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Leroux D.,French National Institute for Agricultural Research | Rahmani A.,French National Institute for Agricultural Research | Jasson S.,French National Institute for Agricultural Research | Ventelon M.,EURALIS SEMENCES | And 3 more authors.
Theoretical and Applied Genetics | Year: 2014

Key message: We enhance power and accuracy of QTL mapping in multiple related families, by clustering the founders of the families on their local genomic similarity. MCQTL is a linkage mapping software application that allows the joint QTL mapping of multiple related families. In its current implementation, QTLs are modeled with one or two parameters for each parent that is a founder of the multi-cross design. The higher the number of parents, the higher the number of model parameters which can impact the power and the accuracy of the mapping. We propose to make use of the availability of denser and denser genotyping information on the founders to lessen the number of MCQTL parameters and thus boost the QTL discovery. We developed clusthaplo, an R package (http://cran.r-project.org/web/packages/clusthaplo/index.html), which aims to cluster haplotypes using a genomic similarity that reflects the probability of sharing the same ancestral allele. Computed in a sliding window along the genome and followed by a clustering method, the genomic similarity allows the local clustering of the parent haplotypes. Our assumption is that the haplotypes belonging to the same class transmit the same ancestral allele. So their putative QTL allelic effects can be modeled with the same parameter, leading to a parsimonious model, that is plugged in MCQTL. Intensive simulations using three maize data sets showed the significant gain in power and in accuracy of the QTL mapping with the ancestral allele model compared to the classical MCQTL model. MCQTL_LD (clusthaplo outputs plug in MCQTL) is a versatile and powerful tool for QTL mapping in multiple related families that makes use of linkage and linkage disequilibrium (web site http://carlit.toulouse.inra.fr/MCQTL/). © 2014 The Author(s).


Maury P.,National Polytechnic Institute of Toulouse | Maury P.,French National Institute for Agricultural Research | Andrianasolo F.N.,National Polytechnic Institute of Toulouse | Andrianasolo F.N.,French National Institute for Agricultural Research | And 10 more authors.
OCL - Oilseeds and fats | Year: 2015

This study was carried out on very early sowing of soybean in order to improve potential yield and/or reduce water requirements. Three varieties belonging to different maturity groups were selected to identify varietal traits of interest in very early sowing. A set of multi-location irrigated trials consisting in two sowing dates was performed from 2010 to 2014. Yield and water requirements were determined; crop development and growth was monitored on cv. Santana. The combined effects of low temperatures and photoperiod in very early sowing resulted in limited aboveground biomass production during vegetative period and increased grain filling duration. Maximal values for yield were observed in very early sowing modality, although yield was slightly lower in very early sowing compared to conventional one (3.7 t/ha vs. 3.9 t/ha). The amount of water brought by irrigation for meeting ETM conditions was slightly lower in very early sowing (170 mm vs. 182 mm). A late variety (maturity group II) appears better adapted to very early sowing compared to a maturity group I variety. This study stands as the first agronomical reference for evaluating early sowing of soybean and suggests that late-varietal type could improve soybean potential yield for early sowing in irrigated cropping conditions of South-Western France. © P. Maury et al., published by EDP Sciences, 2015.


Picot A.,ARVALIS Institute du Vegetal | Picot A.,French National Institute for Agricultural Research | Picot A.,University of California Kearney Research and Extension Center | Atanasova-Penichon V.,French National Institute for Agricultural Research | And 8 more authors.
Journal of Agricultural and Food Chemistry | Year: 2013

The potential involvement of antioxidants (α-tocopherol, lutein, zeaxanthin, β-carotene, and ferulic acid) in the resistance of maize varieties to Fusarium ear rot was the focus of this study. These antioxidants were present in all maize kernel stages, indicating that the fumonisin-producing fungi (mainly Fusarium verticillioides and Fusarium proliferatum) are likely to face them during ear colonization. The effect of these compounds on fumonisin biosynthesis was studied in F. verticillioides liquid cultures. In carotenoid-treated cultures, no inhibitory effect of fumonisin accumulation was observed while a potent inhibitory activity was obtained for sublethal doses of α-tocopherol (0.1 mM) and ferulic acid (1 mM). Using a set of genotypes with moderate to high susceptibility to Fusarium ear rot, ferulic acid was significantly lower in immature kernels of the very susceptible group. Such a relation was nonexistent for tocopherols and carotenoids. Also, ferulic acid in immature kernels ranged from 3 to 8.5 mg/g, i.e., at levels consistent with the in vitro inhibitory concentration. Overall, our data support the fact that ferulic acid may contribute to resistance to Fusarium ear rot and/or fumonisin accumulation. © 2013 American Chemical Society.


