Abstract
Plant and animal domestication that was initiated approximately 10,000 years ago led to the dramatic evolution of human society and rapid speciation of plants and animals co-evolving with humans.
Keywords
- Quantitative Trait Locus
- Rice Cultivar
- Artificial Selection
- Major Quantitative Trait Locus
- Abscission Zone
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References
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles E, Qian Q, Kitano H, Matuoka M (2005) Cytokinin oxicase regulates rice grain production. Science 309:741–745
Azhanguvel P, Komatsusa T (2007) A phylogenetic analysis based on nucleotide sequence of a marker linked to the brittle rachis locus indicates a diphyletic origin of barley. Ann Bot 100:1009–1015
Beadle GW (1939) Teosinte and the origin of maize. J Hered 30:245–247
Cheng C, Motohashi R, Tsuchimoto S, Fukuta Y, Ohtsubo H, Ohstubo E (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20:67–75
Chuck G, Meeley R, Irish E, Sakai H, Hake S (2007) The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spkelet1. Nat Genet 39:1517–1521
Clark RM, Linton E, Messing J, Doebley JF (2004) Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Aced Sci USA 101:700–707
Clark RM, Wagler TN, Quijada P, Doebley JF (2006) A distant upstream enhance at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet 38:594–597
Cunniff J, Osborne CP, Ripley BS, Charles M, Jones G (2008) Response of wild C4 crop progenitors to subambient CO2 highlights a possible role in the origin of agriculture. Glob Change Biol 14:576–587
Darwin CR (1859) On the origin of species by means of natural selection. Jone Murray, London
Diamond J (2002) Evolution, consequences and future of plant and animal domestication. Nature 418:700–707
Doebley JF (2001) George Beadle’s other hypothesis: one-gene, one-trait. Genetics 158:487–493
Doebley JF (2004) The genetics of maize evolution. Ann Rev Genet 38:37–59
Doebley JF, Lukens L (1998) Transcriptional regulators and the evolution of plant form. Plant Cell 10:1075–1082
Doebley JF, Stec A, Hubbard L (1997) The evolution of apical dominance in maize. Nature 386:485–488
Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321
Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: a sequence-driven grass model system. Plant Physiol 149:137–141
Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171
Fargione J, Hill J, Tilman D, Polasky S, Hawthorne P (2008) Land clearing and the biofuel carbon debt. Science 319:1235–1238
Faris JD, Simons KJ, Zhang Z, Gill BS (2006) The wheat super domestication gene Q. Wheat Information Service—Frontiers of Wheat Bioscience 100:129–148. (http://www.shigen.nig.ac.jp/wheat/wis/No100/100.html)
Fuller DQ, Qin L, Zheng Y, Zhao Z, Chen X, Hosoya LA, Sun GP (2009) The domestication process and domestication rate in rice: spikelet bases from the lower Yangtze. Science 323:1607–1610
Furukawa T, Maekawa M, Oki T, Suda I, Lida S, Shimada H, Takamure I, Kadowaki K (2007) The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp. Plant Journal 49:91–102
Ge S, Sang T (2011) Inappropriate model rejects independent domestications of indica and japonica rice. Proc Natl Acad Sci USA 108:E75
Gu XY, Kianian SF, Hareland GA, Hoffer BL, Foley ME (2005) Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa). Theor Appl Genet 110:1108–1118
Hancock JF (2004) Plant evolution and the origin of crop species, 2nd edn. CABI Publishing, Cambridge
Harlan JR (1992) Crops and man, 2nd edn. American Society of Agronomy and Crop Science Society of America, Madison
He Z, Zhai W, Wen H, Tan T, Wang Y, Lu X, Greenburg AJ, Hudson RR, Wu C-I, Shi S (2011) Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet 7:e1002100
Heaton EA, Flavell RB, Mascia PN, Thomas SR, Dohleman FG, Long SP (2008) Herbaceous energy crop development: recent progress and future prospects. Curr Opin Biotech 19:202–209
Huang XH, Feng Q, Qian Q, Zhao Q, Wang L, Wang AH, Guan JP, Fan DL, Weng QJ, Huang T, Dong GJ, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076
Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967
Hubbard L, McSteen P, Doebley J, Hake S (2002) Expression patterns and mutant phenotype of teosinte branched1 correlate with growth suppression in maize and teosinte. Genetics 162:1927–1935
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800
Jantasuriyarat C, Vales MI, Watson CJW, Riera-Lizarazu O (2004) Identification and mapping of genetic loci affecting the free-threshing habit and spike compactness. Theor Appl Genet 108:261–273
Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541–544
Jin J, Huang W, Gao J-P, Yang J, Shi M, Zhu M-Z, Luo D, Lin H-X (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40:1365–1369
Karp A, Shield I (2008) Bioenergy from plants and the sustainable yield challenge. New Phytol 179:15–32
