Socio-ecological factors determine crop performance in agricultural systems

Agricultural production systems are affected by complex interactions between social and ecological factors, which are often hard to integrate in a common analytical framework. We evaluated differences in crop production among farms by integrating components of several related research disciplines in a single socio-ecological analysis. Specifically, we evaluated spring barley (Hordeum vulgare, L.) performance on 34 farms (organic and conventional) in two agro-ecological zones to unravel the importance of ecological, crop and management factors in the performance of a standard crop. We used Projections to Latent Structures (PLS), a simple but robust analytical tool widely utilized in research disciplines dealing with complex systems (e.g. social sciences and chemometrics), but infrequently in agricultural sciences. We show that barley performance on organic farms was affected by previous management, landscape structure, and soil quality, in contrast to conventional farms where external inputs were the main factors affecting biomass and grain yield. This indicates that more complex management strategies are required in organic than in conventional farming systems. We conclude that the PLS method combining socio-ecological and biophysical factors provides improved understanding of the various interacting factors determining crop performance and can help identify where improvements in the agricultural system are most likely to be effective

Performance and inheritance of yield and maize streak virus disease resistance in white maize and yellow conversions

In sub Saharan Africa, past effort has registered success in developing high yielding and foliar disease resistant maize ( Zea mays L.) varieties, which are deficient in pro-vitamin A. A new initiative is to develop maize varieties, tolerant to foliar diseases and rich in pro-vitamin A carotenoids. To achieve this, yellow conversions of white testers and other elite maize varieties have been developed by the International Center for Maize and Wheat Development (CIMMYT). Unlike the white lines, limited information on agronomic performance and disease resistance is available for yellow maize conversions. This study was conducted to evaluate the performance of white maize and their corresponding yellow maize conversions for yield and tolerance to Maize streak virus (MSV) disease; and determine the inheritance patterns of these traits. Fourty seven three-way hybrids generated in a Line by tester mating design (North Carolina 2), 12 inbred lines (used as male parents), 4 single crosses (used as female parents) and 3 commercials checks were screened for resistance to Maize streak virus (MSV) disease at the National Crop Resources Research Institute (NaCRRI) in Uganda. The same genotypes were evaluated in a 9x5 alpha lattice design in three locations of Uganda (National Crop Resources Research Institute (NACRRI), National Semi Arid Resources Research Institute (NaSARRI) and Bulambuli) for agronomic performance. Results confirmed tolerance to MSV in testers CML202, CML395, CML444, CML445 and CML312-SR (white). Genotypes performed significantly differently for yield, anthesis days, plant height, ear height, husk cover, grain texture, reaction to Gray leaf spot (GLS) (P<0.001) and ear aspect (P<0.01). However, pairwise comparison of white and yellow conversions indicated no significant difference (P>0.05) in agronomic performance and tolerance to diseases. General combining ability (GCA) was more important than specific combining ability (SCA) for most traits, except for anthesis days, Turcicum leaf blight (TLB), GLS and yield. GCA effects for yield were not significant in both lines (male parents) and single cross testers (female parents) of white and yellow conversions. However, two unique cases were observed for diseases; yellow conversion of line CML444 significantly combined for susceptibility to TLB; while tester CML312/CML442 combined for resistance to GLS. Additionally, there was low heritably estimates for tolerance to MSV and yield. Generally, there was no significant