National Graduate School of Agronomy, Toulouse
Auzeville-Tolosane, France
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Vitezica Z.G.,National Graduate School of Agronomy, Toulouse | Vitezica Z.G.,French National Institute for Agricultural Research | Legarra A.,French National Institute for Agricultural Research | Toro M.A.,Technical University of Madrid | And 2 more authors.
Genetics | Year: 2017

Genomic prediction methods based on multiple markers have potential to include nonadditive effects in prediction and analysis of complex traits. However, most developments assume a Hardy-Weinberg equilibrium (HWE). Statistical approaches for genomic selection that account for dominance and epistasis in a general context, without assuming HWE (e.g., crosses or homozygous lines), are therefore needed. Our method expands the natural and orthogonal interactions (NOIA) approach, which builds incidence matrices based on genotypic (not allelic) frequencies, to include genome-wide epistasis for an arbitrary number of interacting loci in a genomic evaluation context. This results in an orthogonal partition of the variances, which is not warranted otherwise. We also present the partition of variance as a function of genotypic values and frequencies following Cockerham’s orthogonal contrast approach. Then we prove for the first time that, even not in HWE, the multiple-loci NOIA method is equivalent to construct epistatic genomic relationship matrices for higher-order interactions using Hadamard products of additive and dominant genomic orthogonal relationships. A standardization based on the trace of the relationship matrices is, however, needed. We illustrate these results with two simulated F1 (not in HWE) populations, either in linkage equilibrium (LE), or in linkage disequilibrium (LD) and divergent selection, and pure biological dominant pairwise epistasis. In the LE case, correct and orthogonal estimates of variances were obtained using NOIA genomic relationships but not if relationships were constructed assuming HWE. For the LD simulation, differences were smaller, due to the smaller deviation of the F1 from HWE. Wrongly assuming HWE to build genomic relationships and estimate variance components yields biased estimates, inflates the total genetic variance, and the estimates are not empirically orthogonal. The NOIA method to build genomic relationships, coupled with the use of Hadamard products for epistatic terms, allows the obtaining of correct estimates in populations either in HWE or not in HWE, and extends to any order of epistatic interactions. © 2017 by the Genetics Society of America.

Ruiz P.,CNRS Functional Ecology & Environment Laboratory | Laplanche C.,National Graduate School of Agronomy, Toulouse
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2010

We present a Bayesian hierarchical model to estimate the abundance and the biomass of brown trout (Salmo trutta fario) by using removal sampling and biometric data collected at several stream sections. The model accounts for (i) variability of the abundance with fish length (as a distribution mixture), (ii) spatial variability of the abundance, (iii) variability of the catchability with fish length (as a logit regression model), (iv) spatial variability of the catchability, and (v) residual variability of the catchability with fish. Model measured variables are the areas of the stream sections as well as the length and the weight of the caught fish. We first test the model by using a simulated dataset before using a 3-location, 2- removal sampling dataset collected in the field. Fifteen model alternatives are compared with an index of complexity and fit by using the field dataset. The selected model accounts for variability of the abundance with fish length and stream section and variability of the catchability with fish length. By using the selected model, 95% credible interval estimates of the abundances at the three stream sections are (0.46,0.59), (0.90,1.07), and (0.56,0.69) fish/m2. Respective biomass estimates are (9.68, 13.58), (17.22, 22.71), and (12.69, 17.31) g/m2.

Barraud-Didier V.,National Graduate School of Agronomy, Toulouse | Henninger M.-C.,University of Management and Economics | Akremi A.E.,Toulouse 1 University Capitole
International Food and Agribusiness Management Review | Year: 2012

This paper aims to explain the participative behavior of farmers-members of agricultural cooper-atives in the governance of the latter. The study introduces two concepts from the organizational behavior literature: trust and organizational commitment. It tests a mediator effect of commit-ment in the relationship between the trust a farmer has in the cooperative and his/her participa-tive behavior in its governance. Based on a sample of 259 members of French agricultural coop-eratives, results showed that affective commitment had a mediating role in the relationship be-tween trust and participation in the governance of cooperatives, notwithstanding the cognitive or affective nature of trust. © 2012 International Food and Agribusiness Management Association (IFAMA).

Atoui A.,Lebanese Atomic Energy Commission CNRS | El Khoury A.,Saint - Joseph University | Kallassy M.,Saint - Joseph University | Lebrihi A.,National Graduate School of Agronomy, Toulouse
International Journal of Food Microbiology | Year: 2012

Zearalenone (ZEA) is a mycotoxin produced by some species of Fusarium, especially by Fusarium graminearum and F. culmorum. ZEA induces hyperoestrogenic responses in mammals and can result in reproductive disorders in farm animals. In the present study, a real-time PCR (qPCR) assay has been successfully developed for the detection and quantification of Fusarium graminearum based on primers targeting the gene PKS13 involved in ZEA biosynthesis. A standard curve was developed by plotting the logarithm of known concentrations of F. graminearum DNA against the cycle threshold (Ct) value. The developed real time PCR system was also used to analyze the occurrence of zearalenone producing F. graminearum strains on maize. In this context, DNA extractions were performed from thirty-two maize samples, and subjected to real time PCR. Maize samples also were analyzed for zearalenone content by HPLC. F. graminearum DNA content (pg DNA/ mg of maize) was then plotted against ZEA content (ppb) in maize samples. The regression curve showed a positive and good correlation (R 2=0.760) allowing for the estimation of the potential risk from ZEA contamination. Consequently, this work offers a quick alternative to conventional methods of ZEA quantification and mycological detection and quantification of F. graminearum in maize. © 2011.

