From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development
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Slate, 2010, Gene mapping in the wild with SNPs: guidelines and future directions (vol 136, pg 97, 2009), Genetica, 138, 467, 10.1007/s10709-010-9445-0
Manolio, 2009, Finding the missing heritability of complex diseases, Nature, 461, 747, 10.1038/nature08494
Robinson, 2014, Explaining additional genetic variation in complex traits, Trends Genet, 30, 124, 10.1016/j.tig.2014.02.003
Zhang, 2012, Progress of genome wide association study in domestic animals, J Anim Sci Biotechnol, 3
Ingvarsson, 2011, Association genetics of complex traits in plants, New Phytol, 189, 909, 10.1111/j.1469-8137.2010.03593.x
Rafalski, 2010, Association genetics in crop improvement, Curr Opin Plant Biol, 13, 174, 10.1016/j.pbi.2009.12.004
Weigel, 2012, Natural variation in Arabidopsis: from molecular genetics to ecological genomics, Plant Physiol, 158, 2, 10.1104/pp.111.189845
Bergelson, 2010, Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana, Nat Rev Genet, 11, 867, 10.1038/nrg2896
Atwell, 2010, Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines, Nature, 465, 627, 10.1038/nature08800
Aranzana, 2005, Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes, PLoS Genet, 1, 531, 10.1371/journal.pgen.0010060
Brachi, 2010, Linkage and association mapping of Arabidopsis thaliana flowering time in nature, PLoS Genet, 6
Li, 2010, Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana, Proc Natl Acad Sci U S A, 107, 21199, 10.1073/pnas.1007431107
Brachi, 2013, Investigation of the geographical scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana, Mol Ecol, 22, 4222, 10.1111/mec.12396
Brachi, 2013, Genome-wide association mapping of flowering time in Arabidopsis thaliana in nature: genetics for underlying components and reaction norms across two successive years, Acta Bot Gallica, 160, 205, 10.1080/12538078.2013.807302
Li, 2014, Genetic variation for life history sensitivity to seasonal warming in Arabidopsis thaliana, Genetics, 196, 569, 10.1534/genetics.113.157628
Hung, 2012, ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize, Proc Natl Acad Sci U S A, 109, E1913, 10.1073/pnas.1203189109
Yang, 2013, CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize, Proc Natl Acad Sci U S A, 110, 16969, 10.1073/pnas.1310949110
Putterill, 1995, The constants gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc-finger transcription factors, Cell, 80, 847, 10.1016/0092-8674(95)90288-0
Hao, 2011, Identification of functional genetic variations underlying drought tolerance in maize using SNP markers, J Integr Plant Biol, 53, 641, 10.1111/j.1744-7909.2011.01051.x
Van Inghelandt, 2012, Genome-wide association mapping of flowering time and northern corn leaf blight (Setosphaeria turcica) resistance in a vast commercial maize germplasm set, BMC Plant Biol, 12
Bouchet, 2013, Adaptation of maize to temperate climates: mid-density genome-wide association genetics and diversity patterns reveal key genomic regions, with a major contribution of the Vgt2 (ZCN8) locus, PLoS ONE, 8
Romay, 2013, Comprehensive genotyping of the USA national maize inbred seed bank, Genome Biol, 14
Xue, 2013, Genome-wide association analysis for nine agronomic traits in maize under well-watered and water-stressed conditions, Theor Appl Genet, 126, 2587, 10.1007/s00122-013-2158-x
Zhao, 2011, Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa, Nat Commun, 2
Huang, 2012, Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm, Nat Genet, 44, 32, 10.1038/ng.1018
Zanke, 2014, Genetic architecture of main effect QTL for heading date in European winter wheat, Front Plant Sci, 5
Le Gouis, 2012, Genome-wide association analysis to identify chromosomal regions determining components of earliness in wheat, Theor Appl Genet, 124, 597, 10.1007/s00122-011-1732-3
