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Background Auxin is a major phytohormone involved in many developmental processes by controlling gene expression through a network of transcriptional regulators. In Arabidopsis thaliana, the auxin signalling network is made of 52 potentially interacting transcriptional regulators, activating or repressing gene expression. All the possible interactions were tested in two-way yeast-2-hybrid experiments. Our objective was to characterise this auxin signalling network and to quantify the influence of the dimerisation sequence dissimilarities on the interaction between transcriptional regulators. Results We applied model-based graph clustering methods relying on connectivity profiles between transcriptional regulators. Incorporating dimerisation sequence dissimilarities as explanatory variables, we modelled their influence on the auxin network topology using mixture of linear models for random graphs. Our results provide evidence that the network can be simplified into four groups, three of them being closely related to biological groups. We found that these groups behave differently, depending on their dimerisation sequence dissimilarities, and that the two dimerisation sub-domains might play different roles. Conclusions We propose here the first pipeline of statistical methods combining yeast-2-hybrid data and protein sequence dissimilarities for analysing protein-protein interactions. We unveil using this pipeline of analysis the transcriptional regulator interaction modes. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0254-7) contains supplementary material, which is available to authorized users.

The performances at typical ages P10 (weight at 10 days), P30, P70, DwG10/30 (average daily weight gain between 10 and 30 days) and DwG30/70 of 9642 Barbarine lambs were calculated according to F2, the conventional protocol, or a simplified protocol based on fitting von Bertalanffy’s function to two measurements at 42-day intervals, the first taking place between 2 and 60 days after birth of the lamb, and the actual birth weight (ABw: controlled at birth), a fixed Bw (FBw), i.e. the same for all lambs (FBw = 3.4 kg), or an estimated Bw (EBw) based on the first measurement (w) and the interval between birth and the first measurement (D) [(EBw = 2.71009 + 0.208313 w – 0.00578 w (60 – D) + 0.00016 w (60 – D)2]. The average loss of precision associated with the calculation of weights at typical ages was high for P10 (40– 45%), moderate for P30 (6–7%) and low for P70 (2–3%). The loss of precision associated with DwG10/30 was lower than that of the conventional protocol for an interval between birth and the first control between 15 and 45 days (15% maximum), and similar between 7 and 15 days’ intervals (20% maximum). These results suggest simplifying the F2 protocol to two or three measurements and a birth weight. The first measurement should be postponed to 46 days after birth, whereas the inter-val between successive controls may vary between 30 and 40 days, depending on an acceptable loss of precision on the estimation of performances at typical ages.

Growth monitoring data of two experimental sheep herds of Barbarine breed, collected during 31 years on 9642 lambs weighed at birth, then six times at 21-day intervals, were analyzed. Estimates obtained by fitting a global growth curve were compared to assessments carried within the “F2” conventional protocol of growth. Brody, logistic, Gompertz and von Bertalanffy functions were adequately adjusted to the seven controls. The fitting factors, coefficients of determination (R²) and residual sums of squares were estimated at 0.997 and 2.9, 0.997 and 3.0, 0.996 and 3.8, and 0.996 and 3.8, respectively, for the functions of von Bertalanffy, Gompertz, Logistic and Brody. The average weights at typical ages, estimated by the conventional method, were 3.4, 5.5, 9.1, 15.5, 18.2 and 22.2 kg at birth, 10, 30, 70, 90 and 120 days of age, respectively. The calculation of performances at typical ages by the conventional method was accompanied by a small loss of precision of 5, 2, 0.8 and 0.5% at 30, 70, 90 and 120 days, and by a sizeable drop of 25, 19, 12 and 10% of DWG10/30 (daily weight gain between 10 and 30 days), DWG30/70, DWG30/90 and DWG30/120, respectively. The loss of precision associated with DWG10/30 exceeded 50% for the interval birth - first control at 21 days because of a lower and imprecise extrapolation of the weight at 10 days.

