% Encoding: windows-1252


@Article{asreml_2009,
  title={ASReml-R reference manual},
  author={Butler, DG and Cullis, Brian R and Gilmour, AR and Gogel, BJ},
  journal={The State of Queensland, Department of Primary Industries and Fisheries, Brisbane},
  year={2009}
}


@Article{bardol_2013,
  title={Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism},
  author={Bardol, N and Ventelon, M and Mangin, B and Jasson, S and Loywick, V and Couton, F and Derue, C and Blanchard, P and Charcosset, A and Moreau, Laurence},
  journal={Theoretical and applied genetics},
  volume={126},
  number={11},
  pages={2717--2736},
  year={2013},
  publisher={Springer}
}

@Article{bauer_2013,
  title={Intraspecific variation of recombination rate in maize},
  author={Bauer, Eva and Falque, Matthieu and Walter, Hildrun and Bauland, Cyril and Camisan, Christian and Campo, Laura and Meyer, Nina and Ranc, Nicolas and Rincent, Renaud and Schipprack, Wolfgang and others},
  journal={Genome Biol},
  volume={14},
  number={9},
  pages={R103},
  year={2013}
}

@Article{bink_2008,
  title={Bayesian analysis of complex traits in pedigreed plant populations},
  author={Bink, MCAM and Boer, MP and Ter Braak, CJF and Jansen, J and Voorrips, RE and Van de Weg, WE},
  journal={Euphytica},
  volume={161},
  number={1-2},
  pages={85--96},
  year={2008},
  publisher={Springer}
}

@Article{bink2002multiple,
  title={Multiple QTL mapping in related plant populations via a pedigree-analysis approach},
  author={Bink, MCAM and Uimari, P and Sillanp{\"a}{\"a}, M and Janss, L and Jansen, R},
  journal={Theoretical and Applied Genetics},
  volume={104},
  number={5},
  pages={751--762},
  year={2002},
  publisher={Springer}
}

@Article{bink2012qtl,
  title={QTL linkage analysis of connected populations using ancestral marker and pedigree information},
  author={Bink, Marco CAM and Totir, L Radu and ter Braak, Cajo JF and Winkler, Christopher R and Boer, Martin P and Smith, Oscar S},
  journal={Theoretical and Applied Genetics},
  volume={124},
  number={6},
  pages={1097--1113},
  year={2012},
  publisher={Springer}
}

@Article{blanc_2006,
  title={Connected populations for detecting quantitative trait loci and testing for epistasis: an application in maize},
  author={Blanc, G and Charcosset, A and Mangin, B and Gallais, A and Moreau, L},
  journal={Theoretical and Applied Genetics},
  volume={113},
  number={2},
  pages={206--224},
  year={2006},
  publisher={Springer}
}

@article{bradbury2007tassel,
  title={TASSEL: software for association mapping of complex traits in diverse samples},
  author={Bradbury, Peter J and Zhang, Zhiwu and Kroon, Dallas E and Casstevens, Terry M and Ramdoss, Yogesh and Buckler, Edward S},
  journal={Bioinformatics},
  volume={23},
  number={19},
  pages={2633--2635},
  year={2007},
  publisher={Oxford Univ Press}
}


@Article{broman_rqtl,
  title={R/qtl: QTL mapping in experimental crosses},
  author={Broman, Karl W and Wu, Hao and Sen, {\'S}aunak and Churchill, Gary A},
  journal={Bioinformatics},
  volume={19},
  number={7},
  pages={889--890},
  year={2003},
  publisher={Oxford Univ Press}
}


@article{cavanagh2008mutations,
  title={From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants},
  author={Cavanagh, Colin and Morell, Matthew and Mackay, Ian and Powell, Wayne},
  journal={Current opinion in plant biology},
  volume={11},
  number={2},
  pages={215--221},
  year={2008},
  publisher={Elsevier}
}



@Article{char_iQTLm,
  title={Heterosis in maize investigated using connected RIL populations},
  author={Charcosset, A and Mangin, B and Moreau, L and Combes, L and Jourjon, MF and Gallais, A},
  journal={COLLOQUES-INRA},
  pages={89--98},
  year={2001},
  publisher={INRA; 1999}
}

