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Sébastien Tisné,
Yann Serrand,
Liên Bach,
Elodie Gilbault,
Rachid Ben Ameur,
Hervé Balasse,
Roger Voisin,
David Bouchez,
Mylène Durand-Tardif,
Philippe Guerche,
Gaël Chareyron,
Jérôme Da Rugna,
Christine Camilleri, Olivier Loudet
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ABSTRACT: Increased phenotyping accuracy and throughput are necessary to improve our understanding of quantitative variation and to be able to decompose complex traits like those involved in growth response to the environment. Still, only a few facilities are known to handle individual plants of small stature for non-destructive, real-time phenotype acquisition from plants grown in precisely adjusted and variable experimental conditions. Here, we describe Phenoscope, a high-throughput phenotyping platform that has the unique feature of continuously rotating 735 individual pots over a table. It can automatically adjust watering and is equipped with a zenithal imaging system to monitor rosette size and expansion rate during the vegetative stage, thanks to automatic image analysis allowing manual correction. Applied to Arabidopsis thaliana, we show that rotating the pots strongly reduced micro-environmental disparity: heterogeneity in evaporation was cut by a factor of 2.5 and the number of replicates needed to detect a specific mild genotypic effect was reduced by a factor of 3. In addition, by controlling a large part of the micro-environmental variance, other tangible sources of variance become noticeable. Overall, Phenoscope makes it possible to perform large-scale experiments that would not be viable or reproducible by hand. Applied to typical QTL mapping experiment, we show that our mapping power may be more limited by genetic complexity than by phenotyping accuracy. This should help to draw a more general picture as to how genetic diversity shapes phenotypic variation. To see the robot in action: http://www.inra.fr/vast/Files/PhenoFilm.avi © 2013 The Authors. The Plant Journal © 2013 Blackwell Publishing Ltd.
The Plant Journal 03/2013; · 6.16 Impact Factor
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ABSTRACT: As sessile organisms, plants have to cope with diverse environmental constraints that may vary through time and space, eventually leading to changes in the phenotype of populations through fixation of adaptive genetic variation. To fully comprehend the mechanisms of evolution and make sense of the extensive genotypic diversity currently revealed by new sequencing technologies, we are challenged with identifying the molecular basis of such adaptive variation. Here, we have identified a new variant of a molybdenum (Mo) transporter, MOT1, which is causal for fitness changes under artificial conditions of both Mo-deficiency and Mo-toxicity and in which allelic variation among West-Asian populations is strictly correlated with the concentration of available Mo in native soils. In addition, this association is accompanied at different scales with patterns of polymorphisms that are not consistent with neutral evolution and show signs of diversifying selection. Resolving such a case of allelic heterogeneity helps explain species-wide phenotypic variation for Mo homeostasis and potentially reveals trade-off effects, a finding still rarely linked to fitness.
PLoS Genetics 07/2012; 8(7):e1002814. · 8.69 Impact Factor
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ABSTRACT: Epigenetic variation is currently being investigated with the aim of deciphering its importance in both adaptation and evolution [1]. In plants, epimutations can underlie heritable phenotypic diversity [2-4], and epigenetic mechanisms might contribute to reproductive barriers between [5] or within species [6]. The extent of epigenetic variation begins to be appreciated in Arabidopsis [7], but the origin of natural epialleles and their impact in the wild remain largely unknown. Here we show that a genetic incompatibility among Arabidopsis thaliana strains is related to the epigenetic control of a pair of duplicate genes involved in fitness: a transposition event results in a rearranged paralogous structure that causes DNA methylation and transcriptional silencing of the other copy. We further show that this natural, strain-specific epiallele is stable over numerous generations even after removal of the duplicated, rearranged gene copy through crosses. Finally, we provide evidence that the rearranged gene copy triggers de novo DNA methylation and silencing of the unlinked native gene by RNA-directed DNA methylation. Our findings suggest an important role of naturally occurring epialleles originating from structural variation in rapidly establishing genetic incompatibilities following gene duplication events.
