Darwin C. The variation of animals and plants under domestication, vol. 2: O. In: Judd; 1868.
Google Scholar
Darwin C. On the origin of species, 1859: Routledge; 2004.
Brown TA, Jones MK, Powell W, Allaby RG. The complex origins of domesticated crops in the Fertile Crescent. Trends Ecol Evol. 2009;24(2):103–9.
Article
Google Scholar
Driscoll CA, Macdonald DW, O'Brien SJ. From wild animals to domestic pets, an evolutionary view of domestication. Proc Natl Acad Sci U S A. 2009;106(Suppl 1):9971–8.
Article
CAS
Google Scholar
Wilkins AS, Wrangham RW, Fitch WT. The "domestication syndrome" in mammals: a unified explanation based on neural crest cell behavior and genetics. Genetics. 2014;197(3):795–808.
Article
Google Scholar
Li C, Zhou A, Sang T. Rice domestication by reducing shattering. Science. 2006;311(5769):1936–9.
Article
CAS
Google Scholar
Haberer G, Mayer KF. Barley: from brittle to stable harvest. Cell. 2015;162(3):469–71.
Article
CAS
Google Scholar
Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD. fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science. 2000;289(5476):85–8.
Article
CAS
Google Scholar
Dong Y, Zhang X, Xie M, Arefnezhad B, Wang Z, Wang W, Feng S, Huang G, Guan R, Shen W, et al. Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC Genomics. 2015;16:431.
Article
Google Scholar
Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Luo D, Lin HX. Genetic control of rice plant architecture under domestication. Nat Genet. 2008;40(11):1365–9.
Article
CAS
Google Scholar
Sang T, Ge S. Understanding rice domestication and implications for cultivar improvement. Curr Opin Plant Biol. 2013;16(2):139–46.
Article
Google Scholar
Meyer RS, Purugganan MD. Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet. 2013;14(12):840–52.
Article
CAS
Google Scholar
Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS: the effects of artificial selection on the maize genome. Science 2005, 308(5726):1310–1314.
Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, Li W, Yu Y, Shu L, Zhao Y, Ma Y, et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat Biotechnol. 2015;33(4):408–14.
Article
CAS
Google Scholar
Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, et al. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet. 2007;3(9):1745–56.
Article
CAS
Google Scholar
Olsen KM, Wendel JF. A bountiful harvest: genomic insights into crop domestication phenotypes. Annu Rev Plant Biol. 2013;64:47–70.
Article
CAS
Google Scholar
Xu P, Wu X, Wang B, Luo J, Liu Y, Ehlers JD, Close TJ, Roberts PA, Lu Z, Wang S, et al. Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. Unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies. Heredity. 2012;109(1):34–40.
Article
CAS
Google Scholar
Wang GD, Zhai W, Yang HC, Fan RX, Cao X, Zhong L, Wang L, Liu F, Wu H, Cheng LG, et al. The genomics of selection in dogs and the parallel evolution between dogs and humans. Nat Commun. 2013;4:1860.
Article
Google Scholar
Li M, Tian S, Jin L, Zhou G, Li Y, Zhang Y, Wang T, Yeung CK, Chen L, Ma J, et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet. 2013;45(12):1431–8.
Article
CAS
Google Scholar
Swinnen G, Goossens A, Pauwels L. Lessons from domestication: targeting Cis-regulatory elements for crop improvement. Trends Plant Sci. 2016;21(6):506–15.
Article
CAS
Google Scholar
Li Q, Wang N, Du Z, Hu X, Chen L, Fei J, Wang Y, Li N. Gastrocnemius transcriptome analysis reveals domestication induced gene expression changes between wild and domestic chickens. Genomics. 2012;100(5):314–9.
Article
CAS
Google Scholar
Albert FW, Somel M, Carneiro M, Aximu-Petri A, Halbwax M, Thalmann O, Blanco-Aguiar JA, Plyusnina IZ, Trut L, Villafuerte R, et al. A comparison of brain gene expression levels in domesticated and wild animals. PLoS Genet. 2012;8(9):e1002962.
Article
CAS
Google Scholar
Fang SM, Hu BL, Zhou QZ, Yu QY, Zhang Z. Comparative analysis of the silk gland transcriptomes between the domestic and wild silkworms. BMC Genomics. 2015;16:60.
Article
Google Scholar
Lu X, Li QT, Xiong Q, Li W, Bi YD, Lai YC, Liu XL, Man WQ, Zhang WK, Ma B. The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication. Plant J. 2016;86(6):530–44.
Article
CAS
Google Scholar
Olson MV. When less is more: gene loss as an engine of evolutionary change. Am J Hum Genet. 1999;64(1):18–23.
Article
CAS
Google Scholar
Karl H. Das domestikationssyndrom. Die Kulturpflanze. 1984;32(1):11–34.
Article
Google Scholar
Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S. Genetic structure and diversity in Oryza sativa L. Genetics. 2005;169(3):1631–8.
Article
CAS
Google Scholar
Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L, et al. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet. 2017.
Lemmon ZH, Bukowski R, Sun Q, Doebley JF. The role of cis regulatory evolution in maize domestication. PLoS Genet. 2014;10(11):e1004745.
Article
Google Scholar
Bellucci E, Bitocchi E, Ferrarini A, Benazzo A, Biagetti E, Klie S, Minio A, Rau D, Rodriguez M, Panziera A, et al. Decreased nucleotide and expression diversity and modified Coexpression patterns characterize domestication in the common bean. Plant Cell. 2014;26(5):1901–12.
