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Rincent R.,French National Institute for Agricultural Research | Rincent R.,Kleinwanzlebener Saatzucht Saat AG | Rincent R.,British Petroleum | Moreau L.,French National Institute for Agricultural Research | And 15 more authors.
Genetics | Year: 2014

Association mapping has permitted the discovery of major QTL in many species. It can be applied to existing populations and, as a consequence, it is generally necessary to take into account structure and relatedness among individuals in the statistical model to control false positives. We analytically studied power in association studies by computing noncentrality parameter of the tests and its relationship with parameters characterizing diversity (genetic differentiation between groups and allele frequencies) and kinship between individuals. Investigation of three different maize diversity panels genotyped with the 50k SNPs array highlighted contrasted average power among panels and revealed gaps of power of classical mixed models in regions with high linkage disequilibrium (LD). These gaps could be related to the fact that markers are used for both testing association and estimating relatedness. We thus considered two alternative approaches to estimating the kinship matrix to recover power in regions of high LD. In the first one, we estimated the kinship with all the markers that are not located on the same chromosome than the tested SNP. In the second one, correlation between markers was taken into account to weight the contribution of each marker to the kinship. Simulations revealed that these two approaches were efficient to control false positives and were more powerful than classical models. © 2014 by the Genetics Society of America.


Giraud H.,University Paris - Sud | Lehermeier C.,TU Munich | Bauer E.,TU Munich | Falque M.,French National Institute for Agricultural Research | And 15 more authors.
Genetics | Year: 2014

Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R2= 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R2< 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production. © 2014 by the Genetics Society of America.


Hirth M.,Friedrich - Schiller University of Jena | Dietzel L.,Friedrich - Schiller University of Jena | Dietzel L.,Goethe University Frankfurt | Steiner S.,Friedrich - Schiller University of Jena | And 6 more authors.
Frontiers in Plant Science | Year: 2013

In this study we assessed the ability of the C4 plant maize to perform long-term photosynthetic acclimation in an artificial light quality system previously used for analyzing short-term and long-term acclimation responses (LTR) in C3 plants. We aimed to test if this light system could be used as a tool for analyzing redox-regulated acclimation processes in maize seedlings. Photosynthetic parameters obtained from maize samples harvested in the field were used as control. The results indicated that field grown maize performed a pronounced LTR with significant differences between the top and the bottom levels of the plant stand corresponding to the strong light gradients occurring in it. We compared these data to results obtained from maize seedlings grown under artificial light sources preferentially exciting either photosystem II or photosystem I. In C3 plants, this light system induces redox signals within the photosynthetic electron transport chain which trigger state transitions and differential phosphorylation of LHCII (light harvesting complexes of photosystem II). The LTR to these redox signals induces changes in the accumulation of plastid psaA transcripts, in chlorophyll (Chl) fluorescence values Fs/Fm, in Chl a/b ratios and in transient starch accumulation in C3 plants. Maize seedlings grown in this light system exhibited a pronounced ability to perform both short-term and long-term acclimation at the level of psaA transcripts, Chl fluorescence values Fs/Fm and Chl a/b ratios. Interestingly, maize seedlings did not exhibit redox-controlled variations of starch accumulation probably because of its specific differences in energy metabolism. In summary, the artificial laboratory light system was found to be well-suited to mimic field light conditions and provides a physiological tool for studying the molecular regulation of the LTR of maize in more detail. © 2013 Hirth, Dietzel, Steiner, Ludwig, Weidenbach, Pfalz and Pfannschmidt.


PubMed | Kleinwanzlebener Saatzucht Saat AG, Centro Investigacions Agrarias Mabegondo, University of Hohenheim, Syngenta and 4 more.
Type: Journal Article | Journal: Genetics | Year: 2014

Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R(2) = 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R(2) < 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production.

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