Current biology: CB 02/2012; 22(4):326-31. · 10.99 Impact Factor
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ABSTRACT: One of the main strengths of Arabidopsis thaliana as a model species is the impressive number of public resources available to the scientific community. Exploring species genetic diversity – and therefore adaptation – relies on collections of individuals from natural populations taken from diverse environments. Nevertheless, due to a few mislabeling events or genotype mixtures, some variants available in stock centers have been misidentified, causing inconsistencies and limiting the potential of genetic analyses. To improve the identification of natural accessions, we genotyped 1311 seed stocks from our Versailles Arabidopsis Stock Center and from other collections to determine their molecular profiles at 341 single nucleotide polymorphism markers. These profiles were used to compare genotypes at both the intra- and inter-accession levels. We confirmed previously described inconsistencies and revealed new ones, and suggest likely identities for accessions whose lineage had been lost. We also developed two new tools: a minimal fingerprint computation to quickly verify the identity of an accession, and an optimized marker set to assist in the identification of unknown or mixed accessions. These tools are available on a dedicated web interface called ANATool (https://www.versailles.inra.fr/ijpb/crb/anatool) that provides a simple and efficient means to verify or determine the identity of A. thaliana accessions in any laboratory, without the need for any specific or expensive technology.
The Plant Journal 12/2011; 69(6):1094 - 1101. · 6.16 Impact Factor
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ABSTRACT: Sessile organisms such as plants have to develop adaptive responses to face environmental change. In Arabidopsis thaliana populations, natural variation for stress responses have been observed at different levels of integration and the genetic bases of those variations have been analysed using two strategies: classical linkage and association (LD) mapping. The strength of Arabidopsis resides in the huge amount of genomic data and molecular tools available leading to the identification of many polymorphisms responsible for phenotypic variation. Remaining limitations to clearly understand how Arabidopsis adapts to its environment, that is the complexity of the genetic architecture and the lack of ecological data, should be partially solved thanks to the development of new methods and the acquisition of new data.
Current opinion in plant biology 06/2011; 14(3):225-31. · 10.33 Impact Factor
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ABSTRACT: A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 x Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent--but still functional-combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation polymorphisms using high-throughput sequencing, because it remains challenging to distinguish allelic from paralogous variation at this scale.
PLoS Genetics 05/2010; 6(5):e1000945. · 8.69 Impact Factor
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Alexander Platt,
Matthew Horton,
Yu S Huang,
Yan Li,
Alison E Anastasio,
Ni Wayan Mulyati,
Jon Agren,
Oliver Bossdorf,
Diane Byers,
Kathleen Donohue, [......],
Valérie Le Corre, Olivier Loudet,
Fabrice Roux,
Norman Warthmann,
Detlef Weigel,
Luz Rivero,
Randy Scholl,
Magnus Nordborg,
Joy Bergelson,
Justin O Borevitz
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ABSTRACT: The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.
PLoS Genetics 01/2010; 6(2):e1000843. · 8.69 Impact Factor
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ABSTRACT: Genetic incompatibilities resulting from interactions between two loci represent a potential source of postzygotic barriers and may be an important factor in evolution when they impair the outcome of interspecific crosses. We show that, in crosses between strains of the plant Arabidopsis thaliana, loci interact epistatically, controlling a recessive embryo lethality. This interaction is explained by divergent evolution occurring among paralogs of an essential duplicate gene, for which the functional copy is not located at the same locus in different accessions. These paralogs demonstrate genetic heterogeneity in their respective evolutionary trajectories, which results in widespread incompatibility among strains. Our data suggest that these passive mechanisms, gene duplication and extinction, could represent an important source of genetic incompatibilities across all taxa.
Science 02/2009; 323(5914):623-6. · 31.20 Impact Factor
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Sureshkumar Balasubramanian,
Christopher Schwartz,
Anandita Singh,
Norman Warthmann,
Min Chul Kim,
Julin N Maloof, Olivier Loudet,
Gabriel T Trainer,
Tsegaye Dabi,
Justin O Borevitz,
Joanne Chory,
Detlef Weigel
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ABSTRACT: Even when phenotypic differences are large between natural or domesticated strains, the underlying genetic basis is often complex, and causal genomic regions need to be identified by quantitative trait locus (QTL) mapping. Unfortunately, QTL positions typically have large confidence intervals, which can, for example, lead to one QTL being masked by another, when two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs).
We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb. The advanced intercrossing design led to expansion of the genetic map in the two populations, which contain recombination events corresponding to 50 kb/cM in an F(2) population. We used the AI-RILs to map QTL for light response and flowering time, and to identify segregation distortion in one of the AI-RIL populations due to a negative epistatic interaction between two genomic regions.
The two new AI-RIL populations, EstC and KendC, derived from crosses of Columbia (Col) to Estland (Est-1) and Kendallville (Kend-L) provide an excellent resource for high precision QTL mapping. Moreover, because they have been genotyped with over 100 common markers, they are also excellent material for comparative QTL mapping.
