Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes

Evidence for dosage compensation in Silene latifolia, a plant with 10-million-year-old sex chromosomes, reveals that dosage compensation can evolve rapidly in young XY systems and is not an animal-specific phenomenon

Application of structural equation modeling for assessing relationships between organic carbon and soil properties in semiarid Mediterranean region

Restoration of atmospheric carbon in soils has principal many good effects. Arid lands cover more than 40 % of the global earth area, but only stock 16 % from the global carbon stock. It seems to be a suitable solution for this environmental issue, but still all variables controlling organic carbon in such kinds of soil, was ignored. This study aims to develop two models of organic carbon under clayey and sandy soils in semi-arid Mediterranean zones basing on physical and chemical soil properties. For establishing both models, structural equation modeling was used. For modeling organic carbon, two Tunisian soil databases composed from clayey and sandy soils made respectively, of 450 and 602 soil horizons were used. Using the two databases for all properties, the principal component analysis shows two components for clayey soil; (i) chemical properties and bulk density and (ii) physical properties. For the sandy soil it reveals two components; (i) chemical properties and (ii) physical properties. According to the derived components for each soil category, two models have been built. Structural equation modeling results show that clayey model has proved that organic carbon was controlled by chemical properties and bulk density more than physical properties and sandy model has proved that organic carbon was controlled by chemical properties more than physical properties. The root mean square errors of approximation were 0.079 and 0.050 for the clayey and sandy models, respectively. Then these two models were validated with two other databases from Tunisian dryland soils

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

Background: Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes. Results: Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of similar to 70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome. Conclusions: Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %

The intercropping cowpea-maize improves soil phosphorus availability and maize yields in an alkaline soil

Aim: This study assessed whether growing cowpea can increase phosphorus (P) availability in the rhizosphere and improve the yield of legume-cereal systems. In alkaline Mediterranean soils with P deficiency, it is assumed that legumes increase inorganic P availability.Methods: A field experiment was conducted at the Staoueli experimental station, in Algiers province, Algeria, to compare the growth, grain yield, P availability, and P uptake by plants with sole-cropped cowpea (Vigna unguiculata L. cv. Moh Ouali) and maize (Zea mays L. cv. ILT), intercropped cowpea-maize, and fallow. Results: P availability in the rhizosphere was increased in both sole cropping and intercropping systems compared with fallow. It was highest in intercropping. The increase in P availability was associated with (i) significant pH changes of the rhizosphere of cowpea in sole cropping and intercropping systems, with the rhizosphere acidification significantly higher in intercropping (−0.73 units) than in sole cropping (−0.42 units); (ii) significant increase in the rhizosphere pH of intercropped maize (+0.49 units) compared to fallow; (iii) increased soil respiration (C-CO2 from microbial and root activity) in intercropping compared with sole cropping and fallow; and (iv) higher efficiency in utilization of the rhizobial symbiosis in intercropping than in sole-cropped cowpea. Conclusion With cowpea-maize intercropping, cowpea increased the P uptake, by increasing the P availability by rhizosphere pH changes in an alkaline soil. Overall, this study showed that intercropping cowpea improved the plant biomass and grain yield of maize in this soil

Determination of potential denitrification in a range of tropical topsoils using near infrared reflectance spectroscopy (NIRS)