@Book{chatterjee_2012,
  title={Regression analysis by example 5th edition},
  author={Chatterjee, Samprit and Hadi, Ali S},
  year={2012},
  publisher={John Wiley \& Sons}
}

@ArtiCLE{chur_1994,
  author = {Churchill, Gary A and Doerge, Rebecca W},
  title = {Empirical threshold values for quantitative trait mapping.},
  journal = {Genetics},
  year = {1994},
  volume = {138},
  pages = {963--971},
  number = {3},
  publisher = {Genetics Soc America}
}

@Article{coles_2010,
  title={Genetic control of photoperiod sensitivity in maize revealed by joint multiple population analysis},
  author={Coles, Nathan D and McMullen, Michael D and Balint-Kurti, Peter J and Pratt, Richard C and Holland, James B},
  journal={Genetics},
  volume={184},
  number={3},
  pages={799--812},
  year={2010},
  publisher={Genetics Soc America}
}


@Article{covarrubias_sommer_2016,
    title = {Genome assisted prediction of quantitative traits using the R package sommer},
    author = {Covarrubias-Pazaran, G},
    journal = {PLoS ONE},
    year = {2016},
    volume = {11},
    pages = {1-15},
  }

@Book{cox_1989,
  title={Analysis of binary data},
  author={Cox, David Roxbee and Snell, E Joyce},
  volume={32},
  year={1989},
  publisher={CRC Press}
}



@Article{crepieux_2004_IBD,
  title={Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs Recovering QTL Identical-by-Descent Status Information From Marker Data},
  author={Crepieux, S{\'e}bastien and Lebreton, Claude and Servin, Bertrand and Charmet, Gilles},
  journal={Genetics},
  volume={168},
  number={3},
  pages={1737--1749},
  year={2004},
  publisher={Genetics Soc America}
}

@Article{crepieux_2005_application,
  title={Application of a new IBD-based QTL mapping method to common wheat breeding population: analysis of kernel hardness and dough strength},
  author={Crepieux, Sebastien and Lebreton, Claude and Flament, Pascal and Charmet, Gilles},
  journal={Theoretical and applied genetics},
  volume={111},
  number={7},
  pages={1409--1419},
  year={2005},
  publisher={Springer}
}


@article{doerge2002mapping,
  title={Mapping and Analysis of Quantitative Trait Loci in Experimental Populations},
  author={Doerge, Rebecca W},
  journal={Nature Reviews Genetics},
  volume={3},
  number={1},
  pages={43--52},
  year={2002},
  publisher={Nature Publishing Group}
}



@Article{fisher_1918,
  title={The Correlation between Relatives on the Supposition of Mendelian Inheritance.},
  author={Fisher, Ronald A},
  journal={Transactions of the royal society of Edinburgh},
  volume={52},
  number={02},
  pages={399--433},
  year={1918},
  publisher={Cambridge Univ Press}
}

@book{friedman2001elements,
  title={The elements of statistical learning},
  author={Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert},
  volume={1},
  year={2001},
  publisher={Springer series in statistics Springer, Berlin}
}

@Article{ganal_2011,
  title={A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome},
  author={Ganal, Martin W and Durstewitz, Gregor and Polley, Andreas and B{\'e}rard, Aur{\'e}lie and Buckler, Edward S and Charcosset, Alain and Clarke, Joseph D and Graner, Eva-Maria and Hansen, Mark and Joets, Johann and others},
  journal={PloS one},
  volume={6},
  number={12},
  pages={e28334},
  year={2011},
  publisher={Public Library of Science}
}

@article{gapit2012,
  title={GAPIT: genome association and prediction integrated tool},
  author={Lipka, Alexander E and Tian, Feng and Wang, Qishan and Peiffer, Jason and Li, Meng and Bradbury, Peter J and Gore, Michael A and Buckler, Edward S and Zhang, Zhiwu},
  journal={Bioinformatics},
  volume={28},
  number={18},
  pages={2397--2399},
  year={2012},
  publisher={Oxford Univ Press}
}

@article{genabel2007,
  title={GenABEL: an R library for genome-wide association analysis},
  author={Aulchenko, Yurii S and Ripke, Stephan and Isaacs, Aaron and Van Duijn, Cornelia M},
  journal={Bioinformatics},
  volume={23},
  number={10},
  pages={1294--1296},
  year={2007},
  publisher={Oxford Univ Press}
}

