Methylation Status of Arabidopsis DNA Repair Gene Promoters During Agrobacterium Infection Reveals Epigenetic Changes in Three Generations

Joseph, Thannickal J.; Chandhini, S.; Das, Swati; Mysore, Sumukh; Shah, Meera

doi:10.1007/s11105-021-01287-6

Cited by 13 publications

(5 citation statements)

References 76 publications

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“…In our study, we validated these genes in V. radiata under the biotic stress of Agrobacterium infection. Previously 24-h infection of A. thaliana with A. tumefaciens altered DNA repair gene expression [39]. We also intend to perform similar studies in V. radiata.…”

Section: Selection Of Candidate Reference Genes Specificity and Effic...mentioning

confidence: 94%

Standardization of reference genes for real-time PCR analysis of Vigna radiata L. under Agrobacterium tumefaciens infection

Nivya,

Shah

2024

J App Biol Biotech

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Gene expression analysis using real-time polymerase chain reaction (PCR) requires the validation of a stable reference gene for normalization. Previously reported candidates may not be suitable for novel crops. Vigna radiata is a protein-rich legume crop used in many countries across the world. As this crop is recalcitrant to transformation such as most legumes, we were interested in V. radiata-Agrobacterium interaction studies. Toward this end, we wanted to identify a suitable reference for normalization under Agrobacterium-infections conditions. We selected seven candidate genes (Actin, Tubulin, Glyceraldehyde 3-phosphate dehydrogenase, Ubiquitin 10, Cyclophilin, 18S Ribosomal RNA, and F-box protein) and performed temporal-expression analysis using real-time PCR at 3 h, 24 h, and 4-day post-infection. When their Ct values were compared using the routinely used four algorithms, Normfinder, geNorm, Bestkeeper, and RefFinder, each suggested a different candidate gene. We narrowed-down to Cyclophilin by taking the statistical approach of using analysis of variance and Tukey honestly significant difference. Thus, our report signifies the use of additional statistical analyses in case of situations of discrepancies due to variable suggestions by software.

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Section: Selection Of Candidate Reference Genes Specificity and Effic...mentioning

confidence: 94%

Standardization of reference genes for real-time PCR analysis of Vigna radiata L. under Agrobacterium tumefaciens infection

Nivya,

Shah

2024

J App Biol Biotech

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“…Preliminary reports suggest that frequencies of SNVs and indels in Arabidopsis transformants are similar to background levels (Schouten et al., 2017), but comet assays suggest that tissues exposed to Agrobacterium experience some level of DNA damage. However, whether this is single‐stranded or double‐stranded damage remains unclear (Joseph et al., 2021).…”

Section: Insertion Of T‐dna Into Plant Genomesmentioning

confidence: 99%

Genomic consequences associated with Agrobacterium‐mediated transformation of plants

Thomson,

Dickinson,

Jacob

2023

The Plant Journal

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SUMMARYAttenuated strains of the naturally occurring plant pathogen Agrobacterium tumefaciens can transfer virtually any DNA sequence of interest to model plants and crops. This has made Agrobacterium‐mediated transformation (AMT) one of the most commonly used tools in agricultural biotechnology. Understanding AMT, and its functional consequences, is of fundamental importance given that it sits at the intersection of many fundamental fields of study, including plant‐microbe interactions, DNA repair/genome stability, and epigenetic regulation of gene expression. Despite extensive research and use of AMT over the last 40 years, the extent of genomic disruption associated with integrating exogenous DNA into plant genomes using this method remains underappreciated. However, new technologies like long‐read sequencing make this disruption more apparent, complementing previous findings from multiple research groups that have tackled this question in the past. In this review, we cover progress on the molecular mechanisms involved in Agrobacterium‐mediated DNA integration into plant genomes. We also discuss localized mutations at the site of insertion and describe the structure of these DNA insertions, which can range from single copy insertions to large concatemers, consisting of complex DNA originating from different sources. Finally, we discuss the prevalence of large‐scale genomic rearrangements associated with the integration of DNA during AMT with examples. Understanding the intended and unintended effects of AMT on genome stability is critical to all plant researchers who use this methodology to generate new genetic variants.

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“…Arabidopsis roots infected by cyst showed a huge change in DNA methylation and small RNA. In general, at the stage of infection, dynamic shifts take place ( Joseph et al, 2021 ). However, DNA methylation change can be associated with several regions; transcriptional and epigenetic changes are related to each other and affect genes responsible for defense ( Hewezi et al, 2017 ).…”

Section: Dynamics During Biotic Stressesmentioning

confidence: 99%

Moving Beyond DNA Sequence to Improve Plant Stress Responses

Saeed

Chaudhry²,

Bakhsh³

et al. 2022

Front. Genet.

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Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.

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Methylation Status of Arabidopsis DNA Repair Gene Promoters During Agrobacterium Infection Reveals Epigenetic Changes in Three Generations

Cited by 13 publications

References 76 publications

Standardization of reference genes for real-time PCR analysis of Vigna radiata L. under Agrobacterium tumefaciens infection

Standardization of reference genes for real-time PCR analysis of Vigna radiata L. under Agrobacterium tumefaciens infection

Genomic consequences associated with Agrobacterium‐mediated transformation of plants

Moving Beyond DNA Sequence to Improve Plant Stress Responses

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