difference between white and corresponding yellow maize conversion, implying that there is no significant loss in MSV resistance and yield performance while converting white into yellow maize.En Afrique sub-Saharienne, les efforts ant\ue9rieurs ont connu de grands succ\ue8s dans le d\ue9veloppement des vari\ue9t\ue9s tr\ue8s productives et tol\ue9rantes aux maladies foliaires du ma\uefs ( Zea mays L.), mais qui sont pauvres en provitamine A. La nouvelle vision est de d\ue9velopper des vari\ue9t\ue9s de ma\uefs r\ue9sistantes aux principales maladies foliaires, et riche en carot\ue9no\uefdes provitamine A. Pour y arriver, les conversions jaunes issues des testeurs blancs de ma\uefs ainsi que les vari\ue9t\ue9s \ue9lite ont \ue9t\ue9 d\ue9velopp\ue9es par le Centre International pour l\u2019Am\ue9lioration du Ma\uefs et du Bl\ue9 (CIMMYT). Contrairement aux lign\ue9es blanches de ma\uefs, la performance agronomique et le niveau de r\ue9sistance aux maladies des lign\ue9es jaunes reste m\ue9connue. Cette \ue9tude a \ue9t\ue9 men\ue9e dans le but d\u2019\ue9valuer la performance au niveau du rendement et la r\ue9sistance \ue0 la maladie des bandes (MSV) des vari\ue9t\ue9s de ma\uefs \ue0 grain de couleur blanche et leurs conversions de couleur jaune et d\ue9terminer le mode d\u2019h\ue9ritabilit\ue9 de ces deux param\ue8tres \ue9tudi\ue9s. Quarante-sept hybrides trois voies produits dans un mode de croisement Lign\ue9e par testeur (North Carolina II), 12 lign\ue9es \ue9pur\ue9es (utilis\ue9es comme parents m\ue2les), 4 hybrides simples (utilis\ue9s comme parents femelles) et 3 t\ue9moins ont \ue9t\ue9 inocul\ue9s par l\u2019agent causal de la maladie des bandes \ue0 NaCRRI (National Crop Ressources Research Institute) en Ouganda. La performance agronomique des m\ueames g\ue9notypes a \ue9t\ue9 \ue9valu\ue9e dans un dispositif exp\ue9rimental d\u2019alpha lattice (5parcelles \ue9l\ue9mentaires x 9 blocks) dans 3 sites de l\u2019Ouganda \ue0 savoir NaCRRI (National Crop Ressources Research Institute), NaSARRI (National Semi Arid Resources Research Institute) et Bulambuli. Les r\ue9sultats ont confirm\ue9 la tol\ue9rance \ue0 la MSV des testeurs \ue0 grains blancs CML202, CML395, CML444, CML445 et CML 312-SR. La performance des g\ue9notypes \ue9tait hautement significativement diff\ue9rente pour le rendement, le nombre de jours de floraison m\ue2le, la hauteur des plants, le niveau d\u2019insertion des \ue9pis sur les plants, la couverture des \ue9pis par les spathes, la texture des grains, la r\ue9action \ue0 la GLS (Glay leaf spot) (P<0.001) ainsi que pour l\u2019aspect des \ue9pis (P<0.01). Cependant, la comparaison entre le ma\uefs blanc et sa conversion jaune a montr\ue9 une diff\ue9rence non significative (P>0.05) au niveau de leur performance agronomique et la tol\ue9rance aux maladies. L\u2019aptitude g\ue9n\ue9rale \ue0 la combinaison (GCA) \ue9tait plus importante que l\u2019aptitude sp\ue9cifique \ue0 la combinaison (SCA) pour la plupart des param\ue8tres \ue0 l\u2019exception du nombre de jours \ue0 floraison m\ue2le, la tol\ue9rance \ue0 l\u2019helminthosporiose (TLB), GLS et le rendement. Les effets dus \ue0 la GCA pour le rendement n\u2019\ue9taient pas significatifs pour les parents m\ue2les (lign\ue9es) et femelles (hybrides simples) des g\ue9notypes \ue0 grain de couleur blanche et leurs conversions \ue0 grain de couleur jaune. N\ue9anmoins, deux cas exceptionnels ont \ue9t\ue9 observ\ue9s pour la tol\ue9rance aux maladies: la conversion jaune de la lign\ue9e CML444 \ue9tait un mauvais combinateur pour la TLB, alors que le testeur CML312/CML442 combinait bien pour la tol\ue9rance \ue0 la GLS. En plus, l\u2019h\ue9ritabilit\ue9 \ue9tait faible pour la tol\ue9rance \ue0 la MSV et le rendement. En g\ue9n\ue9ral, il n\u2019y avait pas de diff\ue9rence significative entre les g\ue9notypes \ue0 grain blanc et leurs conversions jaunes respectives, ce qui signifie que, lors de la conversion des vari\ue9t\ue9s \ue0 grain blanc en vari\ue9t\ue9s \ue0 grain jaune, il n\u2019y a aucune perte significative en ce qui est de la tol\ue9rance \ue0 la MSV et la performance en rendement des grains