@Article{giraud_2014,
  title={Linkage Disequilibrium with Linkage Analysis of Multiline Crosses Reveals Different Multiallelic QTL for Hybrid Performance in the Flint and Dent Heterotic Groups of Maize},
  author={Giraud, H{\'e}lo{\"\i}se and Lehermeier, Christina and Bauer, Eva and Falque, Matthieu and Segura, Vincent and Bauland, Cyril and Camisan, Christian and Campo, Laura and Meyer, Nina and Ranc, Nicolas and others},
  journal={Genetics},
  volume={198},
  number={4},
  pages={1717--1734},
  year={2014},
  publisher={Genetics Soc America}
}

@Article{grubbs_1950,
  title={Sample criteria for testing outlying observations},
  author={Grubbs, Frank E},
  journal={The Annals of Mathematical Statistics},
  pages={27--58},
  year={1950},
  publisher={JSTOR}
}

@Article{guo_2006,
  title={Pooled analysis of data from multiple quantitative trait locus mapping populations},
  author={Guo, B and Sleper, DA and Sun, J and Nguyen, HT and Arelli, PR and Shannon, JG},
  journal={Theoretical and applied genetics},
  volume={113},
  number={1},
  pages={39--48},
  year={2006},
  publisher={Springer}
}

@article{haldane1919combination,
  title={The combination of linkage values and the calculation of distances between the loci of linked factors},
  author={Haldane, JBS},
  journal={J Genet},
  volume={8},
  number={29},
  pages={299--309},
  year={1919}
}

@Article{haley_1992,
  title={A simple regression method for mapping quantitative trait loci in line crosses using flanking markers},
  author={Haley, Chris S and Knott, Sarah A},
  journal={Heredity},
  volume={69},
  number={4},
  pages={315--324},
  year={1992}
}

@Article{han2015choice,
  title={Choice of models for QTL mapping with multiple families and design of the training set for prediction of Fusarium resistance traits in maize},
  author={Han, Sen and Utz, H Friedrich and Liu, Wenxin and Schrag, Tobias A and Stange, Michael and W{\"u}rschum, Tobias and Miedaner, Thomas and Bauer, Eva and Sch{\"o}n, Chris-Carolin and Melchinger, Albrecht E},
  journal={Theoretical and Applied Genetics},
  pages={1--14},
  year={2015},
  publisher={Springer}
}

@article{haseman1972investigation,
  title={The investigation of linkage between a quantitative trait and a marker locus},
  author={Haseman, JK and Elston, RC},
  journal={Behavior genetics},
  volume={2},
  number={1},
  pages={3--19},
  year={1972},
  publisher={Springer}
}

@article{huang2011analysis,
  title={Analysis of natural allelic variation in Arabidopsis using a multiparent recombinant inbred line population},
  author={Huang, Xueqing and Paulo, Maria-Jo{\~a}o and Boer, Martin and Effgen, Sigi and Keizer, Paul and Koornneef, Maarten and van Eeuwijk, Fred A},
  journal={Proceedings of the National Academy of Sciences},
  volume={108},
  number={11},
  pages={4488--4493},
  year={2011},
  publisher={National Acad Sciences}
}

@article{huang2012multiparent,
  title={A multiparent advanced generation inter-cross population for genetic analysis in wheat},
  author={Huang, Bevan E and George, Andrew W and Forrest, Kerrie L and Kilian, Andrzej and Hayden, Matthew J and Morell, Matthew K and Cavanagh, Colin R},
  journal={Plant biotechnology journal},
  volume={10},
  number={7},
  pages={826--839},
  year={2012},
  publisher={Wiley Online Library}
}


@Manual{JabRef_software,
  title = {JabRef},
  author = {{JabRef Development Team}},
  year = {2016},
  url = {http://www.jabref.org}
}


@Article{jannink_2003,
  title={Estimating allelic number and identity in state of QTLs in interconnected families},
  author={Jannink, Jean-luc and Wu, Xiao-Lin},
  journal={Genetical research},
  volume={81},
  number={02},
  pages={133--144},
  year={2003},
  publisher={Cambridge Univ Press}
}

