The empirical bias of estimates by restricted maximum likelihood, Bayesian method, and method R under selection for additive, maternal, and dominance models.

Bayesian analysis via Gibbs sampling, restricted maximum likelihood (REML), and Method R were used to estimate variance components for several models of simulated data. Four simulated data sets that included direct genetic effects and different combinations of maternal, permanent environmental, and dominance effects were used. Parents were selected randomly, on phenotype across or within contemporary groups, or on BLUP of genetic value. Estimates by Bayesian analysis and REML were always empirically unbiased in large data sets. Estimates by Method R were biased only with phenotypic selection across contemporary groups; estimates of the additive variance were biased upward, and all the other estimates were biased downward. No empirical bias was observed for Method R under selection within contemporary groups or in data without contemporary group effects. The bias of Method R estimates in small data sets was evaluated using a simple direct additive model. Method R gave biased estimates in small data sets in all types of selection except BLUP. In populations where the selection is based on BLUP of genetic value or where phenotypic selection is practiced mostly within contemporary groups, estimates by Method R are likely to be unbiased. In this case, Method R is an alternative to single-trait REML and Bayesian analysis for analyses of large data sets when the other methods are too expensive to apply.     

Identification of a major gene (Mex-1) from Coffea canephora conferring resistance to Meloidogyne exigua in Coffea arabica

Among the most damaging root-knot nematode species, Meloidogyne exigua is especially common in Latin America and constitutes a major agronomic constraint in all major coffee-growing ( Coffea arabica ) areas. Growing nematode-resistant coffee represents the most promising option for control of the pest. The present study aimed to determine the mode of inheritance of the M. exigua resistance transferred into C. arabica from a related species, Coffea canephora , and to identify associated molecular markers. Segregation data analysis of F ₂ progeny derived from a cross between the resistant introgression line T5296 and the susceptible accession Et6 showed that the resistance to M. exigua is controlled by a simply inherited major gene (designated the Mex -1 locus). The gall index distribution exhibited by the F ₂ individuals suggested incomplete dominant expression. Fourteen AFLP markers were found associated with the resistance to M. exigua and a localized genetic map of the chromosome segment carrying Mex -1 was constructed. Furthermore, the association of the identified AFLP markers with Mex -1 was confirmed by analysis of a set of genotypes involving 28 introgression Arabica lines either resistant or susceptible to M. exigua in field conditions. These results represent an important starting point to enhance backcross breeding programmes and to perform an early selection of resistant seedlings.     

Echinococcus multilocularis and Toxocara canis in urban red foxes (Vulpes vulpes) in Brussels, Belgium

During the last decades, European red foxes (Vulpes vulpes) have been implicated in the transmission of several viral or parasitic pathogenic agents to domestic animals and humans. In urban areas, risks of zoonoses transmission are likely to increase as a result of a higher rate of intra- and inter-species contacts. Foxes occur on 35% of the Brussels-Capital Region area and local densities reach up to 4 family groups per square kilometre. According to the directive 2003/99/ECC, a first survey for the presence in foxes of Echinococcus multilocularis and Toxocara canis was conducted in Brussels from 2001 to 2004. None of 160 foxes were found to be infected with E. multilocularis and 24 of 134 foxes were found to be infected with T. canis. Considering numbers of examined foxes, the sensitivity and the specificity of tests used for diagnosis, the 95% credibility intervals for the true prevalence of E. multilocularis and T. canis were estimated in a Bayesian framework to be 0 to 1.87% (median value of 0%) and 12.7 to 26% (median value of 18.7%), respectively. For T. canis, a significantly higher risk to be a carrier occurs in cubs and a significantly lower risk in adults.     

