Ensemble yield simulations: crop and climate uncertainties, sensitivity to temperature and genotypic adaptation to climate change

Estimates of the response of crops to climate change rarely quantify the uncertainty inherent in the simulation of both climate and crops. We present a crop simulation ensemble for a location in India, perturbing the response of both crop and climate under both baseline (12 720 simulations) and doubled-CO2 (171 720 simulations) climates. Some simulations used parameter values representing genotypic adaptation to mean temperature change. Firstly, observed and simulated yields in the baseline climate were compared. Secondly, the response of yield to changes in mean temperature was examined and compared to that found in the literature. No consistent response to temperature change was found across studies. Thirdly, the relative contribution of uncertainty in crop and climate simulation to the total uncertainty in projected yield changes was examined. In simulations without genotypic adaptation, most of the uncertainty came from the climate model parameters. Comparison with the simulations with genotypic adaptation and with a previous study suggested that the relatively low crop parameter uncertainty derives from the observational constraints on the crop parameters used in this study. Fourthly, the simulations were used, together with an observed dataset and a simple analysis of crop cardinal temperatures and thermal time, to estimate the potential for adaptation using existing cultivars. The results suggest that the germplasm for complete adaptation of groundnut cultivation in western India to a doubled-CO2 environment may not exist. In conjunction with analyses of germplasm and local management practices, results such as this can identify the genetic resources needed to adapt to climate change

Integrated analysis for genotypic adaptation in rice

Development of varieties with high yield potential coupled with wide adaptability is an important plant breeding objective. The presence of genotype by environment (GxE) interaction plays a crucial role in determining the performance of genetic materials, tested at different locations and in different years. This study was undertaken to assess yield performance, stability and adaptability of thirty-six rice genotypes of three different maturity groups evaluated over 12 environments. There were highly significant (P<0.05) genotype-environment interaction in three different maturity groups. The AMMI analysis of variance in the maturity groups also showed significant genotype, location and G\ub4L. Stability in yield performance was predicted using nine stability parameters (b, S2d , CV, SF, R1, R2, W, S1 and ASV). The rank correlation coefficient among nine parameters indicated that the stability parameters were dissimilar in for all the maturity groups. Stability index (STI) computed by integrating all the nine stability parameters indicated that genotypes Lalat and OR 2006-12 of mid-early group, genotypes OR 1912-25, OR 2310-12 and MTU 1001 of mid-late group, and genotypes OR 1898-3-16, OR 1901-14-32, OR 2109-2, OR 2001-1, Mahanadi and Jagabandhu of late group yielded higher consistently over the 3 years in the different agroclimatic zones.Le d\ue9veloppement de vari\ue9t\ue9s \ue0 potentiel \ue9lev\ue9 de rendement coupl\ue9 \ue0 une large adaptabilit\ue9 est un objectif important de l'am\ue9lioration des plantes. La pr\ue9sence de g\ue9notype par interaction avec l'environnement (GxE) joue un r\uf4le crucial dans la d\ue9termination des performances de mat\ue9riels g\ue9n\ue9tiques test\ue9s dans diff\ue9rentes localisations et dans des ann\ue9es diff\ue9rentes. Cette'\ue9tude \ue9tait entreprise pour \ue9valuer la performance en rendement, la stabilit\ue9 et l'adaptabilit\ue9 de trente six g\ue9notypes de riz de trois groupes de maturit\ue9 diff\ue9rente \ue9valu\ue9es sur 12 environnements. L'interaction g\ue9notype-environnement \ue9tait significativement \ue9lev\ue9 (P<0.05) dans trois groupes de maturit\ue9 diff\ue9rente. L'analyse AMM de la variance dans les groupes de maturit\ue9 avait aussi montr\ue9 un effet significatif du g\ue9notype, localisation et G'L. La stabilit\ue9 en performance de rendement \ue9tait pr\ue9dite utilisant neuf param\ue8tres de stabilit\ue9 (b, S2d, CV, SF, R1, R2, W, S1 et ASV). Le rang du co\ue9fficient de corr\ue9lation parmi les neuf param\ue8tres a indiqu\ue9 que les param\ue8tres de stabilit\ue9\ue9taient dissemblables pour tous les groupes de maturit\ue9. L'index de stabilit\ue9 (STI) calcul\ue9 en int\ue9grant tous les neuf param\ue8tres de stabilit\ue9 a indiqu\ue9 que les g\ue9notypes Lalat et OR 2006-12 du mi-premier groupe, les g\ue9notypes OR 1912-25, OR 2310-12 et MTU 1001 du mi-dernier groupe et les g\ue9notypes OR 1898-3-16, OR 1901-14-32, OR 2109-2, OR 2001-1, Mahanadi et Jagabandhu du dernier groupe ont produit consid\ue9rablement de rendements tr\ue8s \ue9lev\ue9s au cours des 3 ans dans diff\ue9rentes zones agroclimatiques

