Genome-wide association mapping for root cone angle in rice

Background

Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years.

Results

To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/?50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes.

Conclusions

The present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation.

     

Environmental determinants of fish community structure in gravel pit lakes

Gravel pit lakes are increasingly common, and there is an urgent need to better understand the functioning of these artificial and disconnected ecosystems. However, our knowledge of the environmental determinants of fish community structure within these types of lakes remains poor. In this study, we quantified the taxonomic diversity, fish species and life‐stage composition in 17 gravel pit lakes sampled in 2012 and 2013 located in south‐west France to determine the potential role of environmental variables (i.e. lake morphology, productivity, water quality and human‐use intensity) as drivers of fish community structure and composition. Our results demonstrated that fish community structure significantly differed between gravel pit lakes, and we notably found that lakes managed for angling hosted higher levels of taxonomic diversity. We also found that young and large lakes supported higher native species biomass and were dominated by native European perch (Perca fluviatilis). Older, smaller and more productive lakes, located closer to the main urban area, supported a higher biomass of non‐native species such as largemouth bass (Micropterus salmoides). Native and non‐native sport fishing species such as northern pike (Esox lucius), pikeperch (Sander lucioperca), common carp (Cyprinus carpio) and cyprinid prey species were positively associated with fishery management effort, suggesting that management practices play also a critical role in shaping fish species composition. Overall, our study demonstrated that fish community composition followed a predictable shift along environmental gradients associated with the maturation of gravel pit lakes and the associated human practices.     

Serological evidence of caprine herpesvirus 1 infection in Mediterranean France

Caprine herpesvirus 1 (CpHV-1) is responsible of a systemic disease in kids and genital diseases inducing abortions in adult goats. In Europe, CpHV-1 is widespread in Mediterranean countries such as Greece, Italy and Spain. As France is geographically close to these countries, a survey was conducted to investigate the presence of CpHV-1 in goats in a Mediterranean department (Corse-du-Sud) and in continental departments (Dordogne and Vendée) of this country. Taking into account the close antigenic and genetic relationships between bovine herpesvirus 1 (BoHV-1) and CpHV-1, the serological detection was performed by using BoHV-1 glycoproteins B (gB) and E (gE) blocking ELISAs. The analysis of 2548 serum samples in a BoHV-1 gB blocking ELISA revealed that a ruminant alphaherpesvirus infection related to BoHV-1 was widespread in Corse-du-Sud whereas no positive animals was detected in Dordogne and Vendée. Furthermore, the specificity and the sensitivity of the BoHV-1 gB blocking ELISA to detect a BoHV-1 related infection in goats were evaluated. A subsequent analysis by a BoHV-1 gE blocking ELISA demonstrated that 22.6% of gB-positive serum samples were also gE-positive. Cross-seroneutralisation assays afforded the unambiguous identification of antibodies against CpHV-1 in gB-positive goats. The likely presence of CpHV-1 in Corse-du-Sud supported by a high seroprevalence (61.9%) in all investigated flocks extends the number of countries infected with CpHV-1. Moreover, the difference observed between Corse-du-Sud and Dordogne and Vendée suggests that CpHV-1 is more prevalent in Mediterranean countries or regions than in central and northern Europe.     

A focus on the European hamster to illustrate how to monitor endangered species

Agriculture intensification, marked by the generalization of crop monoculture, by the increase in plot size and by the reduction of plant diversity, has led to huge decline in wildlife in European farmlands. In such habitat, research has long been biased towards birds and invertebrates, while very few studies have investigated the effect on small mammals. Considering the European hamster, Cricetus cricetus, we therefore review the different techniques that can be used to investigate the impact of environmental changes and conservation measures in small and endangered wild mammals. We suggest that only a multidisciplinary approach will allow exploration of these effects, combining experimental laboratory work on captive‐bred animals with the monitoring of wild individuals. In particular, individual energy balance has to be investigated and measured as accurately as possible, through either biochemical or bio‐logging techniques. It is, indeed, the most affected physiological trait in a changing environment, as it determines both the reproductive output and the survival of the individual. We also discuss the inconvenience of capture–release approaches for such an endangered species and emphasize the disturbance that experimental protocols could impose on the hamster.     

