Choice of shrinkage parameter and prediction of genomic breeding values in elite maize breeding populations

Genomic selection (GS) is a promising alternative to marker‐assisted selection particularly for quantitative traits. In this study, we examined the prediction accuracy of genomic breeding values by using ridge regression best linear unbiased prediction in combination with fivefold cross‐validation based on empirical data of a commercial maize breeding programme. The empirical data is composed of 930 testcross progenies derived from 11 segregating families evaluated at six environments for grain yield and grain moisture. Accuracy to predict genomic breeding values was affected by the choice of the shrinkage parameter λ², by unbalanced family size, by size of the training population and to a lower extent by the number of markers. Accuracy of genomic breeding values was high suggesting that the selection gain can be improved implementing GS in elite maize breeding programmes.     

Effects of edaphic conditions on site quality for Salix purpurea ‘Hotel’ plantations across a large climatic gradient in Canada

Willow has been identified as a possible species for supplying large quantities of biomass for bioenergy and wood fibers in Canada. However, before site selection occurs, there is a need to know how the soils and climate of the prairies and central regions affect willow productivity. Soil, foliar, and climatic variables were therefore measured along with yields at nine “first rotation” Salix purpurea ‘Hotel’ plantations from central Alberta to southern Ontario. Correlation analysis was used to identify those parameters having the most influence on yields. Relationships between soil and climate and growth were established by regression analysis. The acid–base status of the soil as dictated by bulk elemental composition, in particular the presence of Ca, was found to be the dominant factor affecting productivity (r = 0.967, P < 0.001 total Ca vs. yields) despite large regional differences in climate. From a nutritional standpoint, total soil N (r = 0.743, P = 0.048) and foliar K (r = 0.938, P = 0.009 for sites with adequate moisture) were positively correlated with growth. S. purpurea ‘Hotel’ yields were found to be primarily limited by water availability at the two lowest productivity prairie sites. Soil total Ca concentration, pH and total organic C concentration were all generally correlated with higher yields. Additional deficiencies appeared in the following order of importance: water > N and K > Mg. As a whole, soil properties were the dominant predictors of ‘Hotel’ growth in this study, which suggests that, even at the regional scale, growth was governed in large part by the capacity of soils to retain water and/or nutrients. Climate played a lesser role, except perhaps at two sites which appeared to receive inadequate moisture.     

Nutrient concentration and allometric models for hybrid eucalyptus planted in France

Context

Short rotation coppice (SRC) of hybrid Eucalyptus has been developed in France for almost 30 years for the production of pulp and paper and, since a few years, for energy purposes. In the traditional pulp production, only the stems are harvested, whereas the whole biomass may be harvested for energy purposes. Thus, a range of different harvest scenarios need to be considered with higher plantation densities or younger age of harvest for example.

Aims

The objective of this study was to build models to estimate biomass and nutrient content of eucalyptus at different ages and so to estimate the production and the nutrient exportation of a SRC, depending on the different harvest scenarios.

Methods

Over 250 trees were sampled in 16 stands at ages from 1 to 15 years. For each tree, biomass of different compartments and nutrient contents were recorded.

Results

A complete set of equations for the four compartments (wood, bark, branches, and leaves) of aboveground biomass and for nutrient concentration was set up.

Conclusion

Biomass and its allocation to different compartments and nutrient concentrations depended on the dimension and/or the age of the tree. In particular, nutrient concentration decreased with increasing tree diameter.     

