Association Mapping in Crop Plants

Advances in Genetics - Tập 85 - Trang 109-147 - 2014
Pushpendra K. Gupta1, Pawan L. Kulwal2, Vandana Jaiswal1
1Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, UP, India
2State Level Biotechnology Centre, Mahatma Phule Agricultural University, Rahuri, MS, India

Tài liệu tham khảo

Amin, 2007, A genomic background based method for association analysis in related individuals, PLoS One, 2, e1274, 10.1371/journal.pone.0001274 Anderson, 2011, Synthetic associations are unlikely to account for many common disease genome-wide association signals, PLoS Biology, 9, e1000580, 10.1371/journal.pbio.1000580 Asimit, 2010, Rare variant association analysis methods for complex traits, Annual Review of Genetics, 44, 293, 10.1146/annurev-genet-102209-163421 Aulchenko, 2007, Genome-wide rapid association using mixed model and regression: A fast and simple method for genome-wide pedigree-based quantitative trait loci association analysis, Genetics, 177, 577, 10.1534/genetics.107.075614 Balding, 2006, A tutorial on statistical methods for population association studies, Nature Reviews Genetics, 7, 781, 10.1038/nrg1916 Bancroft, 2013, Association genetics and more from crop transcriptome sequences, ISB News Report Bancroft, 2011, Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing, Nature Biotechnology, 29, 762, 10.1038/nbt.1926 Bandillo, 2013, Multi-parent advanced generation inter-cross (MAGIC) populations in rice: Progress and potential for genetics research and breeding, Rice, 6, 11, 10.1186/1939-8433-6-11 Bansal, 2010, Statistical analysis strategies for association studies involving rare variants, Nature Reviews Genetics, 11, 773, 10.1038/nrg2867 Beaumont, 2004, The Bayesian revolution in genetics, Nature Reviews Genetics, 5, 251, 10.1038/nrg1318 Benjamini, 1995, Controlling the false discovery rate: A practical and powerful approach to multiple testing, Journal of Royal Statistical Society, 57, 289 Benjamini, 2006, Adaptive linear step-up procedures that control the false discovery rate, Biometrika, 93, 491, 10.1093/biomet/93.3.491 Bentsink, 2010, Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways, Proceedings of the National Academy of Sciences USA, 107, 4264, 10.1073/pnas.1000410107 Bernardo, 1993, Estimation of coefficient of coancestry using molecular markers in maize, Theoretical and Applied Genetics, 85, 1055, 10.1007/BF00215047 Bernardo, 2008, Molecular markers and selection for complex traits in plants: Learning from the last 20 years, Crop Science, 48, 1649, 10.2135/cropsci2008.03.0131 Bernardo, 2013, Genome-wide markers for controlling background variation in association mapping, The Plant Genome, 6, 1, 10.3835/plantgenome2012.11.0028 Blanc, 2006, Connected populations for detecting quantitative trait loci and testing for epistasis: An application in maize, Theoretical and Applied Genetics, 113, 206, 10.1007/s00122-006-0287-1 Blott, 2003, Molecular dissection of a quantitative trait locus: A phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition, Genetics, 163, 253, 10.1093/genetics/163.1.253 Bonferroni, 1936, Teoria statisti ca delle classi e calcolo delle probabilità, Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze, 8, 3 Brachi, 2010, Linkage and association mapping of Arabidopsis thaliana flowering time in nature, PLoS Genetics, 6, 1, 10.1371/journal.pgen.1000940 Brachi, 2011, Genome-wide association studies in plants: The missing heritability is in the field, Genome Biology, 12, 232, 10.1186/gb-2011-12-10-232 Bradbury, 2007, TASSEL: Software for association mapping of complex traits in diverse samples, Bioinformatics, 23, 2633, 10.1093/bioinformatics/btm308 Breseghello, 2006, Association analysis as a strategy for improvement of quantitative traits in plants, Crop Science, 46, 1323, 10.2135/cropsci2005.09-0305 Buckler, 2009, The genetic architecture of maize flowering time, Science, 325, 714, 10.1126/science.1174276 Cantor, 2010, Prioritizing GWAS results: A review of statistical methods and recommendations for their application, American Journal of Human Genetics, 86, 6, 