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.     

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.     

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.     

Genetic and non-genetic factors influencing KLH binding natural antibodies and specific antibody response to Newcastle disease in Kenyan chicken populations

This study aimed at investigating the influence of genetic and non-genetic factors on immune traits to inform on possibilities of genetic improvement of disease resistance traits in local chicken of Kenya. Immune traits such as natural and specific antibodies are considered suitable indicators of an individual's health status and consequently, used as indicator traits of disease resistance. In this study, natural antibodies binding to Keyhole Limpet Hemocyanin (KLH-NAbs) was used to measure general disease resistance. Specific antibodies binding to Newcastle disease virus (NDV-IgG) post vaccination was used to measure specific disease resistance. Titers of KLH-NAbs isotypes (KLH-IgM, KLH-IgG and KLH-IgA) and NDV-IgG were measured in 1,540 chickens of different ages ranging from 12 to 56 weeks. A general linear model was fitted to determine the effect of sex, generation, population type, phylogenetic cluster, line, genotype and age on the antibody traits. A multivariate animal mixed model was fitted to estimate heritability and genetic correlations among the antibody traits. The model constituted of non-genetic factors found to have a significant influence on the antibody traits as fixed effects, and animal and residual effects as random variables. Overall mean (±SE) concentration levels for KLH-IgM, KLH-IgG, KLH-IgA and NDV-IgG were 10.33 ± 0.04, 9.08 ± 0.02, 6.00 ± 0.02 and 10.12 ± 0.03, respectively. Sex, generation and age (linear covariate) significantly (p < 0.05) influenced variation across all the antibody traits. Genotype effects (p < 0.05) were present in all antibody traits, apart from KLH-IgA. Interaction between generation and line was significant (p < 0.05) in KLH-IgM and NDV-IgG while nesting phylogenetic cluster within population significantly (p < 0.05) influenced all antibody traits, apart from KLH-IgA. Heritability estimates for KLH-IgM, KLH-IgG, KLH-IgA and NDV-IgG were 0.28 ± 0.08, 0.14 ± 0.06, 0.07 ± 0.04 and 0.31 ± 0.06, respectively. There were positive genetic correlations (0.40–0.61) among the KLH-NAbs while negative genetic correlations (−0.26 to −0.98) were observed between the KLH-NAbs and NDV-IgG. Results from this study indicate that non-genetic effects due to biological and environmental factors influence natural and specific antibodies and should be accounted for to reduce bias and improve accuracy when evaluating the traits. Subsequently, the moderate heritability estimates in KLH-IgM and NDV-IgG suggest selection possibilities for genetic improvement of general and specific immunity, respectively, and consequently disease resistance. However, the negative correlations between KLH-NAbs and NDV-IgG indicate the need to consider a suitable approach that can optimally combine both traits in a multiple trait selection strategies.     

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.