Description of a new procedure to estimate the carbon stocks of all forest pools and impact assessment of methodological choices on the estimates

Forest ecosystems play a major role in atmospheric carbon sequestration and emission. Comparable organic carbon stock estimates at temporal and spatial scales for all forest pools are needed for scientific investigations and political purposes. Therefore, we developed a new carbon stock (CS) estimation procedure that combines forest inventory and soil and litter geodatabases at a regional scale (southern Belgium). This procedure can be implemented in other regions and countries on condition that available external carbon soil and litter data can be linked to forest inventory plots. The presented procedure includes a specific CS estimation method for each of the following forest pools and subpools (in brackets): living biomass (aboveground and belowground), deadwood (dead trees and snags, coarse woody debris and stumps), litter, and soil. The total CS of the forest was estimated at 86 Tg (185 Mg ha^?1). Soil up to 0.2 m depth, living biomass, litter, and deadwood CSs account, respectively, for 48, 47, 4, and 1 % of the total CS. The analysis of the CS variation within the pools across ecoregions and forest types revealed in particular that: (1) the living biomass CS of broadleaved forests exceeds that of coniferous forests, (2) the soil and litter CSs of coniferous forest exceed those of broadleaved forests, and (3) beech stands come at the top in carbon stocking capacity. Because our estimates differ sometimes significantly from the previous studies, we compared different methods and their impacts on the estimates. We demonstrated that estimates may vary highly, from ?16 to +12 %, depending on the selected methods. Methodological choices are thus essential especially for estimating CO₂ fluxes by the stock change approach. The sources of error and the accuracy of the estimates were discussed extensively.     

Natural enemies of the South American moth, Tuta absoluta, in Europe, North Africa and Middle East, and their potential use in pest control strategies

The South American tomato leafminer, Tuta absoluta Meyrick (Lepidoptera: Gelechiidae), is an invasive Neotropical pest. After its first detection in Europe, it rapidly invaded more than 30 Western Palaearctic countries becoming a serious agricultural threat to tomato production in both protected and open-field crops. Among the pest control tactics against exotic pests, biological control using indigenous natural enemies is one of the most promising. Here, available data on the Afro-Eurasian natural enemies of T. absoluta are compiled. Then, their potential for inclusion in sustainable pest control packages is discussed providing relevant examples. Collections were conducted in 12 countries, both in open-field and protected susceptible crops, as well as in wild flora and/or using infested sentinel plants. More than 70 arthropod species, 20 % predators and 80 % parasitoids, were recorded attacking the new pest so far. Among the recovered indigenous natural enemies, only few parasitoid species, namely, some eulophid and braconid wasps, and especially mirid predators, have promising potential to be included in effective and environmentally friendly management strategies for the pest in the newly invaded areas. Finally, a brief outlook of the future research and applications of indigenous T. absoluta biological control agents are provided.     

Population structure of the fish pathogen Flavobacterium psychrophilum at whole-country and model river levels in Japan

The bacterium Flavobacterium psychrophilum is a serious problem for salmonid farming worldwide. This study investigates by multilocus sequence typing (MLST) the population structure of this pathogen in Japan where it is also a major concern for ayu, a popular game fish related to salmoniforms. A total of 34 isolates collected across the country and 80 isolates sampled in a single model river by electrofishing were genotyped. The data accounting for 15 fish species allowed identifying 35 distinct sequence types (ST) in Japan. These ST are distinct from those reported elsewhere, except for some ST found in rainbow trout and coho salmon, two fish that have been the subject of intensive international trade. The pattern of polymorphism is, however, strikingly similar across geographical scales (model river, Japan, world) in terms of the fraction of molecular variance linked to the fish host (~50%) and of pairwise nucleotide diversity between ST (~5 Kbp^-1). These observations go against the hypothesis of a recent introduction of F. psychrophilum in Japan. Two findings were made that are important for disease control: 1) at least two independent F. psychrophilum lineages infect ayu and 2) co-infections of the same individual fish by different strains occur.     