Microbial denitrification plays a central role in nitrous oxide (N2O)-emitting processes, which are involved in ecosystem services such as crop production and climate regulation. Field characterization of N2O-emitting processes being time-consuming due to great variability, laboratory determination of potential denitrification (upon incubation) is often used as a valuable test. Near infrared reflectance spectroscopy (NIRS) is a time- and cost-effective approach that has been reported to allow accurate determination of several soil properties. The objective of the present study was to assess the interest of NIRS for determining potential denitrification over a set of 460 topsoils sampled under crops, tree plantations, savanna or rainforest, originating from Madagascar, Congo-Brazzaville, Brazil, and French Guiana. Prediction of potential denitrification using NIRS was satisfying over the total set, especially with LOCAL calibration, which builds a model for each sample separately using its spectral neighbours in the calibration subset (R-2=0.79 for validation). For the other sets, either textural or geographical, global calibration only was performed, involving for each set a unique prediction model built with all calibration samples. The accuracy of NIRS determination depended on the sample set, decreasing in the following order: Malagasy clayey set > total set approximate to. Brazilian sandy loam set > coarse-textured set (Congo-Brazil) approximate to Guianese sandy clay loam set approximate to Congolese sandy set > non-clayey set (Congo-Brazil-Guiana), with cross-validation R-2 ranging from 0.88 to 0.44 (external validation was not carried out for small-sized sets). Thus NIRS prediction was more accurate over the clayey homogeneous set than over the non-clayey heterogeneous set. As a result of global calibration, potential denitrification was expressed as a linear combination of absorbance at every wavelength. Wavelengths that contributed most to NIRS prediction of soil potential denitrification corresponded to wavelengths that literature has assigned to organic nitrogenous compounds, amide-containing ones especially, and to carbonaceous compounds such as cellulose or including CH3 or CH2 groups. This related to the importance of amides in soil organic nitrogen and microbial biomass, and to the dependence of denitrification on soil organic matter. In short, NIRS is a time- and cost-effective approach that proved relevant for determining soil potential denitrification with acceptable accuracy, especially for clayey samples or when LOCAL calibration was performed

Genomic prediction in a multiploid crop: genotype by environment interaction and allele dosage effects on predictive ability in banana

Improving the efficiency of selection in conventional crossbreeding is a major priority in banana ( spp.) breeding. Routine application of classical marker assisted selection (MAS) is lagging in banana due to limitations in MAS tools. Genomic selection (GS) based on genomic prediction models can address some limitations of classical MAS, but the use of GS in banana has not been reported to date. The aim of this study was to evaluate the predictive ability of six genomic prediction models for 15 traits in a multi-ploidy training population. The population consisted of 307 banana genotypes phenotyped under low and high input field management conditions for two crop cycles. The single nucleotide polymorphism (SNP) markers used to fit the models were obtained from genotyping by sequencing (GBS) data. Models that account for additive genetic effects provided better predictions with 12 out of 15 traits. The performance of BayesB model was superior to other models particularly on fruit filling and fruit bunch traits. Models that included averaged environment data were more robust in trait prediction even with a reduced number of markers. Accounting for allele dosage in SNP markers (AD-SNP) reduced predictive ability relative to traditional bi-allelic SNP (BA-SNP), but the prediction trend remained the same across traits. The high predictive values (0.47- 0.75) of fruit filling and fruit bunch traits show the potential of genomic prediction to increase selection efficiency in banana breeding.status: publishe

Effet de la gestion des feuilles d'élagage du palmier à huile sur le stock de carbone et les propriétés physico-chimiques du sol dans les palmeraies villageoises du Bénin

Description of the subject: In Benin, oil palm plantations are widely managed by smallholder farmers. The study addresses the impact on soil properties of the recycling of pruned fronds from these trees. Objectives: The study aims to assess the effect of two modes of management of pruned fronds on the carbon stock and physico-chemical properties of soil. Method. Six oil palm plantations were selected to represent two age classes (7-12 years and 13-24 years) in southeastern Benin. They were used to compare the soil properties of two areas: the areas of total recycling of pruned fronds (TR) and the areas of no recycling of the fronds (NR), which represented the control. In each plantation, soil samples were collected under the two treatments, from holes of up to 50 cm depth, near six oil palm trees. The soil properties were determined using conventional laboratory methods and near-infrared spectroscopy method. Results: Carbon and nitrogen stocks under TR of adult plantations were 58 Mg.ha(-1) and 4.3 Mg.ha(-1), respectively, and were significantly higher than the stocks in all other treatments (34.6 Mg C.ha(-1) and 2.9 Mg N.ha(-1)). Recycling of pruned fronds improved soil fertility at a depth of up to 20 cm in the adult plantations. The porosity and bulk density of the soil were also improved. Conclusions: The management of the pruned fronds in the smallholders' oil palm plantations modified the soil properties, which were significantly improved in the top soil after 10 years of frond recycling