Livestock production in central Mali: Reproduction,growth and mortality of domestic fowl under traditional management

In an 18-month study the domestic fowl in 42 households in three traditional management systems were recorded to determine reproduction, growth and mortality parameters. There were significant differences for all systems combined in the number of clutches started per month with the lowest number being laid in the cool dry season of January and February. Mean number of eggs per clutch was 8.8; the number of eggs increased significantly throughout the career of the hen but there were no significant systems differences. Egg weight was 34.4g there being no significant differences due to age of hen or system. Intervals between clutches were 92 days, annual egg output was 35 per hen (assuming that birds were present in the flock for a year) equivalent to about 118% of mean adult hen body weight: hens actually in the flocks during the study had produced 2.1 clutches on average. Hatchability of eggs was 69.1% there being significant seasonal and systems differences in this parameter, lowest hatchability being in the hot dry season (March to June) and in the rainfed millet system. Mortality rates to eight weeks were 56% of chicks hatched. Growth to 10 weeks averaged 4g/d. Mature cocks weighted 1.60 kg and mature hens 1.02 kg: hen weights were significantly affected by reproductive state, laying hens being heavier than both incubating hens and those rearing chicks, while those rearing chicks were heavier than those incubating. Suggestions for improving productivity are made.     

Gastrointestinal parasite egg excretion in young calves in periurban livestock production in Mali

To acquire the information needed to improve parasite control in periurban cattle production in Mali, repeated sampling of faeces of 694 calves kept around Bamako was done in 2003/2004. The effects of season, age, breed, management type, parasite control and presence of sheep on egg and oocyst counts were determined. A Bayesian model was used with a negative binomial distribution and herd and individual effects, to account for the clustering of calves in herds and the repeated sampling. Interviews were conducted to report the current control strategies. We found eggs of Strongyloides papillosus (Age class 0-1 month: prevalence 39%, 2-3 months: 59%, 5-6 months: 42%), strongyles (14%, 24%, 36%), coccidian oocysts (37%, 68%, 64%) and at low prevalence eggs of Toxocara vitulorum, Moniezia sp., Trichuris sp. and Paramphistomum sp. Season and age effects occurred. Reported utilisation of parasite control was high (92%) but monthly recorded use was significantly lower (61%).     

Inheritance of flour paste viscosity is associated with a rice Waxy gene exon 10 SNP marker

Apparent amylose content is a key element for characterizing a rice (Oryza sativa L.) cultivar for cooking quality. However, cultivars with similar apparent amylose content can have widely varying quality attributes, including major parameters of flour paste viscosity. It has been postulated that the presence of a rice Waxy gene single nucleotide polymorphism (SNP) marker is associated with elevated Rapid Visco Analyser (RVA) properties in specific high amylose rice cultivars. A mapping population derived from a cross between two varieties, Cocodrie and Dixiebelle, having similar high apparent amylose contents, but with different paste viscosity properties and Waxy gene markers was analyzed for the genetic segregation of various pasting properties, measured with RVA instrumentation. Marker inheritance analyses revealed that the Waxy exon 10 SNP marker was associated with the proportion of soluble to insoluble apparent amylose and most RVA pasting measurements. Waxy gene markers can be used to efficiently improve the selection of rice with desirable characteristics, particularly for superior parboiling and canning quality.     

Short-term forecasting of daily crop evapotranspiration using the ‘Kc-ETo’ approach and public weather forecasts

Short-term forecasting of daily crop evapotranspiration (ET_c) is essential for real-time irrigation management. This study proposed a methodology to forecast short-term daily ET_c using the ‘K_c-ET_o’ approach and public weather forecasts. Daily reference evapotranspiration (ET_o) forecasts were obtained using a locally calibrated version of the Hargreaves-Samani (HS) model and temperature forecasts, while the crop coefficient (K_c) was estimated from observed daily ET_o and ET_c. The methodology was evaluated by comparing the daily ET_c forecasts with measured ET_c values from a field irrigation experiment during 2012–2014 in Yongkang Irrigation Experimental Station, China. The overall average of the statistical indices was in the range of 0.96–1.27 mm d^?1 for the mean absolute error (MAE), 1.53–2.55 mm d^?1 for the mean square error (MSE), 1.77–2.30 mm d^?1 for the normalized mean square error (NMSE), 27.5–29.4% for the mean relative error (MRE), 0.71–0.44 for the correlation coefficient (R) and 0.46–0.05 for the mean square error skill score (MSESS). Sources of error werewere K_c estion, temperature forecasts and HS model that does not consider wind speed and humidity, and.the largesourceof error is K_c determination, which suggested that care should be taken when forecasting ET_c with estimated K_c values in the study area.     