International audience; Crop models and decision support system can be useful tools for researchers, teachers, scientists, extension educators, policy makers and planners to help or support the application and evaluation of sustainable and long term alternative management practices. Sunflower is an important oilseed crop that has the potential to bridge the gap between the consumption and domestic production of edible oil in developing countries such as Pakistan. Limited research has been conducted on the application of the OILCROP-SUN model for the simulation of growth and development of sunflower under different environmental conditions, especially in developing countries. Field experiments were conducted in three environments to study the impact of nitrogen (N) fertilizer on grain yield and quality. The objective of the present study was to evaluate the performance of the OILCROP-SUN model and to determine the effect of N on sunflower for three contrasting environments. The results showed that OILCROP-SUN model simulated well for growth, development and yield of sunflower hybrids in these three contrasting environments and under different management practices that included several genotypes and different nitrogen fertilizer application rates. The d values (index of agreement) for leaf area index (LAI) ranged from 88 to 97 under arid, 78 to 85 under semi- arid and 71 to 81 under sub- humid conditions. Similarly, d values for total dry matter (TDM) ranged between 90 and 94 under arid, 81 and 88 under semi-arid and 90 and 96 under sub-humid conditions, respectively while the percentage difference for grain yield ranged from 8.5 to 21% for different ecological conditions. The model also simulated LAI, TDM, grain yield and oil quality well under different environmental conditions of Pakistan and further studies should focus on application of the OILCROP-SUN model for variable agro-climatic regions where sunflower is an important crop.

Summary Growth regulation is an important aspect of plant adaptation during environmental perturbations. Here, the role of MULTIPASS (OsMPS), an R2R3-type MYB transcription factor of rice, was explored. OsMPS is induced by salt stress and expressed in vegetative and reproductive tissues. Over-expression of OsMPS reduces growth under non-stress conditions, while knockdown plants display increased biomass. OsMPS expression is induced by abscisic acid and cytokinin, but is repressed by auxin, gibberellin and brassinolide. Growth retardation caused by OsMPS over-expression is partially restored by auxin application. Expression profiling revealed that OsMPS negatively regulates the expression of EXPANSIN (EXP) and cell-wall biosynthesis as well as phytohormone signaling genes. Furthermore, the expression of OsMPS-dependent genes is regulated by auxin, cytokinin and abscisic acid. Moreover, we show that OsMPS is a direct upstream regulator of OsEXPA4, OsEXPA8, OsEXPB2, OsEXPB3, OsEXPB6 and the endoglucanase genes OsGLU5 and OsGLU14. The multiple responses of OsMPS and its target genes to various hormones suggest an integrative function of OsMPS in the cross-talk between phytohormones and the environment to regulate adaptive growth.

Publis013-agap-074; The ability to assimilate C and allocate non-structural carbohydrates (NSCs) to the most appropriate organs is crucial to maximize plant ecological or agronomic performance. Such C source and sink activities are differentially affected by environmental constraints. Under drought, plant growth is generally more sink than source limited as organ expansion or appearance rate is earlier and stronger affected than C assimilation. This favors plant survival and recovery but not always agronomic performance as NSC are stored rather than used for growth due to a modified metabolism in source and sink leaves. Such interactions between plant C and water balance are complex and plant modeling can help analyzing their impact on plant phenotype. This paper addresses the impact of trade-offs between C sink and source activities and plant production under drought, combining experimental and modeling approaches. Two contrasted monocotyledonous species (rice, oil palm) were studied. Experimentally, the sink limitation of plant growth under moderate drought was confirmed as well as the modifications in NSC metabolism in source and sink organs. Under severe stress, when C source became limiting, plant NSC concentration decreased. Two plant models dedicated to oil palm and rice morphogenesis were used to perform a sensitivity analysis and further explore how to optimize C sink and source drought sensitivity to maximize plant growth. Modeling results highlighted that optimal drought sensitivity depends both on drought type and species and that modeling is a great opportunity to analyze such complex processes. Further modeling needs and more generally the challenge of using models to support complex trait breeding are discussed.

