Limits...
Seed after-ripening is a discrete developmental pathway associated with specific gene networks in Arabidopsis.

Carrera E, Holman T, Medhurst A, Dietrich D, Footitt S, Theodoulou FL, Holdsworth MJ - Plant J. (2007)

Bottom Line: Both metabolism and perception of the phytohormone abscisic acid (ABA) are important in the initiation and maintenance of dormancy.However, molecular mechanisms that regulate the capacity for dormancy or germination through AR are unknown.It was shown that secondary dormancy states reinstate AR status-specific gene expression patterns.

View Article: PubMed Central - PubMed

Affiliation: Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.

ABSTRACT
After-ripening (AR) is a time and environment regulated process occurring in the dry seed, which determines the germination potential of seeds. Both metabolism and perception of the phytohormone abscisic acid (ABA) are important in the initiation and maintenance of dormancy. However, molecular mechanisms that regulate the capacity for dormancy or germination through AR are unknown. To understand the relationship between ABA and AR, we analysed genome expression in Arabidopsis thaliana mutants defective in seed ABA synthesis (aba1-1) or perception (abi1-1). Even though imbibed mutant seeds showed no dormancy, they exhibited changes in global gene expression resulting from dry AR that were comparable with changes occurring in wild-type (WT) seeds. Core gene sets were identified that were positively or negatively regulated by dry seed storage. Each set included a gene encoding repression or activation of ABA function (LPP2 and ABA1, respectively), thereby suggesting a mechanism through which dry AR may modulate subsequent germination potential in WT seeds. Application of exogenous ABA to after-ripened WT seeds did not reimpose characteristics of freshly harvested seeds on imbibed seed gene expression patterns. It was shown that secondary dormancy states reinstate AR status-specific gene expression patterns. A model is presented that separates the action of ABA in seed dormancy from AR and dry storage regulated gene expression. These results have major implications for the study of genetic mechanisms altered in seeds as a result of crop domestication into agriculture, and for seed behaviour during dormancy cycling in natural ecosystems.

Show MeSH
Venn diagram representations identifying after-ripening (AR)-regulated and AR-independent gene sets in 24-h imbibed seeds. Datasets are derived from Table S1; in each case ‘>’ indicates the upregulated gene set in the comparison. In each case sets used for comparison are indicated next to associated circles. The numbers of genes represented in the gene sets are shown within the intersecting and non-intersecting segments of the sets. Gene lists for all comparisons are presented in Table S2a,b. In all cases AR and dormant (D) refer to datasets of Ler wild-type seeds. (a) Identification of a gene set associated solely with germination potential in imbibed seeds (‘germination’ upregulated). (b) Identification of a gene set associated solely with stored (S)/AR imbibed seeds. (c) Identification of a gene set associated solely with fresh (F)/non-AR (dormant) imbibed seeds. A box-plot analysis showing statistical data associated with the different gene groups is given in Figure S1.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2254144&req=5

fig03: Venn diagram representations identifying after-ripening (AR)-regulated and AR-independent gene sets in 24-h imbibed seeds. Datasets are derived from Table S1; in each case ‘>’ indicates the upregulated gene set in the comparison. In each case sets used for comparison are indicated next to associated circles. The numbers of genes represented in the gene sets are shown within the intersecting and non-intersecting segments of the sets. Gene lists for all comparisons are presented in Table S2a,b. In all cases AR and dormant (D) refer to datasets of Ler wild-type seeds. (a) Identification of a gene set associated solely with germination potential in imbibed seeds (‘germination’ upregulated). (b) Identification of a gene set associated solely with stored (S)/AR imbibed seeds. (c) Identification of a gene set associated solely with fresh (F)/non-AR (dormant) imbibed seeds. A box-plot analysis showing statistical data associated with the different gene groups is given in Figure S1.

Mentions: Cohorts of genes that were AR-associated or expressed independently of AR were obtained from comparisons of differentially regulated genes (Figure 3). Comparison of genes from F, D or S AR differentially expressed gene sets (Table S1) identified 15 of which expression was AR-independent and associated solely with germination potential (‘Germination’, Figure 3a; Table S2), 19 genes common to all S-AR sets (AR upregulated, Figure 3b, which includes the gene LPP2 that removes sensitivity to ABA during germination) and 103 common to F-D sets (AR downregulated, Figure 3c, which includes ABA1, involved in ABA synthesis). The expression patterns of representative members of each set was measured in WT and mutant seeds from 0–48 h of imbibition using quantitative (Q)RT-PCR (Figure S2). For each gene, similar biases in expression in F and S seeds were seen to those observed in transcriptome experiments.


