Alonso-Blanco C, El-Assal SE, Coupland G, Koornneef M: Analysis of natural allelic variation at flowering time loci in the Landsberg erecta and Cape Verde Islands ecotypes of Arabidopsis thaliana. Genetics. 1998, 149 (2): 749-764.
PubMed Central
CAS
PubMed
Google Scholar
Clarke JH, Mithen R, Brown JK, Dean C: QTL analysis of flowering time in Arabidopsis thaliana. Mol Gen Genet. 1995, 248 (3): 278-286. 10.1007/BF02191594.
Article
CAS
PubMed
Google Scholar
Kowalski SP, Lan TH, Feldmann KA, Paterson AH: QTL mapping of naturally-occurring variation in flowering time of Arabidopsis thaliana. Mol Gen Genet. 1994, 245 (5): 548-555.
Article
CAS
PubMed
Google Scholar
Koornneef M, Alonso-Blanco C, Vreugdenhil D: Naturally occurring genetic variation in Arabidopsis thaliana. Annu Rev Plant Biol. 2004, 55: 141-172. 10.1146/annurev.arplant.55.031903.141605.
Article
CAS
PubMed
Google Scholar
Borevitz JO, Nordborg M: The impact of genomics on the study of natural variation in Arabidopsis. Plant Physiol. 2003, 132 (2): 718-725. 10.1104/pp.103.023549.
Article
PubMed Central
CAS
PubMed
Google Scholar
Balasubramanian S, Schwartz C, Singh A, Warthmann N, Kim MC, Maloof JN, Loudet O, Trainer GT, Dabi T, Borevitz JO: QTL mapping in new Arabidopsis thaliana advanced intercross-recombinant inbred lines. PLoS One. 2009, 4 (2): e4318-10.1371/journal.pone.0004318.
Article
PubMed Central
PubMed
Google Scholar
Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R: A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet. 2009, 5 (7): e1000551-10.1371/journal.pgen.1000551.
Article
PubMed Central
PubMed
Google Scholar
Huang X, Paulo MJ, Boer M, Effgen S, Keizer P, Koornneef M, van Eeuwijk FA: Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population. Proc Natl Acad Sci USA. 2011, 108 (11): 4488-4493. 10.1073/pnas.1100465108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Weigel D: Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol. 2012, 158 (1): 2-22. 10.1104/pp.111.189845.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brachi B, Faure N, Horton M, Flahauw E, Vazquez A, Nordborg M, Bergelson J, Cuguen J, Roux F: Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet. 2010, 6 (5): e1000940-10.1371/journal.pgen.1000940.
Article
PubMed Central
PubMed
Google Scholar
Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P: An Arabidopsis example of association mapping in structured samples. PLoS Genet. 2007, 3 (1): e4-10.1371/journal.pgen.0030004.
Article
PubMed Central
PubMed
Google Scholar
Hirschhorn JN, Daly MJ: Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005, 6 (2): 95-108.
Article
CAS
PubMed
Google Scholar
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA: Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA. 2009, 106 (23): 9362-9367. 10.1073/pnas.0903103106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT: Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010, 465 (7298): 627-631. 10.1038/nature08800.
Article
PubMed Central
CAS
PubMed
Google Scholar
Flint J, Eskin E: Genome-wide association studies in mice. Nat Rev Genet. 2012, 13 (11): 807-817. 10.1038/nrg3335.
Article
PubMed Central
CAS
PubMed
Google Scholar
Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, Li W, Guo Y, Deng L, Zhu C: Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet. 2012, 44 (1): 32-39.
Article
Google Scholar
Ranc N, Munos S, Xu J, Le Paslier MC, Chauveau A, Bounon R, Rolland S, Bouchet JP, Brunel D, Causse M: Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. G3 (Bethesda). 2012, 2 (8): 853-864. 2012.
Article
CAS
Google Scholar
Wang M, Jiang N, Jia T, Leach L, Cockram J, Comadran J, Shaw P, Waugh R, Luo Z: Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet. 2012, 124 (2): 233-246. 10.1007/s00122-011-1697-2.
Article
PubMed
Google Scholar
Olsen HG, Hayes BJ, Kent MP, Nome T, Svendsen M, Larsgard AG, Lien S: Genome-wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12. Anim Genet. 2011, 42 (5): 466-474. 10.1111/j.1365-2052.2011.02179.x.