Coconut is a cross pollinating palm, propagated only by seeds. Tissue culture is the only vegetative propagation method available for coconut. Consistent callogenesis was obtained by culturing unfertilised ovaries at -4 stage in CRI 72 medium containing 100 mu M 2,4-dichlorophenoxyacetic acid (2,4-D) and 0.1% activated charcoal. Callusing was improved by application of 9 mu M thidiazuron (TDZ). Embryogenic calli were subcultured onto somatic embryogenesis induction medium containing 66 mu M 2,4-D. Stunted growth was observed in the somatic embryos after subculture onto CRI 72 medium containing abscisic acid (ABA). Maturation of somatic embryos could be achieved in Y-3 medium without growth regulators. Conversion of somatic embryos was induced by adding gibberellic acid (GA(3)) to conversion medium containing 5 mu M 6-benzyladenine (BA) while 2-isopentyl adenine (2iP) increased the frequency of plant regeneration. A total of 83 plantlets was produced from 32 cultured ovaries.

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International audience; Using a genomic clone encoding a rice lipid transfer protein, LTP1, we analysed the activity of the 5 region of the Ltp1 gene in transgenic rice (Oryza sativa L.) during plant development and under pathogen attack. The −1176/+13, −556/+13 and −284/+13 regions of the promoter were fused upstream from the uidA reporter gene and nos 3 polyadenylation signal, resulting in the p 1176Gus, p 556Gus and p 284Gus constructs which were transferred to rice by microprojectile bombardment. Histochemical and fluorometric GUS assays and in situ detection of uidA transcripts in transgenic homozygous lines harbouring the p 1176Gus construct demonstrated that the Ltp1 promoter is preferentially active in aerial vegetative and reproductive organs and that both specificity and level of expression are regulated during organ development. In leaf sheath, GUS activity which is initially strictly localized in the epidermis of growing tissue, becomes restricted to the vascular system in mature tissues. In expanded leaf blade, expression of the uidA gene was restricted to the cutting level suggesting inducibility by wounding. Strong activity was detected in lemma and palea, sterile glumes, and immature anther walls and microspores but not in female reproductive organs. No GUS activity was detected during seed embryo maturation whereas the uidA gene was strongly expressed at early stages of somatic embryogenesis in scutellum tissue. The Ltp1 transcripts were found to strongly accumulate in response to inoculation with the fungal agent of the blast disease, Magnaporthe grisea, in two rice cultivars exhibiting compatible or incompatible host-pathogen interactions. Analysis of p 1176Gus leaf samples inoculated with the blast fungus demonstrated that the Ltp1 promoter is induced in all cell types of tissues surrounding the lesion and notably in stomata guard cells. In plants harbouring the Ltp1 promoter deletion construct p 556Gus, activity was solely detected in the vascular system of mature leaves whereas no uidA gene expression was observed in p 284Gus plants. These observations are consistent with the proposed role of LTP1 in strenghtening of structural barriers and organ protection against mechanical disruption and pathogen attack.

Genetic control of fruit shape in Cucumis melo was studied using QTL analysis in two Recombinant Inbred (RI) populations consisting of 163 and 63 individuals, respectively, obtained by crossing the same round-fruited parent with two different elongated-fruit lines. Fruit shape is mainly explained by fruit length in these two populations. Most QTLs for fruit shape and ovary shape detected were found to co-segregate, thus demonstrating early control of fruit shape during ovary development. A high level of correlation between fruit shape and ovary shape was also found in 14 unrelated genetic lines, a finding which suggests that control of fruit shape by gene(s) active early in the ovary is a general feature in C. melo. Two major flower genes, a ( monoecious) and p ( pentamerous), were shown to have major effects on fruit shape. Major tightly linked QTLs for fruit and ovary shape were found close to the a and p genes, probably reflecting their pleiotropic effect on fruit shape. Moreover, one of the two QTLs detected in the Védrantais x PI 414723 population was also found in the Védrantais x PI 161375 population. Variation of fruit shape in melon could be due to variations having quantitative effects on a large set of genes that are probably involved in ovary development.

