An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison

Desiccation tolerance (DT) is the capacity to withstand total loss of cellular water. It is acquired during seed filling and lost just after germination. However, in many species, a germinated seed can regain DT under adverse conditions such as osmotic stress. The genes, proteins and metabolites that are required to establish this DT is referred to as the desiccome. It includes both a range of protective mechanisms and underlying regulatory pathways that remain poorly understood. As a first step toward the identification of the seed desiccome of Medicago truncatula, using updated microarrays we characterized the overlapping transcriptomes associated with acquisition of DT in developing seeds and the re-establishment of DT in germinated seeds using a polyethylene glycol treatment (−1.7 MPa). The resulting list contained 740 and 2829 transcripts whose levels, respectively, increased and decreased with DT. Fourty-eight transcription factors (TF) were identified including MtABI3, MtABI5 and many genes regulating flowering transition and cell identity. A promoter enrichment analysis revealed a strong over-representation of ABRE elements together with light-responsive cis-acting elements. In Mtabi5 Tnt1 insertion mutants, DT could no longer be re-established by an osmotic stress. Transcriptome analysis on Mtabi5 radicles during osmotic stress revealed that 13 and 15% of the up-regulated and down-regulated genes, respectively, are mis-regulated in the mutants and might be putative downstream targets of MtABI5 implicated in the re-establishment of DT. Likewise, transcriptome comparisons of the desiccation sensitive Mtabi3 mutants and hairy roots ectopically expressing MtABI3 revealed that 35 and 23% of the up-regulated and down-regulated genes are acting downstream of MtABI3. Our data suggest that ABI3 and ABI5 have complementary roles in DT. Whether DT evolved by co-opting existing pathways regulating flowering and cellular phase transition and cell identity is discussed

Improving Strategies via SMT Solving

We consider the problem of computing numerical invariants of programs by abstract interpretation. Our method eschews two traditional sources of imprecision: (i) the use of widening operators for enforcing convergence within a finite number of iterations (ii) the use of merge operations (often, convex hulls) at the merge points of the control flow graph. It instead computes the least inductive invariant expressible in the domain at a restricted set of program points, and analyzes the rest of the code en bloc. We emphasize that we compute this inductive invariant precisely. For that we extend the strategy improvement algorithm of [Gawlitza and Seidl, 2007]. If we applied their method directly, we would have to solve an exponentially sized system of abstract semantic equations, resulting in memory exhaustion. Instead, we keep the system implicit and discover strategy improvements using SAT modulo real linear arithmetic (SMT). For evaluating strategies we use linear programming. Our algorithm has low polynomial space complexity and performs for contrived examples in the worst case exponentially many strategy improvement steps; this is unsurprising, since we show that the associated abstract reachability problem is Pi-p-2-complete

Characterization of function of the GlgA2 glycogen/starch synthase in Cyanobacterium sp. Clg1 highlights convergent evolution of glycogen metabolism into starch granule aggregation

At variance with the starch-accumulating plants and most of the glycogen-accumulating cyanobacteria, Cyanobacterium sp. CLg1 synthesizes both glycogen and starch. We now report the selection of a starchless mutant of this cyanobacterium that retains wild-type amounts of glycogen. Unlike other mutants of this type found in plants and cyanobacteria, this mutant proved to be selectively defective for one of the two types of glycogen/starch synthase: GlgA2. This enzyme is phylogenetically related to the previously reported SSIII/SSIV starch synthase that is thought to be involved in starch granule seeding in plants. This suggests that, in addition to the selective polysaccharide debranching demonstrated to be responsible for starch rather than glycogen synthesis, the nature and properties of the elongation enzyme define a novel determinant of starch versus glycogen accumulation. We show that the phylogenies of GlgA2 and of 16S ribosomal RNA display significant congruence. This suggests that this enzyme evolved together with cyanobacteria when they diversified over 2 billion years ago. However, cyanobacteria can be ruled out as direct progenitors of the SSIII/SSIV ancestral gene found in Archaeplastida. Hence, both cyanobacteria and plants recruited similar enzymes independently to perform analogous tasks, further emphasizing the importance of convergent evolution in the appearance of starch from a preexisting glycogen metabolism network.Peer Reviewe

Identification of a molecular dialogue between developing seeds of Medicago truncatula and seedborne xanthomonads.

