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Annual Review of Plant Biology

Volume 64, 2013

A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

Abstract

Human selection during crop domestication has resulted in remarkable transformations of plant phenotypes, providing a window into the genetic basis of morphological evolution. Recent progress in our understanding of the genetic architecture of novel plant traits has emerged from combining advanced molecular technologies with improved experimental designs, including nested association mapping, genome-wide association studies, population genetic screens for signatures of selection, and candidate gene approaches. These studies reveal a diversity of underlying causative mutations affecting phenotypes important in plant domestication and crop improvement, including coding sequence substitutions, presence/absence and copy number variation, transposon activation leading to novel gene structures and expression patterns, diversification following gene duplication, and polyploidy leading to altered combinatorial capabilities. The genomic regions unknowingly targeted by human selection include both structural and regulatory genes, often with results that propagate through the transcriptome as well as to other levels in the biosynthetic and morphogenetic networks.

Keyword(s): association mapping, crop improvement, evo-devo, evolutionary genomics, human-mediated selection
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2013-04-29
2024-10-05
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Literature Cited

  1. Akhunov ED, Akhunova AR, Anderson OD, Anderson J, Blake N. 1.  et al. 2010. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics 11:702 [Google Scholar]
  2. 2. Arabidopsis Genome Init 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815 [Google Scholar]
  3. Asano K, Yamasaki M, Takuno S. 3.  2011. Artificial selection for a green revolution gene during japonica rice domestication. Proc. Natl. Acad. Sci. USA 108:11034–39 [Google Scholar]
  4. Bao Y, Hu G, Flagel LE, Salmon A, Bezanilla M. 4.  et al. 2011. Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium). Proc. Natl. Acad. Sci. USA 108:21152–57 [Google Scholar]
  5. Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW. 5.  et al. 2008. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol. 25:2445–55 [Google Scholar]
  6. Beló A, Beatty MK, Hondred D, Fengler K, Li B, Rafalski A. 6.  2010. Allelic genome structural variations in maize detected by array comparative genome hybridization. Theor. Appl. Genet. 120:355–67 [Google Scholar]
  7. Benjak A, Boué S, Forneck A, Casacuberta JM. 7.  2009. Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.). Genome Biol. Evol. 1:75–84 [Google Scholar]
  8. Benjak A, Forneck A, Casacuberta JM. 8.  2008. Genome-wide analysis of the “cut-and-paste” transposons of grapevine. PLoS ONE 3:e3107 [Google Scholar]
  9. Blackman BK, Rasmussen D, Strasburg JL, Raduski AR, Burke JM. 9.  et al. 2011. Contributions of flowering time genes to sunflower domestication and improvement. Genetics 187:271–87 [Google Scholar]
  10. Blackman BK, Strasburg JL, Raduski AR, Michaels SD, Rieseberg LH. 10.  2010. The role of recently derived FT paralogs in sunflower domestication. Curr. Biol. 20:629–35 [Google Scholar]
  11. Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE. 11.  2005. The gene for fragrance in rice. Plant Biotechnol. J. 3:363–70 [Google Scholar]
  12. Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ. 12.  et al. 2011. Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genet. 7:e1002383 [Google Scholar]
  13. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ. 13.  et al. 2009. The genetic architecture of maize flowering time. Science 325:714–18 [Google Scholar]