Occurrence of somatic embryogenesis in in vitro cultures of Calamus merrillii and Calamus subinermis, two major largecaned rattan species, was scientifically demonstrated for the first time. Tissue responsiveness varied markedly according to the species and the type of primary explants used when initiated on 10.4–31.2 μM picloram-enriched Murashige and Skoog callus induction media. In C. merrillii, within 6 wk after inoculation, 84% of the leaf and 90% of the zygotic embryo explants produced friable embryogenic calluses, by contrast with those formed by 74% of the root explants. In C. subinermis, callogenesis was observed only 6 mo. after inoculation in 68% of root and 48% of zygotic explants. Leaf explants did not respond at all. Only root-derived calluses developed into nodular embryogenic structures. Irrespective of these initial differences, the further steps of the somatic embryogenesis developmental pattern was similar for both species. Histological analyses established that callus formation took place in the perivascular zones, and could give rise to embryogenic isolated cells from which the proembryos were derived. Reducing the picloram concentration stimulated the maturation process resulting ultimately in the germination of somatic embryos that exhibited bipolar development, despite an apparent lack of starch and protein reserves. The somatic embryo-derived plantlets of C. merrillii, overall more prone to somatic embryogenesis than C. subinermis in the given conditions, were successfully acclimatized to outdoor conditions.

*INRA Station d'Hydrobiologie Lacustre, Thonon-Les-Bains Diffusion du document : INRA Station d'Hydrobiologie Lacustre, Thonon-Les-Bains; National audience

The effects of conventional and reduced impact logging (RIL) practices on tree growth, mortality, and recruitment were assessed in a lowland dipterocarp forest of East Kalimantan, Indonesia. All trees >or= 10 cm dbh were measured in 12 - four hectare permanent plots, before and after logging, during the period 1986-1994. Volume extracted during selection logging ranged from 51 to 247.8 m3/ha in areas using conventional harvesting practices, compared to 23.5-217.8 m3/ha where RIL techniques were applied. On average, conventional logging damaged 48% of the pre-harvest stems, versus 25% using RIL measures with a felling intensity < 8 trees /ha. Where RIL practices exceeded a felling intensity of 8 trees/ha, the effectiveness of RIL in limiting forest damage was significantly reduced. Two years after logging, areas with the highest level of damage had the highest annual tree mortality (3%), whereas sites exhibiting basal area removals of < 20% had annual mortality rates similar to undisturbed primary forest (1.6%). Mean annual diameter increment in undisturbed forest was 2.2 mm/year with dipterocarp growing faster than the other species (3 mm/year). Two years after logging, there was a significant increase of growth of both all the remaining tree population (3.9 mm/year) and dipterocarps (5.1 mm/year). Based on these findings and growth rates increments as well, a second harvest volume of 56 M3 /ha can be expected 60 years following logging in primary forest, where RIL measures remove less than 8 trees/ha during the initial harvest event. Limiting the intensity of the harvest to < 8 trees/ha, and applying RIL techniques leads to faster stand recovery and greater second rotation harvest volumes compared to conventional logging practices. However, neither system yields acceptable harvest volumes on 35 year rotations, as recommended by the Indonesian forest management regulations

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Plant structure components related to variation in yield between 25 thaï cotton fields grown at low density were investigated in the cotton growing area of Chaibadan District, Lopburi Province, Thailand during 1994 and 1995. Despite a low contribution of P1 bolls to yield and a high number of sympodia, survival of P1 fruits of the first ten fruiting nodes together with the change in Height to Node Ratio (HNR) provided a meaningful appraisal of the origin of yield variation between farm plots. The relevance of these criteria was validated with data from an additional 75 plots surveyed in 1993. Standards for predicting yield and adjusting crop management decisions to actual plant structure were generated.

