An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment

Castano-Duque, Lina; Ghosal, S.; Quilloy, Fergie Ann; Mitchell‐Olds, Thomas; Dixit, Shalabh

doi:10.1093/plphys/kiab100

Cited by 16 publications

(10 citation statements)

References 65 publications

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“…We noted that rice CHR722 (Os07g0692600) and CHR742 (Os05g0392400) were similar to AtCLSY1 and AtCLSY4 , respectively (Fig.1D). The CHR722 was already denoted as OsCLSY1 , where it was implicated in anaerobic germination and seedling growth (Castano-Duque et al, 2021). In Arabidopsis , CLSYs have tissue-specific expression, while AtCLSY1 , AtCLSY2 are majorly expressed in leaf and flower buds, whereas AtCLSY3 , AtCLSY4 are majorly expressed in unfertilized ovules (Zhou et al, 2022).…”

Section: Resultsmentioning

confidence: 99%

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Pal,

Sundar G,

et al. 2023

Preprint

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Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable elements (TEs) and repeat-derived small(s)RNAs mediate epigenetic changes in plants. In imprinting, uniparental gene expression arises due to parent-specific epigenetic marks on one allele but not on the other. The importance of sRNAs and their regulation in endosperm development or in imprinting is poorly understood in crops. Here we show that a previously uncharacterized CLASSY (CLSY)-family chromatin remodeler named OsCLSY3 is essential for rice endosperm development and imprinting, acting as an upstream player in sRNA pathway. Comparative transcriptome and genetic analysis indicated its endosperm-preferred expression and its paternally imprinted nature. These important features were modulated by RNA-directed DNA methylation (RdDM) of tandemly arranged TEs in its promoter. Upon perturbation of OsCLSY3 in transgenic lines we observed defects in endosperm development and loss of around 70% of all sRNAs. Interestingly, well-conserved endosperm-specific sRNAs (siren) that are vital for reproductive fitness in angiosperms were dependent on OsCLSY3. We also observed many imprinted genes and seed development-associated genes under the control of CLSY3-dependent RdDM. These results support an essential role of OsCLSY3 in rice endosperm development and imprinting, and propose similar regulatory strategies involving CLSY3 homologs among other cereals.

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Section: Resultsmentioning

confidence: 99%

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Pal,

Sundar G,

et al. 2023

Preprint

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“…In the same study, an RIL population derived from a cross between 'Nipponbare' and IR64 highlighted a QTL on chromosome 1 (Hsu & Tung, 2015). Castano-Duque et al (2021) performed GWAS analysis using the 3K rice genome panel and identified a number of SNPs and revealed the involvement of CLASSY 1 (CLSY1), a gene involved in the RNA-directed DNA methylation pathway, in flooding during germination.…”

Section: Core Ideasmentioning

confidence: 99%

Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis

Thapa

Tabien²,

Thomson

et al. 2022

The Plant Genome

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The success of rice (Oryza sativa L.) germination and survival under submerged conditions is mainly determined by the rapid growth of the coleoptile to reach the water surface. Previous reports have shown the presence of genetic variability within rice accessions in the levels of flooding tolerance during germination or anaerobic germination (AG). Although many studies have focused on the physiological mechanisms of oxygen stress, few studies have explored the breadth of natural variation in AG tolerance‐related traits in rice. In this study, we evaluated the coleoptile lengths of a geographically diverse rice panel of 241 accessions, including global accessions along with elite breeding lines and released cultivars from the United States, under the normal and flooded conditions in laboratory and greenhouse environments. A genome‐wide association study (GWAS) was performed using a 7K single‐nucleotide polymorphism (SNP) array and the phenotypic data of normal coleoptile length, flooded coleoptile length, flooding tolerance index, and survival at 14 d after seeding (DAS). Out of the 30 significant GWAS quantitative trait loci (QTL) regions identified, 14 colocalized with previously identified candidate genes of AG tolerance, whereas 16 were potentially novel. Two rice accessions showing contrasting phenotypic responses to AG stress were selected for the transcriptomics study. The combined approach of GWAS and transcriptomics analysis identified 77 potential candidate genes related to AG tolerance. The findings of our study may assist rice improvement programs in developing rice cultivars with robust tolerance under flooding stress during germination and the early seedling stage.

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“…The modified RDA method from Forester et al, 2018 was done by replacing the genotype variable with the gene expression matrix and replacing its various environments with maize line, fungal treatment, and time after inoculation matrixes. This type of modified GEA-RDA analysis has been performed in rice by using gene expression data and independent variables such as flooded and nonflooded environments and different rice genotypes (Castano-Duque et al, 2021). These modifications allowed us to detect the groups of expressed genes that are significantly influenced by the maize line, treatment, and time simultaneously.…”

Section: Multivariate Linear Analysismentioning

confidence: 99%

Flavonoids Modulate the Accumulation of Toxins From Aspergillus flavus in Maize Kernels

et al. 2021

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Aspergillus flavus is an opportunistic fungal pathogen capable of producing aflatoxins, potent carcinogenic toxins that accumulate in maize kernels after infection. To better understand the molecular mechanisms of maize resistance to A. flavus growth and aflatoxin accumulation, we performed a high-throughput transcriptomic study in situ using maize kernels infected with A. flavus strain 3357. Three maize lines were evaluated: aflatoxin-contamination resistant line TZAR102, semi-resistant MI82, and susceptible line Va35. A modified genotype-environment association method (GEA) used to detect loci under selection via redundancy analysis (RDA) was used with the transcriptomic data to detect genes significantly influenced by maize line, fungal treatment, and duration of infection. Gene ontology enrichment analysis of genes highly expressed in infected kernels identified molecular pathways associated with defense responses to fungi and other microbes such as production of pathogenesis-related (PR) proteins and lipid bilayer formation. To further identify novel genes of interest, we incorporated genomic and phenotypic field data from a genome wide association analysis with gene expression data, allowing us to detect significantly expressed quantitative trait loci (eQTL). These results identified significant association between flavonoid biosynthetic pathway genes and infection by A. flavus. In planta fungal infections showed that the resistant line, TZAR102, has a higher fold increase of the metabolites naringenin and luteolin than the susceptible line, Va35, when comparing untreated and fungal infected plants. These results suggest flavonoids contribute to plant resistance mechanisms against aflatoxin contamination through modulation of toxin accumulation in maize kernels.

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An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment

Cited by 16 publications

References 65 publications

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis

Flavonoids Modulate the Accumulation of Toxins From Aspergillus flavus in Maize Kernels

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