Seed maturation associated transcriptional programs and regulatory networks underlying genotypic difference in seed dormancy and size/weight in wheat (Triticum aestivum L.)

Abstract

Background: Maturation forms one of the critical seed developmental phases and it is characterized mainly by programmed cell death, dormancy and desiccation, however, the transcriptional programs and regulatory networks underlying acquisition of dormancy and deposition of storage reserves during the maturation phase of seed development are poorly understood in wheat. The present study performed comparative spatiotemporal transcriptomic analysis of seed maturation in two wheat genotypes with contrasting seed weight/size and dormancy phenotype.

Results: The embryo and endosperm tissues of maturing seeds appeared to exhibit genotype-specific temporal shifts in gene expression profile that might contribute to the seed phenotypic variations. Functional annotations of gene clusters suggest that the two tissues exhibit distinct but genotypically overlapping molecular functions. Motif enrichment predicts genotypically distinct abscisic acid (ABA) and gibberellin (GA) regulated transcriptional networks contribute to the contrasting seed weight/size and dormancy phenotypes between the two genotypes. While other ABA responsive element (ABRE) motifs are enriched in both genotypes, the prevalence of G-box-like motif specifically in tissues of the dormant genotype suggests distinct ABA mediated transcriptional mechanisms control the establishment of dormancy during seed maturation. In agreement with this, the bZIP transcription factors that co-express with ABRE enriched embryonic genes differ with genotype. The enrichment of SITEIIATCYTC motif specifically in embryo clusters of maturing seeds irrespective of genotype predicts a tissue specific role for the respective TCP transcription factors with no or minimal contribution to the variations in seed dormancy.

Conclusion: The results of this study advance our understanding of the seed maturation associated molecular mechanisms underlying variation in dormancy and weight/size in wheat seeds, which is a critical step towards the designing of molecular strategies for enhancing seed yield and quality.

Keywords: Embryo; Endosperm; Genotype; Seed maturation; Transcriptome; Triticum aestivum; Wheat.

Fig. 1

Maturing seeds of wheat. Seeds of AC Domain and RL4452 genotypes from 20 to 50 DAA (a); changes in seed fresh weight, dry weight and moisture content during maturation - data are means ± SE (n = 20–23) and asterisks indicate statistically significant difference in seed fresh weight, dry weight and moisture content between the two genotypes (P < 0.05; t-Student test) (b); and difference in seed size and dormancy/germination phenotypes between mature seeds of the two genotypes (c)

Fig. 2

Number of probesets expressed in the embryo and/or endosperm during seed maturation. Probesets expressed at one or more time points (a, f) and at each time point (b–e, g–j) in the tissues of AC Domain (a–e) and RL4452 (f–j) were determined using MAS5.0 (P < 0.05)

Fig. 3

Principal component analysis of seed maturation transcripts. Embryo and endosperm of maturing AC Domain (a) and RL4452 (b) seeds. Aem, AC Domain embryo; Aen, AC Domain endosperm; Rem, RL4452 embryo; Ren, RL4452 endosperm at 20, 30, 40 and 50 days after anthesis. Principal components (PC)1 representing tissue identity (64.65% in AC Domain and 63.61% in RL4452) and PC2 representing developmental stages (19.74% in AC Domain and 18.55% in RL4452) with a cumulative percentage > 80% in each genotype

Fig. 4

Co-expression gene clusters of AC Domain (A). All probesets expressed in the embryo (a), endosperm (b) or both (c) at one or more time points were clustered based on the peak expression at a given time point(s) during seed maturation. The expression level of probesets in each of the embryo (em) (a), endosperm (en) (b) or both (mn) (c) tissues was determined relative to a time point with the highest RMA-normalized signal intensity, which was arbitrarily set to a value of 1 and represented by red color in the red-green scale shown on the left side of the heat map

Fig. 5

Co-expression gene clusters of RL4452 (R). Clustering of probesets expressed in the embryo (em) (a), endosperm (en) (b) or both (mn) (c) at one or more time points. Figure descriptions are as shown in Fig. 4

Fig. 6

Gene ontology enrichment in the co-expression clusters of maturing AC Domain (A) seeds. The GO terms listed are consistently enriched (P < 10e⁻³) in the embryo (em) or endosperm (en) clusters and the corresponding clusters of both (mn) tissues; P value is shown by the color scale at the top (1/log10). Enriched GO terms and the respective P values can be found in Additional file 8: Table S2. Black, grey and striped bars represent clusters with peak expression at early (20 DAA), mid (30 and 40 DAA) and late (50 DAA) phases of seed maturation, respectively. The white bar represents gene clusters with constitutive/random expression patterns

Fig. 7

Gene ontology enrichment in the co-expression clusters of maturing RL4452 (R) seeds. Figure descriptions are as shown in Fig. 6

Fig. 8

Promoter motif enrichment in the co-expression clusters of maturing AC Domain (A) seeds. Motif enrichments (P < 10e⁻³) are found in embryo (em) and endosperm (en) clusters corresponding to the same seed maturation phase or in tissue specific clusters; P value (1/log10) is shown by the color scale at the top. Enriched motifs and the respective P values can be found in Additional file 9: Table S3. Black, grey and striped bars represent clusters with peak expression at early (20 DAA), mid (30 and 40 DAA) and late (50 DAA) phases of seed maturation, respectively. The white bar represents gene clusters with constitutive/random expression patterns. Degenerate characters in the consensus sequence: K = G/T, S = C/G, R = G/A, Y = C/T

Fig. 9

Promoter motif enrichment in the co-expression clusters of maturing RL4452 (R) seeds. Figure descriptions are as shown in Fig. 8

Fig. 10

Predicted ABI5-ABRE mediated gene regulatory network during seed maturation. The transcription factor ABI5 is represented by the green parallelogram, the ABRE motif by the light blue hexagon, the seed maturation gene clusters by grey oval, and GO terms by the orange rectangles. Solid lines connect GO terms and motifs enriched in the respective gene cluster (P < 10e⁻³); the thickness of solid lines represent the P value in which thicker lines correspond to lower P values. Slash lines represent co-expression of ABI5 with the corresponding gene cluster. Dashed lines connect the ABI5 transcription factor with the predicted binding motifs

Fig. 11

Predicted TCP-Site II mediated gene regulatory network during seed maturation. The transcription factor TCP is represented by the green parallelogram, the Site II motif by the light blue hexagon, the seed maturation gene clusters by grey ovals and GO terms by the orange rectangles. Solid lines connect GO terms and motifs enriched in the respective gene cluster (P < 10e⁻³); the thickness of solid lines represent the P value in which thicker lines correspond to lower P values. Dashed lines connect the TCP transcription factor with the predicted binding motifs