@Article{jansen_2003,
  title={Mapping quantitative trait loci in plant breeding populations},
  author={Jansen, Ritsert C and Jannink, Jean-Luc and Beavis, William D},
  journal={Crop Science},
  volume={43},
  number={3},
  pages={829--834},
  year={2003},
  publisher={Crop Science Society of America}
}

@Article{jourjon_2005,
  title={MCQTL: multi-allelic QTL mapping in multi-cross design},
  author={Jourjon, Marie-Fran{\c{c}}oise and Jasson, Sylvain and Marcel, Jacques and Ngom, Baba and Mangin, Brigitte},
  journal={Bioinformatics},
  volume={21},
  number={1},
  pages={128--130},
  year={2005},
  publisher={Oxford Univ Press}
}

@Article{kohler_1982,
  title={The Relation Among the Likelihood Ratio-, Wald-, and Lagrange Multiplier Tests and Their Applicability to Small Samples},
  author={Kohler, Daniel F},
  year={1982},
  publisher={Rand Corporation}
}

@Article{kover_2009,
  title={A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana},
  author={Kover, Paula X and Valdar, William and Trakalo, Joseph and Scarcelli, Nora and Ehrenreich, Ian M and Purugganan, Michael D and Durrant, Caroline and Mott, Richard and others},
  journal={PLoS Genet},
  volume={5},
  number={7},
  pages={e1000551},
  year={2009}
}

@Article{land_1989,
  title={Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.},
  author={Lander, Eric S and Botstein, David},
  journal={Genetics},
  volume={121},
  number={1},
  pages={185--199},
  year={1989},
  publisher={Genetics Soc America}
}

@Article{lehermeier_2014,
  title={Usefulness of multiparental populations of maize (Zea mays L.) for genome-based prediction},
  author={Lehermeier, Christina and Kr{\"a}mer, Nicole and Bauer, Eva and Bauland, Cyril and Camisan, Christian and Campo, Laura and Flament, Pascal and Melchinger, Albrecht E and Menz, Monica and Meyer, Nina and others},
  journal={Genetics},
  volume={198},
  number={1},
  pages={3--16},
  year={2014},
  publisher={Genetics Soc America}
}




@Article{leroux_2014,
  title={Clusthaplo: a plug-in for MCQTL to enhance QTL detection using ancestral alleles in multi-cross design},
  author={Leroux, Damien and Rahmani, Abdelaziz and Jasson, Sylvain and Ventelon, Marjolaine and Louis, Florence and Moreau, Laurence and Mangin, Brigitte},
  journal={Theoretical and Applied Genetics},
  volume={127},
  number={4},
  pages={921--933},
  year={2014},
  publisher={Springer}
}

@Article{li_2005,
  title={Combining data from multiple inbred line crosses improves the power and resolution of quantitative trait loci mapping},
  author={Li, Renhua and Lyons, Malcolm A and Wittenburg, Henning and Paigen, Beverly and Churchill, Gary A},
  journal={Genetics},
  volume={169},
  number={3},
  pages={1699--1709},
  year={2005},
  publisher={Genetics Soc America}
}

@Article{li_2005_haplo,
  title={Haplotype-based linkage disequilibrium mapping via direct data mining},
  author={Li, Jing and Jiang, Tao},
  journal={Bioinformatics},
  volume={21},
  number={24},
  pages={4384--4393},
  year={2005},
  publisher={Oxford Univ Press}
}

@Article{li_2011_joint,
  title={Joint QTL linkage mapping for multiple-cross mating design sharing one common parent},
  author={Li, Huihui and Bradbury, Peter and Ersoz, Elhan and Buckler, Edward S and Wang, Jiankang},
  journal={PLoS One},
  volume={6},
  number={3},
  pages={e17573},
  year={2011},
  publisher={Public Library of Science}
}

@Article{liu_2012,
  title={Comparison of biometrical approaches for QTL detection in multiple segregating families},
  author={Liu, Wenxin and Reif, Jochen C and Ranc, Nicolas and Della Porta, Giovanni and W{\"u}rschum, Tobias},
  journal={Theoretical and Applied Genetics},
  volume={125},
  number={5},
  pages={987--998},
  year={2012},
  publisher={Springer}
}