10.1016/j.ajhg.2009.11.017 Cavanagh, 2008, From mutations to MAGIC: Resources for gene discovery, validation and delivery in crop plants, Current Opinion in Plant Biology, 11, 215, 10.1016/j.pbi.2008.01.002 Chan, 2010, Understanding the evolution of defense metabolites in Arabidopsis thaliana using genome-wide association mapping, Genetics, 185, 991, 10.1534/genetics.109.108522 Churchill, 2004, The collaborative cross, a community resource for the genetic analysis of complex traits, Nature Genetics, 36, 1133, 10.1038/ng1104-1133 Cook, 2012, Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels, Plant Physiology, 158, 824, 10.1104/pp.111.185033 Cordell, 2002, Epistasis: What it means, what it does not mean, and statistical methods to detect it in humans, Human Molecular Genetics, 11, 2463, 10.1093/hmg/11.20.2463 Das, 2011, A dynamic model for genome-wide association studies, Human Genetics, 129, 629, 10.1007/s00439-011-0960-6 Das, 2012, A Bayesian framework for functional mapping through joint modeling of longitudinal and time-to-event data, International Journal of Plant Genomics, 10.1155/2012/680634 de Bakker, 2008, Practical aspects of imputation-driven meta-analysis of genome-wide association studies, Human Molecular Genetics, 17, R122, 10.1093/hmg/ddn288 Devlin, 1999, Genomic control for association studies, Biometrics, 55, 997, 10.1111/j.0006-341X.1999.00997.x Dickson, 2010, Rare variants create synthetic genome-wide associations, PLoS Biology, 8, e1000294, 10.1371/journal.pbio.1000294 Doerge, 2002, Mapping and analysis of quantitative trait loci in experimental populations, Nature Reviews Genetics, 3, 43, 10.1038/nrg703 Edwards, 2013, Sequence based DNA markers and genotyping for cereal genomics and breeding, 57 Ehrenreich, 2009, Candidate gene association mapping of Arabidopsis flowering time, Genetics, 183, 325, 10.1534/genetics.109.105189 Eichler, 2010, Missing heritability and strategies for finding the underlying causes of complex disease, Nature Reviews Genetics, 11, 446, 10.1038/nrg2809 Elshire, 2011, A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species, PLoS One, 6, e19379, 10.1371/journal.pone.0019379 Evangelou, 2013, Meta-analysis methods for genome-wide association studies and beyond, Nature Reviews Genetics, 14, 379, 10.1038/nrg3472 Fernando, 2013, Bayesian methods applied to GWAS, Vol. 1019, 237 Gibson, 2012, Rare and common variants: Twenty arguments, Nature Reviews Genetics, 13, 135, 10.1038/nrg3118 Guo, 2013, Family-based association mapping in crop species, Theoretical and Applied Genetics, 126, 1419, 10.1007/s00122-013-2100-2 Han, 2012, Interpreting meta-analyses of genome-wide association studies, PLoS Genetics, 8, e1002555, 10.1371/journal.pgen.1002555 Hao, 2012, Association mapping and haplotype analysis of a 3.1-Mb genomic region involved in Fusarium head blight resistance on wheat chromosome 3BS, PLoS One, 7, e46444, 10.1371/journal.pone.0046444 Harper, 2012, Associative transcriptomics of traits in the polyploid crop species, Brassica napus, Nature Biotechnology, 30, 798, 10.1038/nbt.2302 He, 2010, Mapping genes for plant structure, development and evolution: Functional mapping meets ontology, Trends in Genetics, 26, 39, 10.1016/j.tig.2009.11.004 Hoggart, 2008, Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies, PLoS Genetics, 4, e1000130, 10.1371/journal.pgen.1000130 Holm, 1979, A simple sequentially rejective multiple test procedure, Scandinavian Journal of Statistics, 6, 65 Huang, 2010, Genome-wide association studies of 14 agronomic traits in rice landraces, Nature Genetics, 42, 961, 10.1038/ng.695 Huang, 2012, A multiparent advanced generation inter-cross population for genetic analysis in wheat, Plant Biotechnology Journal, 10, 826, 10.1111/j.1467-7652.2012.00702.x Huff, 2012, Crohn’s disease and genetic hitchhiking at IBD5, Molecular Biology and Evolution, 29, 101, 10.1093/molbev/msr151 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 Biology, 12, 56, 10.1186/1471-2229-12-56 Iwata, 2007, Bayesian association mapping of multiple quantitative trait loci and its application to the analysis of genetic