BioMercator: integrating genetic maps and QTL towards discovery of candidate genes

Arcade, Anne; Labourdette, Aymeric; Falque, Matthieu; Mangin, Brigitte; Chardon, Fabien; Charcosset, Alain; Joets, Johann

doi:10.1093/bioinformatics/bth230

Cited by 429 publications

(345 citation statements)

References 6 publications

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“…In systems where more QTL studies have been conducted, more formal meta-analyses and computation of a composite map combining several densely genotyped panels may further improve the confidence of QTL/candidate gene colocalization and thus also improve the efficiency of this approach (Arcade et al 2004;Chardon et al 2004). Several observations suggest that genetic hitchhiking is a concern that impacts how effectively improvement loci can be identified, however.…”

Section: Discussionmentioning

confidence: 99%

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

et al. 2011

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Determining the identity and distribution of molecular changes leading to the evolution of modern crop species provides major insights into the timing and nature of historical forces involved in rapid phenotypic evolution. In this study, we employed an integrated candidate gene strategy to identify loci involved in the evolution of flowering time during early domestication and modern improvement of the sunflower (Helianthus annuus). Sunflower homologs of many genes with known functions in flowering time were isolated and cataloged. Then, colocalization with previously mapped quantitative trait loci (QTLs), expression, or protein sequence differences between wild and domesticated sunflower, and molecular evolutionary signatures of selective sweeps were applied as step-wise criteria for narrowing down an original pool of 30 candidates. This process led to the discovery that five paralogs in the FLOWERING LOCUS T/TERMINAL FLOWER 1 gene family experienced selective sweeps during the evolution of cultivated sunflower and may be the causal loci underlying flowering time QTLs. Our findings suggest that gene duplication fosters evolutionary innovation and that natural variation in both coding and regulatory sequences of these paralogs responded to a complex history of artificial selection on flowering time during the evolution of cultivated sunflower.

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Section: Discussionmentioning

confidence: 99%

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

et al. 2011

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“…The Haldane mapping function was used to convert recombination frequencies into map distances (Haldane 1919). The chart of the linkage map was generated using BioMERCATOR v.3.1 (Arcade et al 2004). QTL analysis QTL analyses using the SSR-SNP linkage map and all available genotypic and phenotypic data were performed with the MapQTL®5 software (Van Ooijen 2004).…”

Section: Linkage Mappingmentioning

confidence: 99%

“…For the hybrid parent SA65T, the species origin of the QTL marker alleles were identified, and the allelic effects at the QTL were therefore estimated by contrast of E. oleifera (grandparent SA49D) against E. guineensis (grandparent LM2466P). The QTLs (position, confidence interval, variation explained) were visualized on the linkage map using BioMERCATOR v.3.1 (Arcade et al 2004).…”

Section: Linkage Mappingmentioning

confidence: 99%

Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.)

Montoya¹,

Lopes

Flori

et al. 2013

Tree Genetics & Genomes

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“…This statistical approach enables QTL results from independent studies to be combined into a single result using only published QTL data. Software packages based on this methodology are available such as BioMercator (Arcade et al 2004) and Meta-QTL (Veyrieras et al 2007), a new software that removes some of the limitations of BioMercator in the number of QTLs it can handle at once. Meta-QTL analyses for flowering time in maize ), resistance to a nematode in soybean (Guo et al 2006), earliness in bread wheat (Hanocq et al 2007), and N uptake in maize (Coque et al 2008) have already shown the usefulness of this approach in determining the number of "true" QTLs underlying the observed QTLs and in positioning consensus QTLs with more precision.…”

Section: Introductionmentioning

confidence: 99%

Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database

Courtois

Ahmadi

Khowaja

et al. 2009

Rice

251

185

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During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number, maximum root length, root thickness, root/ shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published between 1995 and 2007. The physical position on the pseudochromosomes of the markers flanking each QTL was determined. An overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of "hot spots," The 32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones, encompassed only a few genes.

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BioMercator: integrating genetic maps and QTL towards discovery of candidate genes

Abstract: Available upon request (http://moulon/~bioinfo/BioMercator/). Free of charge for academic use.

Cited by 429 publications

References 6 publications

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.)

Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database

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