@Book{malecot_1948,
  title={Les math{\'e}matiques de l'h{\'e}r{\'e}dit{\'e}},
  author={Mal{\'e}cot, Gustave},
  year={1948},
  publisher={Masson}
}

@article{meuwissen2002fine,
  title={Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping},
  author={Meuwissen, Theo HE and Karlsen, Astrid and Lien, Sigbj{\o}rn and Olsaker, Ingrid and Goddard, Mike E},
  journal={Genetics},
  volume={161},
  number={1},
  pages={373--379},
  year={2002},
  publisher={Genetics Soc America}
}

@Book{mcculloch2001,
  title={Generalized, linear, and mixed models},
  author={McCulloch, Charles E and Searle, Shayle R},
  year={2001},
  publisher={Wiley Online Library}
}

@Article{mcmullen_2009,
  title={Genetic properties of the maize nested association mapping population},
  author={McMullen, Michael D and Kresovich, Stephen and Villeda, Hector Sanchez and Bradbury, Peter and Li, Huihui and Sun, Qi and Flint-Garcia, Sherry and Thornsberry, Jeffry and Acharya, Charlotte and Bottoms, Christopher and others},
  journal={Science},
  volume={325},
  number={5941},
  pages={737--740},
  year={2009},
  publisher={American Association for the Advancement of Science}
}


@Article{meuw_1992,
  title={Computing inbreeding coefficients in large populations},
  author={Luo, Z and others},
  journal={Genetics Selection Evolution},
  volume={24},
  number={4},
  pages={305--313},
  year={1992},
  publisher={EDP Sciences}
}

@Article{muranty_1996,
  title={Power of tests for quantitative trait loci detection using full-sib families in different schemes},
  author={Muranty, Helene},
  journal={Heredity},
  volume={76},
  number={2},
  pages={156--165},
  year={1996},
  publisher={London: Oliver and Boyd, 1947-}
}

@Article{myles_2009,
  title={Association mapping: critical considerations shift from genotyping to experimental design},
  author={Myles, Sean and Peiffer, Jason and Brown, Patrick J and Ersoz, Elhan S and Zhang, Zhiwu and Costich, Denise E and Buckler, Edward S},
  journal={The Plant Cell},
  volume={21},
  number={8},
  pages={2194--2202},
  year={2009},
  publisher={Am Soc Plant Biol}
}

@Article{nei_1979,
  title={Mathematical model for studying genetic variation in terms of restriction endonucleases},
  author={Nei, Masatoshi and Li, Wen-Hsiung},
  journal={Proceedings of the National Academy of Sciences},
  volume={76},
  number={10},
  pages={5269--5273},
  year={1979},
  publisher={National Acad Sciences}
}

@Article{nicholson_2002,
  title={Assessing population differentiation and isolation from single-nucleotide polymorphism data},
  author={Nicholson, George and Smith, Albert V and J{\'o}nsson, Frosti and G{\'u}stafsson, {\'O}mar and Stef{\'a}nsson, K{\'a}ri and Donnelly, Peter},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={64},
  number={4},
  pages={695--715},
  year={2002},
  publisher={Wiley Online Library}
}

@Article{ogut2015,
  title={Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population},
  author={Ogut, Funda and Bian, Yang and Bradbury, Peter J and Holland, James B},
  journal={Heredity},
  volume={114},
  number={6},
  pages={552--563},
  year={2015},
  publisher={Nature Publishing Group}
}



@Article{orel_1998,
  title={Empirical genetic laws published in Brno before Mendel was born},
  author={Orel, Y and Wood, RJ},
  journal={Journal of Heredity},
  volume={89},
  number={1},
  pages={79--82},
  year={1998},
  publisher={Am Genetic Assoc}
}

@Article{powell_2010,
  title={Reconciling the analysis of IBD and IBS in complex trait studies},
  author={Powell, Joseph E and Visscher, Peter M and Goddard, Michael E},
  journal={Nature Reviews Genetics},
  volume={11},
  number={11},
  pages={800--805},
  year={2010},
  publisher={Nature Publishing Group}
}