Understanding effects of multiple farm management practices on barley performance

Because of the complexity of farming systems, the combined effects of farm management practices on nitrogen availability, nitrogen uptake by the crop and crop performance are not well understood. To evaluate the effects of the temporal and spatial variability of management practices, we used data from seventeen farms and projections to latent structures analysis (PLS) to examine the contribution of 11 farm characteristics and 18 field management practices on barley performance during the period 2009-2012. Farm types were mixed (crop livestock) and arable and were categorized as old organic, young organic or conventional farms. The barley performance indicators included nitrogen concentrations in biomass (in grain and whole biomass) and dry matter at two growing stages. Fourteen out of 29 farm characteristics and field management practices analysed best explained the variation of the barley performance indicators, at the level of 56%, while model cross-validation revealed a goodness of prediction of 31%. Greater crop diversification on farm, e.g., a high proportion of rotational leys and pasture, which was mostly observed among old organic farms, positively affected grain nitrogen concentration. The highest average grain nitrogen concentration was found in old organic farms (2.3% vs. 1.7 and 1.4% for conventional and young organic farms, respectively). The total nitrogen translocated in grain was highest among conventional farms (80 kg ha(-1) vs. 33 and 39 kg ha(-1) for young and old organic farms, respectively). The use of mineral fertilizers and pesticides increased biomass leading to significant differences in average grain yield which became more than double for conventional farms (477 +/- 24 g m(-2)) compared to organic farms (223 +/- 37 and 196 +/- 32 g m(-2) for young and old organic farms, respectively). In addition to the importance of weed control, management of crop residues and the organic fertilizer application methods in the current and three previous years, were identified as important factors affecting the barley performance indicators that need closer investigation. With the PLS approach, we were able to highlight the management practices most relevant to barley performance in different farm types. The use of mineral fertilizers and pesticides on conventional farms was related to high cereal crop biomass. Organic management practices in old organic farms increased barley N concentration but there is a need for improved management practices to increase biomass production and grain yield. Weed control, inclusion of more leys in rotation and organic fertilizer application techniques are some of the examples of management practices to be improved for higher N concentrations and biomass yields on organic farms

Geo-additive modelling of malaria in Burundi

Abstract Background Malaria is a major public health issue in Burundi in terms of both morbidity and mortality, with around 2.5 million clinical cases and more than 15,000 deaths each year. It is still the single main cause of mortality in pregnant women and children below five years of age. Because of the severe health and economic burden of malaria, there is still a growing need for methods that will help to understand the influencing factors. Several studies/researches have been done on the subject yielding different results as which factors are most responsible for the increase in malaria transmission. This paper considers the modelling of the dependence of malaria cases on spatial determinants and climatic covariates including rainfall, temperature and humidity in Burundi. Methods The analysis carried out in this work exploits real monthly data collected in the area of Burundi over 12 years (1996-2007). Semi-parametric regression models are used. The spatial analysis is based on a geo-additive model using provinces as the geographic units of study. The spatial effect is split into structured (correlated) and unstructured (uncorrelated) components. Inference is fully Bayesian and uses Markov chain Monte Carlo techniques. The effects of the continuous covariates are modelled by cubic p-splines with 20 equidistant knots and second order random walk penalty. For the spatially correlated effect, Markov random field prior is chosen. The spatially uncorrelated effects are assumed to be i.i.d. Gaussian. The effects of climatic covariates and the effects of other spatial determinants are estimated simultaneously in a unified regression framework. Results The results obtained from the proposed model suggest that although malaria incidence in a given month is strongly positively associated with the minimum temperature of the previous months, regional patterns of malaria that are related to factors other than climatic variables have been identified, without being able to explain them. Conclusions In this paper, semiparametric models are used to model the effects of both climatic covariates and spatial effects on malaria distribution in Burundi. The results obtained from the proposed models suggest a strong positive association between malaria incidence in a given month and the minimum temperature of the previous month. From the spatial effects, important spatial patterns of malaria that are related to factors other than climatic variables are identified. Potential explanations (factors) could be related to socio-economic conditions, food shortage, limited access to health care service, precarious housing, promiscuity, poor hygienic conditions, limited access to drinking water, land use (rice paddies for example), displacement of the population (due to armed conflicts).</p

