Economical optimization of a breeding scheme by selective phenotyping of the calibration set in a multi-trait context: application to bread making quality.

KEY MESSAGE: Trait-assisted genomic prediction approach is a way to improve genetic gain by cost unit, by reducing budget allocated to phenotyping or by increasing the program's size for the same budget. This study compares different strategies of genomic prediction to optimize resource allocation in breeding schemes by using information from cheaper correlated traits to predict a more expensive trait of interest. We used bread wheat baking score (BMS) calculated for French registration as a case study. To conduct this project, 398 lines from a public breeding program were genotyped and phenotyped for BMS and correlated traits in 11 locations in France between 2000 and 2016. Single-trait (ST), multi-trait (MT) and trait-assisted (TA) strategies were compared in terms of predictive ability and cost. In MT and TA strategies, information from dough strength (W), a cheaper trait correlated with BMS (r = 0.45), was evaluated in the training population or in both the training and the validation sets, respectively. TA models allowed to reduce the budget allocated to phenotyping by up to 65% while maintaining the predictive ability of BMS. TA models also improved the predictive ability of BMS compared to ST models for a fixed budget (maximum gain: + 0.14 in cross-validation and + 0.21 in forward prediction). We also demonstrated that the budget can be further reduced by approximately one fourth while maintaining the same predictive ability by reducing the number of phenotypic records to estimate BMS adjusted means. In addition, we showed that the choice of the lines to be phenotyped can be optimized to minimize cost or maximize predictive ability. To do so, we extended the mean of the generalized coefficient of determination (CDmean) criterion to the multi-trait context (CDmulti).

Mice carrying a humanized Foxp2 knock-in allele show region-specific shifts of striatal Foxp2 expression levels.

Genetic and clinical studies of speech and language disorders are providing starting points to unravel underlying neurobiological mechanisms. The gene encoding the transcription factor FOXP2 has been the first example of a gene involved in the development and evolution of this human-specific trait. A number of autosomal-dominant FOXP2 mutations are associated with developmental speech and language deficits indicating that gene dosage plays an important role in the disorder. Comparative genomics studies suggest that two human-specific amino acid substitutions in FOXP2 might have been positively selected during human evolution. A knock-in mouse model carrying these two amino acid changes in the endogenous mouse Foxp2 gene (Foxp2hum/hum) shows profound changes in striatum-dependent behaviour and neurophysiology, supporting a functional role for these changes. However, how this affects Foxp2 expression patterns in different striatal regions and compartments has not been assessed. Here, we characterized Foxp2 protein expression patterns in adult striatal tissue in Foxp2hum/hum mice. Consistent with prior reports in wildtype mice, we find that striatal neurons in Foxp2hum/hum mice and wildtype littermates express Foxp2 in a range from low to high levels. However, we observe a shift towards more cells with higher Foxp2 expression levels in Foxp2hum/hum mice, significantly depending on the striatal region and the compartment. As potential behavioural readout of these shifts in Foxp2 levels across striatal neurons, we employed a morphine sensitization assay. While we did not detect differences in morphine-induced hyperlocomotion during acute treatment, there was an attenuated hyperlocomotion plateau during sensitization in Foxp2hum/hum mice. Taken together, these results suggest that the humanized Foxp2 allele in a mouse background is associated with a shift in striatal Foxp2 protein expression pattern.

Optimization of multi-environment trials for genomic selection based on crop models.

KEY MESSAGE: We propose a statistical criterion to optimize multi-environment trials to predict genotype × environment interactions more efficiently, by combining crop growth models and genomic selection models. Genotype × environment interactions (GEI) are common in plant multi-environment trials (METs). In this context, models developed for genomic selection (GS) that refers to the use of genome-wide information for predicting breeding values of selection candidates need to be adapted. One promising way to increase prediction accuracy in various environments is to combine ecophysiological and genetic modelling thanks to crop growth models (CGM) incorporating genetic parameters. The efficiency of this approach relies on the quality of the parameter estimates, which depends on the environments composing this MET used for calibration. The objective of this study was to determine a method to optimize the set of environments composing the MET for estimating genetic parameters in this context. A criterion called OptiMET was defined to this aim, and was evaluated on simulated and real data, with the example of wheat phenology. The MET defined with OptiMET allowed estimating the genetic parameters with lower error, leading to higher QTL detection power and higher prediction accuracies. MET defined with OptiMET was on average more efficient than random MET composed of twice as many environments, in terms of quality of the parameter estimates. OptiMET is thus a valuable tool to determine optimal experimental conditions to best exploit MET and the phenotyping tools that are currently developed.

