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.     

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.     

Technical note: recombinant LHRH fusion protein suppresses estrus in heifers

A recombinant luteinizing hormone-releasing hormone (LHRH) fusion protein was evaluated for its effectiveness in suppression of estrus in heifers. Eight heifers were randomly assigned to two equal treatment groups. Treatments consisted of recombinant ovalbumin-LHRH-7 or recombinant ovalbumin (control). This recombinant chimeric fusion protein consisted of ovalbumin with seven LHRH peptides (ovalbumin-LHRH-7). The plasmid for this protein was expressed in E. coli and was collected and purified as an insoluble protein. One milligram of the respective proteins was suspended in 2 mL of Z-Max adjuvant and administered by intramammary injection three times at 7-wk intervals. Luteinizing hormone-releasing hormone antibody binding was elevated in heifers treated with ovalbumin-LHRH-7 compared to ovalbumin-treated heifers (P < .05). Serum progesterone concentrations (< 1 ng/mL) indicate that the estrous cycle of the four heifers treated with ovalbumin-LHRH-7 was suppressed for a time period ranging from 60 to 238 d, which was different from control heifers (P < .01). Serum progesterone for the control heifers continued to exhibit cyclic profiles over the experimental period. This preliminary study in heifers demonstrated that a chimeric LHRH fusion protein induced elevated concentrations of circulating LHRH antibodies that suppressed estrus for an average of 122 +/- 41 d.     

Annual, career or single race records for breeding value estimation in race horses

The racing careers of 2, 3, 4, and 5-year-old Thoroughbreds and French trotters born in France between 1995 and 1999 were analysed. The horses were evaluated on a set of traits, with particular attention to annual or career earnings and number of starts.

As expected, the distributions of earnings corrected for year, age and sex are very skew and thus inappropriate for breeding value estimations. However, Log transformation results in near normal distributions more suitable for this purpose.

Another problem of annual or career earnings required a more complex approach. As most horses did not win any money in France (67% of the trotters and 41% of the Thoroughbreds), it is difficult to correctly evaluate these horses. On the other hand, a linear adjustment of the Log of earnings by the Log of the number of starts (exponential adjustment of the earning index) leads to regression coefficients close to 1. It justified the use of the Log of earnings per start and explained its higher heritability in literature. A quadratic adjustment of the Log of earnings by the Log of the number of starts (sigmoid adjustment of the earning index) improves the adjustment for the Thoroughbred only and should be implemented for these horses.

The probability of a horse to be placed according to the number of starts was also studied. It is shown that the observed percentage of non-placed horses p_s according to the number of starts, s, is in all cases inferior to the expected percentage (p_s < p₁^s). Therefore, races of the same horse cannot be considered as independent events. The percentage of horses placed and the mean earnings for each age can be combined in order to estimate the economical weights for each age class. Economical weights for the French trotter were 0.00, 0.21, 0.40, and 0.39 for 2, 3, 4, and 5-year olds respectively. They were 0.11, 0.45, 0.26 and 0.18 respectively for Thoroughbreds of the same age categories. The current tendency to move from annual or career criteria towards criteria at the race level is discussed. However, the question on how to evaluate the important proportion of horses born that never appeared in a race still remains open and should focus future research.     

Somaclonal variation in Coffea arabica: effects of genotype and embryogenic cell suspension age on frequency and phenotype of variants

We determined how age of embryogenic cell suspensions affects somaclonal variation in five F1 hybrids of Coffea arabica L. Batches of plants were produced either directly from embryogenic callus, or after 3, 6, 9 and 12 months of embryogenic cell suspension culture. Seven phenotypic variants were characterized. Based on vigor and productivity of the regenerated plants, we classified the variants in order of increasing severity of physiological disorders as: Juvenile leaf color, Giant, Dwarf, Thick leaf (Bullata), Variegata, Angustifolia, and Multi-stem. The Dwarf, Angustifolia and Multi-stem variants were the most frequent among the regenerated plants (1.4, 4.8 and 2.9%, respectively). The frequency (f) of variants increased exponentially with the age (t) of the embryogenic suspension, in accordance with the function f = 0.99e(0.267t). For all genotypes, somaclonal variation was low (1.3%) in plants produced from embryogenic callus or 3-month-old cell suspensions and increased in frequency with increasing suspension age (6, 10 and 25% in plants produced from cell suspensions aged 6, 9 and 12 months, respectively). Large differences in somaclonal variation among genotypes were found only in plants produced from 12-month-old cell suspensions. For two genotypes, the oldest suspensions produced a majority of somaclonal variants (80-90%), whereas somaclonal variation ranged between 8 and 18% in the other genotypes. Cell suspension age and genotype also affected the type of variant produced. The severity of somaclonal variations increased with cell suspension age. For all genotypes combined, the Angustifolia variant was the most common. The other somaclonal variations were specific to certain genotypes or distributed randomly among the genotypes.     

Influence of ozone on cold acclimation in sugar maple seedlings

During summer 1994, sugar maple (Acer saccharum Marsh.) seedlings were grown in open-top chambers supplied with air containing near ambient ozone concentration (control, low O(3)) or three times the ambient ozone concentration (high O(3)). The rate of CO(2) assimilation was significantly reduced by chronic exposure to a high concentration of ozone during the summer. During fall, seedlings were removed from the open-top chambers and acclimated to cold under natural conditions. In both species during cold acclimation, the starch concentration decreased, whereas the sucrose concentration increased. There was no treatment effect on the freezing tolerance of roots, even though roots in the high-O(3) treatment accumulated higher concentrations of the cryoprotective oligosaccharides raffinose and stachyose than control roots. Cold acclimation occurred earlier and stachyose concentration of stems was higher in high-O(3)-treated seedlings than in low-O(3)-treated seedlings. Cold acclimation was associated with an earlier accumulation of ABA in the xylem sap of high-O(3)-treated seedlings compared with low-O(3)-treated seedlings.     

From small-scale habitat loopholes to decadal cycles: a habitat-based hypothesis explaining fluctuation in pelagic fish populations off Peru

The Peru‐Humboldt Current system (HCS) supports the world's largest pelagic fisheries. Among the world's eastern boundary current systems, it is the most exposed to high climatic stress and is directly affected by El Niño and La Niña events. In this volatile ecosystem, fish have been led to develop adaptive strategies in space and time. In this paper, we attempt to understand the mechanisms underlying such strategies, focusing on the El Niño 1997–98 in Peru from which an extensive set of hydrographic, capture and acoustic survey data are available. An integrated analysis of the data is crucial, as each has substantial shortcomings individually; for example, both catch data and acoustic surveys may easily lead to wrong conclusions. Existing hypotheses on anchovy and sardine alternations lead us to a ‘habitat‐based’ synthetic hypothesis. Using our data, an integrated approach evaluated how fish responded to habitat variation, and determined the consequences in terms of fish‐population variability. Various factors occurring at a range of different spatio‐temporal scales were considered: interdecadal regime (warm ‘El Viejo’/cool ‘La Vieja’ decadal scale); strength and the duration of the El Niño Southern Oscillation event (interannual scale); population condition before the event (interannual scale); fishing pressure and other predation (annual scale); changes in reproductive behaviour (intra‐annual scale); presence of local upwelling (local scale). During El Niño 1997–98, anchovy was able to exploit a small‐scale temporal and spatial ‘loophole’ inside the general unfavourable conditions. Moreover, sardine did not do better than anchovy during this El Niño and was not able to take advantage of the ‘loophole’ opened by this short‐term event. Our results question the traditional view that El Niño is bad for anchovy and good for sardine.