  14. Burger JC, Chapman MA, Burke JM. 14.  2008. Molecular insights into the evolution of crop plants. Am. J. Bot. 95:113–22 [Google Scholar]
  15. Burke JM, Burger JC, Chapman M. 15.  2007. Crop evolution: from genetics to genomics. Curr. Opin. Genet. Dev. 17:525–32 [Google Scholar]
  16. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A. 16.  et al. 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet. 3:1745–56 [Google Scholar]
  17. Carroll SB. 17.  2008. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134:25–36 [Google Scholar]
  18. Chantret N, Cenci A, Sabot F, Anderson O, Dubcovsky J. 18.  2004. Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice. Mol. Genet. Genomics 271:377–86 [Google Scholar]
  19. Chapman MA, Pashley CH, Wenzler J, Hvala J, Tang S. 19.  et al. 2008. A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus). Plant Cell 20:2931–45 [Google Scholar]
  20. Chaudhary B, Hovav R, Flagel L, Mittler R, Wendel JF. 20.  2009. Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium). BMC Genomics 10:378 [Google Scholar]
  21. Chia J-M, Song C, Bradbury PJ, Costich D, de Leon N. 21.  et al. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44:803–7 [Google Scholar]
  22. Chuck G, Cigan AM, Saeteurn K, Hake S. 22.  2007. The heterochronic maize mutant Corngrass1 results from overexpression of a tandem microRNA. Nat. Genet. 39:544–49 [Google Scholar]
  23. Clotault J, Thuillet A-C, Buiron M, De Mita S, Couderc M. 23.  et al. 2012. Evolutionary history of pearl millet (Pennisetum glaucum [L.] R. Br.) and selection on flowering genes since its domestication. Mol. Biol. Evol. 29:1199–212 [Google Scholar]
  24. Cong B, Barrero LS, Tanksley SD. 24.  2008. Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat. Genet. 40:800–4 [Google Scholar]
  25. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O. 25.  et al. 2010. Origins and functional impact of copy number variation in the human genome. Nature 464:704–12 [Google Scholar]
  26. Cook JP, McMullen MD, Holland JB, Tian F, Bradbury P. 26.  et al. 2012. Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiol. 158:824–34 [Google Scholar]
  27. Cornille A, Gladieux P, Smulders MJM, Roldán-Ruiz I, Laurens F. 27.  et al. 2012. New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet. 8:e1002703 [Google Scholar]
  28. Darwin C. 28.  1859. On the Origin of Species London: Murray [Google Scholar]
  29. D'Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F. 29.  et al. 2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488:213–17 [Google Scholar]
  30. Díaz A, Zikhali M, Turner AS, Isaac P, Laurie DA. 30.  2012. Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PLoS ONE 7:e33234 [Google Scholar]
  31. Distelfeld A, Tranquilli G, Li C, Yan L, Dubcovsky J. 31.  2009. Genetic and molecular characterization of the VRN2 loci in tetraploid wheat. Plant Physiol. 149:245–57 [Google Scholar]
  32. Doebley JF, Gaut BS, Smith BD. 32.  2006. The molecular genetics of crop domestication. Cell 127:1309–21 [Google Scholar]
  33. Doebley JF, Stec A, Hubbard L. 33.  1997. The evolution of apical dominance in maize. Nature 386:485–88 [Google Scholar]
  34. Doebley JF, Stec A, Wendel J, Edwards M. 34.  1990. Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. Proc. Natl. Acad. Sci. USA 87:9888–92 [Google Scholar]
  35. Doi K, Izawa T, Fuse T, Yamanouchi U. 35.  2004. Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev. 2:926–36 [Google Scholar]
  36. Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE. 36.  et al. 2008. Evolutionary genetics of genome merger and doubling in plants. Annu. Rev. Genet. 42:443–61 [Google Scholar]
  37. Dubcovsky J, Dvorak J. 37.  2007. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316:1862–66 [Google Scholar]
  38. Dvorak J, Deal KR, Luo M-C, You FM, von Borstel K, Dehghani H. 38.  2012. The origin of spelt and free-threshing hexaploid wheat. J. Hered. 103:426–41 [Google Scholar]