ACVIM consensus statement on the diagnosis of immune‐mediated hemolytic anemia in dogs and cats

Immune‐mediated hemolytic anemia (IMHA) is an important cause of morbidity and mortality in dogs. IMHA also occurs in cats, although less commonly. IMHA is considered secondary when it can be attributed to an underlying disease, and as primary (idiopathic) if no cause is found. Eliminating diseases that cause IMHA may attenuate or stop immune‐mediated erythrocyte destruction, and adverse consequences of long‐term immunosuppressive treatment can be avoided. Infections, cancer, drugs, vaccines, and inflammatory processes may be underlying causes of IMHA. Evidence for these comorbidities has not been systematically evaluated, rendering evidence‐based decisions difficult. We identified and extracted data from studies published in the veterinary literature and developed a novel tool for evaluation of evidence quality, using it to assess study design, diagnostic criteria for IMHA, comorbidities, and causality. Succinct evidence summary statements were written, along with screening recommendations. Statements were refined by conducting 3 iterations of Delphi review with panel and task force members. Commentary was solicited from several professional bodies to maximize clinical applicability before the recommendations were submitted. The resulting document is intended to provide clinical guidelines for diagnosis of, and underlying disease screening for, IMHA in dogs and cats. These should be implemented with consideration of animal, owner, and geographical factors.     

Redox potential: An intrinsic parameter of the rumen environment

The ruminal ecosystem is a fermentative milieu which is interesting to discuss in terms of its redox status as a reflection of an intense bacterial activity. The objective of this systematic literature review is to quantitatively analyze data collected on redox potential (Eh) in the rumen and to explore relationship between ruminal Eh, nature of the diet fed to ruminants, and ruminal fermentation parameters. Data obtained from 15 studies comprising 24 different diets was used in the analysis. Studies included in the data file were selected based on the criteria of: (i) the nature of the reference electrode was specified, (ii) the ruminal Eh was recorded simultaneously to pH, (iii) animal body weight (BW) and dry matter intake (DMI) were reported and (iv) the composition of the diet was precisely described. Results showed a high variability in ruminal Eh values. However, all recorded values are markedly negative reflecting the absence of oxygen and the strong reducing power of the rumen environment. The main factors contributing to the variation were the method of Eh measurement and the nature of the diet fed to ruminants. Redox potential was positively correlated with DMI and proportion of concentrate in the diet, and tended to be positively correlated with soluble carbohydrates content. In contrast, it was negatively correlated with neutral detergent fibre from forages. The hierarchical ascendant classification discriminated two groups of diets leading to significant change in ruminal Eh level. Ruminal Eh was negatively correlated with pH, total volatile fatty acids produced and proportion of acetate, and positively correlated with proportion of propionate. This review revealed Eh to be dependent on the diet composition and DMI, at least within the range of diets included in the database.     

Differential aphicidal effects of chitinase inhibitors on the polyphagous homopteran Myzus persicae (Sulzer)

Four chitinase inhibitors, cyclo-(Proline-Tyrosine), cyclo-(Histidine-Proline), allosamidin and psammaplin A, were selected for in vitro feeding experiments with the peach-potato aphid, Myzus persicae (Sulzer), under controlled photoperiod and temperature conditions. Artificial diets were used to provide chitinase inhibitors at 10, 50 and 100 microg mL(-1) to M. persicae. Except for cyclo-(Proline-Tyrosine), which did not modify aphid demographic parameters, chitinase inhibitors induced differential aphicidal effects on M. persicae. At all doses, cyclo-(Histidine-Proline) induced significant effects affecting daily fecundity, intrinsic rate of natural increase (r(m)) and doubling time of population. When compared with the control diet, allosamidin decreased nymph survival and daily fecundity, increasing the doubling time of population from 1 to 1.5 days. Psammaplin A was the most toxic inhibitor when delivered via artificial diet, as it induced the death of all aphids reared at 50 and 100 microg mL(-1). The results demonstrate the potential use of chitinase inhibitors as aphid management tools.