variation among Oryza sativa L. germplasms, Theoretical and Applied Genetics, 114, 1437, 10.1007/s00122-007-0529-x Jannink, 2003, Estimating allelic number and identity in state of QTLs in interconnected families, Genetical Research, 81, 133, 10.1017/S0016672303006153 Jannink, 2001, Using complex plant pedigrees to map valuable genes, Trends in Plant Science, 6, 337, 10.1016/S1360-1385(01)02017-9 Kang, 2008, Efficient control of population structure in model organism association mapping, Genetics, 178, 1709, 10.1534/genetics.107.080101 Kang, 2010, Variance component model to account for sample structure in genome-wide association studies, Nature Genetics, 42, 348, 10.1038/ng.548 Kent, 2011, Rare variants, common markers: Synthetic association and beyond, Genetic Epidemiology, 35, S80, 10.1002/gepi.20655 Korte, 2012, A mixed-model approach for genome-wide association studies of correlated traits in structured populations, Nature Genetics, 44, 1066, 10.1038/ng.2376 Kover, 2009, A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana, PLoS Genetics, 5, e1000551, 10.1371/journal.pgen.1000551 Kulwal, 2012, Association mapping for pre-harvest sprouting resistance in white winter wheat, Theoretical and Applied Genetics, 125, 793, 10.1007/s00122-012-1872-0 Kump, 2011, Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population, Nature Genetics, 43, 163, 10.1038/ng.747 Larsson, 2013, Lessons from Dwarf8 on the strengths and weaknesses of structured association mapping, PLoS Genetics, 9, e1003246, 10.1371/journal.pgen.1003246 Lee, 2002, Expanding the genetic map of maize with the intermated B73×Mo17 (IBM) population, Plant Molecular Biology, 48, 453, 10.1023/A:1014893521186 Li, 2011, Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms, BMC Plant Biology, 11, 146, 10.1186/1471-2229-11-146 Li, 2010, To identify associations with rare variants, just WHaIT: Weighted haplotype and imputation-based tests, American Journal of Human Genetics, 87, 728, 10.1016/j.ajhg.2010.10.014 Li, 2006, Mach 1.0: Rapid haplotype reconstruction and missing genotype inference, American Journal of Human Genetics, 79, S2290 Li, 2011, Detecting epistasis effects in genome-wide association studies based on ensemble approaches, Bioinformatics, 27, 222, 10.1093/bioinformatics/btr227 Li, 2010, Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana, Proceedings of the National Academy of Sciences USA, 107, 21199, 10.1073/pnas.1007431107 Li, 2008, Methods for detecting associations with rare variants for common diseases: Application to analysis of sequence data, American Journal of Human Genetics, 83, 311, 10.1016/j.ajhg.2008.06.024 Lipka, 2013, Genome-wide association study and pathway-level analysis of tocochromanol level in maize grain, Genes Genome Genetics, 3, 1287, 10.1534/g3.113.006148 Lipka, 2012, GAPIT: Genome Association and Prediction Integrated Tool, Bioinformatics, 28, 2397, 10.1093/bioinformatics/bts444 Lippert, 2011, FaST linear mixed models for genome-wide association studies, Nature Methods, 8, 833, 10.1038/nmeth.1681 Liu, 2011, Association mapping in an elite maize breeding population, Theoretical and Applied Genetics, 123, 847, 10.1007/s00122-011-1631-7 Liu, 2013 Liu, 2008, Haplotype-association analysis, Advances in Genetics, 60, 335, 10.1016/S0065-2660(07)00414-2 Lu, 2011, Epistatic association mapping in homozygous crop cultivars, PLoS One, 6, e17773, 10.1371/journal.pone.0017773 Lu, 2010, Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize, Proceedings of the National Academy of Sciences USA, 107, 19585, 10.1073/pnas.1006105107 Lynch, 1988, Estimation of relatedness by DNA fingerprinting, Molecular Biology and Evolution, 5, 584 Mackay, 2009, The genetics of quantitative traits: Challenges and prospects, Nature Reviews Genetics, 10, 565, 10.1038/nrg2612 Makowsky, 2011, Beyond missing heritability: Prediction of complex traits, PLoS Genetics, 7, e1002051, 10.1371/journal.pgen.1002051 Manolio, 2009, Finding the missing heritability of complex diseases, Nature, 461, 747, 10.1038/nature08494 Marchini, 2010, Genotype imputation for genome-wide association