Revisiting rice breeding methods – evaluating the use of rapid generation advance (RGA) for routine rice breeding

Rice production needs to increase in the future in order to meet increasing demands. The development of new improved and higher yielding varieties more quickly will be needed to meet this demand. However, most rice breeding programmes in the world have not changed in several decades. In this article, we revisit the evidence in favour of using rapid generation advance (RGA) as a routine breeding method. We describe preliminary activities at the International Rice Research Institute (IRRI) to re-establish RGA on a large scale as the main breeding method for irrigated rice breeding. We also describe experiences from the early adoption at the Bangladesh Rice Research Institute. Evaluation of RGA breeding lines at IRRI for yield, flowering time and plant height indicated transgressive segregation for all traits. Some RGA lines were also higher yielding than the check varieties. The cost advantages of using RGA compared to the pedigree method were also empirically determined by performing an economic analysis. This indicated that RGA is several times more cost effective and advantages will be realized after 1 year even if facilities need to be built. Based on our experience, and previous independent research empirically testing the RGA method in rice, we recommend that this method should be implemented for routine rice breeding in order to improve breeding efficiency.     

Carbohydrate and crude protein fractions in perennial ryegrass as affected by defoliation frequency and nitrogen application rate

The objective of this study was to evaluate the effects of defoliation frequency (either at two‐ or three‐leaf stage) and nitrogen (N) application rate (0, 75, 150, 300, 450 kg N ha^?1 year^?1) on herbage carbohydrate and crude protein (CP) fractions, and the water‐soluble carbohydrate‐to‐protein ratio (WSC:CP) in perennial ryegrass swards. Crude protein fractions were analysed according to the Cornell carbohydrate and protein system. Carbohydrate fractions were analysed by ultra‐high‐performance liquid chromatography. Sward defoliation at two‐leaf stage increased the total CP, reduced the buffer‐soluble CP fractions and decreased carbohydrate fractions of herbage (P < 0·001). The effect of defoliation frequency was less marked during early spring and autumn (P < 0·001) than for the rest of the seasons. An increase in N application rate was negatively associated with WSC, fructans and neutral detergent fibre (P < 0·001), and positively associated with CP and nitrate (N‐NO₃) contents of herbage. Nitrogen application rate did not affect CP fractions of herbage (P > 0·05). The fluctuations in CP and WSC contents of herbage resulted in lower WSC:CP ratios during early spring and autumn (0·45:1 and 0·75:1 respectively) than in late spring (1·11:1). The herbage WSC:CP ratio was greater (P < 0·001) at the three‐leaf than the two‐leaf defoliation stage and declined as the N application increased in all seasons (P < 0·001). The results of this study indicate that CP and carbohydrate fractions of herbage can be manipulated by sward defoliation frequency and N application rate. The magnitude of these effects, however, may vary with the season.     

Distribution analyses of Meloidogyne spp. and Pratylenchus coffeae sensu lato in coffee plots in Costa Rica and Guatemala

The distribution of the plant-parasitic nematodes Pratylenchus coffeae sensu lato and Meloidogyne spp. were studied in two plots, one in Guatemala ( P. coffeae and M. paranaensis ) and the other in Costa Rica ( P. coffeae and M. exigua ). The quantity of nematodes per g fresh weight root were counted for each coffee tree sampled. The distributions were aggregated, and generally fitted well to negative binomial distributions. Population aggregation was greater when a smaller number of nematodes were involved, suggesting that initial colonization develops in foci. Analyses of the relationships between population levels of the species suggested that there was competition between Pratylenchus coffeae and Meloidogyne spp. This competition was expressed differently depending on the relative population density of the different species.     

Serological and biochemical follow-up in cattle naturally infected with Fasciola hepatica, and comparison with a climate model for predicting risks of fasciolosis

Several biological parameters were measured in 31 heifers naturally infected with Fasciola hepatica during one grazing season in the Belgian Ardennes. A forecast model based on daily temperature used to assess the risk of fasciolosis was fitted to this assay. Cattle were turned out to two pastures. Each pasture was divided into two plots: one was treated with calcium cyanamide and the other was left untreated. The Lymnaea truncatula snails were counted on three different occasions. The results indicated a poor molluscicide efficiency. Body weight gains, anti-Fasciola antibody levels, faecal egg counts, levels of sorbitol dehydrogenase (SDH) and gamma-glutamyl transferase (gamma GT), packed cell volumes, white blood cells and differential leucocyte counts were determined monthly. No statistically significant difference was observed between animals from the two plots regardless of the recorded data. No correlation was found between body weight gains and other biological data. The sampling date had a significant effect on the antibody responses within a same group, and on the enzymatic levels for all groups combined. The forecast results were consistent with the recorded data. Temperature was a major bioclimatic constraint on the transmission of life cycle, and risk of infection occurred mainly in late spring (May/June) and in early September. Current results might be used to issue advice on the need for flukicide treatment of cattle. The indicators of the infection considered alone were useless and it is concluded that herd diagnosis of fasciolosis may rely on the rise of specific antibody levels, possibly associated with an increase in hepatic enzyme activities.     