Article
CAS
Google Scholar
Axelsson E, Ratnakumar A, Arendt ML, Maqbool K, Webster MT, Perloski M, Liberg O, Arnemo JM, Hedhammar A, Lindblad-Toh K. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature. 2013;495(7441):360–4.
Article
CAS
Google Scholar
Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT, Jiang L, Ingman M, Sharpe T, Ka S, et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature. 2010;464(7288):587–91.
Article
CAS
Google Scholar
Huang X, Kurata N, Wei X, Wang ZX, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, et al. A map of rice genome variation reveals the origin of cultivated rice. Nature. 2012;490(7421):497–501.
Article
CAS
Google Scholar
Hufford MB, Xu X, van Heerwaarden J, Pyhajarvi T, Chia JM, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, et al. Comparative population genomics of maize domestication and improvement. Nat Genet. 2012;44(7):808–11.
Article
CAS
Google Scholar
Xiang H, Liu X, Li M, Zhu Y, Wang L, Cui Y, Liu L, Fang G, Qian H, Xu A, et al. The evolutionary road from wild moth to domestic silkworm. Nat Ecol Evol. 2018;2(8):1268–79.
Article
Google Scholar
Chapman MA, Pashley CH, Wenzler J, Hvala J, Tang S, Knapp SJ, Burke JM. A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus). Plant Cell. 2008;20(11):2931–45.
Article
CAS
Google Scholar
Li JY, Wang J, Zeigler RS. The 3,000 rice genomes project: new opportunities and challenges for future rice research. GigaScience. 2014;3:8.
Article
Google Scholar
Luo J, Liu H, Zhou T, Gu B, Huang X, Shangguan Y, Zhu J, Li Y, Zhao Y, Wang Y, et al. An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice. Plant Cell. 2013;25(9):3360–76.
Article
CAS
Google Scholar
Gu B, Zhou T, Luo J, Liu H, Wang Y, Shangguan Y, Zhu J, Li Y, Sang T, Wang Z, et al. An-2 encodes a Cytokinin synthesis enzyme that regulates awn length and grain production in Rice. Mol Plant. 2015;8(11):1635–50.
Article
CAS
Google Scholar
Jin J, Hua L, Zhu Z, Tan L, Zhao X, Zhang W, Liu F, Fu Y, Cai H, Sun X, et al. GAD1 encodes a secreted peptide that regulates grain number, grain length, and awn development in Rice domestication. Plant Cell. 2016;28(10):2453–63.
Article
CAS
Google Scholar
Saitoh K, Onishi K, Mikami I, Thidar K, Sano Y. Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associated with phenotypes. Genetics. 2004;168(2):997–1007.
Article
CAS
Google Scholar
Zhu Z, Tan L, Fu Y, Liu F, Cai H, Xie D, Wu F, Wu J, Matsumoto T, Sun C. Genetic control of inflorescence architecture during rice domestication. Nat Commun. 2013;4:2200.
Article
Google Scholar
Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evol. 1984;38(6):1358–70.
CAS
Google Scholar
Nei M, Li WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979;76(10):5269–73.
Article
CAS
Google Scholar
Zhang L, Su W, Tao R, Zhang W, Chen J, Wu P, Yan C, Jia Y, Larkin RM, Lavelle D, et al. RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis. Nat Commun. 2017;8(1):2264.
Article
Google Scholar
Bolduc N, Yilmaz A, Mejia-Guerra MK, Morohashi K, O'Connor D, Grotewold E, Hake S. Unraveling the KNOTTED1 regulatory network in maize meristems. Genes Dev. 2012;26(15):1685–90.
Article
CAS
Google Scholar
Vaughan DA, Lu BR, Tomooka N. The evolving story of rice evolution. Plant Sci. 2008;174(4):394–408.
Article
CAS
Google Scholar
Doebley JF, Gaut BS, Smith BD: the molecular genetics of crop domestication. Cell 2006, 127(7):1309–1321.
Qi X, Li MW, Xie M, Liu X, Ni M, Shao G, Song C, Kay-Yuen Yim A, Tao Y, Wong FL, et al. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun. 2014;5:4340.
Article
CAS
Google Scholar
Smith JM, Haigh J. The hitch-hiking effect of a favourable gene. Genet Res. 1974;23(1):23–35.
Article
CAS
Google Scholar
Hufford KM, Canaran P, Ware DH, McMullen MD, Gaut BS: Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci. Plant Physiol 2007, 144(3):1642–1653.
Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy RG, Main D. CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Res. 2014;42(Database issue):D1229–36.
Article
CAS
Google Scholar
Leinonen R, Sugawara H, Shumway M. International nucleotide sequence database C: the sequence read archive. Nucleic Acids Res. 2011;39(Database issue):D19–21.
Article
CAS
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
Google Scholar
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protoc. 2012;7(3):562–78.
Article
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome project data processing S: the sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–9.
Article
CAS
Google Scholar
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106.
Article
CAS
Google Scholar
Li H, Durbin R. Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics. 2010;26(5):589–95.
Article
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.
Article
CAS
Google Scholar
Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res. 2010;20(3):393–402.
Article
CAS
Google Scholar
Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, et al. An integrated physical and genetic map of the rice genome. Plant Cell. 2002;14(3):537–45.
Article
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8.
Article
CAS
Google Scholar