A Regulatory Network-Based Approach Dissects Late Maturation Processes Related to the Acquisition of Desiccation Tolerance and Longevity of Medicago truncatula Seeds

Abstract

In seeds, desiccation tolerance (DT) and the ability to survive the dry state for prolonged periods of time (longevity) are two essential traits for seed quality that are consecutively acquired during maturation. Using transcriptomic and metabolomic profiling together with a conditional-dependent network of global transcription interactions, we dissected the maturation events from the end of seed filling to final maturation drying during the last 3 weeks of seed development in Medicago truncatula. The network revealed distinct coexpression modules related to the acquisition of DT, longevity, and pod abscission. The acquisition of DT and dormancy module was associated with abiotic stress response genes, including late embryogenesis abundant (LEA) genes. The longevity module was enriched in genes involved in RNA processing and translation. Concomitantly, LEA polypeptides accumulated, displaying an 18-d delayed accumulation compared with transcripts. During maturation, gulose and stachyose levels increased and correlated with longevity. A seed-specific network identified known and putative transcriptional regulators of DT, including ABSCISIC ACID-INSENSITIVE3 (MtABI3), MtABI4, MtABI5, and APETALA2/ ETHYLENE RESPONSE ELEMENT BINDING PROTEIN (AtAP2/EREBP) transcription factor as major hubs. These transcriptional activators were highly connected to LEA genes. Longevity genes were highly connected to two MtAP2/EREBP and two basic leucine zipper transcription factors. A heat shock factor was found at the transition of DT and longevity modules, connecting to both gene sets. Gain-and loss-of-function approaches of MtABI3 confirmed 80% of its predicted targets, thereby experimentally validating the network. This study captures the coordinated regulation of seed maturation and identifies distinct regulatory networks underlying the preparation for the dry and quiescent states.

Regulatory network analysis reveals novel regulators of seed desiccation tolerance in Arabidopsis thaliana

“…Our comparative transcriptomic analysis of desiccation-tolerant and -intolerant mutants identified biological processes important for DT acquisition in seeds and coincides with findings from previous reports (3,37). However, there is no information available on TFs that regulate the genetic networks involved in the acquisition of seed DT.…”

“…In angiosperms, DT is acquired at the seed maturation stage, which involves a complex regulatory network (3,4) that activates a large subset of genes involved in a number of mechanisms that influence seed survival in the dry state. The set of genes required for seed DT includes genes encoding protective proteins such as late embryogenesis abundant (LEA) (5,6) and heat shock proteins (HSPs) (7), enzymes involved in scavenging reactive oxygen species (8) and the biosynthesis of protective compounds such as oligosaccharides (3,9), and antioxidants such as tocopherols and flavonoids (10,11).…”

Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways

“…These transcriptional regulators were projected onto MatNet ( Figure 2C, red symbols). Using data from the Medicago Gene Expression Atlas MtGEA (He et al, 2009) and our own transcriptomic data sets (Verdier et al, 2013), we also identified probes preferentially expressed in seeds in comparison to other tissues. Out of the 2912 nodes present in MatNet, 198 had transcription levels >100-fold higher in seed versus non-seed tissues (blue symbols).…”

“…This uncoupling suggests that the acquisition of these traits is controlled in part by independent regulatory pathways. To test this hypothesis and further elucidate the extent to which genes in the DT and longevity modules are under regulation of ABI3, we analyzed the transcriptomes of the desiccation-sensitive seeds of M. truncatula abi3 mutants at 32 and 40 DAP (Delahaie et al, 2013;Verdier et al, 2013) (Supplemental Data Set 5). These time points coincide with an increase in the transcript levels of the longevity-correlated genes in wild-type seeds.…”

“…Also, 14 probes showed transcript levels that significantly increased in the Mtabi3 mutant at either 32 or 40 DAP ( Figure 4A, red nodes). Whether the deregulation of the longevity module genes was due to a direct regulation by ABI3 or further downstream of the ABI3 pathway was investigated through the analysis of the transcriptome of hairy roots ectopically overexpressing M. truncatula ABI3 (GSE44291; Verdier et al, 2013). In the DT module, transcript levels of 43/143 (30%) nodes were significantly affected in the hairy roots, suggesting that their transcript levels are directly regulated by ABI3 ( Figure 4A, blue nodes) (Supplemental Data Set 5).…”