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Boigneville, France

Thepot S.,University Paris - Sud | Thepot S.,French National Institute for Agricultural Research | Restoux G.,University Paris - Sud | Goldringer I.,French National Institute for Agricultural Research | And 4 more authors.
Genetics | Year: 2015

Multiparental populations are innovative tools for fine mapping large numbers of loci. Here we explored the application of a wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population for QTL mapping. This population was created by 12 generations of free recombination among 60 founder lines, following modification of the mating system from strict selfing to strict outcrossing using the ms1b nuclear male sterility gene. Available parents and a subset of 380 SSD lines of the resulting MAGIC population were phenotyped for earliness and genotyped with the 9K i-Select SNP array and additional markers in candidate genes controlling heading date. We demonstrated that 12 generations of strict outcrossing rapidly and drastically reduced linkage disequilibrium to very low levels even at short map distances and also greatly reduced the population structure exhibited among the parents. We developed a Bayesian method, based on allelic frequency, to estimate the contribution of each parent in the evolved population. To detect loci under selection and estimate selective pressure, we also developed a new method comparing shifts in allelic frequency between the initial and the evolved populations due to both selection and genetic drift with expectations under drift only. This evolutionary approach allowed us to identify 26 genomic areas under selection. Using association tests between flowering time and polymorphisms, 6 of these genomic areas appeared to carry flowering time QTL, 1 of which corresponds to Ppd-D1, a major gene involved in the photoperiod sensitivity. Frequency shifts at 4 of 6 areas were consistent with earlier flowering of the evolved population relative to the initial population. The use of this new outcrossing wheat population, mixing numerous initial parental lines through multiple generations of panmixia, is discussed in terms of power to detect genes under selection and association mapping. Furthermore we provide new statistical methods for use in future analyses of multiparental populations. © 2015, Genetics Society of America. All rights reserved.

Debeljak M.,Jozef Stefan Institute | Kuzmanovski V.,Jozef Stefan Institute | Trajanov A.,Jozef Stefan Institute | Dzeroski S.,Jozef Stefan Institute | And 2 more authors.
Proceedings of the 13th International Symposium on Operational Research, SOR 2015 | Year: 2015

The application of pesticides in agriculture is not always safe for human health and the environment. Despite being officialy approved by authorities in terms of ecological risk, they appear in surface and ground water in concentrations above the official thresholds. To reduce and eliminate water pollution with pesticides, a decision support system (DSS) for ecological risk assessment of pesticide applications and ecological risk management, is proposed. The DSS is built by using the framework proposed by the US Environmental Protection Agency and Multi Criteria Decision Analysis (MCDA) implemented into the DEX (Decision EXpert) integrative methodology was implemented to build qualitative multiattribute decision models by the DEXi modelling tool. A conceptual solution is demonstrated on an assessment of a proposed crop management plan for winter wheat, where the herbicide Isoproturon is planned to be applied. The DSS identified that the proposed plan is risky, therefore mitigation measures that have to be included in the proposed crop management plan are proposed.

Melander B.,University of Aarhus | Munier-Jolain N.,CNRS Agroecology Lab | Charles R.,Head of Research Units | Wirth J.,Head of Research Units | And 5 more authors.
Weed Technology | Year: 2013

Noninversion tillage with tine- or disc-based cultivations prior to crop establishment is the most common way of reducing tillage for arable cropping systems with small grain cereals, oilseed rape, and maize in Europe. However, new regulations on pesticide use might hinder further expansion of reduced-tillage systems. European agriculture is asked to become less dependent on pesticides and promote crop protection programs based on integrated pest management (IPM) principles. Conventional noninversion tillage systems rely entirely on the availability of glyphosate products, and herbicide consumption is mostly higher compared to plow-based cropping systems. Annual grass weeds and catchweed bedstraw often constitute the principal weed problems in noninversion tillage systems, and crop rotations concurrently have very high proportions of winter cereals. There is a need to redesign cropping systems to allow for more diversification of the crop rotations to combat these weed problems with less herbicide input. Cover crops, stubble management strategies, and tactics that strengthen crop growth relative to weed growth are also seen as important components in future IPM systems, but their impact in noninversion tillage systems needs validation. Direct mechanical weed control methods based on rotating weeding devices such as rotary hoes could become useful in reduced-tillage systems where more crop residues and less workable soils are more prevalent, but further development is needed for effective application. Owing to the frequent use of glyphosate in reduced-tillage systems, perennial weeds are not particularly problematic. However, results from organic cropping systems clearly reveal that desisting from glyphosate use inevitably leads to more problems with perennials, which need to be addressed in future research. Nomenclature: Catchweed bedstraw, Galium aparine L.; barley, Hordeum vulgare L.; maize, Zea mays L.; oilseed rape, Brassica napus L.; wheat, Triticum aestivum L.

