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ABSTRACT: Association mapping of sequence polymorphisms underlying the phenotypic variability of quantitative agronomical traits is now a widely used method in plant genetics. However, due to the common presence of a complex genetic structure within the plant diversity panels, spurious associations are expected to be highly frequent. Several methods have thus been suggested to control for panel structure. They mainly rely on ad hoc criteria for selecting the number of ancestral groups; which is often not evident for the complex panels that are commonly used in maize. It was thus necessary to evaluate the effect of the selected structure models on the association mapping results. A real maize data set (342 maize inbred lines and 12,000 SNPs) was used for this study. The panel structure was estimated using both Bayesian and dimensional reduction methods, considering an increasing number of ancestral groups. Effect on association tests depends in particular on the number of ancestral groups and on the trait analyzed. The results also show that using a high number of ancestral groups leads to an over-corrected model in which all causal loci vanish. Finally the results of all models tested were combined in a meta-analysis approach. In this way, robust associations were highlighted for each analyzed trait.
Theoretical and Applied Genetics 01/2011; 122(6):1149-60. · 3.30 Impact Factor
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Umar Masood Quraishi,
Michael Abrouk,
Stéphanie Bolot,
Caroline Pont,
Mickael Throude,
Nicolas Guilhot,
Carole Confolent,
Fernanda Bortolini, Sébastien Praud,
Alain Murigneux,
Gilles Charmet,
Jerome Salse
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ABSTRACT: Recent updates in comparative genomics among cereals have provided the opportunity to identify conserved orthologous set (COS) DNA sequences for cross-genome map-based cloning of candidate genes underpinning quantitative traits. New tools are described that are applicable to any cereal genome of interest, namely, alignment criterion for orthologous couples identification, as well as the Intron Spanning Marker software to automatically select intron-spanning primer pairs. In order to test the software, it was applied to the bread wheat genome, and 695 COS markers were assigned to 1,535 wheat loci (on average one marker/2.6 cM) based on 827 robust rice-wheat orthologs. Furthermore, 31 of the 695 COS markers were selected to fine map a pentosan viscosity quantitative trait loci (QTL) on wheat chromosome 7A. Among the 31 COS markers, 14 (45%) were polymorphic between the parental lines and 12 were mapped within the QTL confidence interval with one marker every 0.6 cM defining candidate genes among the rice orthologous region.
Functional & Integrative Genomics 08/2009; 9(4):473-84. · 3.83 Impact Factor
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Catherine Ravel, Sébastien Praud,
Aurélie Canaguier,
Philippe Dufour,
Sandra Giancola,
François Balfourier,
Boulos Chalhoub,
Dominique Brunel,
Laurent Linossier,
Mireille Dardevet,
Michel Beckert,
Michel Rousset,
Alain Murigneux,
Gilles Charmet
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ABSTRACT: Single-nucleotide polymorphisms (SNPs) constitute an abundant source of DNA polymorphisms, which have been successfully used
to identify loci that are associated with a particular phenotype. Additionally, such markers could be efficiently used in
combination with doubled haploid technology to improve the efficiency of breeding programmes. Information on such markers
in plants is still scarce. For bread wheat, SNP data are restricted to a few genes. This can be explained by the hexaploidy
of Triticum aestivum which makes SNP discovery difficult. We developed a novel method for SNP discovery in bread wheat. The strategy is based
on the development of highly specific PCR-primers, which were used to sequence 27 lines. SNPs were discovered from sequence
alignment data. Some SNPs were identified by mass spectrometry in a collection of 113 lines, which were both evaluated for
agronomic traits and genotyped at 42 neutral microsatellite loci. Traits investigated include: protein content, the quantity
of high-molecular-weight glutenins and that of the GluBx subunit. The 42 markers were used to infer population structure,
which was included in linear models for association studies. The results of this preliminary study showed 89 SNPs in approximately
20kbp, i.e., one SNP every 223bp on average. Six SNPs were genotyped: three were located along the sequence of Glu-B1-1, while three non-synonymous SNPs were located along the sequence of the B homoeologous gene coding for SPA (Storage Protein
Activator). The SNPs from Glu-B1-1 had a significant effect on the studied variables, whereas those of SPA had no effect. Such results might indicate that some haplotypes for Glu-B1-1 are linked to higher protein content, through an increased amount of high-molecular-weight glutenins, especially the GluBx
subunit.