Grain characterization and milling behaviour of near-isogenic lines differing by hardness.

Wheat grain hardness is a major factor affecting the milling behaviour and end-product quality although its exact structural and biochemical basis is still not understood. This study describes the development of new near-isogenic lines selected on hardness. Hard and soft sister lines were characterised by near infrared reflectance (NIR) and particle size index (PSI) hardness index, grain protein content, thousand kernel weight and vitreousness. The milling behaviour of these wheat lines was evaluated on an instrumented micromill which also measures the grinding energy and flour particle size distribution was investigated by laser diffraction. Endosperm mechanical properties were measured using compression tests. Results pointed out the respective effect of hardness and vitreousness on those characteristics. Hardness was shown to influence both the mode of fracture and the mechanical properties of the whole grain and endosperm. Thus, this parameter also acts on milling behaviour. On the other hand, vitreousness was found to mainly play a role on the energy required to break the grain. This study allows us to distinguish between consequences of hardness and vitreousness. Hardness is suggested to influence the adhesion forces between starch granules and protein matrix whereas vitreousness would rather be related to the endosperm microstructure.

Effects of food deprivation and particle size of ground wheat on digestibility of food components in broilers fed on a pelleted diet.

The first aim of the experiment was to study the effect of wheat (Triticum aestivum) particle size on the digestibility of starch in a pelleted diet given to broilers. The second aim was to study the consequences of food deprivation before the excreta collection period (from 21 to 24 d). Wheat from a strong hardness cultivar was incorporated at 546.1 g/kg in diets. The other main ingredients were soybean meal (353.5 g/kg) and rapeseed oil (55.0 g/kg). Diets were given as pellets. The experimental design was a 2 x 2 factorial design testing two particle sizes of wheat flour and two procedures of a balance experiment (with or without food deprivation). Birds given diet C (wheat coarse grinding before pelleting) had significantly greater gizzard weight than birds fed on diet F (wheat fine grinding before pelleting). Starch digestibility value was significantly increased when birds were fed on diet F. This effect was halved by food deprivation. No significant effect of grain particle size was observed for protein and lipid digestibility values. However, food deprivation decreased apparent protein digestibility, with an effect which was more pronounced for fine than for coarse grinding. AMEN of the diet was significantly improved by fine grinding of wheat and decreased by food deprivation. However, no significant differences in growth performance were induced by differences in wheat grinding. No significant effect of grinding was observed on the water excretion:feed intake ratio. No significant difference was observed for vent score between treatments. There was over-excretion of starch in the first hours of refeeding following food deprivation.

Relationships between digestibilities of food components and characteristics of wheats (Triticum aestivum) introduced as the only cereal source in a broiler chicken diet.