Rice Yellow Mottle Virus is Seed-borne but not Seed Transmitted in Rice Seeds

Seed transmission of two pathogroups of rice yellow mottle virus from Soudano-Sahelian areas of West Africa was studied in several rice genotypes. The virus was detected by enzyme-linked immunosorbent assay and the highly susceptible rice variety BG 90-2 was used for infectivity assays. In most of the rice genotypes studied (17 out of 21), rice yellow mottle virus was detected in all seed parts including glumella, endosperm and embryo at a rate ranging from 65 to 100%. Nevertheless, no seed-borne infection was found. Infectivity of the virus decreased throughout the process of seed formation suggesting inactivation of the virus as a result of seed maturation and desiccation. It was concluded that rice yellow mottle epidemics do not develop from seed-borne infections in rice seeds.     

Early mortality of lambs in African traditional livestock production systems

Early mortality of lambs is a major constraint on total productivity. In 6 different environments the early death rate varied from 12 to 30% of all lambs born. Cause of death differed among systems but only a proportion could definitely be ascribed to infectious disease: nutrition, management and other environmental factors also contribute to the mortality rate. Mortality can be reduced by isolating solutions due to any of these factors but best results (lowest death rates) would be obtained by an integrated package containing elements of all these aspects.     

Effect of nitrate/ammonium ratio on biomass production,nitrogen accumulation,and use efficiency in sorghums of different origin

Plant nitrogen (N) uptake, growth, and N use efficiency may be affected by N form (NO₃ ^‐or NH₄ ⁺) available to the root. The objectives of this study were to determine the effect of mixed N form on dry matter production and partitioning, N uptake, and biomass N use efficiency defined as total dry matter produced per unit plant N (NUE₁) in U.S. and tropical grain sorghums [Sorghum bicolor (L.) Moench]. The U.S. derived genotype CK 60 and three tropical genotypes, Malisor‐7, M 35–1, and S 34, were evaluated in a greenhouse trial using three nutrient solutions differing in their NO₃ ^‐/NH₄ ⁺ ratio (100/0, 75/25, 50/50). Shoot and root biomass, N accumulation, and NUE, were determined at 10‐leaf and boot stages. Averaged over all genotypes, shoot and root biomass decreased when NH₄ ⁺ concentration was increased in the solution. Shoot biomass was reduced by 11% for 75/25 and 26% for 50/50 ratios, as compared to 100/0 NO₃ ^‐/NH₄ ⁺. Similarly, root biomass reduction was about 34% and 45% for the same ratios, respectively. Increasing NH₄ ⁺ concentration also altered biomass partitioning between shoot and root as indicated by decreasing root/shoot ratio. Total plant N content and NUE₁ were also reduced by mixed N source. Marked genotypic variability was found for tolerance to higher rates of NH₄ ⁺. The tropical line M 35–1 was well adapted to either NO₃ ^‐ as a sole source, or to an N source containing high amounts of NH₄ ⁺. Such a characteristic may exist in some exotic lines and may be used to improve genotypes which do not do well in excessively wet soil conditions where N uptake can be reduced.     

A novel Gateway®-compatible binary vector allows direct selection of recombinant clones in Agrobacterium tumefaciens

Background

In vivo detection of protein-bound genomic regions can be achieved by combining chromatin-immunoprecipitation with next-generation sequencing technology (ChIP-seq). The large amount of sequence data produced by this method needs to be analyzed in a statistically proper and computationally efficient manner. The generation of high copy numbers of DNA fragments as an artifact of the PCR step in ChIP-seq is an important source of bias of this methodology.

Results

We present here an R package for the statistical analysis of ChIP-seq experiments. Taking the average size of DNA fragments subjected to sequencing into account, the software calculates single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the ratio test or the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutations. Computational efficiency is achieved by implementing the most time-consuming functions in C++ and integrating these in the R package. An analysis of simulated and experimental ChIP-seq data is presented to demonstrate the robustness of our method against PCR-artefacts and its adequate control of the error rate.

Conclusions

The software ChIP-seq Analysis in R (CSAR) enables fast and accurate detection of protein-bound genomic regions through the analysis of ChIP-seq experiments. Compared to existing methods, we found that our package shows greater robustness against PCR-artefacts and better control of the error rate.