Genome-wide association mapping of root traits in a japonica rice panel.

Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r(2)>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.

1P19Q loss but not IDH1 mutations influences WHO grade II gliomas spontaneous growth.

Mutations at the codon 132 in the isocitrate dehydrogenase 1 (IDH1) gene occur early, with a high frequency, in World Health Organization (WHO) grade II gliomas. We investigated the impact of IDH1 mutations on spontaneous glioma growth rate, known to be an early prognostic factor.The mean tumor diameter was assessed on the first MRI performed at diagnosis and on a second MRI, performed immediately before surgery, in a series of 64 WHO grade II gliomas. The patients did not undergo treatment before surgery. Because of a frequent association, we jointly analyzed the 1p19q co-deletion and IDH1 mutations effects on tumor velocity of diameter expansion (mm/year) during preoperative spontaneous growth period. 1p19q co-deletion had a significant slowing effect (p = 0.0133) on tumor growth estimated at -1.7760 ± 0.711 mm/year (95% CI -3.154, -0.366), whereas IDH1 mutations estimated effect of +0.036 ± 0.833 mm/year (95% CI -1.668; +1.596) was not significant (p = 0.9654). Our results provide first evidence that IDH1 mutations are not significantly involved in tumor growth rate. By contrast, we confirm that 1p19q co-deletion decreases growth velocity.

Genetic structure among sorghum landraces as revealed by morphological variation and microsatellite markers in three agroclimatic regions of Burkina Faso.

Diversity among 124 sorghum landraces from 10 villages surveyed in 3 regions of Burkina Faso covering different agroecological zones was assessed by 28 agromorphological traits and 29 microsatellite markers. 94.4% of the landraces collected belonged to the botanical race guinea (consisting of 96.6% guinea gambicum and 3.4% guinea margaritiferum), 74.2% had white kernels, 13.7% had orange and 12.1% had red kernels. Compared to the "village nested within zone" factor, the "variety nested within village within zone" factor predominately contributed to the diversity pattern for all nine statistically analysed quantitative traits. The multivariate analyses performed on ten morphological traits identified five landrace groups, and of these, the red kernel sorghum types appeared the most homogenous. 2 to 17 alleles were detected per locus with a mean 4.9 alleles per locus and a gene diversity (He) of 0.37. Landraces from the sub-Sahelian zone had the highest gene diversity (He = 0.38). Cluster analysis revealed that the diversity was weakly stratified and could not be explained by any biophysical criteria. One homogenous guinea margaritiferum group was distinguished from other guinea landraces. The red kernel type appeared to be genetically distinct from all other guinea landraces. The kernel colour was the principal structuring factor. This is an example of a homogeneous group of varieties selected for a specific use (for local beer preparation), mainly grown around the households in compound fields, and presenting particular agromorphological and genetic traits. This is the most original feature of sorghum diversity in Burkina Faso and should be the focus of special conservation efforts.

[Prediction of crop response by linearisation about control approximation]. / Linéarisation autour d'un témoin pour prédire la réponse de cultures.

A new method for modelling genotype x environment interaction: APLAT. The yield predicted by a crop-simulation model is developed as a Taylor series in the neighbourhood of a parameter vector of a control genotype. With this local linearisation, these genotype parameters can be estimated by a linear regression of the observed yield on the derivatives of the crop-simulation model predictions with respect to its parameters.