1. The aim of the experiment was to establish relationships between chemical or physical characteristics of wheats (Triticum aestivum) and digestibilities of food components in broiler chickens fed on wheat-based diets. Twenty-two wheat samples, each differing by their cultivar origin, were included at 550 g/kg in diets offered to male Ross broiler chicks. The other main ingredients were soya bean meal (340 g/kg) and rapeseed oil (68.5 g/kg). Diets were given as pellets. 2. In vitro viscosities of wheats measured as potential applied viscosity (PAV) or real applied viscosity (RAV) varied between 1.91 and 6.03, or between 0.95 and 3.81 ml/g (dry matter basis), respectively. Hardness of wheats varied between 17 (soft) and 95 (very hard), and lipase activity of wheats varied from 1 to 13.6 (relative scale). 3. PAV and RAV values were not significantly correlated with hardness. PAV and RAV values were correlated with (80:20) ethanol:water insoluble, water soluble arabinoxylans (r = 0.961, 0.932, respectively), with the amount of water retained by cell walls (r = 0.656, 0.492, respectively), and with lipase activity (r = 0.600, 0.532, respectively. 4. Hardness was correlated with ash (r = -0.484), nitrogen (r = 0.534), mean particle size of wheat flours (r = 0.631), and specific energy of pelleting (r = -0.574). 5. Wheat diets were evaluated in two assays with 3-week-old chicks, with 11 diets per assay. In each assay, a balance experiment was carried out using the total collection method. Growth performance was also measured during the balance experiment. 6. In vitro viscosity parameters were negatively correlated with diet AMEn (P < 0.05), lipid digestibility (P < 0.05) and, to a lesser extent, protein digestibility (P < 0.05). In vitro viscosity data were positively correlated with food:gain ratio (P < 0.05) and water loss parameters (P < 0.05), and were not significantly (P > 0.05) correlated with starch digestibility. 7. Wheat hardness-related parameters were correlated (P < 0.01) with individual starch digestibility (hardness, proportion of coarse particles in wheat flour, specific energy of pelleting: r = -0.273, -0.305, 0.212, respectively). 8. Wheat lipase activity was negatively correlated with individual lipid (r = -0.179; P < 0.05) and starch (r = -0.225; P < 0.01) digestibilities and with individual diet AMEn (r = -0.266; P < 0.001). Individual diet AMEn values were correlated (r = 0.175) with the values calculated by the EU AMEn prediction equation (Fisher and McNab, 1987). Among the correlations observed between the individual measured AMEn:EU predicted AMEn ratio and wheat parameters (P < 0.05), the correlation obtained with wheat lipase was the highest (r = -0.195). The correlations with lipase could be explained in part by strong correlations between lipase and in vitro viscosity parameters.

Regulation of cyclic adenosine 3',5'-monophosphate-dependent protein kinase activity and regulatory subunit RII beta content by basic fibroblast growth factor (bFGF) during granulosa cell differentiation: possible implication of protein kinase C in bFGF action.

We have previously shown that basic fibroblast growth factor (bFGF) inhibits the FSH-induced differentiation of cultured rat granulosa cells, as manifested by prominent reduction of the LH receptor expression. We now investigate the possible sites and mechanism of action of bFGF. Whereas bFGF decreased the cAMP formation induced by FSH, it enhanced the cAMP production caused by cholera toxin and forskolin, suggesting that bFGF exerted its inhibitory action on cell differentiation at a step to cAMP production. Photoaffinity labeling with 8-azido-[32P]cAMP revealed that bFGF markedly reduced the FSH-induced increase in the level of regulatory subunit RII beta of the cAMP-dependent protein kinase (PKA) type II. In contrast to its striking effect on RII beta expression (70-80% inhibition), bFGF decreased PKA enzymatic activity by only 30%. On the other hand, transforming growth factor-beta (TGF beta) slightly amplified the stimulatory action of FSH and antagonized the bFGF inhibitory effect on both LH receptor expression and RII beta synthesis. We report that the protein kinase C (PKC) activator 12-O-tetradecanoylphorbol-13-acetate (TPA), which impaired granulosa cell differentiation, also abolished the RII beta synthesis induced by FSH. The activation of PKC by bFGF in granulosa cells was supported by the following findings: (i) bFGF markedly enhanced the production of diacylglycerol (2.3-fold stimulation at 5 min), the intracellular activator of PKC; (ii) bFGF promoted tight association of PKC to cellular membranes, a process that is believed to correlate with the enzyme activation; (iii) bFGF induced the phosphorylation of an endogenous M(r) 78,000/pI 4.7 protein that appears as a specific PKC substrate; (iv) bFGF mimicked the TPA-induced transmodulation of the epidermal growth factor (EGF) receptor, reducing by 36% the 125I-EGF binding on granulosa cells. We conclude that bFGF may exert its repressive action on RII beta synthesis, PKA activity, and granulosa cell differentiation by primarily targeting PKC activation.

