Predicting maternal auxin-signaling networks for seed dormancy regulation in Arabidopsis

Abstract

Auxin, like ABA, promotes seed dormancy, but how auxin promotes seed dormancy is not well understood. In studying seed dormancy regulation, we found that AUXIN SIGNALING F-BOX PROTEIN 1 (AFB1) and 5 maternally promoted seed dormancy and AFB1 had a stronger effect than AFB5. AFB1 and 5 were expressed in the funiculus and the chalazal seed coat at the mature embryo stage, and AFB1, not AFB5, was also transiently expressed in a small chalazal seed coat region surrounding the remnant funiculus during seed imbibition. Analysis of publically available datasets for genes expressed in the funiculus and seed coat at the mature embryo stage allowed the assignment of the six AFBs into two groups: TIR1, AFB1 and 4 as the first group with higher expression levels in the funiculus than in the chalazal seed coat, and AFB2, 3 and 5 as the second group with higher expression levels in the chalazal seed coat than in the funiculus. It was then assumed that auxin-upregulated and -downregulated genes associated with the first AFB group should be expressed at higher and lower levels in the funiculus than in the chalazal seed coat, respectively, and the reverse is assumed for those associated with the second AFB group. Three potential auxin-signaling networks including 30 genes were identified based on these assumptions and high linear correlation in expression within each group. These networks do not overlap in components and two-thirds of the genes are known or predicted to function in seed germination either positively or negatively. The presence of both positive and negative regulators in each of the networks is consistent with the plant’s ability to either remain dormant or go into germination in response to environmental conditions. The identified components of the networks also suggest interactions of auxin with other hormones in seed dormancy regulation.