  39. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K. 39.  et al. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379 [Google Scholar]
  40. Fan C, Xing Y, Mao H, Lu T, Han B. 40.  et al. 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. 112:1164–71 [Google Scholar]
  41. Fan L, Bao J, Wang Y, Yao J, Gui Y. 41.  et al. 2009. Post-domestication selection in the maize starch pathway. PLoS ONE 4:e7612 [Google Scholar]
  42. Fan L, Quan L, Leng X, Guo X, Hu W. 42.  et al. 2008. Molecular evidence for post-domestication selection in the Waxy gene of Chinese waxy maize. Mol. Breed. 22:329–38 [Google Scholar]
  43. Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K. 43.  2011. Crop genome sequencing: lessons and rationales. Trends Plant Sci. 16:77–88 [Google Scholar]
  44. Feuk L, Carson AR, Scherer SW. 44.  2006. Structural variation in the human genome. Nat. Rev. Genet. 7:85–97 [Google Scholar]
  45. Flagel LE, Wendel JF. 45.  2009. Gene duplication and evolutionary novelty in plants. New Phytol. 183:557–64 [Google Scholar]
  46. Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD. 46.  2012. Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. Mol. Biol. Evol. 29:675–87 [Google Scholar]
  47. Fournier-Level A, Lacombe T, Le Cunff L, Boursiquot J-M, This P. 47.  2010. Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.). Heredity 104:351–62 [Google Scholar]
  48. Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G. 48.  et al. 2012. The genome of melon (Cucumis melo L.). Proc. Natl. Acad. Sci. USA 109:11872–77 [Google Scholar]
  49. Golovnina KA, Kondratenko EY, Blinov AG, Goncharov NP. 49.  2010. Molecular characterization of vernalization loci VRN1 in wild and cultivated wheats. BMC Plant Biol. 10:168 [Google Scholar]
  50. Gross BL, Olsen KM. 50.  2010. Genetic perspectives on crop domestication. Trends Plant Sci. 15:529–37 [Google Scholar]
  51. Gross BL, Skare KJ, Olsen KM. 51.  2009. Novel Phr1 mutations and the evolution of phenol reaction variation in US weedy rice (Oryza sativa). New Phytol. 184:842–50 [Google Scholar]
  52. Hammer K. 52.  1984. Das Domestikationssyndrom. Kulturpflanze 32:11–34 [Google Scholar]
  53. He Z, Zhai W, Wen H, Tang T, Wang Y. 53.  et al. 2011. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet. 7:e1002100 [Google Scholar]
  54. Hoekstra HE, Coyne JA. 54.  2007. The locus of evolution: evo devo and the genetics of adaptation. Evolution 61:995–1016 [Google Scholar]
  55. Hollister JD, Smith LM, Guo Y-L, Ott F, Weigel D, Gaut BS. 55.  2011. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl. Acad. Sci. USA 108:2322–27 [Google Scholar]
  56. Hovav R, Chaudhary B, Udall JA, Flagel L, Wendel JF. 56.  2008. Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton. Genetics 179:1725–33 [Google Scholar]
  57. Hovav R, Udall JA, Chaudhary B, Hovav E, Flagel L. 57.  et al. 2008. The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism. PLoS Genet. 4:e25 [Google Scholar]
  58. Huang X, Wei X, Sang T, Zhao Q, Feng Q. 58.  et al. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42:961–67 [Google Scholar]
  59. Huang X, Zhao Y, Wei X, Li C, Wang A. 59.  et al. 2012. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat. Genet. 44:32–39 [Google Scholar]
  60. Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, Chia J-M. 60.  et al. 2012. Comparative population genomics of maize domestication and improvement. Nat. Genet. 44:808–11 [Google Scholar]
  61. Hung H-Y, Shannon LM, Tian F, Bradbury PJ, Chen C. 61.  et al. 2012. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proc. Natl. Acad. Sci. USA 109:E1913–21 [Google Scholar]
  62. Hunt HV, Denyer K, Packman LC, Jones MK, Howe CJ. 62.  2010. Molecular basis of the waxy endosperm starch phenotype in broomcorn millet (Panicum miliaceum L.). Mol. Biol. Evol. 27:1478–94 [Google Scholar]