Article
CAS
PubMed
Google Scholar
Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Vilhjalmsson BJ: Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet. 2012, 44 (2): 212-216. 10.1038/ng.1042.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chan EK, Rowe HC, Corwin JA, Joseph B, Kliebenstein DJ: Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana. PLoS Biol. 2011, 9 (8): e1001125-10.1371/journal.pbio.1001125.
Article
PubMed Central
CAS
PubMed
Google Scholar
Filiault DL, Maloof JN: A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response. PLoS Genet. 2012, 8 (3): e1002589-10.1371/journal.pgen.1002589.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chao DY, Silva A, Baxter I, Huang YS, Nordborg M, Danku J, Lahner B, Yakubova E, Salt DE: Genome-wide association studies identify heavy metal ATPase3 as the primary determinant of natural variation in leaf cadmium in Arabidopsis thaliana. PLoS Genet. 2012, 8 (9): e1002923-10.1371/journal.pgen.1002923.
Article
PubMed Central
CAS
PubMed
Google Scholar
Baxter I, Brazelton JN, Yu D, Huang YS, Lahner B, Yakubova E, Li Y, Bergelson J, Borevitz JO, Nordborg M: A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genet. 2010, 6 (11): e1001193-10.1371/journal.pgen.1001193.
Article
PubMed Central
PubMed
Google Scholar
Li Y, Huang Y, Bergelson J, Nordborg M, Borevitz JO: Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proc Natl Acad Sci USA. 2010, 107 (49): 21199-21204. 10.1073/pnas.1007431107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J, Wilczek AM: A map of local adaptation in Arabidopsis thaliana. Science. 2011, 334 (6052): 86-89. 10.1126/science.1209271.
Article
CAS
PubMed
Google Scholar
Seren U, Vilhjalmsson BJ, Horton MW, Meng D, Forai P, Huang YS, Long Q, Segura V, Nordborg M: GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis. Plant Cell. 2012, 24 (12): 4793-4805. 10.1105/tpc.112.108068.
Article
PubMed Central
CAS
PubMed
Google Scholar
Louthan AM, Kay KM: Comparing the adaptive landscape across trait types: larger QTL effect size in traits under biotic selection. BMC Evol Biol. 2011, 11: 60-10.1186/1471-2148-11-60.
Article
PubMed Central
PubMed
Google Scholar
Asimit J, Zeggini E: Rare variant association analysis methods for complex traits. Annu Rev Genet. 2010, 44: 293-308. 10.1146/annurev-genet-102209-163421.
Article
CAS
PubMed
Google Scholar
Gibson G: Rare and common variants: twenty arguments. Nat Rev Genet. 2011, 13 (2): 135-145.
Article
PubMed Central
Google Scholar
Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB: Rare variants create synthetic genome-wide associations. PLoS Biol. 2010, 8 (1): e1000294-10.1371/journal.pbio.1000294.
Article
PubMed Central
PubMed
Google Scholar
Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A: Finding the missing heritability of complex diseases. Nature. 2009, 461 (7265): 747-753. 10.1038/nature08494.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bodmer W, Bonilla C: Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet. 2008, 40 (6): 695-701. 10.1038/ng.f.136.
Article
PubMed Central
CAS
PubMed
Google Scholar
Flint J, Mackay TF: Genetic architecture of quantitative traits in mice, flies, and humans. Genome Res. 2009, 19 (5): 723-733. 10.1101/gr.086660.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, Flint-Garcia S, Rocheford TR, McMullen MD, Holland JB, Buckler ES: Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet. 2011, 43 (2): 159-162. 10.1038/ng.746.
Article
CAS
PubMed
Google Scholar
Sulem P, Gudbjartsson DF, Stacey SN, Helgason A, Rafnar T, Magnusson KP, Manolescu A, Karason A, Palsson A, Thorleifsson G: Genetic determinants of hair, eye and skin pigmentation in Europeans. Nat Genet. 2007, 39 (12): 1443-1452. 10.1038/ng.2007.13.
