Genomic and phenomic predictions help capture low-effect alleles promoting seed germination in oilseed rape in addition to QTL analyses.

KEY MESSAGE: Phenomic prediction implemented on a large diversity set can efficiently predict seed germination, capture low-effect favorable alleles that are not revealed by GWAS and identify promising genetic resources. Oilseed rape faces many challenges, especially at the beginning of its developmental cycle. Achieving rapid and uniform seed germination could help to ensure a successful establishment and therefore enabling the crop to compete with weeds and tolerate stresses during the earliest developmental stages. The polygenic nature of seed germination was highlighted in several studies, and more knowledge is needed about low- to moderate-effect underlying loci in order to enhance seed germination effectively by improving the genetic background and incorporating favorable alleles. A total of 17 QTL were detected for seed germination-related traits, for which the favorable alleles often corresponded to the most frequent alleles in the panel. Genomic and phenomic predictions methods provided moderate-to-high predictive abilities, demonstrating the ability to capture small additive and non-additive effects for seed germination. This study also showed that phenomic prediction estimated phenotypic values closer to phenotypic values than GEBV. Finally, as the predictive ability of phenomic prediction was less influenced by the genetic structure of the panel, it is worth using this prediction method to characterize genetic resources, particularly with a view to design prebreeding populations.

Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species.

Association mapping has been proposed as an efficient approach to assist in the identification of the molecular basis of agronomical traits in plants. For this purpose, we analyzed the phenotypic and genetic diversity of a large collection of tomato accessions including 44 heirloom and vintage cultivars (Solanum lycopersicum), 127 S. lycopersicum var. cerasiforme (cherry tomato) and 17 Solanum pimpinellifolium accessions. The accessions were genotyped using a SNPlex™ assay of 192 SNPs, among which 121 were informative for subsequent analysis. Linkage disequilibrium (LD) of pairwise loci and population structure were analyzed, and the association analysis between SNP genotypes and ten fruit quality traits was performed using a mixed linear model. High level of LD was found in the collection at the whole genome level. It was lower when considering only the 127 S. lycopersicum var. cerasiforme accessions. Genetic structure analysis showed that the population was structured into two main groups, corresponding to cultivated and wild types and many intermediates. The number of associations detected per trait varied, according to the way the structure was taken into account, with 0-41 associations detected per trait in the whole collection and a maximum of four associations in the S. lycopersicum var. cerasiforme accessions. A total of 40 associations (30 %) were co-localized with previously identified quantitative trait loci. This study thus showed the potential and limits of using association mapping in tomato populations.

Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL.

In tomato (Solanum lycopersicum) fruit, the number of locules (cavities containing seeds that are derived from carpels) varies from two to up to 10 or more. Locule number affects fruit shape and size and is controlled by several quantitative trait loci (QTLs). The large majority of the phenotypic variation is explained by two of these QTLs, fasciated (fas) and locule number (lc), that interact epistatically with one another. FAS has been cloned, and mutations in the gene are described as key factors leading to the increase in fruit size in modern varieties. Here, we report the map-based cloning of lc. The lc QTL includes a 1,600-bp region that is located 1,080 bp from the 3' end of WUSCHEL, which encodes a homeodomain protein that regulates stem cell fate in plants. The molecular evolution of lc showed a reduction of diversity in cultivated accessions with the exception of two single-nucleotide polymorphisms. These two single-nucleotide polymorphisms were shown to be responsible for the increase in locule number. An evolutionary model of locule number is proposed herein, suggesting that the fas mutation appeared after the mutation in the lc locus to confer the extreme high-locule-number phenotype.

Genotype-dependent response to carbon availability in growing tomato fruit.

Tomato fruit growth and composition depend on both genotype and environment. This paper aims at studying how fruit phenotypic responses to changes in carbon availability can be influenced by genotype, and at identifying genotype-dependent and -independent changes in gene expression underlying variations in fruit growth and composition. We grew a parental line (Solanum lycopersicum) and an introgression line from Solanum chmielewskii harbouring quantitative trait loci for fresh weight and sugar content under two fruit loads (FL). Lowering FL increased fruit cell number and reduced fruit developmental period in both genotypes. In contrast, fruit cell size was increased only in the parental line. Modifications in gene expression were monitored using microarrays and RT-qPCR for a subset of genes. FL changes induced more deployments of regulation systems (transcriptional and post-transcriptional) than massive adjustments of whole primary metabolism. Interactions between genotype and FL occurred on 99 genes mainly linked to hormonal and stress responses, and on gene expression kinetics. Links between gene expression and fruit phenotype were found for aquaporin expression levels and fruit water content, and invertase expression levels and sugar content. In summary, the present data emphasized age- and genotype-dependent responses of tomato fruit to carbon availability, at phenotypic as well as gene expression level.

Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing.

Molecular markers linked to phenotypically important traits are of great interest especially when traits are difficult and/or costly to be observed. In tomato where a strong focus on resistance breeding has led to the introgression of several resistance genes, resistance traits have become important characteristics in distinctness, uniformity and stability (DUS) testing for Plant Breeders Rights (PBR) applications. Evaluation of disease traits in biological assays is not always straightforward because assays are often influenced by environmental factors, and difficulties in scoring exist. In this study, we describe the development and/or evaluation of molecular marker assays for the Verticillium genes Ve1 and Ve2, the tomato mosaic virus Tm1 (linked marker), the tomato mosaic virus Tm2 and Tm2 ( 2 ) genes, the Meloidogyne incognita Mi1-2 gene, the Fusarium I (linked marker) and I2 loci, which are obligatory traits in PBR testing. The marker assays were evaluated for their robustness in a ring test and then evaluated in a set of varieties. Although in general, results between biological assays and marker assays gave highly correlated results, marker assays showed an advantage over biological tests in that the results were clearer, i.e., homozygote/heterozygote presence of the resistance gene can be detected and heterogeneity in seed lots can be identified readily. Within the UPOV framework for granting of PBR, the markers have the potential to fulfil the requirements needed for implementation in DUS testing of candidate varieties and could complement or may be an alternative to the pathogenesis tests that are carried out at present.

[Evaluation of general practitioners' involvement in the appropriate and good use of prescription drugs]. / Evaluation de l'implication des médecins généralistes libéraux dans le bon usage des médicaments.

Public health policy is committed to support best practice and the good use of prescription drugs. The law passed in August 2004 to reform social health insurance aims to improve the use, consumption and prescription of medication, essentially to fight against the iatrogenic risk due to drug interaction. The study analyses how general practitioners translate this health policy into practice. 528 general practitioners (GPs) in South-Eastern France participated in a telephone-survey. The questionnaire's objective was to assess GPs' involvement in providing information to patients on the risks of self-medication and on the prevention of drug iatrogenicity. Results show that the identification of drug iatrogenicity is well integrated into practice (87,3% of GPs report doing it frequently), although giving information to patients about risks of self-medication is less regular (46%). Rural GPs are more involved in identifying iatrogenic risks rather than their urban counterparts. Heavy workloads, and lack of time and coordination between prescribing doctors seem to be factors which emerge as strongly hindering GPs' involvement into this type of prevention.

Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme.

Genome-wide association mapping is an efficient way to identify quantitative trait loci controlling the variation of phenotypes, but the approach suffers severe limitations when one is studying inbred crops like cultivated tomato (Solanum lycopersicum). Such crops exhibit low rates of molecular polymorphism and high linkage disequilibrium, which reduces mapping resolution. The cherry type tomato (S. lycopersicum var. cerasiforme) genome has been described as an admixture between the cultivated tomato and its wild ancestor, S. pimpinellifolium. We have thus taken advantage of the properties of this admixture to improve the resolution of association mapping in tomato. As a proof of concept, we sequenced 81 DNA fragments distributed on chromosome 2 at different distances in a core collection of 90 tomato accessions, including mostly cherry type tomato accessions. The 81 Sequence Tag Sites revealed 352 SNPs and indels. Molecular diversity was greatest for S. pimpinellifolium accessions, intermediate for S. l. cerasiforme accessions, and lowest for the cultivated group. We assessed the structure of molecular polymorphism and the extent of linkage disequilibrium over genetic and physical distances. Linkage disequilibrium decreased under r(2) = 0.3 within 1 cM, and minimal estimated value (r(2) = 0.13) was reached within 20 kb over the physical regions studied. Associations between polymorphisms and fruit weight, locule number, and soluble solid content were detected. Several candidate genes and quantitative trait loci previously identified were validated and new associations detected. This study shows the advantages of using a collection of S. l. cerasiforme accessions to overcome the low resolution of association mapping in tomato.

A Case Study on the Substitution Effect between the Length of GP Consultation and Drug Prescribing Practices.

The relationship between the length of GP consultation in primary care and drug prescribing practices is still a subject for debate. Patients' morbidity, generating both very long consultation times and large volumes of prescriptions, may mask an underlying substitution among GPs regarding the length of time they offer to patients versus the alternative of prescribing pharmaceuticals. We propose to pursue the debate by analyzing the results of a case vignette, submitted to 1,900 GPs, in which patient morbidity is controlled for by definition. In this case - a hypothetical patient suffering from mild depression - we observe the choice between three types of treatment strategy: psychotherapy, drug therapy and a combination of the two. We observe that the GPs with the highest consultation rates were twice as likely to adopt the drug therapy option as their counterparts with lower rates of consultation. Moreover, for more than 50% of drug prescriptions, the medical decisions contradict clinical practice guidelines.

