Regulation of Wheat Seed Dormancy by After-Ripening Is Mediated by Specific Transcriptional Switches That Induce Changes in Seed Hormone Metabolism and Signaling

<div><p>Treatments that promote dormancy release are often correlated with changes in seed hormone content and/or sensitivity. To understand the molecular mechanisms underlying the role of after-ripening (seed dry storage) in triggering hormone related changes and dormancy decay in wheat (<i>Triticum aestivum</i>), temporal expression patterns of genes related to abscisic acid (ABA), gibberellin (GA), jasmonate and indole acetic acid (IAA) metabolism and signaling, and levels of the respective hormones were examined in dormant and after-ripened seeds in both dry and imbibed states. After-ripening mediated developmental switch from dormancy to germination appears to be associated with declines in seed sensitivity to ABA and IAA, which are mediated by transcriptional repressions of <i>PROTEIN PHOSPHATASE 2C</i>, <i>SNF1-RELATED PROTEIN KINASE2</i>, <i>ABA INSENSITIVE5</i> and <i>LIPID PHOSPHATE PHOSPHTASE2</i>, and <i>AUXIN RESPONSE FACTOR</i> and <i>RELATED TO UBIQUITIN1</i> genes. Transcriptomic analysis of wheat seed responsiveness to ABA suggests that ABA inhibits the germination of wheat seeds partly by repressing the transcription of genes related to chromatin assembly and cell wall modification, and activating that of GA catabolic genes. After-ripening induced seed dormancy decay in wheat is also associated with the modulation of seed IAA and jasmonate contents. Transcriptional control of members of the <i>ALLENE OXIDE SYNTHASE</i>, <i>3-KETOACYL COENZYME A THIOLASE</i>, <i>LIPOXYGENASE</i> and <i>12-OXOPHYTODIENOATE REDUCTASE</i> gene families appears to regulate seed jasmonate levels. Changes in the expression of GA biosynthesis genes, <i>GA 20-OXIDASE</i> and <i>GA 3-OXIDASE</i>, in response to after-ripening implicate this hormone in enhancing dormancy release and germination. These findings have important implications in the dissection of molecular mechanisms underlying regulation of seed dormancy in cereals.</p> </div

Comparison of the transcript abundance of IAA metabolic genes and seed IAA content.

<p>IAA metabolism pathway in plants excluding the Brassicaceae species specific pathway (A). Expression of probesets annotated as IAA metabolic genes in log₂ fold change during imbibition of dormant (D-12/D-0, D-24/D-0 and D-24/D-0) and after-ripened (AR-12/AR-0, AR-24/AR-0 and AR-24/AR-0) seeds as shown in the first column of the heat map, between dormant and after-ripened seeds in both dry and imbibed states (AR-0/D-0, AR-12/D-12 and AR-24/D-24) and between water and ABA imbibed after-ripened seeds (AR-24/AR-24+ABA) as shown in the second column in each heat map (B). Determination of the fold changes in expression of each probeset is as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone-0056570-g002" target="_blank">Figure 2</a>. Log₂ and linear scaled fold changes in expression of the probesets and the respective <i>P</i> values can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone.0056570.s003" target="_blank">Table S2</a>. IAA content of D and AR seeds in dry (0 days after imbibition [HAI]) and imbibed (12 and 24 HAI) states (C). Data are means of IAA measurements from three independent biological replicates ± SE. Trp, tryptophan; TAM, tryptamine; IAAld, indole-3-acetaldehyde; IPA, indole-3-pyruvic acid; IAA, indole-3-acetic acid; IAM, indole-3-acetamide; TAA, tryptophan aminotransferase; YUC, YUCCA; AMI1, indole-3-acetamide hydrolase; ILR, IAA-leucine resistant 1; IAR; IAA-alanine resistant; ILL; IAA-leucine resistant 1-like; TDC, tyrosine decarboxylase.</p

Imbibed dormant (D) and after-ripened (AR) seeds of wheat cv. AC Domain.

<p>Seeds imbibed in water (D and AR) and 50 µM ABA (AR) at 24, 36 and 48 h after imbibition (HAI).</p

Transcript abundance of jasmonate metabolic genes, and seed jasmonic acid (JA) and JA-isoleucine (JA-Ile) content.