Komatsuda T, Maxim P, Senthil N, Mano Y (2004) High-density AFLP map of nonbrittle rachis 1 (btr1) and (btr2) genes in barley (Hordeum vulgare L.). Theor Appl Genet 109:986–995
Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicher T, Tagiri A et al (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104:1424–1429
Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396
Li W, Gill BS (2006) Multiple genetic pathways for seed shattering in the grasses. Funct Integr Genomics 6:300–309
Li X, Qian Q, Fu Z, Wang Y, Xiong G, Zeng D, Wang X, Liu X, Teng S, Hiroshi F, Yuan M, Luo D, Han B, Li J (2003) Control of tillering in rice. Nature 422:618–621
Li C, Zhou A, Sang T (2006a) Rice domestication by reducing shattering. Science 311:1936–1939
Li C, Zhou A, Sang T (2006b) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol 170:185–194
Li P, Wang Y, Qian Q, Fu Z, Wang M, Zeng D, Li B, Wang X, Li J (2007) LAZY1controls rice shoot gravitropism through regulating polar auxin transport. Cell Res 17:402–410
Lin Z, Griffith ME, Li X, Zhu Z, Tan L, Fu Y, Zhang W, Wang X, Xie D, Sun C (2007) Origin of seed shattering in rice (Oryza sativa L.). Planta 226:11–20
Londo JP, Chiang YC, Hung KH, Chiang TY, Schaal BA (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci USA 103:9578–9583
Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404–12410
Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA 107:19579–19584
Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez J, Buckler E, Doebley J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99:6080–6084
Miura K, Ikeda M, Matsubara A, Song X, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M (2010) OsSPL14 promotes paniclebranching and higher grain productivity in rice. Nat Genet 42:545–549
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Rynolds A, Huang P, Jackson SA, Schaal BA, Bustanante CD, Boybo AR, Purugganan MD (2011a) Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci USA 108:8351–8356
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Rynolds A, Huang P, Jackson SA, Schaal BA, Bustanante CD, Boybo AR, Purugganan MD (2011b) Reply to Ge and Sang: a single origin of domesticated rice. Proc Natl Acad Sci USA, doi/10.1073/pnas.1112466108
Morrell PL, Clegg MT (2007) Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent. Proc Natl Acad Sci USA 104:3289–3294
Nalam VJ, Vales MI, Watson CJW, Kianian SF, Riera-Lizarazu O (2006) Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.). Theor Appl Genet 112:373–381
Nalam VJ, Vales MI, Watson CJW, Johnson EB, Riera-Lizarazu O (2007) Map-based analysis of genetic loci on chromosome 2D that affect glume tenacity and threshability, components of the free-threshing habit in common wheat (Triticum aestivum L). Theor Appl Genet 116:135–145
Oliver RJ, Finch JW, Taylor G (2009) Second generation bioenergy crops and climate change: a review of the effects of elevated atmospheric CO2 and drought on water use and the implications for yield. GCB Bioenergy 1:97–114
Onishi K, Horiuchi Y, Ishigoh-Oka N, Takagi K, Ichikawa N, Maruoka M, Sano Y (2007) A QTL cluster for plant architecture and its ecological significance in Asian wild rice. Breeding Sci 57:7–16
Paterson AH, Lin YR, Li Z, Schertz KF, Doebley JF, Pinson SRM, Liu SC, Stansel JW, Irvine JE (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269:1714–1718
Paterson AH et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556
Pourkheirandish M, Komatsuda T (2007) The importance of barley genetics and domestication in a global perspective. Ann Bot 100:999–1008
Pozzi C, Rossini L, Vecchietti A, Salamini F (2004) Gene and genome changes during domestication of cereals. In Gupta PK, Varshney RK (eds) Cereal genomics, pp 165–198
Richerson PJ, Boyd R, Bettinger RL (2001) Was agriculture impossible during the Pleiostocene but mandatory during the Holocene? A climate change hypothesis. Amer Antiq 66:387–411
Robertson GP, Dale VH, Doering OC, Hamburg SP, Melillo JM, Wander MM, Parton WJ, Adler PR, Barney JN, Cruse RM, Duke CS, Fearnside PM, Follett RF, Gibbs HK, Goldember J, Dladenoff DJ, Ojima D, Palmer M, Sharpley A, Wallace L, Weathers KC, Wiens JA, Wilhelm WW (2008) Sustainable biofuels redux. Science 322:49–50
Ross-Ibarra J, Morrell PL, Gaut BS (2007) Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc Natl Acad Sci USA 104:8641–8648
Sage R (1995) Was low atmospheric CO2 during the Pleistocene a limiting factor for the origin of agriculture? Glob Change Biol 1:93–106
Sakuma S, Salomon B, Komatsuda T (2011) The domestication syndrome genes responsible for the major changes in plant form in the Triticeae crops. Plant Cell Physiol 52:738–749
Salamini F, Ozkan H, Brandolini A, Schafer-Pregl R, Marin W (2002) Genetics and geography of wild cereal domestication in the Near East. Nat Rev Genet 3:420–441
Sang T (2009) Genes and mutations underlying domestication transitions in grasses. Plant Physiol 149:63–70