Assessment of aflatoxin and fumonisin contamination levels in maize and mycotoxins awareness and risk factors in Rwanda

Mycotoxins are secondary metabolites of fungi that are toxic to humans and animals when consumed in contaminated food and feed. The Rwandan climate conditions like steady temperature and sufficient rainfall favor the growth of fungi leading to high probability of mycotoxins contamination. Mycotoxins get into maize throughout the value chain from the field to processed products. Maize is&nbsp; promoted in Rwanda under the Crop Intensification Program (CIP), for nutrition and food security. The aim of the study was to evaluate mycotoxins (Aflatoxin and fumonisin) levels in maize and assess awareness and factors associated with mycotoxin contamination in Rwanda. Maize samples (227 kg) from season B 2019 were collected in 15 Districts in five provinces of Rwanda after an interview with a representative of the household or cooperative using a structured questionnaire. The samples were analyzed for aflatoxin and&nbsp; fumonisin using Reveal Q+ and AccuScan Gold Reader. From the interview, most of the respondents were not aware about aflatoxin (59.7 %) and 99 % did not know the effect of mycotoxins on human health. The average of aflatoxin contamination in surveyed districts was 6.69±13 μg/kg. In general, 90.4 % of samples scored below the limit of aflatoxin level regulated in East Africa/Kenya regulation standards (10 μg/kg). The levels of aflatoxin ranged between 0 and 100.9 μg/kg. The means aflatoxin levels within districts ranged between 1.36±0.5 μg/kg and 13.75±25 μg/kg. Among 9.6 % of the samples containing aflatoxins above the EU and Kenyan regulations standard limit, 5.7 % were above the US standards of 20 μg/kg. Within clusters, the level of aflatoxin more than 10 μg/kg was 5 %, 7 % and 18 % for stores, household and market samples, respectively. From the study, as mechanical damage of grains, moisture content of grains and the temperature of the store house increased, Aflatoxin level also increased. Fumonisin analyzed in maize ranged from 0 to 2.3 μg/g and only one sample from market showed a slightly higher level of fumonisin than the EU and US limit of 2 μg/g. More effort for aflatoxin mitigation is needed at the market level. Farmers need to be aware and taught how they can improve their agricultural system and more knowledge on mycotoxin control is needed. The results point to appropriate measures to recommend for control ofmycotoxins in Rwanda and awareness creation. Key words: AccuScan, Aflatoxin, Fumonisin, Fungal, Maize, Mycotoxins, Reveal Q+, Rwand

Phenotypic and genotypic analyses to guide selection of reverse transcriptase inhibitors in second-line HIV therapy following extended virological failure in Uganda

Objectives We investigated phenotypic and genotypic resistance after 2 years of first-line therapy with two HIV treatment regimens in the absence of virological monitoring. Methods NORA [Nevirapine OR Abacavir study, a sub-study of the Development of AntiRetroviral Therapy in Africa (DART) trial] randomized 600 symptomatic HIV-infected Ugandan adults (CD4 cell count <200 cells/mm3) to receive zidovudine/lamivudine plus abacavir (cABC arm) or nevirapine (cNVP arm). All virological tests were performed retrospectively, including resistance tests on week 96 plasma samples with HIV RNA levels ≥1000 copies/mL. Phenotypic resistance was expressed as fold-change in IC50 (FC) relative to wild-type virus. Results HIV-1 RNA viral load ≥1000 copies/mL at week 96 was seen in 58/204 (28.4%) cABC participants and 21/159 (13.2%) cNVP participants. Resistance results were available in 35 cABC and 17 cNVP participants; 31 (89%) cABC and 16 (94%) cNVP isolates had a week 96 FC below the biological cut-off for tenofovir (2.2). In the cNVP arm, 16/17 participants had resistance mutations synonymous with high-level resistance to nevirapine and efavirenz; FC values for etravirine were above the biological cut-off in 9 (53%) isolates. In multivariate regression models, K65R, Y115F and the presence of thymidine analogue-associated mutations were associated with increased susceptibility to etravirine in the cABC arm. Conclusions Our data support the use of tenofovir following failure of a first-line zidovudine-containing regimen and shed further light on non-nucleoside reverse transcriptase inhibitor hypersusceptibility