<p>Jasmonate metabolism pathway in plants (A). Expression of probesets annotated as jasmonate metabolic genes in log₂ fold change during imbibition of dormant (D-12/D-0, D-24/D-0 and D-24/D-0) and after-ripened (AR-12/AR-0, AR-24/AR-0 and AR-24/AR-0) seeds as shown in the first column of the heat map, between dormant and after-ripened seeds in both dry and imbibed states (AR-0/D-0, AR-12/D-12 and AR-24/D-24) and between water and ABA imbibed after-ripened seeds (AR-24/AR-24+ABA) as shown in the second column in each heat map (B). Determination of the fold changes in expression of each probeset is as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone-0056570-g002" target="_blank">Figure 2</a>. Log₂ and linear scaled fold changes in expression of the probesets and the respective <i>P</i> values can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone.0056570.s003" target="_blank">Table S2</a>. JA and JA-Ile content of D and AR seeds in dry (0 days after imbibition [HAI]) and imbibed (12 and 24 HAI) states (C). Data are means of JA and JA-Ile measurements from three independent biological replicates ± SE. DAD, defender against cell death; LOX; lipoxygenase; 13-HPOT,13-hydroperoxylinolenic acid; AOS, allene oxide synthase; 12, 13-EOT, 12,13 epoxy-octadecatrienoic acid; AOC, allene oxide cyclase; cis-(+)-OPDA, cis-(+) -12-oxo phytodienoic acid; OPR3, 12-oxophytodienoate reductase; OPC-8∶0, 3-oxo-2-(2′-<i>Z</i>-pentenyl)-cyclopentane-1-octanoic acid; ACS, acyl-coenzyme A synthetase; ACX, acyl-coenzyme A oxidase; MFP, multifunctional protein; KAT, 3-ketoacyl coenzyme A thiolase; TEase; acyl-coenzyme A thioesterase; JAR, jasmonate resistant.</p

Comparison of the transcript abundance of abscisic acid (ABA) signaling genes.

<p>A model for ABA signaling pathway in plants (A). Expression of probesets annotated as ABA signaling genes in log₂ fold change during imbibition of dormant (D-12/D-0, D-24/D-0 and D-24/D-0) and after-ripened (AR-12/AR-0, AR-24/AR-0 and AR-24/AR-0) seeds as shown in the first column of the heat map, between dormant and after-ripened seeds in both dry and imbibed states (AR-0/D-0, AR-12/D-12 and AR-24/D-24) and between water and ABA imbibed after-ripened seeds (AR-24/AR-24+ABA) as shown in the second column in each heat map (B). Determination of the fold changes in expression of each probeset is as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone-0056570-g002" target="_blank">Figure 2</a>. Log₂ and linear scaled fold changes in expression of the probesets and the respective <i>P</i> values can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone.0056570.s003" target="_blank">Table S2</a>. PYL, pyrabactin resistance like; PP2C, protein phosphatase 2C; SnRK, SNF1-related protein kinase2; AIP, ABI3-interacting protein 2; ABF, ABA responsive element binding factor; LPP; lipid phosphate phosphatase; SKP, S-phase kinase-associated protein; ABI3/4/5, ABA insensitive 3/4/5.</p

Comparison of the transcript abundance of gibberellin (GA) metabolic genes.

<p>The GA metabolism pathway in plants (A). Expression of probesets annotated GA metabolic genes in log₂ fold change during imbibition of dormant (D-12/D-0, D-24/D-0 and D-24/D-0) and after-ripened (AR-12/AR-0, AR-24/AR-0 and AR-24/AR-0) seeds as shown in the first column of the heat map, between dormant and after-ripened seeds in both dry and imbibed states (AR-0/D-0, AR-12/D-12 and AR-24/D-24) and between water and ABA imbibed after-ripened seeds (AR-24/AR-24+ABA) as shown in the second column in each heat map (B). Determination of the fold changes in expression of each probeset is as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone-0056570-g002" target="_blank">Figure 2</a>. Log₂ and linear scaled fold changes in expression of the probesets and the respective <i>P</i> values can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone.0056570.s003" target="_blank">Table S2</a>. Relative transcript level of <i>TaGA3ox2</i> in D-0, D-12 and D-24, and AR-0, AR-12 AR-24 and AR-24+ABA wheat seeds (C). Transcript level was determined using Taβactin as the reference gene, and then expressed relative to that in D-0 seeds, which was arbitrarily set to a value of 1. Data are means of 2 to 3 independent biological replicates ± SE. Different letters between seed samples within each imbibition time indicate statistically significant difference in transcript abundance at <i>P</i>≤0.05. GGDP, geranyl geranyl diphosphate CDP, <i>ent</i>-copalyl diphosphate; CPS, ent-copalyl diphosphate synthase KS, ent-kaurene synthase KO, ent-kaurene oxidase KAO ent-kaurenoic acid oxidase GA20ox, gibberellin 20 oxidase GA3ox, gibberellin 3 oxidase; GA2ox, gibberellin 2 oxidase.</p