Sang T (2011) Toward the domestication of lignocellulosic energy crops: learning from food crop domestication. J Integr Plant Biol 53:96–104
Sang T, Ge S (2007a) The puzzle of rice domestication. J Integr Plant Biol 49:760–768
Sang T, Ge S (2007b) Genetics and phylogenetics of rice domestication. Cur Opin Genet Dev 17:533–538
Sang T, Zhu W-X (2011) China’s bioenergy potential. GCB Bioenergy 3:79–179
Schnable et al (2010) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115
Searchinger T, Heimlich R, Houghton RA, Dong F, Elobeid A, Fabiosa J, Tokgoz S, Hayes D, Yu TH (2008) Use of U.S. croplands for biofuels increases greenhouse gases through emissions from land use change. Science 319:1238–1244
Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028
Simonetti MC, Bellomo MP, Laghetti G, Perrino P, Simeone R, Blanco A (1999) Quantitative trait loci influencing free-threshing habit in tetraploid wheats. Genet Res Crop Evol 46:267–271
Simons KJ, Fellers JP, Trick HN, Zhang Z, Tai YS, Gill BS, Faris JD (2006) Molecular characterization of the major wheat domestication gene Q. Genetics 172:547–555
Somerville C, Yongs H, Taylor C, Davis SC, Long SP (2010) Feedstocks for lignocellulosic biofuels. Science 329:790–792
Sweeney MT, Thomson MJ, Pfeil BE, McCouch SR (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18:283–294
Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch SR (2007) Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet 3:e133
Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S (2009) Evolutionary history of GS3, a gene conferring grain length in rice. Genetics 182:1323–1334
Taketa S, Amano S, Tsujino Y, Sato T, Saisho D, Kakeda K, Nomura M, Suzuki T, Matsumoto T, Sato K et al (2008) Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway. Proc Natl Acad Sci USA 105:4062–4067
Tan L, Li X, Liu F, Sun X, Li C, Zhu Z, Fu Y, Cai H, Wang X, Xie D, Sun C (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40:1360–1364
van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, Sánchez González JJ, Ross-Ibarra J (2011) Genetic signals of origin, spread and introgression in a large sample of maize landraces. Proc Natl Acad Sci USA 108:1088–1092
Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Kresovich S, Matsuoka Y, Doebley J (2002) Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc Natl Acad Sci USA 99:9650–9655
Vitte C, Ishii T, Lamy F, Brar D, Panaud O (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Gen Genet 272:504–511
Wang RL, Stec A, Hey J, Lukens L, Doebley JF (1999) The limits of selection during maize domestication. Nature 398:236–239
Wang H, Nussbaum-Wagler T, Li BL, Zhao Q, Vigouroux Y, Faller M, Bomblies K, Lukens L, Doebley JF (2005) The origin of the naked grains of maize. Nature 436:714–719
Wang L, Wang AH, Huang XH, Zhao Q, Dong GJ, Qian Q, Sang T, Han B (2011) Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombination inbred lines. Theor Appl Genet 122:327–340
Watanabe N, Sugiyama K, Yamagishi Y, Sakata Y (2002) Comparative telosomic mapping of homoeologous genes for brittle rachis in tetraploid and hexaploid wheats. Hereditas 137:180–185
Watanabe N, Fujii Y, Kato N, Ban T, Martinek P (2006) Microsatellite mapping of the genes for brittle rachis on homoeologous group 3 chromosomes in tetraploid and hexaploid wheats. J Appl Genet 47:93–98
Wright SI, Vroh Bi I, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS (2005) The effects of artificial selection on the maize genome. Science 308:1310–1314
Xia Q et al (2009) Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326:433–436
Youens-Clark K, Buckler E, Casstevens T, Chen C, DeClerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D (2011) Gramene database in 2010: updates and extensions. Nucleic Acids Res 39:D1085–D1094
Yu Y, Tang T, Qian Q, Wang Y, Yan M, Zeng D, Han B, Wu C-I, Shi S, Li J (2008) Independent losses of function in a polyphenol oxidase in rice: Differentiation in grain discoloration between subspecies and the role of positive selection under domestication. Plant Cell 20:2946–2959
Zhang L, Zhu Q, Wu Z, Ross-Ibarra J, Gaut BS, Ge S, Sang T (2009) Selection on grain shattering genes and rates of rice domestication. New Phytol 184:708–720
Zhu Q, Ge S (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol 167:249–265
Zhu B, Si L, Wang Z, Zhou Y, Zhu J, Shangguan Y, Lu D, Fan D, Li C, Lin H, Qian Q, Sang T, Zhou B, Minobe Y, Han B (2011) Genetic control of a transition from black to straw-white seed hull in rice domestication. Plant Physiol 155:1301–1311
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Sang, T., Li, J. (2013). Molecular Genetic Basis of the Domestication Syndrome in Cereals. In: Gupta, P., Varshney, R. (eds) Cereal Genomics II. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6401-9_12
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