Metabolism of amino acid amides in Pseudomonas putida ATCC 12633

The metabolism of the natural amino acid L-valine, the unnatural amino acids D-valine, and D-, L-phenylglycine (D-, L-PG), and the unnatural amino acid amides D-, L-phenylglycine amide (D, L-PG-NH2) and L-valine amide (L-Val-NH2) was studied in Pseudomonas putida ATCC 12633. The organism possessed constitutive L-amidase activities towards L-PG-NH2 and L-Val-NH2, both following the same pattern of expression, suggesting the involvement of similarly regulated enzymes, or a common enzyme. Quite surprisingly, growth in mineral media with L-PG-NH2 resulted in variable, long lag phases of growth and strongly reduced L-amidase activities. Conversion of D-PG-NH2 into D-PG and L-PG also occurred and could be attributed to the presence of an inducible D-amidase and the racemization of the amino acid amide in combination with L-amidase activity, respectively. The further degradation of L-PG and D-PG involved constitutive L-PG aminotransferase and inducible D-PG dehydrogenase activities, respectively, both with a high degree of enantioselectivity. Amino acid racemase activity for D- and L-PG was not detected.

CGIAR modeling approaches for resource-constrained scenarios: I. Accelerating crop breeding for a changing climate.

Crop improvement efforts aiming at increasing crop production (quantity, quality) and adapting to climate change have been subject of active research over the past years. But, the question remains 'to what extent can breeding gains be achieved under a changing climate, at a pace sufficient to usefully contribute to climate adaptation, mitigation and food security?'. Here, we address this question by critically reviewing how model-based approaches can be used to assist breeding activities, with particular focus on all CGIAR (formerly the Consultative Group on International Agricultural Research but now known simply as CGIAR) breeding programs. Crop modeling can underpin breeding efforts in many different ways, including assessing genotypic adaptability and stability, characterizing and identifying target breeding environments, identifying tradeoffs among traits for such environments, and making predictions of the likely breeding value of the genotypes. Crop modeling science within the CGIAR has contributed to all of these. However, much progress remains to be done if modeling is to effectively contribute to more targeted and impactful breeding programs under changing climates. In a period in which CGIAR breeding programs are undergoing a major modernization process, crop modelers will need to be part of crop improvement teams, with a common understanding of breeding pipelines and model capabilities and limitations, and common data standards and protocols, to ensure they follow and deliver according to clearly defined breeding products. This will, in turn, enable more rapid and better-targeted crop modeling activities, thus directly contributing to accelerated and more impactful breeding efforts.Online Version of Record before inclusion in an issue

Climate change impact on China food security in 2050

Climate change is now affecting global agriculture and food production worldwide. Nonetheless the direct link between climate change and food security at the national scale is poorly understood. Here we simulated the effect of climate change on food security in China using the CERES crop models and the IPCC SRES A2 and B2 scenarios including CO2 fertilization effect. Models took into account population size, urbanization rate, cropland area, cropping intensity and technology development. Our results predict that food crop yield will increase +3-11 % under A2 scenario and +4 % under B2 scenario during 2030-2050, despite disparities among individual crops. As a consequence China will be able to achieve a production of 572 and 615 MT in 2030, then 635 and 646 MT in 2050 under A2 and B2 scenarios, respectively. In 2030 the food security index (FSI) will drop from +24 % in 2009 to -4.5 % and +10.2 % under A2 and B2 scenarios, respectively. In 2050, however, the FSI is predicted to increase to +7.1 % and +20.0 % under A2 and B2 scenarios, respectively, but this increase will be achieved only with the projected decrease of Chinese population. We conclude that 1) the proposed food security index is a simple yet powerful tool for food security analysis; (2) yield growth rate is a much better indicator of food security than yield per se; and (3) climate change only has a moderate positive effect on food security as compared to other factors such as cropland area, population growth, socio-economic pathway and technology development. Relevant policy options and research topics are suggested accordingly