Ce document fait le point sur le déroulement et les résultats de l'ATP 10/96 dans sa deuxième année d'activité. Le travail de modélisation et de développements informatique a été poursuivi sur l'architecture des palmiers, l'interception de la lumière et calcul de la photosynthèse, couplage du logiciel AMAPsim avec des modules externes. Les observations sur la réponse des parties aérienne et racinaires des cocotiers aux traitements d'ablation et d'élagage au Vanuatu ont été poursuivis et des expériences de simulation des transferts radiatifs ont été effectués. Les principaux résultats de ces travaux sont présentés en annexes

The year-round, spontaneous and continued reproduction of tilapia in captivity was initially regarded as an unexpected asset for African aquaculture development, but it was quickly found to be a serious handicap when farming the fish in ponds due to the resulting population. Various techniques have overcome this obstacle. The reproductive efficiency of tilapia has advantages and disadvantages for the supply of fry to fish farmers. Among the advantages is the possibility for fish farmers to produce their own fry ; among the disadvantages is the difficulty to control the broodstock quality. The low number of eggs in each spawning requires the use of a large number of broodstock and the asynchrony of spawnings makes the simultaneous production of large quantities of graded fry difficult. Finally, the control of undesirable reproduction in farming involves the use of monosex populations. These issues are analyzed and discussed in relation to development strategies, microeconomics and the identification of research themes that can be developed to improve the different options. The data for three species of tilapia (#Oreochromis niloticus$, #Sarotherodon melanotheron$ and #Tilapia guineensis$) are compared to the data for two species of African catfish of the family #Clariidae$ (#Claris gariepinus$ and #Heterobranchus longifilis$) that require induced reproduction techniques, but are far more fertile. (Résumé d'auteur)

In tilapia, there is a sex-related growth difference between males and females. This study tried to detect any correlation between the somatic growth and the plasma endocrine status. For this, individually marked (Floytags) male and female tilapia (BW 82 +/- 10 g) were either starved or fed on different daily food rations (1, 2, or 3% of the biomass) during 15 days. We have found that specific growth rates (SGR) were positively and significantly related to feeding levels. Growth hormone (GH) plasma levels tended to increase with the decrease in food levels, and thus with the decrease in growth rate. No significant correlation was found between GH levels and SGR. Triiodothyronine (T3) levels in well-fed fish were higher than those in restricted fish (0 and 1%), but no differences in thyroxine (T4) levels were observed. No significant relationship was found between plasma levels of steroid hormones and feeding ration, even though 11-ketotestosterone (11-KT) levels tended to increase with the ration in fed males. SGR were not significantly different between males and females at the same feeding level, but taken as a whole, they were significantly different in favor of males (P < 0.05). There was no important difference in GH levels between the two sexes. Steroid hormones were, in general, higher in males for 11-KT and in females for 17 beta-estradiol (17 beta-E2). Males and females exhibited significant differences in T3 levels (respectively 4.25 +/- 0.18 and 2.71 +/- 0.09 pmol/ml), whatever the food ration, but no significant differences in T4 levels were observed except in the high-ration group. The correlation between T3 levels and SGR was low but stronger in males (r2 = 0.21; n = 90) than in females (r2 = 0.10; n = 105). The slope of the log-log regression of T3 levels with body weight was much lower in females (b = 0.87) than in males (b = 1.31). This relationship suggests the involvement of T3 in tilapia growth and probably in the differential growth between males and females. In both males and females, a significant but low correlation was observed between T3 and 11-KT levels (respectively r2 = 0.12; n = 82 and r2 = 0.08; n = 89), while no correlation was found between the levels of T3 and 17 beta-E2. T3 plasma levels were found to be the most different parameter between males and females. This hormone seemed to be involved in the control of somatic growth, and could explain the differential growth rate between males and females.