Cozannet P.,French National Institute for Agricultural Research | Primot Y.,Ajinomoto Co. | Gady C.,ADISSEO France SAS | Metayer J.P.,Institute du Vegetal | And 3 more authors.
British Poultry Science | Year: 2011

1. In recent years, policies encouraging the production of ethanol from maize or wheat have stimulated an increased production of distillers' dried grains with solubles (DDGS) for which the nutritional value for poultry is poorly described, especially in the case of wheat DDGS. 2. DDGS samples (19) were obtained from 7 plants in Europe from June to September 2007. Each sample was analysed for chemical composition and 10 representative samples were measured for amino acid (AA) content and their standardised digestibility (SDD) in caecectomised cockerels. Lightness score (L) of each DDGS was also measured. 3. Results indicated a rather stable crude protein content (327 to 392 g/kg DM) but the AA profile was variable between samples. Lysine (LYS) was the most affected AA with contents ranging between 0·83 and 3·01 g/100 g CP. In addition, only 0·76 of total LYS were free if estimated by the fluoro-dinitro-benzene procedure and 0·85 of total LYS were free if estimated by the furosine procedure. 4. The SDD of LYS was also highly variable (-0·04 to 0·71) with the lowest values observed for DDGS samples with a low LYS content in CP; these latter samples had also a high occurrence of Maillard reactions and low L values (<50). Consequently, both LYS content in CP (r = 0·63) and SDD of LYS (r = 0·64) values were positively related with L. 5. Our data indicate that LYS SDD can be accurately predicted from LYS content in CP according to a quadratic (R2 = 0·94) or a linear-plateau model (R2 = 0·90; breakpoint for 1·9 g/100 g lysine in CP and a 0.63 plateau SDD value). © 2011 British Poultry Science Ltd.

Cozannet P.,French National Institute for Agricultural Research | Cozannet P.,Institute du Vegetal | Primot Y.,Ajinomoto Co. | Gady C.,ADISSEO France SAS | And 5 more authors.
Livestock Science | Year: 2010

In recent years, policies encouraging the production of ethanol from corn or wheat have stimulated an increased production of distillers dried grains with solubles (DDGS) whose nutritional value for pigs is little described. Seventeen wheat DDGS samples were obtained from 7 different plants in Europe from July to September 2007. Each sample was analyzed and 10 representative samples were measured for amino acids (AA) content and their standardized ileal digestibility (SID) in pigs. Lightness score (L) of each DDGS was also measured. Our results indicate a rather stable crude protein content (32.6 to 38.9% DM basis; average: 36.1% DM basis) whereas lysine was the most affected AA with contents ranging between 0.82 and 3.00% of crude protein (CP; N*6.25). In addition, lysine SID was also variable (9 to 82%) with the lowest values observed in DDGS with low lysine level in CP. In fact, samples with low lysine content in CP and low SID of lysine had low lightness values (L < 50) and a subsequent high occurrence of Maillard reactions. Consequently, both lysine content (R = 0.63) and lysine SID (R=0.68) values were positively correlated with lightness and DDGS samples that were lighter in colour had higher total and digestible AA levels. Our data indicate that lysine SID can be accurately predicted from lysine content in CP with a quadratic model (R2 = 0.87) or a linear-plateau model (R2 = 0.80 with a breakpoint for lysine content in CP of 1.9% and SID at plateau of 68%). This also suggests that wheat DDGS with lysine content in CP lower than 1.9% should be avoided in pig diets. © 2010 Elsevier B.V.

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