Genetic and physiological dissection of transpiration efficiency in wheat

OBJECTIVE: To determine the incidence and prevalence of facioscapulohumeral muscular dystrophy (FSHD) in the Netherlands. METHODS: Using 3-source capture-recapture methodology, we estimated the total yearly number of newly found symptomatic individuals with FSHD, including those not registered in any of the 3 sources. To this end, symptomatic individuals with FSHD were available from 3 large population-based registries in the Netherlands if diagnosed within a 10-year period (January 1, 2001 to December 31, 2010). Multiplication of the incidence and disease duration delivered the prevalence estimate. RESULTS: On average, 52 people are newly diagnosed with FSHD every year. This results in an incidence rate of 0.3/100,000 person-years in the Netherlands. The prevalence rate was 12/100,000, equivalent to 2,000 affected individuals. CONCLUSIONS: We present population-based incidence and prevalence estimates regarding symptomatic individuals with FSHD, including an estimation of the number of symptomatic individuals not present in any of the 3 used registries. This study shows that the total number of symptomatic persons with FSHD in the population may well be underestimated and a considerable number of affected individuals remain undiagnosed. This suggests that FSHD is one of the most prevalent neuromuscular disorders

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

<p>Abstract</p> <p>Background</p> <p>Isobutanol is a promising next-generation biofuel with demonstrated high yield microbial production, but the toxicity of this molecule reduces fermentation volumetric productivity and final titer. Organic solvent tolerance is a complex, multigenic phenotype that has been recalcitrant to rational engineering approaches. We apply experimental evolution followed by genome resequencing and a gene expression study to elucidate genetic bases of adaptation to exogenous isobutanol stress.</p> <p>Results</p> <p>The adaptations acquired in our evolved lineages exhibit antagonistic pleiotropy between minimal and rich medium, and appear to be specific to the effects of longer chain alcohols. By examining genotypic adaptation in multiple independent lineages, we find evidence of parallel evolution in <it>marC</it>, <it>hfq</it>, <it>mdh</it>, <it>acrAB, gatYZABCD</it>, and <it>rph </it>genes. Many isobutanol tolerant lineages show reduced RpoS activity, perhaps related to mutations in <it>hfq </it>or <it>acrAB</it>. Consistent with the complex, multigenic nature of solvent tolerance, we observe adaptations in a diversity of cellular processes. Many adaptations appear to involve epistasis between different mutations, implying a rugged fitness landscape for isobutanol tolerance. We observe a trend of evolution targeting post-transcriptional regulation and high centrality nodes of biochemical networks. Collectively, the genotypic adaptations we observe suggest mechanisms of adaptation to isobutanol stress based on remodeling the cell envelope and surprisingly, stress response attenuation.</p> <p>Conclusions</p> <p>We have discovered a set of genotypic adaptations that confer increased tolerance to exogenous isobutanol stress. Our results are immediately useful to further efforts to engineer more isobutanol tolerant host strains of <it>E. coli </it>for isobutanol production. We suggest that <it>rpoS </it>and post-transcriptional regulators, such as <it>hfq</it>, RNA helicases, and sRNAs may be interesting mutagenesis targets for future global phenotype engineering.</p

Variations in agronomic and grain quality traits of rice grown under irrigated lowland conditions in West Africa

Rice breeding in West Africa has been largely skewed toward yield enhancement and stress tolerance. This has led to the variable grain quality of locally produced rice in the region. This study sought to assess variations in the agronomic and grain quality traits of some rice varieties grown in this region, with a view to identifying sources of high grain yield and quality that could serve as potential donors in their breeding programs. Forty‐five varieties were grown under irrigated conditions in Benin and Senegal with two trials in each country. There were wide variations in agronomic and grain quality traits among the varieties across the trials. Cluster analysis using paddy yield, head rice yield, and chalkiness revealed that 68% of the total variation could be explained by five varietal groupings. One group comprising seven varieties (Afrihikari, BG90‐2, IR64, Sahel 108, WAT311‐WAS‐B‐B‐23‐7‐1, WAT339‐TGR‐5‐2, and WITA 10) had high head rice yield and low chalkiness. Of the varieties in this group, Sahel 108 had the highest paddy yield in three of the four trials. IR64 and Afrihikari had intermediate and low amylose content, respectively, with the rest being high‐amylose varieties. Another group of varieties consisting of B6144F‐MR‐6‐0‐0, C74, IR31851‐96‐2‐3‐2‐1, ITA222, Jaya, Sahel 305, WITA 1, and WITA 2 had high paddy yield but poor head rice yield and chalkiness. The use of materials from these two groups of varieties could accelerate breeding for high yielding rice varieties with better grain quality for local production in West Africa