Lorenz, 2010, Performance of single nucleotide polymorphisms versus haplotypes for genome-wide association analysis in barley, PLoS ONE, 5
Cockram, 2010, Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome, Proc Natl Acad Sci U S A, 107, 21611, 10.1073/pnas.1010179107
Pasam, 2012, Genome-wide association studies for agronomical traits in a world wide spring barley collection, BMC Plant Biol, 12
Wang, 2012, Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm, Theor Appl Genet, 124, 111, 10.1007/s00122-011-1691-8
Wang, 2012, Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars, Theor Appl Genet, 124, 233, 10.1007/s00122-011-1697-2
Berger, 2013, Marker-trait associations in Virginia Tech winter barley identified using genome-wide mapping, Theor Appl Genet, 126, 693, 10.1007/s00122-012-2011-7
Munoz-Amatriain, 2014, The USDA barley core collection: genetic diversity. Population structure, and potential for genome-wide association studies, PLoS ONE, 9
Saidou, 2014, Association mapping, patterns of linkage disequilibrium and selection in the vicinity of the PHYTOCHROME C gene in pearl millet, Theor Appl Genet, 127, 19, 10.1007/s00122-013-2197-3
Jia, 2013, A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica), Nat Genet, 45, 957, 10.1038/ng.2673
Galeano, 2012, Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean, BMC Genet, 13
Stanton-Geddes, 2013, Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatula, PLoS ONE, 8
Li, 2014, Genome-wide association study dissects the genetic architecture of seed weight and seed quality in rapeseed (Brassica napus L.), DNA Res, 10.1093/dnares/dsu002
Angelovici, 2013, Genome-wide analysis of branched-chain amino acid levels in Arabidopsis seeds, Plant Cell, 25, 4827, 10.1105/tpc.113.119370
Gonzalez-Jorge, 2013, CAROTENOID CLEAVAGE DIOXYGENASE4 is a negative regulator of beta-carotene content in Arabidopsis seeds, Plant Cell, 25, 4812, 10.1105/tpc.113.119677
Yano, 2013, Combining association mapping and transcriptomics identify HD2B histone deacetylase as a genetic factor associated with seed dormancy in Arabidopsis thaliana, Plant J, 74, 815, 10.1111/tpj.12167
Fournier-Level, 2011, A map of local adaptation in Arabidopsis thaliana, Science, 334, 86, 10.1126/science.1209271
Huang, 2013, Genome-wide association analysis of ten chilling tolerance indices at the germination and seedling stages in maize, J Integr Plant Biol, 55, 735, 10.1111/jipb.12051
Chen, 2014, A high-density SNP genotyping array for rice biology and molecular breeding, Mol Plant, 7, 541, 10.1093/mp/sst135
Yang, 2014, Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice, Nat Commun, 5
Cuesta-Marcos, 2010, Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure, BMC Genomics, 11
Newell, 2012, Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin, Theor Appl Genet, 125, 1687, 10.1007/s00122-012-1945-0
Hwang, 2014, A genome-wide association study of seed protein and oil content in soybean, BMC Genomics, 15
Lucas, 2013, Association studies and legume synteny reveal haplotypes determining seed size in Vigna unguiculata, Front Plant Sci, 4, 1, 10.3389/fpls.2013.00095
Muchero, 2013, Genetic architecture of delayed senescence, biomass, and grain yield under drought stress in cowpea, PLoS ONE, 8
Ranc, 2012, Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme, G3-Genes Genom Genet, 2, 853, 10.1534/g3.112.002667
Shirasawa, 2013, Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato, DNA Res, 20, 593, 10.1093/dnares/dst033
Sauvage, 2014, Genome-wide association in tomato reveals 44 candidate loci for fruit metabolic traits, Plant Physiol, 165, 1120, 10.1104/pp.114.241521
Parchman, 2012, Genome-wide association genetics of an adaptive trait in lodgepole pine, Mol Ecol, 21, 2991, 10.1111/j.1365-294X.2012.05513.x