Longitudinal evaluation of aflatoxin exposure in two cohorts in south-western Uganda

Aflatoxins (AF) are a group of mycotoxins. AF exposure causes acute and chronic adverse health effects such as aflatoxicosis and hepatocellular carcinoma in human populations, especially in the developing world. In this study, AF exposure was evaluated using archived serum samples from human immunodeficiency virus (HIV)-seronegative participants from two cohort studies in south-western Uganda. AFB1-lysine (AFB-Lys) adduct levels were determined via HPLC fluorescence in a total of 713 serum samples from the General Population Cohort (GPC), covering eight time periods between 1989 and 2010. Overall, 90% (642/713) of the samples were positive for AFB-Lys and the median level was 1.58 pg mg(-1) albumin (range = 0.40-168 pg mg(-1) albumin). AFB-Lys adduct levels were also measured in a total of 374 serum samples from the Rakai Community Cohort Study (RCCS), across four time periods between 1999 and 2003. The averaged detection rate was 92.5% (346/374) and the median level was 1.18 pg mg(-1) albumin (range = 0.40-122.5 pg mg(-1) albumin). In the GPC study there were no statistically significant differences between demographic parameters, such as age, sex and level of education, and levels of serum AFB-Lys adduct. In the RCCS study, longitudinal analysis using generalised estimating equations revealed significant differences between the adduct levels and residential areas (p = 0.05) and occupations (p = 0.02). This study indicates that AF exposure in people in two populations in south-western Uganda is persistent and has not significantly changed over time. Data from one study, but not the other, indicated that agriculture workers and rural area residents had more AF exposure than those non-agricultural workers and non-rural area residents. These results suggest the need for further study of AF-induced human adverse health effects, especially the predominant diseases in the region

Bayesian modelling of the effect of climate on malaria in Burundi

<p>Abstract</p> <p>Background</p> <p>In Burundi, malaria is a major public health issue in terms of both morbidity and mortality with around 2.5 million clinical cases and more than 15,000 deaths each year. It is the single main cause of mortality in pregnant women and children below five years of age. Due to the severe health and economic cost of malaria, there is still a growing need for methods that will help to understand the influencing factors. Several studies have been done on the subject yielding different results as which factors are most responsible for the increase in malaria. The purpose of this study has been to undertake a spatial/longitudinal statistical analysis to identify important climatic variables that influence malaria incidences in Burundi.</p> <p>Methods</p> <p>This paper investigates the effects of climate on malaria in Burundi. For the period 1996-2007, real monthly data on both malaria epidemiology and climate in the area of Burundi are described and analysed. From this analysis, a mathematical model is derived and proposed to assess which variables significantly influence malaria incidences in Burundi. The proposed modelling is based on both generalized linear models (GLM) and generalized additive mixed models (GAMM). The modelling is fully Bayesian and inference is carried out by Markov Chain Monte Carlo (MCMC) techniques.</p> <p>Results</p> <p>The results obtained from the proposed models are discussed and it is found that malaria incidence in a given month in Burundi is strongly positively associated with the minimum temperature of the previous month. In contrast, it is found that rainfall and maximum temperature in a given month have a possible negative effect on malaria incidence of the same month.</p> <p>Conclusions</p> <p>This study has exploited available real monthly data on malaria and climate over 12 years in Burundi to derive and propose a regression modelling to assess climatic factors that are associated with monthly malaria incidence. The results obtained from the proposed models suggest a strong positive association between malaria incidence in a given month and the minimum temperature (night temperature) of the previous month. An open question is, therefore, how to cope with high temperatures at night.</p

The Role of Climate Variability in the Spread of Malaria in Bangladeshi Highlands

Malaria is a major public health problem in Bangladesh, frequently occurring as epidemics since the 1990s. Many factors affect increases in malaria cases, including changes in land use, drug resistance, malaria control programs, socioeconomic issues, and climatic factors. No study has examined the relationship between malaria epidemics and climatic factors in Bangladesh. Here, we investigate the relationship between climatic parameters [rainfall, temperature, humidity, sea surface temperature (SST), El Niño-Southern Oscillation (ENSO), the normalized difference vegetation index (NDVI)], and malaria cases over the last 20 years in the malaria endemic district of Chittagong Hill Tracts (CHT)