@Manual{R_Core,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2016},
    url = {https://www.R-project.org/},
  }


@Book{rao_2008, 
title={Linear Models and Generalizations: Least Squares and Alternatives},
author={C. Radhakrishna Rao and Helge Toutenburg and Shalabh and Christian Heumann},
year={2008},
publisher={Springer}
}

@Article{rebai_1993,
  title={Power of tests for QTL detection using replicated progenies derived from a diallel cross},
  author={Reba{\"i}, Ahmed and Goffinet, Bruno},
  journal={Theoretical and Applied Genetics},
  volume={86},
  number={8},
  pages={1014--1022},
  year={1993},
  publisher={Springer}
}


@Article{rebai_2000,
  title={More about quantitative trait locus mapping with diallel designs},
  author={Reba{\"i}, Ahmed and Goffinet, Bruno},
  journal={Genetical research},
  volume={75},
  number={02},
  pages={243--247},
  year={2000},
  publisher={Cambridge Univ Press}
}


@Article{rosenberg_2002,
  title={Genealogical trees, coalescent theory and the analysis of genetic polymorphisms},
  author={Rosenberg, Noah A and Nordborg, Magnus},
  journal={Nature Reviews Genetics},
  volume={3},
  number={5},
  pages={380--390},
  year={2002},
  publisher={Nature Publishing Group}
}

@Article{schwegler_2013,
  title={Multiple-line cross quantitative trait locus mapping in sugar beet (Beta vulgaris L.)},
  author={Schwegler, Diana D and Liu, Wenxin and Gowda, Manje and W{\"u}rschum, Tobias and Schulz, Britta and Reif, Jochen C},
  journal={Molecular breeding},
  volume={31},
  number={2},
  pages={279--287},
  year={2013},
  publisher={Springer}
}

@Article{speed_2012,
  title={Improved heritability estimation from genome-wide SNPs},
  author={Speed, Doug and Hemani, Gibran and Johnson, Michael R and Balding, David J},
  journal={The American Journal of Human Genetics},
  volume={91},
  number={6},
  pages={1011--1021},
  year={2012},
  publisher={Elsevier}
}


@Article{steinhoff_2011,
  title={Multiple-line cross quantitative trait locus mapping in European elite maize},
  author={Steinhoff, Jana and Liu, Wenxin and Maurer, Hans Peter and W{\"u}rschum, Tobias and Friedrich, C and Longin, H and Ranc, Nicolas and Reif, Jochen C},
  journal={Crop science},
  volume={51},
  number={6},
  pages={2505--2516},
  year={2011},
  publisher={The Crop Science Society of America, Inc.}
}

@Article{steinhoff_2012a,
  title={Detection of QTL for flowering time in multiple families of elite maize},
  author={Steinhoff, Jana and Liu, Wenxin and Reif, Jochen C and Della Porta, Giovanni and Ranc, Nicolas and W{\"u}rschum, Tobias},
  journal={Theoretical and Applied Genetics},
  volume={125},
  number={7},
  pages={1539--1551},
  year={2012},
  publisher={Springer}
}


@Article{sun_2010,
  title={Variation explained in mixed-model association mapping},
  author={Sun, G and Zhu, C and Kramer, MH and Yang, SS and Song, W and Piepho, HP and Yu, J},
  journal={Heredity},
  volume={105},
  number={4},
  pages={333--340},
  year={2010},
  publisher={Nature Publishing Group}
}

@Article{ter_2010,
  title={Identity-by-descent matrix decomposition using latent ancestral allele models},
  author={Ter Braak, Cajo JF and Boer, Martin P and Totir, L Radu and Winkler, Christopher R and Smith, Oscar S and Bink, Marco CAM},
  journal={Genetics},
  volume={185},
  number={3},
  pages={1045--1057},
  year={2010},
  publisher={Genetics Soc America}
}

@Article{utz_2000,
  title={Bias and sampling error of the estimated proportion of genotypic variance explained by quantitative trait loci determined from experimental data in maize using cross validation and validation with independent samples},
  author={Utz, H Friedrich and Melchinger, Albrecht E and Sch{\"o}n, Chris C},
  journal={Genetics},
  volume={154},
  number={4},
  pages={1839--1849},
  year={2000},
  publisher={Genetics Soc America}
}

