Identification of GATA Transcription Factors in Brachypodium distachyon and Functional Characterization of BdGATA13 in Drought Tolerance and Response to Gibberellins

Guo, Jie; Bai, Xionghui; Dai, Keli; Yuan, Xiangyang; Guo, Peng; Zhou, Meixue; Shi, Weiping; Hao, Chenyang

doi:10.3389/fpls.2021.763665

Cited by 22 publications

(17 citation statements)

References 46 publications

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“…A GATA transcription factor was identified, and it is another type of zinc finger protein [ 29 ]. Numerous GATA TFs have been cited in literature for abiotic stress tolerance in plants.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress

Czajka

Nkongolo²

2022

PLoS ONE

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Plants have evolved heavy metal tolerance mechanisms to adapt and cope with nickel (Ni) toxicity. Decrypting whole gene expression of Trembling Aspen (Pinus tremuloides) under nickel stress could elucidate the nickel resistance/tolerance mechanisms. The main objectives of the present research were to 1) characterize the P. tremuloides transcriptome, and 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing. Illumina Sequencing generated 27–45 million 2X150 paired-end reads of raw data per sample. The alignment performed with StringTie Software added two groups of transcripts to the draft genome annotation. One group contained 32,677 new isoforms that match to 17,254 genes. The second group contained 17,349 novel transcripts that represent 16,157 novel genes. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. With the high stringency (two-fold change, FDR value ≤ 0.05 and logFC value ≥1 (upregulated) or ≤ -1 (downregulated), after GSEA analysis and filtering for gene set size, 575 gene sets were upregulated and 146 were downregulated in nickel resistant phenotypes compared to susceptible genotypes. For biological process, genes associated with translation were significantly upregulated while signal transduction and cellular protein process genes were downregulated in resistant compared to susceptible genotypes. For molecular function, there was a significant downregulation of genes associated with DNA binding in resistant compared to susceptible lines. Significant upregulation was observed in genes located in ribosome while downregulation of genes in chloroplast and mitochondrion were preponderant in resistant genotypes compared to susceptible. Hence, from a whole transcriptome level, an upregulation in ribosomal and translation activities was identified as the main response to Ni toxicity in the resistant plants. More importantly, this study revealed that a metal transport protein (Potrs038704g29436 –ATOX1-related copper transport) was among the top upregulated genes in resistant genotypes when compared to susceptible plants. Other identified upregulated genes associated with abiotic stress include genes coding for Dirigent Protein 10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar transporter, and thiamine thiazole synthase.

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“…A GATA transcription factor was identified, and it is another type of zinc finger protein [ 29 ]. Numerous GATA TFs have been cited in literature for abiotic stress tolerance in plants.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress

Czajka

Nkongolo²

2022

PLoS ONE

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“…The genes Zm00001d027874 , Zm00001d028936 , and Zm00001d040775 encode nuclear transcription factor Y subunit A1 (NFYA1), bZIP-transcription factor bZIP52, and GATA-transcription factor GATA27, respectively. These transcription factors and transcription factor families play important roles in plant development, growth, and abiotic stress responses ( Zhang et al 2016 ; Guo et al 2021 ; Zhang et al 2021 ; Li et al 2022 )⁠.…”

Section: Resultsmentioning

confidence: 99%

Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize

Crow

Nojoomi

et al. 2022

Molecular Biology and Evolution

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Maize is a staple food of smallholder farmers living in highland regions up to 4,000 meters above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggests the maize’s adaptation to these regions occurred largely independently, providing a case study for convergent evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence in gene regulation. Although the vast majority of evolutionary changes associated with highland adaptation were region-specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.

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“…The genes Zm00001d027874, Zm00001d028936 and Zm00001d040775 encode Nuclear transcription factor Y subunit A1 (NFYA1), bZIP transcription factor bZIP52, and GATA transcription factor GATA27, respectively. These transcription factors and transcription factor families play important roles in plant development, growth, and abiotic stress responses (Zhang et al 2016; Guo et al 2021; Zhang et al 2021; Li et al 2022)□.…”

Section: Resultsmentioning

confidence: 99%

Allele-specific expression reveals multiple paths to highland adaptation in maize

Crow

Nojoomi

et al. 2022

Preprint

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Maize is a staple food of smallholder farmers living in highland regions up to 4,000 meters above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggests the maize's adaptation to these regions occurred largely independently, providing a case study for parallel evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence. Our findings reveal a complex genetic architecture of cis-regulatory alleles underlying adaptation to highlands in maize. Although the vast majority of evolutionary changes associated with highland adaptation were region-specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.

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Identification of GATA Transcription Factors in Brachypodium distachyon and Functional Characterization of BdGATA13 in Drought Tolerance and Response to Gibberellins

Cited by 22 publications

References 46 publications

Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress

Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress

Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize

Allele-specific expression reveals multiple paths to highland adaptation in maize

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