  63. 63. Int. Rice Genome Seq. Proj 2005. The map-based sequence of the rice genome. Nature 436:793–800 [Google Scholar]
  64. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L. 64.  et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473:97–100 [Google Scholar]
  65. Jiao Y, Zhao H, Ren L, Song W, Zeng B. 65.  et al. 2012. Genome-wide genetic changes during modern breeding of maize. Nat. Genet. 44:812–15 [Google Scholar]
  66. Jin J, Huang W, Gao J-P, Yang J, Shi M. 66.  et al. 2008. Genetic control of rice plant architecture under domestication. Nat. Genet. 40:1365–69 [Google Scholar]
  67. Knox AK, Dhillon T, Cheng H, Tondelli A, Pecchioni N, Stockinger EJ. 67.  2010. CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor. Appl. Genet. 121:21–35 [Google Scholar]
  68. Kobayashi S, Goto-Yamamoto N, Hirochika H. 68.  2005. Association of VvMybA1 gene expression with anthocyanin production in grape (Vitis vinifera) skin-color mutants. J. Jpn. Soc. Hortic. Sci. 74:196–203 [Google Scholar]
  69. Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H. 69.  et al. 2007. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc. Natl. Acad. Sci. USA 104:1424–29 [Google Scholar]
  70. Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR. 70.  2009. The origin and evolution of fragrance in rice (Oryza sativa L.). Proc. Natl. Acad. Sci. USA 106:14444–49 [Google Scholar]
  71. Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR. 71.  et al. 2011. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat. Genet. 43:163–68 [Google Scholar]
  72. Lakis G, Navascués M, Rekima S, Simon M, Remigereau M-S. 72.  et al. 2012. Evolution of neutral and flowering genes along pearl millet (Pennisetum glaucum) domestication. PLoS ONE 7:e36642 [Google Scholar]
  73. Lam H-M, Xu X, Liu X, Chen W, Yang G. 73.  et al. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet. 42:1053–59 [Google Scholar]
  74. Li Y, Fan C, Xing Y, Jiang Y, Luo L. 74.  et al. 2011. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat. Genet. 43:1266–69 [Google Scholar]
  75. Lin Z, Li X, Shannon LM, Yeh C-T, Wang ML. 75.  et al. 2012. Parallel domestication of the Shattering1 genes in cereals. Nat. Genet. 44:720–24 [Google Scholar]
  76. Lu L, Yan W, Xue W, Shao D, Xing Y. 76.  2012. Evolution and association analysis of Ghd7 in rice. PLoS ONE 7:e34021 [Google Scholar]
  77. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H. 77.  et al. 2009. Genetic properties of the maize nested association mapping population. Science 325:737–40 [Google Scholar]
  78. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. 78.  2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 17:240–48 [Google Scholar]
  79. Morrell PL, Buckler ES, Ross-Ibarra J. 79.  2011. Crop genomics: advances and applications. Nat. Rev. Genet. 13:85–96 [Google Scholar]
  80. Myles S, Boyko AR, Owens CL, Brown PJ, Grassi F. 80.  et al. 2011. Genetic structure and domestication history of the grape. Proc. Natl. Acad. Sci. USA 108:3530–35 [Google Scholar]
  81. Ni Z, Kim E-D, Ha M, Lackey E, Liu J. 81.  et al. 2009. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457:327–31 [Google Scholar]
  82. Park Y-J, Nemoto K, Nishikawa T, Matsushima K, Minami M, Kawase M. 82.  2010. Waxy strains of three amaranth grains raised by different mutations in the coding region. Mol. Breed. 25:623–35 [Google Scholar]
  83. Paterson AH. 83.  2005. Polyploidy, evolutionary opportunity, and crop adaptation. Genetica 123:191–96 [Google Scholar]
  84. Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, Estill JC. 84.  2006. Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon. Trends Genet. 22:597–602 [Google Scholar]
  85. Paterson AH, Lin YR, Li Z, Schertz KF, Doebley JF. 85.  et al. 1995. Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269:1714–18 [Google Scholar]