Article
CAS
PubMed
Google Scholar
Beleza S, Johnson NA, Candille SI, Absher DM, Coram MA, Lopes J, Campos J, Araujo II, Anderson TM, Vilhjalmsson BJ: Genetic architecture of skin and eye color in an african-European admixed population. PLoS Genet. 2013, 9 (3): e1003372-10.1371/journal.pgen.1003372.
Article
PubMed Central
CAS
PubMed
Google Scholar
Platt A, Vilhjalmsson BJ, Nordborg M: Conditions under which genome-wide association studies will be positively misleading. Genetics. 2010, 186 (3): 1045-1052. 10.1534/genetics.110.121665.
Article
PubMed Central
PubMed
Google Scholar
Segura V, Vilhjalmsson BJ, Platt A, Korte A, Seren U, Long Q, Nordborg M: An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat Genet. 2012, 44 (7): 825-830. 10.1038/ng.2314.
Article
PubMed Central
CAS
PubMed
Google Scholar
Feng T, Zhu X: Detecting rare variants. Methods Mol Biol. 2012, 850: 453-464. 10.1007/978-1-61779-555-8_24.
Article
PubMed
Google Scholar
Dai Y, Guo L, Dong J, Jiang R: Improved power by collapsing rare and common variants based on a data-adaptive forward selection strategy. BMC Proc. 2011, 5 Suppl 9: S114-
Article
PubMed
Google Scholar
Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V: A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol. 2010, 6 (10): e1000954-10.1371/journal.pcbi.1000954.
Article
PubMed Central
PubMed
Google Scholar
Li B, Leal SM: Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008, 83 (3): 311-321. 10.1016/j.ajhg.2008.06.024.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C: Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011, 43 (10): 956-963. 10.1038/ng.911.
Article
CAS
PubMed
Google Scholar
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT: Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature. 2011, 477 (7365): 419-423. 10.1038/nature10414.
Article
CAS
PubMed
Google Scholar
Long R, Meng , Huber , Farlow , Platzer , Zhang , Vilhjalmsson , Korte , Nizhynska , Voronin , Korte , Sedman , Mandakova , Lysak , Seren , Hellmann , Nordborg : Massive genomic variation and strong selection in Swedish Arabidopsis thaliana. Nat Genet. in press
Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker JR, Weigel D, Nordborg M: Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet. 2007, 39 (9): 1151-1155. 10.1038/ng2115.
Article
CAS
PubMed
Google Scholar
Jiao S, Hsu L, Hutter CM, Peters U: The use of imputed values in the meta-analysis of genome-wide association studies. Genet Epidemiol. 2011, 35 (7): 597-605. 10.1002/gepi.20608.
Article
PubMed Central
PubMed
Google Scholar
Taub MA, Schwender H, Beaty TH, Louis TA, Ruczinski I: Incorporating genotype uncertainties into the genotypic TDT for main effects and gene-environment interactions. Genet Epidemiol. 2012, 36 (3): 225-234. 10.1002/gepi.21615.
Article
PubMed Central
PubMed
Google Scholar
Vilhjalmsson BJ, Nordborg M: The nature of confounding in genome-wide association studies. Nat Rev Genet. 2012, 14 (1): 1-2.
Article
PubMed
Google Scholar
Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E: Efficient control of population structure in model organism association mapping. Genetics. 2008, 178 (3): 1709-1723. 10.1534/genetics.107.080101.
Article
PubMed Central
PubMed
Google Scholar
Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB: A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 2006, 38 (2): 203-208. 10.1038/ng1702.
Article
CAS
PubMed
Google Scholar
Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM: Mixed linear model approach adapted for genome-wide association studies. Nat Genet. 2010, 42 (4): 355-360. 10.1038/ng.546.
Article
PubMed Central
CAS
PubMed
Google Scholar
Listgarten J, Lippert C, Kadie CM, Davidson RI, Eskin E, Heckerman D: Improved linear mixed models for genome-wide association studies. Nat Methods. 2012, 9 (6): 525-526. 10.1038/nmeth.2037.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wray NR, Purcell SM, Visscher PM: Synthetic associations created by rare variants do not explain most GWAS results. PLoS Biol. 2011, 9 (1): e1000579-10.1371/journal.pbio.1000579.
Article
PubMed Central
CAS
PubMed
Google Scholar
Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P: Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet. 2009, 5 (6): e1000530-10.1371/journal.pgen.1000530.
