Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process

Li, Jianying; Wang, Maojun; Li, Yajun; Zhang, Qinghua; Lindsey, Keith; Daniell, Henry; Jin, Shuangxia; Zhang, Xianlong

doi:10.1111/pbi.12988

Cited by 112 publications

(92 citation statements)

References 60 publications

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“…Similarly, a decreased methylation level has been reported in the SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK), LEC2, and WUS genes in the embryogenic calli of Boesenbergia rotunda [144]. Hypomethylation at the CHH sites in a promoter has been associated with the activation of some hormone related and WOX genes in G. hirsutum SE [126].…”

Section: Dna Methylationmentioning

confidence: 67%

“…The impact of 2,4-D on DNA methylation has also been confirmed in embryogenic cultures of Picea omorika [120], Malus xiaojinensis [121], and Glycine max [122]. The changes in global 5mC content in the auxin-induced embryogenic cultures of different plants have been associated with a differential gene expression [123], and an extensive modulation of the genes encoding both the methylases and demethylases of DNA has been attributed to the auxin-induced SE-transcriptomes of different plants, i.e., Populus trichocarpa, Arabidopsis, G. hirsutum, and G. max [122,[124][125][126]. In Arabidopsis, DOMAINS REARRANGED METHYLTRANSFERASE1-2 (DRM1-2) are required for de novo methylation via RNA-directed DNA methylation (RdDM) pathway, while METHYLTRANSFERASE1 (MET1) and CHROMOMETHYLASE1-3 (CMT1-3) maintain the methylation pattern during DNA replication.…”

Section: Dna Methylationmentioning

confidence: 99%

“…Several reports have indicated the interplay between DNA and histone methylation in the chromatin remodeling to be associated with the in vitro-induced developmental processes, including SE in G. hirsutum [126]. A decrease in the 5mC level and histone methylation at the H3K9me2 and H3K9me3 markers has been attributed to the positive regulation of gene expression during plant cell dedifferentiation [147,148].…”

Section: Histone Methylationmentioning

confidence: 99%

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Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Wójcikowska

Wójcik

Gaj

2020

IJMS

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Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.

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Section: Dna Methylationmentioning

confidence: 67%

Section: Dna Methylationmentioning

confidence: 99%

Section: Histone Methylationmentioning

confidence: 99%

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Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Wójcikowska

Wójcik

Gaj

2020

IJMS

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“…Plant regeneration via SE is highly genotype dependent [74,77]. Moreover, the growth state of each explant is divergent, thus, the phenotype can be different under the same external environment.…”

Section: Discussionmentioning

confidence: 99%

Full-Length Transcriptome Analysis of the ABCB, PIN/PIN-LIKES, and AUX/LAX Families Involved in Somatic Embryogenesis of Lilium pumilum DC. Fisch.

Song

Wang

Ren

et al. 2020

IJMS

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Plant cell totipotency is one of the 25 major topics in current scientific research, and somatic embryos are good experimental material for studying cell totipotency. Polar auxin transport plays an important regulatory role in somatic embryogenesis (SE). However, little is known about the auxin transport genes and their regulatory mechanisms in Lilium SE. In this study, we applied single-molecule real-time (SMRT) sequencing to Lilium pumilum DC. Fisch. for the first time and obtained a total of 119,649 transcripts, of which 14 encoded auxin transport genes. Correlation analyses between somatic embryo induction and gene expression under different treatments revealed that auxin transport genes, especially ATP-binding cassette (ABC) transporter B family member 21 (ABCB21) and PIN-FORMED (PIN) LIKES 7 (PILS7), may be key players in SE, and the necessary duration of picloram (PIC) treatment to induce SE is as short as 3 days. Our research provides valuable genetic information on Lilium pumilum, elucidating the candidate auxin transport genes involved in SE and their influencing factors. This study lays a foundation for elucidating the regulatory mechanism of auxin transport in SE.

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“…Elite cotton cultivar (Gossypium hirsutum: Jin668) was used as the transformation receptor as described in our previous protocol (Li et al, 2018). Putative transgenic T0 plants were obtained and screened by Polymerase Chain Reaction (PCR) analysis.…”

Section: Agrobacterium-mediated Transformation In Cottonmentioning

confidence: 99%

Whole genome sequencing reveals rare off‐target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9‐edited cotton plants

Manghwar

Liang

et al. 2018

Plant Biotechnology Journal

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173

129

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Summary The CRISPR /Cas9 system has been extensively applied for crop improvement. However, our understanding of Cas9 specificity is very limited in Cas9‐edited plants. To identify on‐ and off‐target mutation in an edited crop, we described whole genome sequencing ( WGS ) of 14 Cas9‐edited cotton plants targeted to three genes, and three negative (Ne) control and three wild‐type ( WT ) plants. In total, 4188–6404 unique single‐nucleotide polymorphisms ( SNP s) and 312–745 insertions/deletions (indels) were detected in 14 Cas9‐edited plants compared to WT , negative and cotton reference genome sequences. Since the majority of these variations lack a protospacer‐adjacent motif ( PAM ), we demonstrated that the most variations following Cas9‐edited are due either to somaclonal variation or/and pre‐existing/inherent variation from maternal plants, but not off‐target effects. Of a total of 4413 potential off‐target sites (allowing ≤5 mismatches within the 20‐bp sg RNA and 3‐bp PAM sequences), the WGS data revealed that only four are bona fide off‐target indel mutations, validated by Sanger sequencing. Moreover, inherent genetic variation of WT can generate novel off‐target sites and destroy PAM s, which suggested great care should be taken to design sg RNA for the minimizing of off‐target effect. These findings suggested that CRISPR /Cas9 system is highly specific for cotton plants.

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Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process

Cited by 112 publications

References 60 publications

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Full-Length Transcriptome Analysis of the ABCB, PIN/PIN-LIKES, and AUX/LAX Families Involved in Somatic Embryogenesis of Lilium pumilum DC. Fisch.

Whole genome sequencing reveals rare off‐target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9‐edited cotton plants

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