studies, Nature Reviews Genetics, 11, 499, 10.1038/nrg2796 Marttinen, 2010, Efficient Bayesian approach for multilocus association mapping including gene-gene interactions, BMC Bioinformatics, 11, 443, 10.1186/1471-2105-11-443 McKinney, 2012, Six degrees of epistasis: Statistical network models for GWAS, Frontiers in Genetics, 2, 1, 10.3389/fgene.2011.00109 Meuwissen, 2001, Prediction of total genetic value using genome-wide dense marker maps, Genetics, 157, 1819, 10.1093/genetics/157.4.1819 Meuwissen, 2002, Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping, Genetics, 161, 373, 10.1093/genetics/161.1.373 Moonesinghe, 2008, Required sample size and nonreplicability thresholds for heterogeneous genetic associations, Proceedings of the National Academy of Sciences USA, 105, 617, 10.1073/pnas.0705554105 Morris, 2013, Population genomic and genome-wide association studies of agroclimatic traits in sorghum, Proceedings of the National Academy of Sciences USA, 110, 453, 10.1073/pnas.1215985110 Mott, 2002, Simultaneous detection and fine mapping of quantitative trait loci in mice using heterogeneous stocks, Genetics, 160, 1609, 10.1093/genetics/160.4.1609 Mott, 2000, A method for fine mapping quantitative trait loci in outbred animal stocks, Proceedings of the National Academy of Sciences USA, 97, 12649, 10.1073/pnas.230304397 Myles, 2009, Association mapping: Critical considerations shift from genotyping to experimental design, The Plant Cell, 21, 2194, 10.1105/tpc.109.068437 Nelson, 2012, An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people, Science, 337, 100, 10.1126/science.1217876 Noble, 2009, How does multiple testing correction work?, Nature Biotechnology, 27, 1135, 10.1038/nbt1209-1135 Ott, 2011, Family-based designs for genome-wide association studies, Nature Reviews Genetics, 12, 465, 10.1038/nrg2989 Panoutsopoulou, 2013, In search of low-frequency and rare variants affecting complex traits, Human Molecular Genetics, 22, R16, 10.1093/hmg/ddt376 Parisseaux, 2004, In silico mapping of quantitative trait loci in maize, Theoretical and Applied Genetics, 109, 508, 10.1007/s00122-004-1666-0 Paulo, 2008, A mixed model QTL analysis for a complex cross population consisting of a half diallel of two-way hybrids in Arabidopsis thaliana: Analysis of simulated data, Euphytica, 161, 107, 10.1007/s10681-008-9665-x Poland, 2011, Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize, Proceedings of the National Academy of Sciences USA, 108, 6893, 10.1073/pnas.1010894108 Poland, 2012, Genotyping-by-sequencing for plant breeding and genetics, The Plant Genome, 5, 92, 10.3835/plantgenome2012.05.0005 Price, 2006, Principal components analysis corrects for stratification in genome-wide association studies, Nature Genetics, 38, 904, 10.1038/ng1847 Pritchard, 2000, Inference of population structure using multilocus genotype data, Genetics, 155, 945, 10.1093/genetics/155.2.945 Qian, 2005, Comparison of false discovery rate methods in identifying genes with differential expression, Genomics, 86, 495, 10.1016/j.ygeno.2005.06.007 Rakitsch, 2013, A lasso multi-marker mixed model for association mapping with population structure correction, Bioinformatics, 29, 206, 10.1093/bioinformatics/bts669 Rebai, 1993, Power of tests for QTL detection using replicated progenies derived from a diallel cross, Theoretical and Applied Genetics, 86, 1014, 10.1007/BF00211055 Rebai, 2000, More about quantitative trait locus mapping with diallel designs, Genetical Research, 75, 243, 10.1017/S0016672399004358 Reeves, 2009, Accurate inference of subtle population structure (and other genetic discontinuities) using principal coordinates, PLoS One, 4, e4269, 10.1371/journal.pone.0004269 Reif, 2011, Association mapping for quality traits in soft winter wheat, Theoretical and Applied Genetics, 122, 961, 10.1007/s00122-010-1502-7 Reif, 2010, Genetic basis of agronomically important traits in sugar beet (Beta vulgaris L.) investigated with joint linkage association mapping, Theoretical and Applied Genetics, 8, 1489, 10.1007/s00122-010-1405-7 Remington, 2001, Structure of linkage