  86. Pickersgill B. 86.  2009. Domestication of plants revisited—Darwin to the present day. Bot. J. Linn. Soc. 161:203–12 [Google Scholar]
  87. Poland JA, Bradbury PJ, Buckler ES, Nelson RJ. 87.  2011. Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc. Natl. Acad. Sci. USA 108:6893–98 [Google Scholar]
  88. Ramsay L, Comadran J, Druka A, Marshall DF, Thomas WTB. 88.  et al. 2011. INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1. Nat. Genet. 43:169–72 [Google Scholar]
  89. Rapp RA, Haigler CH, Flagel L, Hovav RH, Udall JA, Wendel JF. 89.  2010. Gene expression in developing fibres of upland cotton (Gossypium hirsutum L.) was massively altered by domestication. BMC Biol. 8:139 [Google Scholar]
  90. Raquin A-L, Brabant P, Rhoné B, Balfourier F, Leroy P, Goldringer I. 90.  2008. Soft selective sweep near a gene that increases plant height in wheat. Mol. Ecol. 17:741–56 [Google Scholar]
  91. Remigereau M-S, Lakis G, Rekima S, Leveugle M, Fontaine MC. 91.  et al. 2011. Cereal domestication and evolution of branching: evidence for soft selection in the Tb1 orthologue of pearl millet (Pennisetum glaucum [L.] R. Br.). PLoS ONE 6:e22404 [Google Scholar]
  92. Riedelsheimer C, Lisec J, Czedik-Eysenberg A, Sulpice R, Flis A. 92.  et al. 2012. Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize. Proc. Natl. Acad. Sci. USA 109:8872–77 [Google Scholar]
  93. Rizzon C, Ponger L, Gaut BS. 93.  2006. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput. Biol. 2:e115 [Google Scholar]
  94. Rockman MV, Kruglyak L. 94.  2008. Breeding designs for recombinant inbred advanced intercross lines. Genetics 179:1069–78 [Google Scholar]
  95. Saïdou A-A, Mariac C, Luong V, Pham J-L, Bezançon G, Vigouroux Y. 95.  2009. Association studies identify natural variation at PHYC linked to flowering time and morphological variation in pearl millet. Genetics 182:899–910 [Google Scholar]
  96. Saito H, Yuan Q, Okumoto Y, Doi K, Yoshimura A. 96.  et al. 2009. Multiple alleles at Early flowering 1 locus making variation in the basic vegetative growth period in rice (Oryza sativa L.). Theor. Appl. Genet. 119:315–23 [Google Scholar]
  97. Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K. 97.  et al. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–41 [Google Scholar]
  98. Schnable JC, Wang X, Pires JC, Freeling M. 98.  2012. Escape from preferential retention following repeated whole genome duplications in plants. Front. Plant Sci. 3:94 [Google Scholar]
  99. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F. 99.  et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–15 [Google Scholar]
  100. Schranz ME, Osborn TC. 100.  2004. De novo variation in life-history traits and responses to growth conditions of resynthesized polyploid Brassica napus (Brassicaceae). Am. J. Bot. 91:174–83 [Google Scholar]
  101. Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H. 101.  et al. 2008. Deletion in a gene associated with grain size increased yields during rice domestication. Nat. Genet. 40:1023–28 [Google Scholar]
  102. Sigmon B, Vollbrecht E. 102.  2010. Evidence of selection at the ramosa1 locus during maize domestication. Mol. Ecol. 19:1296–311 [Google Scholar]
  103. Simons KJ, Fellers JP, Trick HN, Zhang Z, Tai Y-S. 103.  et al. 2006. Molecular characterization of the major wheat domestication gene Q. Genetics 172:547–55 [Google Scholar]
  104. Soltis DE, Soltis PS, Tate JA. 104.  2003. Advances in the study of polyploidy since Plant Speciation. New Phytol. 161:173–91 [Google Scholar]
  105. Soltis PS, Soltis DE. 105.  2009. The role of hybridization in plant speciation. Annu. Rev. Plant Biol. 60:561–88 [Google Scholar]
  106. Soltis PS, Soltis DE. 106.  2012. Polyploidy and Genome Evolution New York: Springer [Google Scholar]
