### For Introduction

@article{MaCS,
   author = {Chen, Gary K. and Marjoram, Paul and Wall, Jeffery D.},
   title = {Fast and Flexible Simulation of DNA Sequence Data},
   journal = {Genome Research},
   volume = {19},
   pages = {136-142},
   year = {2009},
   URL ={https://genome.cshlp.org/content/19/1/136}
}

@article{AlphaSim,
   author = {Faux, Anne-Michelle andGorjanc, Gregor and Gaynor, R. Chris and Battagin, Mara and Edwards, Stefan M. and Wilson, David L. and Hearne, Sarah J. and Gonen, Serap and Hickey, John M.},
   title = {AlphaSim: Software for Breeding Program Simulation},
   journal = {The Plant Genome},
   volume = {9},
   number = {3},
   year = {2016},
   URL ={https://doi.org/10.3835/plantgenome2016.02.0013}
}

### For theory

@book{Gallais,
    title = {Quantitative Genetics and Breeding Methods in Autopolyploid Plants},
    author = {Gallais, A.},
    year = {2003},
    publisher = {INRA},
    address = {Paris},
    ISBN = {2-7380-1093-8}
}

@book{FalconerMackay,
    title = {Introduction to Quantitative Genetics},
    author = {Falconer, D. S. and Mackay, Trudy F. C.},
    edition = {4},
    year = {1996},
    publisher = {Longman},
    address = {Harlow},
    ISBN = {978-0-582-24302-6}
}

@article{FinlayWilkinson,
		title = {The analysis of adaptation in a plant-breeding programme},
	volume = {14},
	issn = {1444-9838},
	url = {http://www.publish.csiro.au/cp/AR9630742},
	doi = {10.1071/ar9630742},
	language = {en},
	number = {6},
	urldate = {2017-12-13},
	journal = {Australian Journal of Agricultural Research},
	author = {Finlay, K. W. and Wilkinson, G. N.},
	year = {1963},
	pages = {742--754}
}

@article{gaynor_2017,
	title = {A Two-Part Strategy for Using Genomic Selection to Develop Inbred Lines},
	volume = {57},
	issn = {0011-183X},
	url = {https://acsess.onlinelibrary.wiley.com/doi/full/10.2135/cropsci2016.09.0742},
	doi = {10.2135/cropsci2016.09.0742},
	language = {en},
	number = {5},
	urldate = {2017-10-20},
	journal = {Crop Science},
	author = {Gaynor, R. Chris and Gorjanc, Gregor and Bentley, Alison R. and Ober, Eric S. and Howell, Phil and Jackson, Robert and Mackay, Ian J. and Hickey, John M.},
	year = {2017},
	pages = {2372--2386},
}

@article{Falconer_85,
	title = {A note on {Fisher}'s ‘average effect’ and ‘average excess’},
	volume = {46},
	issn = {1469-5073, 0016-6723},
	url = {https://www.cambridge.org/core/journals/genetics-research/article/note-on-fishers-average-effect-and-average-excess/26DFA92B3BA3EA92CD76847BFA21C5C8},
	doi = {10.1017/S0016672300022825},
	language = {en},
	number = {3},
	urldate = {2019-01-03},
	journal = {Genetics Research},
	author = {Falconer, D. S.},
	month = dec,
	year = {1985},
	pages = {337--347}
}

@article{Massman13,
   author = {Massman, Jon M. and Gordillo, Andres and Lorenzana, Robenzon E. and Bernardo, Rex},
   title = {Genomewide Predictions from Maize Single-Cross Data},
   journal = {Theoretical and Applied Genetics},
   volume = {126},
   number = {1},
   pages = {12-22},
   year = {2013},
   URL ={https://doi.org/10.1007/s00122-012-1955-y}
}

@manual{EMMREML,
    title = {EMMREML: Fitting Mixed Models with Known Covariance Structures},
    author = {Akdemir, Deniz and Godfrey, Okeke Uche},
    year = {2015},
    note = {R package version 3.1},
    url = {https://CRAN.R-project.org/package=EMMREML},
}

@article{sommer,
    title = {Genome assisted prediction of quantitative traits using the R package sommer},
    author = {Covarrubias-Pazaran, Giovanny},
    journal = {PLoS ONE},
    year = {2016},
    volume = {11},
    pages = {1-15},
    url = {https://doi.org/10.1371/journal.pone.0156744}
}

@article{xiang_2016,
	title = {Genomic evaluation by including dominance effects and inbreeding depression for purebred and crossbred performance with an application in pigs},
	volume = {48},
	issn = {1297-9686},
	url = {https://doi.org/10.1186/s12711-016-0271-4},
	doi = {10.1186/s12711-016-0271-4},
	number = {1},
	urldate = {2019-04-23},
	journal = {Genetics Selection Evolution},
	author = {Xiang, Tao and Christensen, Ole Fredslund and Vitezica, Zulma Gladis and Legarra, Andres},
	month = nov,
	year = {2016},
	pages = {92}
}

@article{fisher_1919,
  title={XV.—The Correlation between Relatives on the Supposition of Mendelian Inheritance.},
  volume={52},
  DOI={10.1017/S0080456800012163},
  number={2},
  journal={Transactions of the Royal Society of Edinburgh},
  publisher={Royal Society of Edinburgh Scotland Foundation},
  author={Fisher, R. A.},
  year={1919},
  pages={399–433}
}

### MaCS histories

@article{cattle,
  title={Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors},
  volume={30},
  issue={9},
  DOI={https://doi.org/10.1093/molbev/mst125},
  journal={Molecular Biology and Evolution},
  publisher={Royal Society of Edinburgh Scotland Foundation},
  author={MacLeod, Iona M. and Larkin, Denis M. and Lewin, Harris A.and Hayes, Ben J. and Goddard, Mike E.},
  year={2013},
  month=sep,
  pages={2209–2223}
}

@article{hickey_2014,
	title = {Evaluation of Genomic Selection Training Population Designs and Genotyping Strategies in Plant Breeding Programs Using Simulation},
	volume = {54},
	issue = {4},
	doi = {10.2135/cropsci2013.03.0195},
	language = {en},
	journal = {Crop Science},
	author = {Hickey, John M.and Dreisigacker, Susanne and Crossa, Jose and Hearne, Sarah and Babu, Raman and Prasanna, Boddupalli M. and Grondona, Martin and Zambelli, Andres and Windhausen, Vanessa S. and Mathews, Ky and Gorjanc, Gregor},
	year = {2014},
	pages = {1476-1488},
}