Article
PubMed Central
PubMed
Google Scholar
Bergelson J, Roux F: Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat Rev Genet. 2010, 11 (12): 867-879. 10.1038/nrg2896.
Article
CAS
PubMed
Google Scholar
Ehrenreich IM, Stafford PA, Purugganan MD: The genetic architecture of shoot branching in Arabidopsis thaliana: a comparative assessment of candidate gene associations vs. quantitative trait locus mapping. Genetics. 2007, 176 (2): 1223-1236.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cordell HJ: Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet. 2009, 10 (6): 392-404.
Article
PubMed Central
CAS
PubMed
Google Scholar
Marchini J, Donnelly P, Cardon LR: Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet. 2005, 37 (4): 413-417. 10.1038/ng1537.
Article
CAS
PubMed
Google Scholar
Kam-Thong T, Putz B, Karbalai N, Muller-Myhsok B, Borgwardt K: Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs. Bioinformatics. 2011, 27 (13): i214-221. 10.1093/bioinformatics/btr218.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hemani G, Theocharidis A, Wei W, Haley C: EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards. Bioinformatics. 2011, 27 (11): 1462-1465. 10.1093/bioinformatics/btr172.
Article
CAS
PubMed
Google Scholar
Turner SD, Berg RL, Linneman JG, Peissig PL, Crawford DC, Denny JC, Roden DM, McCarty CA, Ritchie MD, Wilke RA: Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks. PLoS One. 2011, 6 (5): e19586-10.1371/journal.pone.0019586.
Article
PubMed Central
CAS
PubMed
Google Scholar
Oh S, Lee J, Kwon MS, Weir B, Ha K, Park T: A novel method to identify high order gene-gene interactions in genome-wide association studies: gene-based MDR. 13 Suppl 9. 2012, 13 Suppl: S5-
Google Scholar
Consortium AIM: Evidence for network evolution in an Arabidopsis interactome map. Science. 2011, 333 (6042): 601-607.
Article
Google Scholar
Thomas D: Gene–environment-wide association studies: emerging approaches. Nat Rev Genet. 2010, 11 (4): 259-272. 10.1038/nrg2764.
Article
PubMed Central
CAS
PubMed
Google Scholar
Korte A, Vilhjalmsson BJ, Segura V, Platt A, Long Q, Nordborg M: A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nat Genet. 2012, 44 (9): 1066-1071. 10.1038/ng.2376.
Article
PubMed Central
CAS
PubMed
Google Scholar
Deary IJ, Yang J, Davies G, Harris SE, Tenesa A, Liewald D, Luciano M, Lopez LM, Gow AJ, Corley J: Genetic contributions to stability and change in intelligence from childhood to old age. Nature. 2012, 482 (7384): 212-215.
CAS
PubMed
Google Scholar
Lacaze X, Hayes PM, Korol A: Genetics of phenotypic plasticity: QTL analysis in barley, Hordeum vulgare. Heredity (Edinb). 2009, 102 (2): 163-173. 10.1038/hdy.2008.76.
Article
CAS
Google Scholar
Pettersson ME, Nelson RM, Carlborg O: Selection on variance-controlling genes: adaptability or stability. Evolution. 2012, 66 (12): 3945-3949. 10.1111/j.1558-5646.2012.01753.x.
Article
PubMed
Google Scholar
Benjamin DJ, Cesarini D, Chabris CF, Glaeser EL, Laibson DI, Guethnason V, Harris TB, Launer LJ, Purcell S, Smith AV: The Promises and Pitfalls of Genoeconomics*. Annu Rev Econom. 2012, 4: 627-662. 10.1146/annurev-economics-080511-110939.
Article
PubMed Central
PubMed
Google Scholar
Hunter DJ: Gene-environment interactions in human diseases. Nat Rev Genet. 2005, 6 (4): 287-298.
Article
CAS
PubMed
Google Scholar
Phillips PC: Epistasis–the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet. 2008, 9 (11): 855-867. 10.1038/nrg2452.
Article
PubMed Central
CAS
PubMed
Google Scholar
Visscher PM, Hill WG, Wray NR: Heritability in the genomics era–concepts and misconceptions. Nat Rev Genet. 2008, 9 (4): 255-266.
Article
CAS
PubMed
Google Scholar