequence of DNA. The epigenetic modifications influence gene expression by changing the state of chromatin, which underpins plant growth and dictates phenotypic responsiveness for extrinsic and intrinsic inputs. Epigenetic modifications, in addition to DNA sequence variation, improve breeding by giving useful markers. Also, it takes epigenome diversity into account to predict plant performance and increase crop production. In this review, emphasis has been given for summarising the role of epigenetic changes in epibreeding for crop improvement.

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The miR164-dependent regulatory pathway in developing maize seed

Cited by 25 publications

References 65 publications

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

Genomic identification and characterization of MYC family genes in wheat (Triticum aestivum L.)

Epigenetics and its role in effecting agronomical traits

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