Atanasova-Penichon V.,French National Institute for Agricultural Research | Pons S.,French National Institute for Agricultural Research | Pons S.,Monsanto Corporation | Pinson-Gadais L.,French National Institute for Agricultural Research | And 9 more authors.
Molecular Plant-Microbe Interactions | Year: 2012

Fusarium graminearum is the causal agent of Gibberella ear rot and produces trichothecene mycotoxins. Basic questions remain unanswered regarding the kernel stages associated with trichothecene biosynthesis and the kernel metabolites potentially involved in the regulation of trichothecene production in planta. In a two-year field study, F. graminearum growth, trichothecene accumulation, and phenolic acid composition were monitored in developing maize kernels of a susceptible and a moderately resistant variety using quantitative polymerase chain reaction and liquid chromatography coupled with photodiode array or mass spectrometry detection. Infection started as early as the blister stage and proceeded slowly until the dough stage. Then, a peak of trichothecene accumulation occurred and infection progressed exponentially until the final harvest time. Both F. graminearum growth and trichothecene production were drastically reduced in the moderately resistant variety. We found that chlorogenic acid is more abundant in the moderately resistant variety, with levels spiking in the earliest kernel stages induced by Fusarium infection. This is the first report that precisely describes the kernel stage associated with the initiation of trichothecene production and provides in planta evidence that chlorogenic acid may play a role in maize resistance to Gibberella ear rot and trichothecene accumulation. © 2012 The American Phytopathological Society.


Cadic E.,French National Institute for Agricultural Research | Cadic E.,French National Center for Scientific Research | Cadic E.,BIOGEMMA SAS | Coque M.,BIOGEMMA SAS | And 20 more authors.
Theoretical and Applied Genetics | Year: 2013

Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0. 08 to 0. 26 cM for a threshold of 0. 20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach. © 2013 Springer-Verlag Berlin Heidelberg.


Bardol N.,University Paris - Sud | Ventelon M.,Euralis Semences | Mangin B.,French National Institute for Agricultural Research | Jasson S.,French National Institute for Agricultural Research | And 6 more authors.
Theoretical and Applied Genetics | Year: 2013

Advancements in genotyping are rapidly decreasing marker costs and increasing marker density. This opens new possibilities for mapping quantitative trait loci (QTL), in particular by combining linkage disequilibrium information and linkage analysis (LDLA). In this study, we compared different approaches to detect QTL for four traits of agronomical importance in two large multi-parental datasets of maize (Zea mays L.) of 895 and 928 testcross progenies composed of 7 and 21 biparental families, respectively, and genotyped with 491 markers. We compared to traditional linkage-based methods two LDLA models relying on the dense genotyping of parental lines with 17,728 SNP: one based on a clustering approach of parental line segments into ancestral alleles and one based on single marker information. The two LDLA models generally identified more QTL (60 and 52 QTL in total) than classical linkage models (49 and 44 QTL in total). However, they performed inconsistently over datasets and traits suggesting that a compromise must be found between the reduction of allele number for increasing statistical power and the adequacy of the model to potentially complex allelic variation. For some QTL, the model exclusively based on linkage analysis, which assumed that each parental line carried a different QTL allele, was able to capture remaining variation not explained by LDLA models. These complementarities between models clearly suggest that the different QTL mapping approaches must be considered to capture the different levels of allelic variation at QTL involved in complex traits. © 2013 Springer-Verlag Berlin Heidelberg.


Delourme R.,French National Institute for Agricultural Research | Falentin C.,French National Institute for Agricultural Research | Fomeju B.F.,French National Institute for Agricultural Research | Boillot M.,Euralis Semences | And 14 more authors.
BMC Genomics | Year: 2013

Background: High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern. Results: We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in " 00" winter oilseed rape types but this was shown to vary greatly along the linkage groups. Conclusions: Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses. © 2013 Delourme et al; licensee BioMed Central Ltd.


PubMed | University of Padua, University of Natural Resources and Life Sciences, Vienna, Saatzucht Streng Engelen GmbH & Co. KG, University of Hohenheim and 17 more.
Type: | Journal: Plant, cell & environment | Year: 2017

Soybean cultivation holds great potential for a sustainable agriculture in Europe, but adaptation remains a central issue. In this large mega-environment (MEV) study, 75 European cultivars from five early maturity groups (MGs 000 - II) were evaluated for maturity related traits at 22 locations in 10 countries across Europe. Clustering of the locations based on phenotypic similarity revealed six mega-environments in latitudinal direction and suggested several more. Analysis of maturity identified several groups of cultivars with phenotypic similarity that are optimally adapted to the different growing regions in Europe. We identified several haplotypes for the allelic variants at the E1, E2, E3 and E4 genes, with each E haplotype comprising cultivars from different MGs. Cultivars with the same E haplotype can exhibit different flowering and maturity characteristics, suggesting that the genetic control of these traits is more complex and that adaptation involves additional genetic pathways, for example temperature requirement. Taken together, our study allowed the first unified assessment of soybean growing regions in Europe and illustrates the strong effect of photoperiod on soybean adaptation and MEV classification, as well as the effects of the E maturity loci for soybean adaptation in Europe. This article is protected by copyright. All rights reserved.

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