Budde, 2014, In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime pine (Pinus pinaster), New Phytol, 201, 230, 10.1111/nph.12483
Muchero, 2009, Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L.) Walp.], Theor Appl Genet, 118, 849, 10.1007/s00122-008-0944-7
Saliba-Colombani, 2001, Genetic analysis of organoleptic quality in fresh market tomato. 1. Mapping QTLs for physical and chemical traits, Theor Appl Genet, 102, 259, 10.1007/s001220051643
Tian, 2011, Genome-wide association study of leaf architecture in the maize nested association mapping population, Nat Genet, 43, 159, 10.1038/ng.746
Chitwood, 2014, A modern ampelography: a genetic basis for leaf shape and venation patterning in grape, Plant Physiol, 164, 259, 10.1104/pp.113.229708
Slovak, 2014, A scalable open-source pipeline for large-scale root phenotyping of Arabidopsis, Plant Cell, 10.1105/tpc.114.124032
Gifford, 2013, Plasticity regulators modulate specific root traits in discrete nitrogen environments, PLoS Genet, 9
Rosas, 2013, Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture, Proc Natl Acad Sci U S A, 110, 15133, 10.1073/pnas.1305883110
Meijon, 2014, Genome-wide association study using cellular traits identifies a new regulator of root development in Arabidopsis, Nat Genet, 46, 77, 10.1038/ng.2824
Korte, 2013, The advantages and limitations of trait analysis with GWAS: a review, Plant Methods, 9
Kang, 2008, Efficient control of population structure in model organism association mapping, Genetics, 178, 1709, 10.1534/genetics.107.080101
Seren, 2012, GWAPP: a web application for genome-wide association mapping in Arabidopsis, Plant Cell, 24, 4793, 10.1105/tpc.112.108068
Bradbury, 2007, TASSEL: software for association mapping of complex traits in diverse samples, Bioinformatics, 23, 2633, 10.1093/bioinformatics/btm308
Benjamini, 2001, The control of the false discovery rate in multiple testing under dependency, Ann Stat, 29, 1165, 10.1214/aos/1013699998
Nordborg, 2002, The extent of linkage disequilibrium in Arabidopsis thaliana, Nat Genet, 30, 190, 10.1038/ng813
Sorkheh, 2008, Linkage disequilibrium, genetic association mapping and gene localization in crop plants, Genet Mol Biol, 31, 805, 10.1590/S1415-47572008000500001
Bush, 2012, Chapter 11: genome-wide association studies, PLoS Comput Biol, 8
Weigel, 2005, Natural variation in Arabidopsis. How do we find the causal genes?, Plant Physiol, 138, 567, 10.1104/pp.104.900157
Gazzarrini, 2003, Cross-talk in plant hormone signalling: what Arabidopsis mutants are telling us, Ann Bot Lond, 91, 605, 10.1093/aob/mcg064
Todesco, 2010, Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana, Nature, 465, 632, 10.1038/nature09083
DeRose-Wilson, 2011, Mapping salinity tolerance during Arabidopsis thaliana germination and seedling growth, PLoS ONE, 6
Nemri, 2010, Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping, Proc Natl Acad Sci U S A, 107, 10302, 10.1073/pnas.0913160107
Pagny, 2012, Family-based linkage and association mapping reveals novel genes affecting Plum pox virus infection in Arabidopsis thaliana, New Phytol, 196, 873, 10.1111/j.1469-8137.2012.04289.x
Huard-Chauveau, 2013, An atypical kinase under balancing selection confers broad-spectrum disease resistance in Arabidopsis, PLoS Genet, 9
Chan, 2010, Understanding the evolution of defense metabolites in Arabidopsis thaliana using genome-wide association mapping, Genetics, 185, 991, 10.1534/genetics.109.108522
Chan, 2010, The complex genetic architecture of the metabolome, PLoS Genet, 6
Baxter, 2010, A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1, PLoS Genet, 6
Chan, 2011, Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana, PLoS Biol, 9
Chao, 2012, Genome-wide association studies identify Heavy Metal ATPase3 as the primary determinant of natural variation in leaf cadmium in Arabidopsis thaliana, PLoS Genet, 8