Immunisation against Theileria parva in eastern Zambia: influence of maternal antibodies and demonstration of the carrier status

Immunisation of calves by the infection and treatment method (I & T) has been extensively used in the eastern province of Zambia to control East Coast fever (ECF), a protozoan tick-borne disease. This paper presents the results of a field longitudinal study, which included a total of 148 Angoni calves. After immunisation against ECF, they were monitored for a full rainy season, coinciding with the main peak of activity of the vector of Theileria parva, the tick Rhipicephalus appendiculatus. Dysimmunisation (acute reaction generated by I & T immunisation), seroconversion and mortality are among the parameters recorded. The effect of maternal antibodies on these parameters was analysed and also studied in experimental conditions on two calves. Before immunisation, young calves had a higher seroprevalence than older animals (maternal antibodies) but their post-immunisation seroprevalence was lower. There was no evidence that their immunoprotection was weaker but this indicates that the post-immunisation seroconversion is probably not a reliable tool to monitor the efficacy of calf immunisation. The carrier state of cattle after immunisation was investigated in experimental conditions on three bovines whereas in the field, the infection prevalence in the ticks was estimated using the relation between the tick burden and the T. parva contacts with the calves. The ability of larval and nymphal R. appendiculatus ticks to pick-up T. parva from carriers and to transmit it to na?ve animals after moulting was assessed. It was found that both instars are able to transmit clinical and lethal ECF but that the prevalence of T. parva infection in nymphs is much lower than in adults, confirming the primary role of adults in the transmission of ECF in endemic conditions. Similar results were obtained from the field whereby the ECF peak corresponds with the peak of adult R. appendiculatus activity. The infection prevalence in the ticks was however much lower in the field than in experimental conditions indicating that an important proportion of them feed on alternative hosts. Old ticks seemed to have lost part of their infectivity.     

Susceptibility of trypanotolerant West African Dwarf goats and F1 crosses with the susceptible Sahelian breed to experimental Trypanosoma congolense infection and interactions with helminth infections and different levels of diet

Forty pure West African Dwarf (WAD) goats and 35 of its F1 crosses with the Sahelian breed were used in a multifactorial experimental design to evaluate the effects of an experimental Trypanosoma congolense infection and interactions with natural helminth infections and different levels of diet on health and productivity of these two breeds. Trypanosome infection caused a severe drop in packed cell volume (PCV), but this was not significantly affected by breed. Neither deworming nor diet had any effect on the course of anaemia after trypanosome infection. The mean score of parasitaemia tended to be higher in crossbreeds than in WAD goats although this was not significant (P>0.05). Similarly, the antibody response to trypanosome infection was not significantly different between breeds. Parasitaemia level was significantly influenced by the level of diet with the group under high supplementation having a higher mean parasitaemia score than the group under low supplementation. Weight loss due to trypanosome infection tended to be greater in crossbreeds than in WAD goats (P>0.05).During this study, there was no difference in mean helminth egg output between crossbred and WAD goats. However, between weeks 4 and 10 after trypanosome infection (corresponding to a period of heavy rainfall and highly infective pastures), the mean egg output was higher in the crossbreeds.The immunosuppressive effect of trypanosome infections was revealed by a lower antibody response to Haemonchus contortus in infected animals compared to the uninfected controls. Trypanosome infection tended to increase strongyle egg output. This study did no reveal any superior trypanotolerance of WAD goats compared to crossbreeds.