In the past 5 years, RNA-Seq has become a powerful tool in transcriptome analysis even though computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. It is, however, now commonly accepted that the choice of a normalization procedure is an important step in such a process, for example in differential gene expression analysis. The present article highlights the similarities between three normalization methods: TMM from edgeR R package, RLE from DESeq2 R package, and MRN. Both TMM and DESeq2 are widely used for differential gene expression analysis. This paper introduces properties that show when these three methods will give exactly the same results. These properties are proven mathematically and illustrated by performing in silico calculations on a given RNA-Seq data set. © 2016 Maza.

Yguel B.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Bailey R.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | Bailey R.,University of Oslo | Tosh N.D.,CNRS Ecosystems, Biodiversity, and Evolution Laboratory | And 8 more authors.
Ecology Letters | Year: 2011

Hosts belonging to the same species suffer dramatically different impacts from their natural enemies. This has been explained by host neighbourhood, that is, by surrounding host-species diversity or spatial separation between hosts. However, even spatially neighbouring hosts may be separated by many million years of evolutionary history, potentially reducing the establishment of natural enemies and their impact. We tested whether phylogenetic isolation of oak hosts from neighbouring trees within a forest canopy reduces phytophagy. We found that an increase in phylogenetic isolation by 100 million years corresponded to a 10-fold decline in phytophagy. This was not due to poorer living conditions for phytophages on phylogenetically isolated oaks. Neither species diversity of neighbouring trees nor spatial distance to the closest oak affected phytophagy. We suggest that reduced pressure by natural enemies is a major advantage for individuals within a host species that leave their ancestral niche and grow among distantly related species. © 2011 Blackwell Publishing Ltd/CNRS.

Jego G.,National Graduate School of Agronomy, Toulouse | Jego G.,French National Institute for Agricultural Research | Jego G.,Agriculture and Agri Food Canada | Sanchez-Perez J.M.,National Graduate School of Agronomy, Toulouse | Justes E.,French National Institute for Agricultural Research
Agricultural Water Management | Year: 2012

The performance of the STICS soil-crop model for the dynamic prediction of soil water content (SWC) and soil mineral nitrogen (SMN) in the root zone (120. cm) of seven agricultural fields was evaluated using field measurements in a coarse-grained alluvial aquifer of the Garonne River floodplain (southwestern France) from 2005 to 2007. The STICS model was used to simulate drainage and nitrate concentration in drainage water in all the agricultural fields of the study area, in order to quantify and assess the temporal and spatial variability of nitrate leaching into groundwater. Simulations of SWC and SMN in the seven monitored fields were found to be satisfactory as indicated by root mean square error (RMSE) and model efficiency being 6.8 and 0.84% for SWC and 22.8 and 0.92% for SMN, respectively. On average, SWC was slightly overestimated by a mean difference of 10. mm (3%) and there was almost no bias in SMN estimations (<0.5%). These satisfactory results demonstrate the potential for using the STICS model to accurately simulate nitrate leaching.Across the study area, simulated drainage and nitrate concentration were extremely variable from one field to another. For some fields, simulated mean annual nitrate concentration in drainage water exceeded 300mgNO 3 -L -1 and predicted nitrate leaching was close to 100kgNha -1, while other fields had very low nitrate losses. About 15% of the farmers' fields were responsible for 60-70% of nitrate leaching. The SMN in late autumn, before winter drainage, was found the main determining factor explaining this variability. This situation may be attributed to unsatisfactory cumulative nitrogen management over the medium term. Ineffective nitrogen management was found to be more detrimental than a single annual incident of overfertilization, particularly in situations of deep soils and in cases of low or highly variable drainage between years. © 2012 Elsevier B.V..