Plant pathogenic bacteria disseminate and survive mainly in association with seeds. This study addresses whether seeds are passive carriers or engage a molecular dialogue with pathogens during their development. We developed two pathosystems using Medicago truncatula with Xanthomonas alfalfae subsp. alfalfae (Xaa), the natural Medicago sp. pathogen and Xanthomonas campestris pv. campestris (Xcc), a Brassicaceae pathogen. Three days after flower inoculation, the transcriptome of Xcc-infected pods showed activation of an innate immune response that was strongly limited in Xcc mutated in the type three secretion system, demonstrating an incompatible interaction of Xcc with the reproductive structures. In contrast, the presence of Xaa did not result in an activation of defence genes. Transcriptome profiling during development of infected seeds exhibited time-dependent and differential responses to Xcc and Xaa. Gene network analysis revealed that the transcriptome of Xcc-infected seeds was mainly affected during seed filling whereas that of Xaa-infected seeds responded during late maturation. The Xcc-infected seed transcriptome exhibited an activation of defence response and a repression of targeted seed maturation pathways. Fifty-one percent of putative ABSCISIC ACID INSENSITIVE3 targets were deregulated by Xcc, including oleosin, cupin, legumin and chlorophyll degradation genes. At maturity, these seeds displayed decreased weight and increased chlorophyll content. In contrast, these traits were not affected by Xaa infection. These findings demonstrate the existence of a complex molecular dialogue between xanthomonads and developing seeds and provides insights into a previously unexplored trade-off between seed development and pathogen defence

Table ronde autres feuillus

The meeting on broad-leaved species other than Eucalyptus which took place at the AFOCEL-IVRO symposium in Bordaux (September 14-18, 1992), was focused more particularly on forest trees of tropical regions and on the development of breeding means and methods. Physiology, state of genetic resources and future breeding programs were discussed. / La table ronde sur le feuillus autres que l'eucalyptus qui a eu lieu lors du colloque de l'AFOCEL-IURO à Bordeaux (14-18 septembre 1992), s'est plus particulièrement intéressée aux arbres forestiers de la zone tropicale et aux moyens et méthodes à développer pour leur amélioration génétique : ont été abordés la physiologie, l'état des ressources génétiques et les programmes d'amélioration à mettre en oeuvre

Le programme de vergers à graines de l'état : une étape dans la stratégie de diffusion des variétés améliorées

The state seed stand program was conceived after the first results obtained in genetic breeding of forestry species. The value of the seeds produced depends mainly on the quality of the original stand. The rapid production of more performing varieties is now possible for some species. However, seed stands must not be considered as an obsolete technique since production stability in time presents advantages for regulatory status, diffusion and reduction of varietal risk. On the contrary, the consequences of production perennation will reduce the odds of producing new varieties of the Laricio Corsica pine of which the stand surface was overestimated. / Le programme des vergers à graines de l'état a été conçu à l'issue des premiers résultats obtenus en amélioration génétique des arbres forestiers. La valeur des graines produites dépend surtout de la qualité de la population initiale d'amélioration. Pour quelques espèces, il est maintenant possible de produire rapidement des variétés plus performantes. Cependant les vergers à graines ne doivent pas être considérés comme une technique obsolète, car la stabilité de la production dans le temps présente des avantages pour le statut réglementaire, la vulgarisation et la réduction du risque variétal. En revanche, les conséquences de la pérennité de la production vont limiter la possibilité de produire de nouvelles variétés pour le pin laricio de Corse dont la surface de verger a été surdimensionné

Synthèse thème 2 (préalable à l'amélioration)

The discussions are centered around the prerequisites to a breeding program; to know the structure of genetic variability; to have access to natural resources; to rapidly release varieties as performing as possible on the market. / Les discussions ont été centrées sur les préalables nécessaires au démarrage d'un programme d'amélioration ; connaître la structure de la variabilité génétique ; avoir accès aux ressources naturelles ; mettre rapidement sur le marché des variétés aussi performantes que possible

Les peupliers et les saules en complément de l'agriculture : rapport de synthèse

Synthesis of national reports presented by 19 countries on the relationships between agriculture and poplar cultivation. The association as cover crops is found only in hot and humid temperate climates. The association as alignments is more frequent in the North of the distribution area of regions submitted to regular wind or in fruit-producing regions. The laying out of trees in line is disappearing in most countries. China remains the country in which this type of association has reached the highest level of complexity. This report was presented in the 19th session of the International Poplar Committee in Spain on September 21-25, 1992. / Synthèse des rapports nationaux présentés par dix neuf pays sur le thème des relations entre populiculture et agriculture. L'association sous forme de cultures intercalaires se rencontre exclusivement sous des climats tempérés chauds et bien arrosés. L'association sous forme d'alignement est par contre plus fréquente au nord de l'aire de répartition dans des zones soumises à des vents réguliers, ou dans les zones de repoduction fruitière. Les plantations d'alignement sont en diminution dans la plupart des pays. La Chine reste le pays dans lequel cette forme d'association a atteint le niveau de complexité le plus élevé. Ce rapport était présenté à la 19ème session de la commission internationale du peuplier qui s'est tenue en Espagne du 21 au 25 septembre 1992