  107. Song X-J, Huang W, Shi M, Zhu M-Z, Lin H-X. 107.  2007. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat. Genet. 39:623–30 [Google Scholar]
  108. Springer NM, Ying K, Fu Y, Ji T, Yeh C-T. 108.  et al. 2009. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet. 5:e1000734 [Google Scholar]
  109. Studer A, Zhao Q, Ross-Ibarra J, Doebley J. 109.  2011. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat. Genet. 43:1160–63 [Google Scholar]
  110. Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H. 110.  et al. 2010. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc. Natl. Acad. Sci. USA 107:5792–97 [Google Scholar]
  111. Swanson-Wagner RA, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J. 111.  et al. 2012. Reshaping of the maize transcriptome by domestication. Proc. Natl. Acad. Sci. USA 109:11878–83 [Google Scholar]
  112. Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC. 112.  et al. 2010. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res. 20:1689–99 [Google Scholar]
  113. Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T. 113.  et al. 2009. Evolutionary history of GS3, a gene conferring grain length in rice. Genetics 182:1323–34 [Google Scholar]
  114. Taketa S, Amano S, Tsujino Y, Sato T, Saisho D. 114.  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 105:4062–67 [Google Scholar]
  115. Tan L, Li X, Liu F, Sun X, Li C. 115.  et al. 2008. Control of a key transition from prostrate to erect growth in rice domestication. Nat. Genet. 40:1360–64 [Google Scholar]
  116. Tang H, Sezen U, Paterson AH. 116.  2010. Domestication and plant genomes. Curr. Opin. Plant Biol. 13:160–66 [Google Scholar]
  117. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES. 117.  2001. Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28:286–89 [Google Scholar]
  118. Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q. 118.  et al. 2011. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43:159–62 [Google Scholar]
  119. Tian Z, Wang X, Lee R, Li Y, Specht JE. 119.  et al. 2010. Artificial selection for determinate growth habit in soybean. Proc. Natl. Acad. Sci. USA 107:8563–68 [Google Scholar]
  120. Udall JA, Wendel JF. 120.  2006. Polyploidy and crop improvement. Crop Sci. 46:Suppl. 13–14 [Google Scholar]
  121. van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM. 121.  et al. 2011. Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proc. Natl. Acad. Sci. USA 108:1088–92 [Google Scholar]
  122. van Heerwaarden J, Hufford MB, Ross-Ibarra J. 122.  2012. Historical genomics of North American maize. Proc. Natl. Acad. Sci. USA 109:12420–25 [Google Scholar]
  123. Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK. 123.  et al. 2012. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30:83–89 [Google Scholar]
  124. Vielle-Calzada J-P, Martínez de la Vega O, Hernández-Guzmán G, Ibarra-Laclette E, Alvarez-Mejía C. 124.  et al. 2009. The Palomero genome suggests metal effects on domestication. Science 326:1078 [Google Scholar]
  125. Walker AR, Lee E, Bogs J, McDavid DAJ, Thomas MR, Robinson SP. 125.  2007. White grapes arose through the mutation of two similar and adjacent regulatory genes. Plant J. 49:772–85 [Google Scholar]
  126. Wang E, Wang J, Zhu X, Hao W, Wang L. 126.  et al. 2008. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat. Genet. 40:1370–74 [Google Scholar]
  127. Wang E, Xu X, Zhang L, Zhang H, Lin L. 127.  et al. 2010. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evol. Biol. 10:108 [Google Scholar]
  128. Wang Q, Dooner HK. 128.  2006. Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proc. Natl. Acad. Sci. USA 103:17644–49 [Google Scholar]
  129. Wang RL, Stec A, Hey J, Lukens L, Doebley J. 129.  1999. The limits of selection during maize domestication. Nature 398:236–69 [Google Scholar]
  130. Wang S, Wu K, Yuan Q, Liu X, Liu Z. 130.  et al. 2012. Control of grain size, shape and quality by OsSPL16 in rice. Nat. Genet. 44:950–54 [Google Scholar]