Dynamics of influenza A virus infections in permanently infected pig farms: evidence of recurrent infections,circulation of several swine influenza viruses and reassortment events

Concomitant infections by different influenza A virus subtypes within pig farms increase the risk of new reassortant virus emergence. The aims of this study were to characterize the epidemiology of recurrent swine influenza virus infections and identify their main determinants. A follow-up study was carried out in 3 selected farms known to be affected by repeated influenza infections. Three batches of pigs were followed within each farm from birth to slaughter through a representative sample of 40 piglets per batch. Piglets were monitored individually on a monthly basis for serology and clinical parameters. When a flu outbreak occurred, daily virological and clinical investigations were carried out for two weeks. Influenza outbreaks, confirmed by influenza A virus detection, were reported at least once in each batch. These outbreaks occurred at a constant age within farms and were correlated with an increased frequency of sneezing and coughing fits. H1N1 and H1N2 viruses from European enzootic subtypes and reassortants between viruses from these lineages were consecutively and sometimes simultaneously identified depending on the batch, suggesting virus co-circulations at the farm, batch and sometimes individual levels. The estimated reproduction ratio R of influenza outbreaks ranged between 2.5 [1.9-2.9] and 6.9 [4.1-10.5] according to the age at infection-time and serological status of infected piglets. Duration of shedding was influenced by the age at infection time, the serological status of the dam and mingling practices. An impaired humoral response was identified in piglets infected at a time when they still presented maternally-derived antibodies.     

Towards a better understanding of Rift Valley fever epidemiology in the south-west of the Indian Ocean

Rift Valley fever virus (Phlebovirus, Bunyaviridae) is an arbovirus causing intermittent epizootics and sporadic epidemics primarily in East Africa. Infection causes severe and often fatal illness in young sheep, goats and cattle. Domestic animals and humans can be contaminated by close contact with infectious tissues or through mosquito infectious bites. Rift Valley fever virus was historically restricted to sub-Saharan countries. The probability of Rift Valley fever emerging in virgin areas is likely to be increasing. Its geographical range has extended over the past years. As a recent example, autochthonous cases of Rift Valley fever were recorded in 2007–2008 in Mayotte in the Indian Ocean. It has been proposed that a single infected animal that enters a naive country is sufficient to initiate a major outbreak before Rift Valley fever virus would ever be detected. Unless vaccines are available and widely used to limit its expansion, Rift Valley fever will continue to be a critical issue for human and animal health in the region of the Indian Ocean.     

Lipid deposition on the tongue after oral processing of medium-chain triglycerides and impact on the perception of mouthfeel

Lipids between the tongue and palate strongly contribute to the sensory impact of a product. Mouthfeel is a sensory attribute responsible for distinguishing reduced fat from full fat food products. The aim of this work was to quantify the distribution, deposition, and retention of lipids on the tongue and palate upon oral processing and relate this to texture. The thickness of lipid deposition was measured in mouth by fluorescence. A trained panel evaluated the perceived intensity of samples to describe lipid Mouthfeel. The thickness of lipid deposition on the tongue shows spatial variation (10-100 microm) and stopped increasing after intakes higher than 8 mL of medium-chain triglycerides (MCTs). After 2 min, only 25% of the lipid deposition was retained on oral surfaces. A difference in the thickness of lipid deposition of 25 microm resulted in significantly different perception. This work describes the in-mouth behavior of food lipids and its influence on texture perception.     

Arsenic Concentration in Tobacco Leaves: A Study on Three Commercially Important Tobacco (Nicotiana tabacum L.) Types

In recent years, arsenic (As) has received increased attention as humans may be exposed to it through occupational and environmental exposure. Tobacco (Nicotiana tabacum L.) like other crops can uptake this element from the soil, which may lead to human exposure. Here, we report on a survey on arsenic in cured or processed tobacco leaves obtained from Africa, Asia, Europe, South and North America. A total of 1,431 leaf samples of flue-cured, burley, and Oriental tobaccos were obtained from various sampling locations during 2002 to 2004. Arsenic concentration in the samples averaged 0.4?±?0.6 μg g^?1 as determined by inductively coupled plasma-mass spectrometry. Recorded values from most samples showed that concentrations of arsenic were usually found at the lower end of the distribution. Significant differences were found among tobacco types, sampling locations, and crop years. Arsenic concentrations were rather low in the majority of regions investigated, which is compatible with data from the literature. However, sample size was small and sampling geographically restricted. Our results would need to be validated with a larger dataset.