Seed after-ripening is a discrete developmental pathway associated with specific gene networks in Arabidopsis.

Carrera E, Holman T, Medhurst A, Dietrich D, Footitt S, Theodoulou FL, Holdsworth MJ - Plant J. (2007)

Venn diagram representations identifying after-ripening (AR)-regulated and AR-independent gene sets in 24-h imbibed seeds. Datasets are derived from Table S1; in each case ‘>’ indicates the upregulated gene set in the comparison. In each case sets used for comparison are indicated next to associated circles. The numbers of genes represented in the gene sets are shown within the intersecting and non-intersecting segments of the sets. Gene lists for all comparisons are presented in Table S2a,b. In all cases AR and dormant (D) refer to datasets of Ler wild-type seeds. (a) Identification of a gene set associated solely with germination potential in imbibed seeds (‘germination’ upregulated). (b) Identification of a gene set associated solely with stored (S)/AR imbibed seeds. (c) Identification of a gene set associated solely with fresh (F)/non-AR (dormant) imbibed seeds. A box-plot analysis showing statistical data associated with the different gene groups is given in Figure S1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2254144&req=5

fig03: Venn diagram representations identifying after-ripening (AR)-regulated and AR-independent gene sets in 24-h imbibed seeds. Datasets are derived from Table S1; in each case ‘>’ indicates the upregulated gene set in the comparison. In each case sets used for comparison are indicated next to associated circles. The numbers of genes represented in the gene sets are shown within the intersecting and non-intersecting segments of the sets. Gene lists for all comparisons are presented in Table S2a,b. In all cases AR and dormant (D) refer to datasets of Ler wild-type seeds. (a) Identification of a gene set associated solely with germination potential in imbibed seeds (‘germination’ upregulated). (b) Identification of a gene set associated solely with stored (S)/AR imbibed seeds. (c) Identification of a gene set associated solely with fresh (F)/non-AR (dormant) imbibed seeds. A box-plot analysis showing statistical data associated with the different gene groups is given in Figure S1.
Mentions: Cohorts of genes that were AR-associated or expressed independently of AR were obtained from comparisons of differentially regulated genes (Figure 3). Comparison of genes from F, D or S AR differentially expressed gene sets (Table S1) identified 15 of which expression was AR-independent and associated solely with germination potential (‘Germination’, Figure 3a; Table S2), 19 genes common to all S-AR sets (AR upregulated, Figure 3b, which includes the gene LPP2 that removes sensitivity to ABA during germination) and 103 common to F-D sets (AR downregulated, Figure 3c, which includes ABA1, involved in ABA synthesis). The expression patterns of representative members of each set was measured in WT and mutant seeds from 0–48 h of imbibition using quantitative (Q)RT-PCR (Figure S2). For each gene, similar biases in expression in F and S seeds were seen to those observed in transcriptome experiments.

Bottom Line: Both metabolism and perception of the phytohormone abscisic acid (ABA) are important in the initiation and maintenance of dormancy.However, molecular mechanisms that regulate the capacity for dormancy or germination through AR are unknown.It was shown that secondary dormancy states reinstate AR status-specific gene expression patterns.

View Article: PubMed Central - PubMed

Affiliation: Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.

ABSTRACT
After-ripening (AR) is a time and environment regulated process occurring in the dry seed, which determines the germination potential of seeds. Both metabolism and perception of the phytohormone abscisic acid (ABA) are important in the initiation and maintenance of dormancy. However, molecular mechanisms that regulate the capacity for dormancy or germination through AR are unknown. To understand the relationship between ABA and AR, we analysed genome expression in Arabidopsis thaliana mutants defective in seed ABA synthesis (aba1-1) or perception (abi1-1). Even though imbibed mutant seeds showed no dormancy, they exhibited changes in global gene expression resulting from dry AR that were comparable with changes occurring in wild-type (WT) seeds. Core gene sets were identified that were positively or negatively regulated by dry seed storage. Each set included a gene encoding repression or activation of ABA function (LPP2 and ABA1, respectively), thereby suggesting a mechanism through which dry AR may modulate subsequent germination potential in WT seeds. Application of exogenous ABA to after-ripened WT seeds did not reimpose characteristics of freshly harvested seeds on imbibed seed gene expression patterns. It was shown that secondary dormancy states reinstate AR status-specific gene expression patterns. A model is presented that separates the action of ABA in seed dormancy from AR and dry storage regulated gene expression. These results have major implications for the study of genetic mechanisms altered in seeds as a result of crop domestication into agriculture, and for seed behaviour during dormancy cycling in natural ecosystems.

Show MeSH