Oeurng C.,National Graduate School of Agronomy, Toulouse | Sauvage S.,National Graduate School of Agronomy, Toulouse | Sauvage S.,Ecolab | Sanchez-Perez J.-M.,National Graduate School of Agronomy, Toulouse | Sanchez-Perez J.-M.,Ecolab
Earth Surface Processes and Landforms | Year: 2010

The dynamics of suspended sediment transport were monitored continuously in a large agricultural catchment in southwest France from January 2007 to March 2009. The objective of this paper is to analyse the temporal variability in suspended sediment transport and yield in that catchment. Analyses were also undertaken to assess the relationships between precipitation, discharge and suspended sediment transport, and to interpret sediment delivery processes using suspended sediment-discharge hysteresis patterns. During the study period, we analysed 17 flood events, with high resolution suspended sediment data derived from continuous turbidity and automatic sampling. The results revealed strong seasonal, annual and inter-annual variability in suspended sediment transport. Sediment was strongly transported during spring, when frequent flood events of high magnitude and intensity occurred. Annual sediment transport in 2007 yielded 16 614 tonnes, representing 15 t km-2 (85% of annual load transport during floods for 16% of annual duration), while the 2008 sediment yield was 77 960 tonnes, representing 70 t km-2 (95% of annual load transport during floods for 20% of annual duration). Analysis of the relationships between precipitation, discharge and suspended sediment transport showed that there were signifi cant correlations between total precipitation, peak discharge, total water yield, flood intensity and sediment variables during the flood events, but no relationship with antecedent conditions. Flood events were classified in relation to suspended sediment concentration (SSC)-discharge hysteretic loops, complemented with temporal dynamics of SSC-discharge ranges during rising and falling flow. The hysteretic shapes obtained for all flood events refl ected the distribution of probable sediment sources throughout the catchment. Regarding the sediment transport during all flood events, clockwise hysteretic loops represented 68% from river deposited sediments and nearby source areas, anticlockwise 29% from distant source areas, and simultaneity of SSC and discharge 3%. © 2010 John Wiley & Sons, Ltd.

Oeurng C.,National Graduate School of Agronomy, Toulouse | Sauvage S.,National Graduate School of Agronomy, Toulouse | Sauvage S.,Ecolab | Sanchez-Perez J.-M.,National Graduate School of Agronomy, Toulouse | Sanchez-Perez J.-M.,Ecolab
Journal of Hydrology | Year: 2011

The Soil and Water Assessment Tool (SWAT, 2005) was used to simulate discharge and sediment transport at daily time steps within the intensively farmed Save catchment in south-west France (1110km2). The SWAT model was applied to evaluate catchment hydrology and sediment and associated particulate organic carbon yield using historical flow and meteorological data for a 10-years (January 1999-March 2009). Daily data on sediment (27months, January 2007-March 2009) and particular organic carbon (15months, January 2008-March 2009) were used to calibrate the model. Data on management practices (crop rotation, planting date, fertiliser quantity and irrigation) were included in the model during the simulation period of 10years. Simulated daily discharge, sediment and particulate carbon values matched the observed values satisfactorily. The model predicted that mean annual catchment precipitation for the total study period (726mm) was partitioned into evapotranspiration (78.3%), percolation/groundwater recharge (14.1%) and abstraction losses (0.5%), yielding 7.1% surface runoff. Simulated mean total water yield for the whole simulation period amounted to 138mm, comparable to the observed value of 136mm. Simulated annual sediment yield ranged from 4.3tkm-2y-1 to 110tkm-2y-1 (annual mean of 48tkm-2y-1). Annual yield of particulate organic carbon ranged from 0.1tkm-2y-1 to 2.8tkm-2y-1 (annual mean of 1.2tkm-2y-1). Thus, the highest annual sediment and particulate carbon yield represented 25 times the minimum annual yield. However, the highest annual water yield represented five times the minimum (222mm and 51mm, respectively). An empirical correlation between annual water yield and annual sediment and organic carbon yield was developed for this agricultural catchment. Potential source areas of erosion were also identified with the model. The range of the annual contributing erosive zones varied spatially from 0.1 to 6tha-1 according to the slope and agricultural practices at the catchment scale. © 2011 Elsevier B.V.

Villanueva M.C.,French Research Institute for Exploitation of the Sea | Ibarra A.A.,National Graduate School of Agronomy, Toulouse
Ecological Indicators | Year: 2016

In order to assess the level of ecological stress caused by the pollution from local disturbances in a stretch of the Garonne River, France, we applied the Abundance-Biomass Comparison (ABC) index, using fish assemblages. Data were collected in a 10-year span (1992-2002) in a reference site and in two pollution-exposed sites. The ABC index mean value in the reference site (S1) was 0.03 ± 0.002 (95% Confidence Interval - CI); for the polluted sites (S2 and S3), the values were -0.09 ± 0.002 (95% CI) and -0.12 ± 0.002 (95% CI), respectively. The ABC index showed that, besides flow variations, both downstream sites are statistically different (p < 0.05) from the reference site, but all three seem to be under moderate stress. Furthermore, we related our ABC scores to water quality and flow regime variables in the reference site and one of the polluted sites by means of a cluster analysis. The results showed that, in the reference site, the ABC scores are closely related to the flow regime, while in the polluted site, downstream a urban area, ABC is related to water quality variables such as phosphates and total phosphorous. We argue that ecological indicators can help decisions on environmental damage liability. © 2016 Elsevier Ltd. All rights reserved.

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