disequilibrium and phenotypic associations in the maize genome, Proceedings of the National Academy of Sciences USA, 98, 11479, 10.1073/pnas.201394398 Rosyara, 2009, Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustration, Theoretical and Applied Genetics, 118, 1617, 10.1007/s00122-009-1010-9 Rutkoski, 2013, Imputation of unordered markers and the impact on genomic selection accuracy, Genes Genomes Genetics, 3, 427, 10.1534/g3.112.005363 Saintenac, 2013, Sequence-based mapping of the polyploid wheat genome, Genes Genomes Genetics, 3, 1105, 10.1534/g3.113.005819 Segura, 2012, An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations, Nature Genetics, 44, 825, 10.1038/ng.2314 Shoemaker, 1999, Bayesian statistics in genetics. A guide for the uninitiated, Trends in Genetics, 15, 354, 10.1016/S0168-9525(99)01751-5 Sneller, 2009, Analytical approaches and population types for finding and utilizing QTL in complex plant populations, Crop Science, 49, 363, 10.2135/cropsci2008.07.0420 Spencer, 2009, Designing genome-wide association studies: Sample size, power, imputation, and the choice of genotyping chip, PLoS Genetics, 5, e1000477, 10.1371/journal.pgen.1000477 Spielman, 1993, Transmission test for linkage disequilibrium: The insulin gene region and insulin-dependent diabetes mellitus (IDDM), American Journal of Human Genetics, 52, 506 Steinhoff, 2011, Multiple-line cross QTL-mapping in European elite maize, Crop Science, 51, 2505, 10.2135/cropsci2011.03.0181 Stephens, 2009, Bayesian statistical methods for genetic association studies, Nature Reviews Genetics, 10, 681, 10.1038/nrg2615 Stich, 2009, Comparison of mating designs for establishing nested association mapping populations in maize and Arabidopsis thaliana, Genetics, 183, 1525, 10.1534/genetics.109.108449 Stich, 2009, Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis, BMC Genomics, 10, 94, 10.1186/1471-2164-10-94 Stich, 2010, An introduction to association mapping in plants, CAB Reviews, 5, 1, 10.1079/PAVSNNR20105039 Stich, 2006, A new test for family-based association mapping with inbred lines from plant breeding programs, Theoretical and Applied Genetics, 113, 1121, 10.1007/s00122-006-0372-5 Stich, 2008, Comparison of mixed-model approaches for association mapping, Genetics, 178, 1745, 10.1534/genetics.107.079707 Storey, 2002, A direct approach to false discovery rates, Journal of Royal Statistical Society Series B, 64, 479, 10.1111/1467-9868.00346 Stracke, 2009, Association mapping reveals gene action and interactions in the determination of flowering time in barley, Theoretical and Applied Genetics, 118, 259, 10.1007/s00122-008-0896-y Svishcheva, 2012, Rapid variance components-based method for whole-genome association analysis, Nature Genetics, 44, 1166, 10.1038/ng.2410 Tachmazidou, 2007, Genetic Association mapping via evolution-based clustering of haplotypes, PLoS Genetics, 3, e111, 10.1371/journal.pgen.0030111 Tennessen, 2012, Evolution and functional impact of rare coding variation from deep sequencing of human exomes, Science, 64, 64, 10.1126/science.1219240 Thompson, 2011, The meta-analysis of genome-wide association studies, Briefings in Bioinformatics, 12, 259, 10.1093/bib/bbr020 Thornsberry, 2001, Dwarf8 polymorphisms associate with variation in flowering time, Nature Genetics, 28, 286, 10.1038/90135 Tian, 2011, Genome-wide association study of leaf architecture in the maize nested association mapping population, Nature Genetics, 43, 159, 10.1038/ng.746 Vilhjálmsson, 2013, The nature of confounding in genome-wide association studies, Nature Reviews Genetics, 14, 1, 10.1038/nrg3382 Wakefield, 2009, Bayes factors for genome-wide association studies: Comparison with P-values, Genetic Epidemiology, 33, 79, 10.1002/gepi.20359 Wan, 2013, The complete compositional epistasis detection in genome-wide association studies, BMC Genetics, 14, 7, 10.1186/1471-2156-14-7 Wang, 2012, Conditional QTL mapping of protein content in wheat with respect to grain yield and its components, Journal of Genetics, 91, 303, 10.1007/s12041-012-0190-2 Wang, 2011, Identifying QTLs and epistasis in structured