PLoS ONE 02/2009; 4(2):e4318. · 4.09 Impact Factor
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ABSTRACT: Growth in plants is modulated by a complex interplay between internal signals and external cues. Although traditional mutagenesis has been a successful approach for the identification of growth regulatory genes, it is likely that many genes involved in growth control remain to be discovered. In this study, we used the phenotypic variation between Bay-0 and Shahdara, two natural strains (accessions) of Arabidopsis thaliana, to map quantitative trait loci (QTL) affecting light- and temperature-regulated growth of the embryonic stem (hypocotyl). Using heterogeneous inbred families (HIFs), the gene underlying one QTL, LIGHT5, was identified as a tandem zinc knuckle/PLU3 domain encoding gene (At5g43630; TZP), which carries a premature stop codon in Bay-0. Hypocotyl growth assays in monochromatic light and microarray analysis demonstrate that TZP controls blue light associated growth in a time-of-day fashion by regulating genes involved in growth, such as peroxidase and cell wall synthesis genes. TZP expression is phased by the circadian clock and light/dark cycles to the beginning of the day, the time of maximal growth in A. thaliana in short-day conditions. Based on its domain structure and localization in the nucleus, we propose that TZP acts downstream of the circadian clock and photoreceptor signaling pathways to directly control genes responsible for growth. The identification of TZP thus provides new insight into how daily synchronization of growth pathways plays a critical role in growth regulation.
Proceedings of the National Academy of Sciences 12/2008; 105(44):17193-8. · 9.68 Impact Factor
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ABSTRACT: Quantitative approaches conducted in a single mapping population are limited by the extent of genetic variation distinguishing the parental genotypes. To overcome this limitation and allow a more complete dissection of the genetic architecture of complex traits, we built an integrated set of 15 new large Arabidopsis thaliana recombinant inbred line (RIL) populations optimized for quantitative trait loci (QTL) mapping, having Columbia as a common parent crossed to distant accessions. Here we present 5 of these populations that were validated by investigating three traits: flowering time, rosette size, and seed production as an estimate of fitness. The large number of RILs in each population (between 319 and 377 lines) and the high density of evenly spaced genetic markers scored ensure high power and precision in QTL mapping even under a minimal phenotyping framework. Moreover, the use of common markers across the different maps allows a direct comparison of the QTL detected within the different RIL sets. In addition, we show that following a selective phenotyping strategy by performing QTL analyses on genotypically chosen subsets of 164 RILs (core populations) does not impair the power of detection of QTL with phenotypic contributions >7%.
Genetics 04/2008; 178(4):2253-64. · 4.01 Impact Factor
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ABSTRACT: In compatible interactions between plants and viruses that result in systemic infection, symptom development is a major phenotypic trait. However, host determinants governing this trait are mostly unknown, and the mechanisms underlying it are still poorly understood. In a previous study on the Arabidopsis thaliana-Plum pox virus (PPV) pathosystem, we showed a large degree of variation in symptom development among susceptible accessions. In particular, Cvi-1 (Cape Verde islands) accumulates viral particules but remains symptomless, Col-0 (Columbia) sometimes shows weak symptoms compared with Ler (Landsberg erecta), which always shows severe symptoms. Genetic analyses of Col x Ler and Cvi x Ler F2 and recombinant inbred line (RIL) populations suggested that symptom development as well as viral accumulation traits are polygenic and quantitative. Three of the symptom quantitative trait loci (QTL) identified could be confirmed in near-isogenic lines, including PSI1 (PPV symptom induction 1), which was identified on the distal part of chromosome 1 in both RIL populations. With respect to viral accumulation, several factors have been detected and, interestingly, in the Col x Ler population, two out of three viral accumulation QTL colocalized with loci controlling symptom development, although correlation analysis showed weak linearity between symptom severity and virus accumulation. In addition, in the Cvi x Ler RIL population, a digenic recessive determinant controlling PPV infection was identified.