Tumor necrosis factor-alpha inhibits follicle-stimulating hormone-induced differentiation in cultured rat granulosa cells.

We have investigated the effects of TNF-alpha on FSH-induced LH receptor expression, cAMP and progesterone production in cultured rat granulosa cells. TNF-alpha (0.5-100 ng/ml) inhibits the stimulating action of FSH on LH receptor formation in a dose-dependent manner with an IC50 of 1 ng/ml and an almost complete suppression of LH receptor induction for 50-100 ng/ml TNF-alpha. The inhibitory effect of TNF-alpha is not due to variations in cell number or viability but rather to a reduction of the LH receptor content per cell with no change in binding affinity (KD = 0.8 x 10(-10)M). TNF-alpha also inhibits the FSH-induced cAMP production but at a lower extent, with a maximum reduction of 60% for 100 ng/ml TNF-alpha. Moreover, TNF-alpha impairs the LH receptor formation induced by forskolin, cholera toxin or 8-Bromo-cAMP, indicating that the cytokine also acts at a step distal to FSH receptor and to cAMP formation. Finally, TNF-alpha decreases dramatically the progesterone synthesis that is stimulated by FSH, with a reduction to undetectable levels on and after 10 ng/ml TNF-alpha. These results suggest that TNF-alpha may drastically reduce the capacity of granulosa cells to differentiate upon FSH stimulation and to respond to LH during the physiological ovarian follicular maturation. Such anti-gonadotropic action of TNF-alpha on granulosa cell differentiation may be also relevant to the alteration of ovarian function during physiopathological processes like inflammatory or infection diseases.

Fibroblast growth factor regulates the expression of luteinizing hormone receptors in cultured rat granulosa cells.

We have investigated the effects of bFGF on both the FSH-induced LH receptor expression and cAMP production in cultured rat granulosa cells. Concentrations of pure FGF, from 10(-12) M to 10(-10) M, progressively inhibit the stimulatory actions of FSH with an ED50 of approximately 4 x 10(-12) M for both parameters. Higher FGF concentrations, from 4 x 10(-10) M to 10(-8) M, lead to a gradual reduction of the growth factor inhibitory effect. The effects of FGF are more prominent on the modulation of LH receptors than on the FSH-induced cAMP production. Moreover, FGF impairs the LH receptor formation induced by cholera toxin or 8-Bromo-cAMP, indicating that the growth factor also acts at a step distal to cAMP formation. The inhibitory effect of FGF on LH receptor expression increases during the entire course of granulosa cell differentiation, from 24 to 96 h, and is not due to variations in cell number or viability, but rather to a change in the content of LH receptors with no significant modification of binding affinity (KD congruent to 0.8 x 10(-10) M). These results suggest that bFGF may acutely regulate the capacity of granulosa cells to differentiate upon FSH stimulation and to respond to LH during the ovarian follicular maturation.

TPA induces subcellular translocation and subsequent down-regulation of both phorbol ester binding and protein kinase C activities in MCF-7 cells.

Phorbol ester TPA has been previously shown to induce a rapid translocation, followed by a progressive decline of protein kinase C activity in MCF-7 cells (J.M. Darbon et al, 1986, Biochem. Biophys. Res. Comm. 137: 1159-1166). We show now a parallel TPA-induced movement of phorbol ester binding sites from the cytosolic to the particulate fraction with no change in the binding affinities for the (3H) PDBu probe (KD congruent to 2 nM). The subcellular redistribution process is followed by a rapid decrease of the phorbol ester binding capacity at the membrane level. The concomitant decline in both phorbol ester binding and protein kinase C activities that we observed during the course of TPA treatment strongly argues for a real down-regulation of the enzyme in phorbol ester-treated MCF-7 cells. The molecular mechanisms of these events and their relations to the inhibition of cell growth remain to be clarified.