Research ArticlePLANT SCIENCES

Transcriptional landscapes of floral meristems in barley

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Science Advances  28 Apr 2021:
Vol. 7, no. 18, eabf0832
DOI: 10.1126/sciadv.abf0832
  • Fig. 1 Tissue-specific transcriptomes of barley meristems and organs.

    (A) Profile views of barley spike developmental stages from the vegetative apex (VA) to white anther (WA) stage used for RNA-seq analysis (assembled images). Colors depict spike tissues that were captured by LCM for transcriptome profiling. Meristematic tissues from vegetative organs [leaf, 21 days after germination (DAG) (LB); root tip at 5 DAG (RT)] were used as control samples. (B) Representative cryosections with marked tissues (green or red) at different developmental stages (top right) for LCM-based isolation. (C) Merged numbers of transcripts expressed in individual spike subregions and complete spikes (R2) during development (TPM ≥ 1). Number of high confidence (HC) and sum of low confidence (LC) and HC genes (All) are given in bar charts. (D) Data representation by PCA for all samples, including reference and control samples, and spike tissues. (E) Heatmap of the top 50 domain-specific genes up- or down-regulated in IM, CS, and LS during spike development found by Pearson correlation. Normalized, log2-transformed expression values are depicted by color code ranging from blue (low expression) to red (high expression). AP, awn primordia; GP, glume primordia; LP, lemma primordia; R1, reference/provascular tissue; SP, stamen primordia.

  • Fig. 2 Expression profiles of domain-specific genes displayed by the barley spike meristem eFP browser and verification by WISH.

    (A to C) Candidate genes HORVU2Hr1G095210 [homeobox-leucine zipper family/HvHD-zip (A)], HORVU7Hr1G054220 [HvMADS7 (B)], and HORVU4Hr1G007040 [VRS5/HvTB1 (C)] were selected on the basis of their specific expression in spike subdomains according to our transcript dataset. Spikes treated with antisense (T7) and sense/T3 (negative control) probes are shown in insets, and arrows depict digoxigenin (DIG) signals. Data can be queried from the ePlant browser through http://bar.utoronto.ca/eplant_barley/.

  • Fig. 3 Transcriptional signatures of VA and IM as well as LRs and SRs reflect floral transition and formation of reproductive meristems.

    (A) Differential expression of gene family members between VA and IM defines floral transition. (I) GO term enrichment in DEGs (log2 FC > 1; FDR-adjusted P < 0.05) between VA and IM. Heatmap depicts the top 20 enriched categories in DEGs, and color saturation corresponds to degree of enrichment. (II) Heatmap display of gene expression levels of the top 50 differentially expressed TFs in VA and IM according to fold changes. Main TF families are assigned on the left. (B) The transcriptome LR and SR shows distinct differences associated with formation of reproductive meristems. (I) GO term enrichment in DEGs between LR and SR. Heatmap depicts the top 20 significantly enriched categories in DEGs, and color saturation corresponds to degree of enrichment. (II) Heatmap display of gene expression levels of DEGs between LR and SR. Unit variance–scaled, median-centered TPM values for each biological replicate are depicted by color code: red, high; blue, low expression. Labeled SEM pictures depict captured tissues used for comparison.

  • Fig. 4 Differential transcriptomes of CS and LS tissues.

    The UpSet plots showing genes up-regulated in CS (A) and LS (B) tissues at TM, GP, LP, SP, and AP stages. Set size on the x axis defines the total number of DEGs identified in each developmental stage, whereas the interaction size on the y axis depicts the number of DEGs unique to each stage or common DEGs across developmental time points. (C) Coexpression clusters of DEGs identified by K-means clustering of CS and LS tissues. (D) Enriched GO terms (scaled −log10 FDR-adjusted P > 1.30) in the coexpression clusters identified from Fig. 1C. (E) Row-type gene expression in CS and LS from TM to AP.

  • Fig. 5 WGCNA coexpression modules for CS and LS.

    (A) Expression shapes of eight LS-specific modules. Expression patterns of CS and LS tissues are depicted in white and orange, respectively. LS up-regulated modules labeled as LS-up-early or LS-up-late. (B) Gene regulatory network of the LS-M1 module. Network hub nodes are highlighted as yellow ellipses or triangles (TFs). Nodes in green indicate genes essential for organ boundary formation/signaling or meristem maintenance. Small ellipses or triangles in the periphery represent remaining nodes in the LS-M1 coexpression network. Gray lines connecting nodes represent edges of the network. (C) Descriptions for hub nodes and other nodes deemed to be involved in organ boundary formation/meristem maintenance in LS-M1 module. (D) Expression heatmap of genes known to be involved in organ boundary formation/signaling and meristem maintenance. The heatmap is partitioned into three groups based on expression patterns in CS and LS tissues. The first group has similar expression tendencies in CS and LS. The second group shows higher expression in LS at TM, GP, LP, SP, and AP stages. The third group depicts higher expression in LS mainly at the TM stage. Genes highlighted with asterisks represent characterized genes involved in organ boundary formation and meristem maintenance (table S11).

  • Fig. 6 Phenotypes of novel regulators for LS development.

    Expression patterns of HvDEP1 (A, I), HvBOP1/2/CUL4 (B, I), and HvSPL14/IPA1 (C, I) identified from laser microdissected tissues of CS and LS. Spikes of Bowman and DEP1 allele BW-NIL(ari-e.1) (A, II), Flare and uniculm 4.24 (B, II), and Golden Promise (GP) and HvSPL14 RGEN KOs (C, II). LSs of Bowman and BW-NIL(ari-e.1) (A, II), Flare and uniculm 4.24 (B, II), and GP and HvSPL14 KOs (C, II). Morphometric comparison of LSs of Bowman and BW-NIL(ari-e.1) [A, III; n = 10 (wild type), 13 (mutant)], Flare and cul4.24 [B, III; n = 8 (wild type), 10 (mutant)], and Golden Promise and HvSPL14 KOs [C, III; n = 5 (wild type), 9 (mutant)]. Scale bars in (A, II), (B, II), and (C, II) depict the LS length excluding pedicel. ***P < 0.001; **P < 0.01. NS, not significant (two-tailed Student’s t test).

Supplementary Materials

  • Supplementary Materials

    Transcriptional landscapes of floral meristems in barley

    J. Thiel, R. Koppolu, C. Trautewig, C. Hertig, S. M. Kale, S. Erbe, M. Mascher, A. Himmelbach, T. Rutten, E. Esteban, A. Pasha, J. Kumlehn, N. J. Provart, S. Vanderauwera, C. Frohberg, T. Schnurbusch

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