  131. Wang Y, Shen D, Bo S, Chen H, Zheng J. 131.  et al. 2010. Sequence variation and selection of small RNAs in domesticated rice. BMC Evol. Biol. 10:119 [Google Scholar]
  132. Wendel JF. 132.  2000. Genome evolution in polyploids. Plant Mol. Biol. 42:225–49 [Google Scholar]
  133. Wingen LU, Münster T, Faigl W, Deleu W, Sommer H. 133.  et al. 2012. Molecular genetic basis of pod corn (Tunicate maize). Proc. Natl. Acad. Sci. USA 109:7115–20 [Google Scholar]
  134. Wittkopp PJ, Kalay G. 134.  2012. cis-Regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat. Rev. Genet. 13:59–69 [Google Scholar]
  135. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF. 135.  et al. 2005. The effects of artificial selection on the maize genome. Science 308:1310–14 [Google Scholar]
  136. Wu Y, Li X, Xiang W, Zhu C, Lin Z. 136.  et al. 2012. Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1. Proc. Natl. Acad. Sci. USA 109:10281–86 [Google Scholar]
  137. Würschum T, Maurer HP, Kraft T, Janssen G, Nilsson C, Reif JC. 137.  2011. Genome-wide association mapping of agronomic traits in sugar beet. Theor. Appl. Genet. 123:1121–31 [Google Scholar]
  138. Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E. 138.  2008. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319:1527–30 [Google Scholar]
  139. Xu P, Wu X, Wang B, Luo J, Liu Y. 139.  et al. 2012. Genome wide linkage disequilibrium in Chinese asparagus bean (Vigna. unguiculata ssp. sesquipedialis) germplasm: implications for domestication history and genome wide association studies. Heredity 109:34–40 [Google Scholar]
  140. Xu X, Liu X, Ge S, Jensen JD, Hu F. 140.  et al. 2012. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol. 30:105–11 [Google Scholar]
  141. Xue W, Xing Y, Weng X, Zhao Y, Tang W. 141.  et al. 2008. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat. Genet. 40:761–67 [Google Scholar]
  142. Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W. 142.  et al. 2004. The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–44 [Google Scholar]
  143. Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J. 143.  2003. Positional cloning of the wheat vernalization gene VRN1. Proc. Natl. Acad. Sci. USA 100:6263–68 [Google Scholar]
  144. Yu B, Lin Z, Li H, Li X, Li J. 144.  et al. 2007. TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J. 52:891–98 [Google Scholar]
  145. Yu J, Holland JB, McMullen MD, Buckler ES. 145.  2008. Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–51 [Google Scholar]
  146. Yu Y, Tang T, Qian Q, Wang Y, Yan M. 146.  et al. 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 20:2946–59 [Google Scholar]
  147. Zerjal T, Rousselet A, Mhiri C, Combes V, Madur D. 147.  et al. 2012. Maize genetic diversity and association mapping using transposable element insertion polymorphisms. Theor. Appl. Genet. 124:1521–37 [Google Scholar]
  148. Zhang Z, Belcram H, Gornicki P, Charles M, Just J. 148.  et al. 2011. Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat. Proc. Natl. Acad. Sci. USA 108:18737–42 [Google Scholar]
  149. Zhao K, Tung C-W, Eizenga GC, Wright MH, Ali ML. 149.  et al. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat. Commun. 2:467 [Google Scholar]
  150. Zhu B-F, Si L, Wang Z, Zhou Y, Zhu J. 150.  et al. 2011. Genetic control of a transition from black to straw-white seed hull in rice domestication. Plant Physiol. 155:1301–11 [Google Scholar]
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A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes
Annual Review of Plant Biology 64, 47 (2013); https://doi.org/10.1146/annurev-arplant-050312-120048
/content/journals/10.1146/annurev-arplant-050312-120048
/content/journals/10.1146/annurev-arplant-050312-120048
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