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Key message: We propose new methods to predict genotype × environment interaction by selecting relevant environmental covariates and using an AMMI decomposition of the interaction. Abstract: Farmers are asked to produce more efficiently and to reduce their inputs in the context of climate change. They have to face more and more limiting factors that can combine in numerous stress scenarios. One solution to this challenge is to develop varieties adapted to specific environmental stress scenarios. For this, plant breeders can use genomic predictions coupled with environmental characterization to identify promising combinations of genes in relation to stress covariates. One way to do it is to take into account the genetic similarity between varieties and the similarity between environments within a mixed model framework. Molecular markers and environmental covariates (EC) can be used to estimate relevant covariance matrices. In the present study, based on a multi-environment trial of 220 European elite winter bread wheat (Triticum aestivum L.) varieties phenotyped in 42 environments, we compared reference regression models potentially including ECs, and proposed alternative models to increase prediction accuracy. We showed that selecting a subset of ECs, and estimating covariance matrices using an AMMI decomposition to benefit from the information brought by the phenotypic records of the training set are promising approaches to better predict genotype-by-environment interactions (G × E). We found that using a different kinship for the main genetic effect and the G × E effect increased prediction accuracy. Our study also demonstrates that integrative stress indexes simulated by crop growth models are more efficient to capture G × E than climatic covariates.

International audience; Wheat (Triticum aestivum L.) is the most widely cultivated crop worldwide and faces a wide range of stresses. To make effective crop improvement decisions, environmental characterization is of paramount importance. This study presents a new methodology for characterizing the environment that enables replacing the conventional arbitrary classification of the environment by a series of environmental covariates that capture and describe the stresses the plant encounters. Three CIMMYT bread wheat populations, combining complementary heat and drought adaptive traits, were grown over 3 yr in northwestern Mexico under limited irrigation, heat stress, and irrigated conditions. The network comprised 15 trials representing seven treatment x year combinations as experimental environments, referred to here as the "Environment". Environmental characterization was performed at the trial scale. Twelve stress thresholds related to eight environmental factors were combined to obtain 11 potential growth limiting factors. Thirty-three environmental covariates were obtained by calculating when these limiting factors occurred for each of three key-developmental-phases across all trials. Cluster analysis allowed grouping environmental covariates into six distinct clusters corresponding to six "environmental scenarios". One representative environmental covariate was extracted from each cluster and taken together explained more than 90% of the variance for yield in the Environment. Principal component analysis discriminated the seven experimental environments and identified its stress characteristics. We conclude that the method developed characterized the main stresses and their impact on average population performance, and the representative covariates efficiently replaced the Environment. As such, they will facilitate the dissection of genotype x environment interaction (GEI) for yield-related traits.

Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R2 = 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R2 < 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production.

International audience; We assessed the effects of vitreousness and particle size of maize grain on ruminal and intestinal in sacco degradation of dry matter, starch and nitrogen. Six maize grain (Zea mays) genotypes characterized by differing vitreousness (proportion of vitreous in total endosperm) were ground (3-min screen; Gr, ground particles, mean particle size (MPS): 526 mu m) and cracked with a roller mill using two gap width settings (CS, cracked small particles, MPS: 1360 mu m; CL, cracked large particles, MPS: 2380 mu m). The ruminal and intestinal in sacco degradation of dry matter, starch and nitrogen was measured on three dry Holstein cows, fitted with rumen, proximal duodenum and terminal ileum cannulas, fed maize silage ad libitum twice daily. The ruminal starch degradability and intestinal digestibility differed among genotypes (P

International audience; BACKGROUND: Oxidative stress is implicated in the etiology of many diseases, but most of clinical trials failed to demonstrate beneficial effects of antioxidant supplementation. METHODS: In the present experiment, we assessed the mean-term effect of wheat germ supplementation, as a dietary source of vitamin E, on antioxidant protection in rat. RESULTS: Feeding rats a 20% wheat germ diet significantly increased plasma and liver vitamin E levels, compared to the low vitamin E basal diet. Concurrently, wheat germ diet consumption strongly decreased the susceptibility of heart and liver lipids to oxidation, as well as the plasma. Wheat germ feeding did not change triglycerides (TG) nor total cholesterol concentrations in plasma or liver, resulting in higher vitamin E/TG ratio compared to controls. Similar results were found with a diet in which wheat germ oil provided the same amount of vitamin E. CONCLUSIONS: Wheat germ appears thus very effective to improve antioxidant defense status, especially in tissues, irrespective of modifications of lipids status.

International audience; Whole wheat bread represents an important source of dietary fibre and micronutrients such as minerals and vitamins (B1, B2, B6). Thus it is important to control losses of vitamins during milling and breadmaking. The classical (yeast) breadmaking process is a relatively severe, leading to a 48% loss of thiamine in white bread. Longer fermentation times (white bread) led to higher thiamine concentrations (2.5 mu g/g) than shorter fermentations (1.4 mu g/g). In whole wheat bread, separate yeast or sourdough fermentations maintained vitamin B1 levels close to that of the original flour (5.5 mu g/g). Whole wheat breadmaking with yeast (from kneading to final bread), in long fermentations, resulted in a 30% enrichment in riboflavin. The pyridoxine concentration of whole wheat flour is 5-fold higher than white flour, but classical fermentations resulted in a severe depletion in pyridoxine (-47%). The use of mixed fermentation conditions (yeast plus sourdough) had no synergistic impact on B vitamin levels. The classical breadmaking protocol is time-saving but does not result in maximal vitamin retention. Highest levels of B vitamins were achieved by long yeast fermentations.