Molecular Plant-Microbe Interactions 03/2008; 21(2):198-207. · 4.43 Impact Factor
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ABSTRACT: The Arabidopsis thaliana accession Shahdara was identified as a rare naturally occurring mutant that does not liberate seed mucilage on imbibition. The defective locus was found to be allelic to the mum2-1 and mum2-2 mutants. Map-based cloning showed that MUCILAGE-MODIFIED2 (MUM2) encodes the putative beta-D-galactosidase BGAL6. Activity assays demonstrated that one of four major beta-D-galactosidase activities present in developing siliques is absent in mum2 mutants. No difference was observed in seed coat epidermal cell structure between wild-type and mutant seed; however, weakening of the outer tangential cell wall by chemical treatment resulted in the release of mucilage from mum2 seed coat epidermal cells, and the mum2 mucilage only increased slightly in volume, relative to the wild type. Consistent with the absence of beta-D-galactosidase activity in the mutant, the inner layer of mucilage contained more Gal. The allocation of polysaccharides between the inner and outer mucilage layers was also modified in mum2. Mass spectrometry showed that rhamnogalacturonan I in mutant mucilage had more branching between rhamnose and hexose residues relative to the wild type. We conclude that the MUM2/BGAL6 beta-D-galactosidase is required for maturation of rhamnogalacturonan I in seed mucilage by the removal of galactose/galactan branches, resulting in increased swelling and extrusion of the mucilage on seed hydration.
The Plant Cell 01/2008; 19(12):3990-4006. · 8.99 Impact Factor
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ABSTRACT: Light and temperature are key external factors in the control of Arabidopsis thaliana seed germination and dormancy mechanisms. Perception and response to these stimuli have to ensure that seedling emergence and growth occur at the most advantageous time for correct establishment. Analysis of over 300 Arabidopsis accessions identified 14, from 12 different geographical locations, that were able to germinate to greater than 20% at 6 degrees C in the dark. This natural variation was exploited to identify genetic loci responsible for cold-tolerant, dark germination. A quantitative trait loci approach was used on recombinant inbred line progeny of a cross between Bay-0 and Shahdara. Six distinct quantitative trait loci were identified, three of which were major loci, each responsible for 17-25% of the phenotypic variability in this trait. Parental phenotypes indicated that the majority of the cold-tolerant, dark-germination characteristics are related to light responses. Validation of the three major loci using heterogeneous inbred families confirmed the feasibility of fine mapping and cloning the genes at the quantitative trait loci responsible for cold-tolerant, dark germination.
Molecular plant 01/2008; 1(1):145-54. · 5.55 Impact Factor
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ABSTRACT: Most agronomic traits of importance, whether physiological (such as nutrient use efficiency) or developmental (such as flowering time), are controlled simultaneously by multiple genes and their interactions with the environment. Here, we show that variation in sulfate content between wild Arabidopsis thaliana accessions Bay-0 and Shahdara is controlled by a major quantitative trait locus that results in a strong interaction with nitrogen availability in the soil. Combining genetic and biochemical results and using a candidate gene approach, we have cloned the underlying gene, showing how a single-amino acid substitution in a key enzyme of the assimilatory sulfate reduction pathway, adenosine 5'-phosphosulfate reductase, is responsible for a decrease in enzyme activity, leading to sulfate accumulation in the plant. This work illustrates the potential of natural variation as a source of new alleles of known genes, which can aid in the study of gene function and metabolic pathway regulation. Our new insights on sulfate assimilation may have an impact on sulfur fertilizer use and stress defense improvement.
Nature Genetics 08/2007; 39(7):896-900. · 35.53 Impact Factor
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ABSTRACT: Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 x Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci. A major QTL for fructose content (FR3.4) and a QTL for starch content (ST3.4) were confirmed in heterogeneous inbred families. Several genes associated with carbon (C) metabolism colocalize with the identified QTL. QTLs for senescence-related traits, and for flowering time, water status, and nitrogen-related traits, previously detected with the same genetic material, colocalize with C-related QTLs. These colocalizations reflect the complex interactions of C metabolism with other physiological processes. QTL fine-mapping and cloning could thus lead soon to the identification of genes potentially involved in the control of different connected physiological processes.
Plant physiology 09/2006; 141(4):1630-43. · 6.53 Impact Factor
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ABSTRACT: Quantitative trait loci (QTL) analysis was used to identify genes underlying natural variation in primary cell wall composition in Arabidopsis (Arabidopsis thaliana). The cell walls of dark-grown seedlings of a Bay-0 x Shahdara recombinant inbred line population were analyzed using three miniaturized global cell wall fingerprinting techniques: monosaccharide composition analysis by gas chromatography, xyloglucan oligosaccharide mass profiling, and whole-wall Fourier-transform infrared microspectroscopy. Heritable variation and transgression were observed for the arabinose-rhamnose ratio, xyloglucan side-chain composition (including O-acetylation levels), and absorbance for a subset of Fourier-transform infrared wavenumbers. In total, 33 QTL, corresponding to at least 11 different loci controlling dark-grown hypocotyl length, pectin composition, and levels of xyloglucan fucosylation and O-acetylation, were identified. One major QTL, accounting for 51% of the variation in the arabinose-rhamnose ratio, affected the number of arabinan side chains presumably attached to the pectic polysaccharide rhamnogalacturonan I, paving the way to positional cloning of the first gene underlying natural variation in pectin structure. Several QTL were found to be colocalized, which may have implications for the regulation of xyloglucan metabolism. These results demonstrate the feasibility of combining fingerprinting techniques, natural variation, and quantitative genetics to gain original insight into the molecular mechanisms underlying the structure and metabolism of cell wall polysaccharides.