Euphytica 11/2007; 158(3):331-336. · 1.55 Impact Factor
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ABSTRACT: Wheat prolamin-box binding factor (WPBF) was shown to be an activator of Triticum aestivum L. storage protein genes. Three homoeologous genes encoding this transcription factor were isolated from a bacterial artificial chromosome genomic library and sequenced. The genes all have two exons separated by an intron of approximately 1,000 bp where the second exon contains the entire coding sequence. Many differences were found between homoeologous sequences, but none of them is predicted to significantly alter the sequence of the putative encoded protein. The three homoeologous genes are specifically expressed in grain from 3 to 39 days after anthesis. The allelic variation of a genetically diverse collection of 27 bread wheat lines was assessed. One, five, and one single-nucleotide polymorphisms (SNPs) were detected in the wPbf genes for the A, B, and D genomes, respectively. Physical and genetic mapping utilizing some of the SNPs identified confirmed that wPbf genes are located close to the centromeres on the homoeologous group 5 chromosomes. The low level of allelic diversity found in wPbf genes may suggest that these genes play a key role and are thus constrained by selection.
Functional and Integrative Genomics 11/2006; 6(4):310-21. · 2.84 Impact Factor
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Catherine Ravel, Sébastien Praud,
Alain Murigneux,
Aurélie Canaguier,
Frédéric Sapet,
Delphine Samson,
François Balfourier,
Philippe Dufour,
Boulos Chalhoub,
Dominique Brunel,
Michel Beckert,
Gilles Charmet
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ABSTRACT: Information on single-nucleotide polymorphisms (SNPs) in hexaploid bread wheat is still scarce. The goal of this study was to detect SNPs in wheat and examine their frequency. Twenty-six bread wheat lines from different origins worldwide were used. Specific PCR-products were obtained from 21 genes and directly sequenced. SNPs were discovered from the alignment of these sequences. The overall sequence polymorphism observed in this sample appears to be low; 64 single-base polymorphisms were detected in approximately 21.5 kb (i.e., 1 SNP every 335 bp). The level of polymorphism is highly variable among the different genes studied. Fifty percent of the genes studied contained no sequence polymorphism, whereas most SNPs detected were located in only 2 genes. As expected, taking into account a synthetic line created with a wild Triticum tauschii parent increases the level of polymorphism (101 SNPs; 1 SNP every 212 bp). The detected SNPs are available at http://urgi.versailles.inra.fr/GnpSNP">http://urgi.versailles.inra.fr/GnpSNP. Data on linkage disequilibrium (LD) are still preliminary. They showed a significant level of LD in the 2 most polymorphic genes. To conclude, the genome size of hexaploid wheat and its low level of polymorphism complicate SNP discovery in this species.
Genome 09/2006; 49(9):1131-9. · 1.65 Impact Factor
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ABSTRACT: A previous study in wheat (Triticum aestivum L.) identified two candidate genes controlling a quantitative trait locus (QTL) for high-molecular-weight glutenin subunit (HMW-GS) GluBx. These candidates were Glu-B1-1, the structural gene coding for Glu1Bx, and the B homoeologous gene coding for SPA (spa-B), a seed storage protein activator. The goal of this study was to identify the best candidate gene for this QTL. Single nucleotide polymorphisms (SNPs) are an abundant source of DNA polymorphisms that have been successfully used to identify loci associated with particular phenotypes. As no linkage disequilibrium was detected between Glu-B1-1 and spa-B, we performed an association study to identify the individual gene responsible for the QTL. Six SNPs, three located in Glu-B1-1 and three in spa-B, were genotyped by mass spectrometry in a collection of 113 bread wheat lines. These lines were also evaluated for protein content as well as the total quantity of HMW-GSs and of each HMW-GS in seed samples from two harvest years. Significant associations were detected only between Glu-B1-1 polymorphism and most of the traits evaluated. Spa-B was unambiguously discarded as a candidate. To our knowledge, this is the first report on an association study that was successfully used to discriminate between two candidate genes.
Theoretical and Applied Genetics 03/2006; 112(4):738-43. · 3.30 Impact Factor