plant populations using adaptive mixed LASSO, Journal of Agricultural, Biological and Environmental Statistics, 16, 170, 10.1007/s13253-010-0046-2 Weber, 2009, Using association mapping in teosinte to investigate the function of maize selection-candidate genes, PLoS One, 4, e8227, 10.1371/journal.pone.0008227 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, e29229, 10.1371/journal.pone.0029229 Westfall, 1993 Wray, 2011, Synthetic associations created by rare variants do not explain most GWAS results, PLoS Biology, 9, e1000579, 10.1371/journal.pbio.1000579 Wu, 2009, Genome-wide association analysis by lasso penalized logistic regression, Bioinformatics, 25, 714, 10.1093/bioinformatics/btp041 Wu, 1999, Time related mapping of quantitative trait loci underlying tiller number in rice, Genetics, 151, 297, 10.1093/genetics/151.1.297 Wu, 2006, Functional mapping – how to map and study the genetic architecture of dynamic complex traits, Nature Reviews Genetics, 7, 229, 10.1038/nrg1804 Wurschum, 2012, Mapping QTL for agronomic traits in breeding populations, Theoretical and Applied Genetics, 125, 201, 10.1007/s00122-012-1887-6 Wurschum, 2012, Comparison of biometrical models for joint linkage association mapping, Heredity, 108, 332, 10.1038/hdy.2011.78 Wurschum, 2011, Genome-wide association mapping reveals epistasis and genetic interaction networks in sugar beet, Theoretical and Applied Genetics, 123, 109, 10.1007/s00122-011-1570-3 Xu, 1998, Mapping quantitative trait loci using multiple families of line crosses, Genetics, 148, 517, 10.1093/genetics/148.1.517 Yu, 2006, Genetic association mapping and genome organization of maize, Current Opinion in Biotechnology, 17, 155, 10.1016/j.copbio.2006.02.003 Yu, 2008, Genetic design and statistical power of nested association mapping in maize, Genetics, 178, 539, 10.1534/genetics.107.074245 Yu, 2011, Association mapping and gene–gene interaction for stem rust resistance in spring wheat germplasm, Theoretical and Applied Genetics, 123, 1257, 10.1007/s00122-011-1664-y Yu, 2006, A unified mixed-model method for association mapping that accounts for multiple levels of relatedness, Nature Genetics, 38, 203, 10.1038/ng1702 Zhang, 2009, Software engineering the mixed model for genome-wide association studies on large samples, Briefings in Bioinformatics, 10, 664, 10.1093/bib/bbp050 Zhang, 2010, Mixed linear model approach adapted for genome-wide association studies, Nature Genetics, 42, 355, 10.1038/ng.546 Zhang, 2011, Association mapping of dynamic developmental plant height in common wheat, Planta, 234, 891, 10.1007/s00425-011-1434-8 Zhang, 2013, Efficacy of pyramiding elite alleles for dynamic development of plant height in common wheat, Molecular Breeding, 32, 327, 10.1007/s11032-013-9873-5 Zhang, 2001, Test of association for quantitative traits in general pedigrees: The quantitative pedigree disequilibrium test, Genetic Epidemiology, 21, 370, 10.1002/gepi.2001.21.s1.s370 Zhao, 2007, An Arabidopsis example of association mapping in structured samples, PLoS Genetics, 3, E4, 10.1371/journal.pgen.0030004 Zhao, 2011, Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa, Nature Communications, 2, 467, 10.1038/ncomms1467 Zheng, 2008, A phenylalanine in DGAT is a key determinant of oil content and composition in maize, Nature Genetics, 40, 367, 10.1038/ng.85 Zhou, 2012, Genome-wide efficient mixed-model analysis for association studies, Nature Genetics, 44, 821, 10.1038/ng.2310 Zhu, 1995, Analysis of conditional genetic effects and variance components in developmental genetics, Genetics, 141, 1633, 10.1093/genetics/141.4.1633 Zhu, 2011, A genome-wide comparison of the functional properties of rare and common genetic variants in humans, American Journal of Human Genetics, 88, 458, 10.1016/j.ajhg.2011.03.008 Zhu, 2008, Status and prospects of association mapping in plants, The Plant Genome, 1, 5, 10.3835/plantgenome2008.02.0089 Zuk, 2012, The mystery of missing heritability: Genetic interactions create phantom heritability, Proceedings of the National Academy of Sciences USA, 109, 1193, 10.1073/pnas.1119675109