Plant physiology 08/2006; 141(3):1035-44. · 6.53 Impact Factor
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ABSTRACT: For the first time in Arabidopsis thaliana, this work proposes the identification of quantitative trait loci (QTLs) associated with leaf senescence and stress response symptoms such as yellowing and anthocyanin-associated redness. When Arabidopsis plants were cultivated under low nitrogen conditions, we observed that both yellowing of the old leaves of the rosette and whole rosette redness were promoted. Leaf yellowing is a senescence symptom related to chlorophyll breakdown. Redness is a symptom of anthocyanin accumulation related to whole plant ageing and nutrient limitation. In this work, Arabidopsis is used as a model system to dissect the genetic variation of these parameters by QTL mapping in the 415 recombinant inbred lines of the Bay-0xShahdara population. Fifteen new QTLs and two epistatic interactions were described in this study. The yellowing of the rosette, estimated by visual notation and image processing, was controlled by four and five QTLs, respectively. The visual estimation of redness allowed us to detect six QTLs among which the major one explained 33% of the total variation. Two main QTLs were confirmed in near-isogenic lines (heterogenous inbred family; HIF), thus confirming the relevance of the visual notation of these traits. Co-localizations between QTLs for leaf yellowing, redness and nitrogen use efficiency described in a previous publication indicate complex interconnected pathways involved in both nitrogen management and senescence- and stress-related processes. No co-localization between QTLs for leaf yellowing and redness has been found, suggesting that the two characters are genetically independent.
Plant and Cell Physiology 02/2006; 47(1):74-83. · 4.70 Impact Factor
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ABSTRACT: Arabidopsis thaliana provides a scientifically attractive and simple model for studying root growth and architecture and, subsequently, for discovering new genes involved in the control of these characters in plants. We have used the natural variation available in Arabidopsis accessions and mapped quantitative trait loci (QTLs) for primary root length (PRL), lateral root number (LRN) and density (LRD) and for total length of the lateral root system (LRL) in the Bay-0 x Shahdara population. Total phenotypic variation was very large, and despite the importance of the environmental component we were able to map 13 QTLs and one epistatic interaction between QTLs. Our results highlight the biological relevance and genetic control of lateral root density in this material. We were also able to show that variation in the extent of the lateral root system depends mainly on the growth of the existing lateral roots rather than in a change in LRN. Factors controlling lateral root growth seemed to have no major effect on primary root growth. Moreover, Shahdara QTL alleles always increased the length of the lateral roots, which may be taken as an adaptation to its very dry natural environment in Tadjikistan. A QTL for PRL was confirmed using a type of near-isogenic line called a heterogeneous inbred family (HIF), and this QTL is a candidate for further fine-mapping and cloning.
Theoretical and Applied Genetics 03/2005; 110(4):742-53. · 3.30 Impact Factor
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ABSTRACT: Genetic analysis of natural variation in ecotypes of Arabidopsis thaliana can facilitate the discovery of new genes or of allelic variants of previously identified genes controlling physiological processes in plants. We mapped quantitative trait loci (QTL) for light response in recombinant inbred lines (RILs) derived from the Columbia and Kashmir accessions via two methods: composite interval mapping and eXtreme array mapping (XAM). After measuring seedling hypocotyl lengths in blue, red, far-red, and white light, and in darkness, eight QTL were identified by composite interval mapping and five localized near photoreceptor loci. Two QTL in blue light were associated with CRY1 and CRY2, two in red light were near PHYB and PHYC, and one in far-red light localized near PHYA. The RED2 and RED5 QTL were verified in segregating lines. XAM was tested for the identification of QTL in red light with pools of RILs selected for extreme phenotypes. Thousands of single feature polymorphisms detected by differential DNA hybridized to high-density oligo-nucleotide arrays were used to estimate allele frequency differences between the pools. The RED2 QTL was identified clearly; differences exceeded a threshold of significance determined by simulations. The sensitivities of XAM to population type and size and genetic models were also determined by simulation analysis.
Genetics 07/2004; 167(2):907-17. · 4.01 Impact Factor