Drug reimbursement and GPs' prescribing decisions: a randomized case-vignette study about the pharmacotherapy of obesity associated with type 2 diabetes: how GPs react to drug reimbursement.

This study sought to identify the effect of drug reimbursability--a decision made in France by the National Authority for Health--on physicians' prescribing practices for a diet drug such as rimonabant, approved for obese or overweight patients with type-2 diabetes. A cross-sectional survey of French general practitioners (GPs) presented a case-vignette about a patient for whom this drug is indicated in two alternative versions, differing only in its reimbursability, to two separate randomized subsamples of GPs in early 2007, before any decision was made about reimbursement. The results indicate that (i) more than 20% of GPs in private practice would be willing to prescribe a non-reimbursed diet drug for patients with obesity complicated by type 2 diabetes; (ii) the number of GPs willing to prescribe it would increase by 47.6% if the drug were reimbursed, and (iii) such a drug would be adopted at a higher rate by GPs who have regular contacts with pharmaceutical sales representatives. In France, unlike most other countries, drug reimbursement status is a signal of quality. However, our results suggest that a significant proportion of GPs would spontaneously adopt anti-obesity drugs even if they were not reimbursed. Decisions about reimbursement of pharmaceutical products should be made taking into account that reimbursement is likely to intensify prescription.

Positive attitudes of French general practitioners towards A/H1N1 influenza-pandemic vaccination: a missed opportunity to increase vaccination uptakes in the general public?

Attitudes of general practitioners (GPs) towards A/H1N1 pandemic vaccination are unknown. We conducted a cross-sectional survey with computer-assisted telephone interviewing in the French Regional Panel of General Practices from June 16 to September 22, 2009. Of 1434 respondents representative of GPs in four French regions, 885 (61.7%) were willing to accept A/H1N1 pandemic vaccination for themselves. The personal history of seasonal flu vaccination was the strongest independent predictive factor of willingness to accept A/H1N1 pandemic vaccination (p<.0001). GPs receiving seasonal vaccines every year were more likely to accept A/H1N1 pandemic vaccination than those who were never vaccinated in the prior 3 years (adjusted OR=4.38; 95% CI, 2.44-4.67). Willingness to accept pandemic vaccination was also significantly associated with being on call for emergencies; positive attitudes towards other protective measures against A/H1N1 influenza virus in the practice; and a higher readiness to provide additional consultations in response to the pandemic. In conclusion, GPs showed a high acceptability of A/H1N1 pandemic vaccination. GPs' involvement in the mass vaccination campaign, which has been neglected by French public health authorities, may have increased uptake rates in the general public.

Desulfurobacterium crinifex sp. nov., a novel thermophilic, pinkish-streamer forming, chemolithoautotrophic bacterium isolated from a Juan de Fuca Ridge hydrothermal vent and amendment of the genus Desulfurobacterium.

A novel thermophilic, chemolithoautotrophic bacterium, designated as NE1206(T), was isolated from a Juan de Fuca Ridge hydrothermal vent sample (tubes of the annelid polychaete Paralvinella sulfincola attached to small pieces of hydrothermal chimney). The cells were rod-shaped (1.2-3.5 x 0.4-0.7 microm), occurring as single motile rods or forming macroscopic aggregates visible as pinkish to brownish streamers. The new isolate was anaerobic. It grew between 50 and 70 degrees C (optimum 60-65 degrees C; doubling time approximately 1 h 15 min at 60 degrees C), between pH 5.0 and 7.5 (optimum pH around 6.0-6.5) and at sea salts concentrations between 20 and 40 g l(-1 )(optimum 30 g l(-1)). Cells grew chemolithoautotrophically in an H(2)/CO(2) atmosphere (80/20, v/v; 200 kPa). Molecular hydrogen was the sole electron donor used by the strain. Nitrate and elemental sulfur served as electron acceptors, yielding ammonia and hydrogen sulfide, respectively (nitrate reduction supported higher growth rates than sulfur reduction). The G+C content of the genomic DNA was 36.7+/-0.8 mol%. Phylogenetic analyses of the 16S rRNA gene located the strain within the genus Desulfurobacterium. However, the novel isolate possesses physiological and biochemical characteristics that differ from the previously described species of this genus. We propose that the isolate represents a novel species, Desulfurobacterium crinifex sp. nov. The type strain is NE1206(T) (DSM 15218(T), CIP 107649(T)). An amendment of the genus Desulfurobacterium description is proposed, based on the phenotypic characteristics of the novel species.