Percentage germination of dormant and after-ripened seeds of wheat cv. AC Domain imbibed in water and ABA solution.

a<p>Data are means ± SE, n = 3 (n refers to a batch of 25 seeds).</p>b<p>Seeds were imbibed with 50 µM ABA solution.</p

Probesets differentially expressed in dormant (D) and after-ripened (AR) seeds in dry and imbibed states.

<p>Comparisons of imbibed/dry (24 HAI D/Dry D, 24 HAI AR/Dry AR and 24 HAI AR+ABA/Dry AR) and imbibed/imbibed (24 HAI AR/24 HAI D, 24HAI AR+ABA/24 HAI D, 24 HAI AR/24 HAI AR+ABA) samples of D and AR seeds (A, B). The Venn diagrams show the number of significantly upregulated and downregulated probesets in each comparison (cutoff values fourfold change and <i>P</i>≤0.05). Probesets regulated in common are shown by the overlapping/intersecting region. Principal component analysis applied to the transcriptome dataset derived from seven samples (C); dry dormant seeds (D-0), dormant seeds imbibed in water for 12 (D-12) and 24 (D-24) h; dry after-ripened seeds (AR-0), after-ripened seeds imbibed in water for 12 (AR-12) and 24 (AR-24) h, and after ripened seeds imbibed for 24 h in 50 µM ABA (AR-24+ABA).</p

Comparison of the transcript abundance of auxin signaling genes.

<p>Molecular model for IAA signaling pathways in plants (A). Expression of probesets annotated as IAA signaling genes in log₂ fold change during imbibition of dormant (D-12/D-0, D-24/D-0 and D-24/D-0) and after-ripened (AR-12/AR-0, AR-24/AR-0 and AR-24/AR-0) seeds as shown in the first column of the heat map, between dormant and after-ripened seeds in both dry and imbibed states (AR-0/D-0, AR-12/D-12 and AR-24/D-24) and between water and ABA imbibed after-ripened seeds (AR-24/AR-24+ABA) as shown in the second column in each heat map (B). Determination of the fold changes in expression of each probeset is as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone-0056570-g002" target="_blank">Figure 2</a>. Log₂ and linear scaled fold changes in expression of the probesets and the respective <i>P</i> values can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone.0056570.s003" target="_blank">Table S2</a>. TIR, transport inhibitor response; AXR; auxin-resistant; Aux/IAA, auxin/indole-3-acetic acid; RUB, related to ubiquitin; SCF; Skp1-cullin-F-box; ARF, auxin response factor; ABP, auxin binding protein.</p

Comparison of the transcript abundance of gibberellin (GA) signaling genes.

<p>Molecular model for GA signaling pathways in plants (A). Changes in expression of probesets annotated as GA signaling genes in log₂ fold change during imbibition of dormant (D-12/D-0, D-24/D-0 and D-24/D-0) and after-ripened (AR-12/AR-0, AR-24/AR-0 and AR-24/AR-0) seeds as shown in the first column of the heat map, between dormant and after-ripened seeds in both dry and imbibed states (AR-0/D-0, AR-12/D-12 and AR-24/D-24) and between water and ABA imbibed after-ripened seeds (AR-24/AR-24+ABA) as shown in the second column in each heat map (B). Determination of the fold changes in expression of each probeset is as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone-0056570-g002" target="_blank">Figure 2</a>. Log₂ and linear scaled fold changes in expression of the probesets and the respective <i>P</i> values can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056570#pone.0056570.s003" target="_blank">Table S2</a>. GPA, G protein α-sub unit; GID, GA insensitive dwarf; SCF; Skp1-cullin-F-box; SLY, sleepy1; Rht, reduced height; GAMYB, GA-regulated MYB transcription factor; KGM; kinase associated with GAMYB; PKL, pickel; SPY, spindly.</p