@Article{van_2010,
  title={Mixed model approaches for the identification of QTLs within a maize hybrid breeding program},
  author={van Eeuwijk, Fred A and Boer, Martin and Totir, L Radu and Bink, Marco and Wright, Deanne and Winkler, Christopher R and Podlich, Dean and Boldman, Keith and Baumgarten, Andy and Smalley, Matt and others},
  journal={Theoretical and applied genetics},
  volume={120},
  number={2},
  pages={429--440},
  year={2010},
  publisher={Springer}
}


@article{varshney2015analytical,
  title={Analytical and decision support tools for genomics-assisted breeding},
  author={Varshney, Rajeev K and Singh, Vikas K and Hickey, John M and Xun, Xu and Marshall, David F and Wang, Jun and Edwards, David and Ribaut, Jean-Marcel},
  journal={Trends in plant science},
  year={2015},
  publisher={Elsevier}
}


@Article{verhoeven_2006,
  title={Using mating designs to uncover QTL and the genetic architecture of complex traits},
  author={Verhoeven, KJF and Jannink, JL and McIntyre, LM},
  journal={Heredity},
  volume={96},
  number={2},
  pages={139--149},
  year={2006},
  publisher={Nature Publishing Group}
}

@Article{wald_1943,
  title={Tests of statistical hypotheses concerning several parameters when the number of observations is large},
  author={Wald, Abraham},
  journal={Transactions of the American Mathematical society},
  volume={54},
  number={3},
  pages={426--482},
  year={1943},
  publisher={JSTOR}
}

@Article{walling_2000,
  title={Combined analyses of data from quantitative trait loci mapping studies: chromosome 4 effects on porcine growth and fatness},
  author={Walling, Grant A and Visscher, Peter M and Andersson, Leif and Rothschild, Max F and Wang, Lizhen and Moser, Gerhard and Groenen, Martien AM and Bidanel, Jean-Pierre and Cepica, Stanislav and Archibald, Alan L and others},
  journal={Genetics},
  volume={155},
  number={3},
  pages={1369--1378},
  year={2000},
  publisher={Genetics Soc America}
}

@Article{weeks_1964,
  title={A note on the determination of connectedness in an N-way cross classification},
  author={Weeks, David L and Williams, Donald R},
  journal={Technometrics},
  volume={6},
  number={3},
  pages={319--324},
  year={1964},
  publisher={Taylor \& Francis}
}

@Article{wei_2015,
  title={A Random Model Approach to QTL Mapping in Multi-parent Advanced Generation Inter-cross (MAGIC) Populations},
  author={Wei, Julong and Xu, Shizhong},
  journal={Genetics},
  pages={genetics--115},
  year={2015},
  publisher={Genetics Soc America}
}


@Article{wurschum_2012_comp,
  title={Comparison of biometrical models for joint linkage association mapping},
  author={W{\"u}rschum, T and Liu, W and Gowda, M and Maurer, HP and Fischer, S and Schechert, A and Reif, JC},
  journal={Heredity},
  volume={108},
  number={3},
  pages={332--340},
  year={2012},
  publisher={Nature Publishing Group}
}

@Article{wurschum_2012_fam,
  title={Mapping QTL for agronomic traits in breeding populations},
  author={W{\"u}rschum, Tobias},
  journal={Theoretical and Applied Genetics},
  volume={125},
  number={2},
  pages={201--210},
  year={2012},
  publisher={Springer}
}

@Article{xavierNAM2015,
    title = {{NAM}: association studies in multiple populations},
    author = {Alencar Xavier and Shizhong Xu and William Muir and Katy Rainey},
    journal = {Bioinformatics},
    publisher = {Oxford University Press},
    year = {2015},
    pages = {btv448},
  }

@Article{xie_1998,
  title={Combining different line crosses for mapping quantitative trait loci using the identical by descent-based variance component method},
  author={Xie, Chongqing and Gessler, Damian DG and Xu, Shizhong},
  journal={Genetics},
  volume={149},
  number={2},
  pages={1139--1146},
  year={1998},
  publisher={Genetics Soc America}
}