Verslues, 2014, Genome-wide association mapping combined with reverse genetics identifies new effectors of low water potential-induced proline accumulation in Arabidopsis, Plant Physiol, 164, 144, 10.1104/pp.113.224014
Filiault, 2012, A genome-wide association study identifies variants underlying the Arabidopsis thaliana shade avoidance response, PLoS Genet, 8
Long, 2013, Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden, Nat Genet, 45, 884, 10.1038/ng.2678
Weng, 2011, Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines, PLoS ONE, 6
Strigens, 2013, Association mapping for chilling tolerance in elite flint and dent maize inbred lines evaluated in growth chamber and field experiments, Plant Cell Environ, 36, 1871, 10.1111/pce.12096
Kump, 2011, Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population, Nat Genet, 43, 163, 10.1038/ng.747
Weng, 2012, Molecular mapping of the major resistance quantitative trait locus qHS2.09 with simple sequence repeat and single nucleotide polymorphism markers in maize, Phytopathology, 102, 692, 10.1094/PHYTO-12-11-0330
Zila, 2013, A genome-wide association study reveals genes associated with Fusarium ear rot resistance in a maize core diversity panel, G3-Genes Genom Genet, 3, 2095, 10.1534/g3.113.007328
Olukolu, 2013, A connected set of genes associated with programmed cell death implicated in controlling the hypersensitive response in maize, Genetics, 193, 609, 10.1534/genetics.112.147595
Liu, 2014, Genome-wide association study of resistance to rough dwarf disease in maize, Eur J Plant Pathol, 139, 205, 10.1007/s10658-014-0383-z
Riedelsheimer, 2012, Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize, Proc Natl Acad Sci U S A, 109, 8872, 10.1073/pnas.1120813109
Li, 2012, Genome-wide association studies identified three independent polymorphisms associated with alpha-tocopherol content in maize kernels, PLoS ONE, 7
Lipka, 2013, Genome-wide association study and pathway-level analysis of tocochromanol levels in maize grain, G3-Genes Genom Genet, 3, 1287, 10.1534/g3.113.006148
Waugh, 2010, Whole-genome association mapping in elite inbred crop varieties, Genome, 53, 967, 10.1139/G10-078
Ramsay, 2011, INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1, Nat Genet, 43, 169, 10.1038/ng.745
Long, 2013, Association mapping of salt tolerance in barley (Hordeum vulgare L.), Theor Appl Genet, 126, 2335, 10.1007/s00122-013-2139-0
Massman, 2011, Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm, Mol Breeding, 27, 439, 10.1007/s11032-010-9442-0
Visioni, 2013, Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.), BMC Genomics, 14
Shu, 2012, Genome-wide association study of resistant starch (RS) phenotypes in a barley variety collection, J Agr Food Chem, 60, 10302, 10.1021/jf3031875
Shu, 2014, Quantification of amylose, amylopectin and β-glucan in the search for genes controlling the three major quality traits in barley using genome-wide association studies, Front Plant Sci, 5
Famoso, 2011, Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping, PLoS Genet, 7
Huang, 2012, A map of rice genome variation reveals the origin of cultivated rice, Nature, 490, 497, 10.1038/nature11532
Porth, 2013, Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms, New Phytol, 200, 710, 10.1111/nph.12422
La Mantia, 2013, Association analysis identifies Melampsora xcolumbiana poplar leaf rust resistance SNPs, PLoS ONE, 8
Morris, 2013, Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits, G3-Genes Genom Genet, 3, 2085, 10.1534/g3.113.008417
Wurschum, 2011, Genome-wide association mapping of agronomic traits in sugar beet, Theor Appl Genet, 123, 1121, 10.1007/s00122-011-1653-1
Zhang, 2014, The acid phosphatase-encoding gene GmACP1 contributes to soybean tolerance to low-phosphorus stress, PLoS Genet, 10
Uitdewilligen JGAML, 2013, A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato, PLoS ONE, 8