@Article{xu_1995,
  title={A random model approach to interval mapping of quantitative trait loci.},
  author={Xu, Shizhong and Atchley, William R},
  journal={Genetics},
  volume={141},
  number={3},
  pages={1189--1197},
  year={1995},
  publisher={Genetics Soc America}
}


@Article{xu_1998,
  title={Mapping quantitative trait loci using multiple families of line crosses},
  author={Xu, Shizhong},
  journal={Genetics},
  volume={148},
  number={1},
  pages={517--524},
  year={1998},
  publisher={Genetics Soc America}
}

@Article{yang_2010,
  title={Common SNPs explain a large proportion of the heritability for human height},
  author={Yang, Jian and Benyamin, Beben and McEvoy, Brian P and Gordon, Scott and Henders, Anjali K and Nyholt, Dale R and Madden, Pamela A and Heath, Andrew C and Martin, Nicholas G and Montgomery, Grant W and others},
  journal={Nature genetics},
  volume={42},
  number={7},
  pages={565--569},
  year={2010},
  publisher={Nature Publishing Group}
}

@Article{yang_2014,
  title={Advantages and pitfalls in the application of mixed-model association methods},
  author={Yang, Jian and Zaitlen, Noah A and Goddard, Michael E and Visscher, Peter M and Price, Alkes L},
  journal={Nature genetics},
  volume={46},
  number={2},
  pages={100--106},
  year={2014},
  publisher={Nature Publishing Group}
}

@Article{yi_2001bayesian,
  title={Bayesian mapping of quantitative trait loci under complicated mating designs},
  author={Yi, Nengjun and Xu, Shizhong},
  journal={Genetics},
  volume={157},
  number={4},
  pages={1759--1771},
  year={2001},
  publisher={Genetics Soc America}
}

@Article{yu_2006,
  title={A unified mixed-model method for association mapping that accounts for multiple levels of relatedness},
  author={Yu, Jianming and Pressoir, Gael and Briggs, William H and Bi, Irie Vroh and Yamasaki, Masanori and Doebley, John F and McMullen, Michael D and Gaut, Brandon S and Nielsen, Dahlia M and Holland, James B and others},
  journal={Nature genetics},
  volume={38},
  number={2},
  pages={203--208},
  year={2006},
  publisher={Nature Publishing Group}
}

@Article{yu_2008_NAM,
  title={Genetic design and statistical power of nested association mapping in maize},
  author={Yu, Jianming and Holland, James B and McMullen, Michael D and Buckler, Edward S},
  journal={Genetics},
  volume={178},
  number={1},
  pages={539--551},
  year={2008},
  publisher={Genetics Soc America}
}

@Article{zeng_1993,
  title={Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci},
  author={Zeng, Zhao-Bang},
  journal={Proceedings of the National Academy of Sciences},
  volume={90},
  number={23},
  pages={10972--10976},
  year={1993},
  publisher={National Acad Sciences}
}

@Article{zeng_1994,
  title={Precision mapping of quantitative trait loci.},
  author={Zeng, Zhao-Bang},
  journal={Genetics},
  volume={136},
  number={4},
  pages={1457--1468},
  year={1994},
  publisher={Genetics Soc America}
}

@Article{zheng2014general,
  title={A general modeling framework for genome ancestral origins in multiparental populations},
  author={Zheng, Chaozhi and Boer, Martin P and van Eeuwijk, Fred A},
  journal={Genetics},
  volume={198},
  number={1},
  pages={87--101},
  year={2014},
  publisher={Genetics Soc America}
}

@Article{zheng2015reconstruction,
  title={Reconstruction of genome ancestry blocks in multiparental populations},
  author={Zheng, Chaozhi and Boer, Martin P and van Eeuwijk, Fred A},
  journal={Genetics},
  volume={200},
  number={4},
  pages={1073--1087},
  year={2015},
  publisher={Genetics Soc America}
}

@Article{,
  author =    {Alencar Xavier and Shizhong Xu and William Muir and Katy Rainey},
  title =     {{NAM}: {A}ssociation {S}tudies in {M}ultiple {P}opulations},
  journal =   {Bioinformatics},
  year =      {2015},
  pages =     {btv448},
  publisher = {Oxford University Press}
}

@Comment{jabref-meta: databaseType:bibtex;}
