1932

Abstract

Crops feed the world's population and shape human civilization. The improvement of crop productivity has been ongoing for almost 10,000 years and has evolved from an experience-based to a knowledge-driven practice over the past three decades. Natural alleles and their reshuffling are long-standing genetic changes that affect how crops respond to various environmental conditions and agricultural practices. Decoding the genetic basis of natural variation is central to understanding crop evolution and, in turn, improving crop breeding. Here, we review current advances in the approaches used to map the causal alleles of natural variation, provide refined insights into the genetics and evolution of natural variation, and outline how this knowledge promises to drive the development of sustainable agriculture under the dome of emerging technologies.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-arplant-080720-090632
2021-06-17
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/arplant/72/1/annurev-arplant-080720-090632.html?itemId=/content/journals/10.1146/annurev-arplant-080720-090632&mimeType=html&fmt=ahah

Literature Cited

  1. 1. 
    Abdelghani AH, Parzies HK, Omary A, Geiger HH. 2004. Estimating the outcrossing rate of barley landraces and wild barley populations collected from ecologically different regions of Jordan. Theor. Appl. Genet. 109:588–95
    [Google Scholar]
  2. 2. 
    Alonge M, Wang X, Benoit M, Soyk S, Pereira L et al. 2020. Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell 182:145–61.e23
    [Google Scholar]
  3. 3. 
    Alpert KB, Tanksley SD 1996. High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2: a major fruit weight quantitative trait locus in tomato. PNAS 93:15503–7
    [Google Scholar]
  4. 4. 
    Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y et al. 2019. Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat. Biotechnol. 37:139–43
    [Google Scholar]
  5. 5. 
    Auer PL, Lettre G. 2015. Rare variant association studies: considerations, challenges and opportunities. Genome Med 7:16
    [Google Scholar]
  6. 6. 
    Bai X, Huang Y, Hu Y, Liu H, Zhang B et al. 2017. Duplication of an upstream silencer of FZP increases grain yield in rice. Nat. Plants 3:885–93
    [Google Scholar]
  7. 7. 
    Barrero JM, Cavanagh CR, Verbyla KL, Tibbits J, Verbyla AP et al. 2015. Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL. Genome Biol 16:93
    [Google Scholar]
  8. 8. 
    Benke KK, Tomkins B. 2017. Future food-production systems: vertical farming and controlled-environment agriculture. Sustain. Sci. Pract. Policy 13:13–26
    [Google Scholar]
  9. 9. 
    Bommert P, Nagasawa NS, Jackson D. 2013. Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat. Genet. 45:334–37
    [Google Scholar]
  10. 10. 
    Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ et al. 2009. The genetic architecture of maize flowering time. Science 325:714–18
    [Google Scholar]
  11. 11. 
    Cannon ME, Mohlke KL. 2018. Deciphering the emerging complexities of molecular mechanisms at GWAS loci. Am. J. Hum. Genet. 103:637–53
    [Google Scholar]
  12. 12. 
    Chakrabarti M, Zhang N, Sauvage C, Munos S, Blanca J et al. 2013. A cytochrome P450 regulates a domestication trait in cultivated tomato. PNAS 110:17125–30
    [Google Scholar]
  13. 13. 
    Chen L, Liu Y. 2014. Male sterility and fertility restoration in crops. Annu. Rev. Plant Biol. 65:579–606Reviews the mechanisms underlying male sterility, fertility restoration, and hybrid compatibility (see also 122).
    [Google Scholar]
  14. 14. 
    Comadran J, Kilian B, Russell J, Ramsay L, Stein N et al. 2012. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat. Genet. 44:1388–92
    [Google Scholar]
  15. 15. 
    Cui X, Wise RP, Schnable PS. 1996. The rf2 nuclear restorer gene of male-sterile T-cytoplasm maize. Science 272:1334–36
    [Google Scholar]
  16. 16. 
    Dai X, Ding Y, Tan L, Fu Y, Liu F et al. 2012. LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon). J. Integr. Plant Biol. 54:790–99
    [Google Scholar]
  17. 17. 
    De Wiel CCMV, Lotz LAP. 2006. Outcrossing and coexistence of genetically modified with (genetically) unmodified crops: a case study of the situation in the Netherlands. NJAS Wagen. J. Life Sci. 54:17–35
    [Google Scholar]
  18. 18. 
    Dixon LE, Greenwood JR, Bencivenga S, Zhang P, Cockram J et al. 2018. TEOSINTE BRANCHED1 regulates inflorescence architecture and development in bread wheat (Triticum aestivum). Plant Cell 30:563–81
    [Google Scholar]
  19. 19. 
    Doebley JF, Gaut BS, Smith BD. 2006. The molecular genetics of crop domestication. Cell 127:1309–21
    [Google Scholar]
  20. 20. 
    Doebley JF, Stec A, Hubbard L. 1997. The evolution of apical dominance in maize. Nature 386:485–88
    [Google Scholar]
  21. 21. 
    Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T et al. 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 18:926–36
    [Google Scholar]
  22. 22. 
    Dong Y, Yang X, Liu J, Wang B, Liu BL, Wang Y. 2014. Pod shattering resistance associated with domestication is mediated by a NAC gene in soybean. Nat. Commun. 5:3352
    [Google Scholar]
  23. 23. 
    Dong Z, Xiao Y, Govindarajulu R, Feil R, Siddoway ML et al. 2019. The regulatory landscape of a core maize domestication module controlling bud dormancy and growth repression. Nat. Commun. 10:3810
    [Google Scholar]
  24. 24. 
    Douglas AE. 2018. Strategies for enhanced crop resistance to insect pests. Annu. Rev. Plant Biol. 69:637–60
    [Google Scholar]
  25. 25. 
    Elichukwu NC. 2019. Applications of artificial intelligence in agriculture: a review. Eng. Technol. Appl. Sci. Res. 9:4377–83
    [Google Scholar]
  26. 26. 
    Enjalbert J, David JL. 2000. Inferring recent outcrossing rates using multilocus individual heterozygosity: application to evolving wheat populations. Genetics 156:1973–82
    [Google Scholar]
  27. 27. 
    Eom JS, Luo D, Atienza-Grande G, Yang J, Ji C et al. 2019. Diagnostic kit for rice blight resistance. Nat. Biotechnol. 37:1372–79
    [Google Scholar]
  28. 28. 
    Eshed Y, Zamir D. 1995. An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141:1147–62
    [Google Scholar]
  29. 29. 
    Fang J, Zhang F, Wang H, Wang W, Zhao F et al. 2019. Ef-cd locus shortens rice maturity duration without yield penalty. PNAS 116:18717–22
    [Google Scholar]
  30. 30. 
    Faris JD 2014. Wheat domestication: key to agricultural revolutions past and future. Genomics of Plant Genetic Resources, Vol. 1: Managing, Sequencing and Mining Genetic Resources R Tuberosa, A Graner, E Frison 439–64 Dordrecht, Neth: Springer
    [Google Scholar]
  31. 31. 
    Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B et al. 2000. fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88
    [Google Scholar]
  32. 32. 
    Fridman E, Pleban T, Zamir D 2000. A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. PNAS 97:4718–23
    [Google Scholar]
  33. 33. 
    Funatsuki H, Suzuki M, Hirose A, Inaba H, Yamada T et al. 2014. Molecular basis of a shattering resistance boosting global dissemination of soybean. PNAS 111:17797–802
    [Google Scholar]
  34. 34. 
    Gao H, Gadlage MJ, Lafitte HR, Lenderts B, Yang M et al. 2020. Superior field performance of waxy corn engineered using CRISPR-Cas9. Nat. Biotechnol. 38:579–81
    [Google Scholar]
  35. 35. 
    Gao H, Jin M, Zheng XM, Chen J, Yuan D et al. 2014. Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice. PNAS 111:16337–42
    [Google Scholar]
  36. 36. 
    Gao L, Gonda I, Sun H, Ma Q, Bao K et al. 2019. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat. Genet. 51:1044–51
    [Google Scholar]
  37. 37. 
    Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T et al. 2019. Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol 20:69
    [Google Scholar]
  38. 38. 
    Geddes BA, Paramasivan P, Joffrin A, Thompson AL, Christensen K et al. 2019. Engineering trans-kingdom signalling in plants to control gene expression in rhizosphere bacteria. Nat. Commun. 10:3430
    [Google Scholar]
  39. 39. 
    Glémin S, François CM, Galtier N 2019. Genome evolution in outcrossing versus selfing versus asexual species. Evolutionary Genomics: Statistical and Computational Methods M Anisimova 331–69 New York: SpringerIllustrates the profound influences of mating system on population genetic processes and genome evolution.
    [Google Scholar]
  40. 40. 
    Gong Z. 2020. Flowering phenology as a core domestication trait in soybean. J. Integr. Plant Biol. 62:546–49
    [Google Scholar]
  41. 41. 
    Guo J, Xu C, Wu D, Zhao Y, Qiu Y et al. 2018. Bph6 encodes an exocyst-localized protein and confers broad resistance to planthoppers in rice. Nat. Genet. 50:297–306
    [Google Scholar]
  42. 42. 
    Guo L, Wang X, Zhao M, Huang C, Li C et al. 2018. Stepwise cis-regulatory changes in ZCN8 contribute to maize flowering-time adaptation. Curr. Biol. 28:3005–15.e4Provides an example of stepwise selection and wild introgression that help maize adapt temperate regions.
    [Google Scholar]
  43. 43. 
    Hammer K. 1984. Das Domestikationsyndrom [The domestication syndrome]. Kulturpflanze 32:11–34
    [Google Scholar]
  44. 44. 
    Han L, Usher S, Sandgrind S, Hassall K, Sayanova O et al. 2020. High level accumulation of EPA and DHA in field-grown transgenic Camelina—a multi-territory evaluation of TAG accumulation and heterogeneity. Plant Biotechnol. J. 18:2280–91
    [Google Scholar]
  45. 45. 
    Harlan JR 1992. The dynamics of domestication. Crops and Man JR Harlan 115–33 Madison, WI: Am. Soc. Agron. , 2nd ed..
    [Google Scholar]
  46. 46. 
    Hu J, Wang Y, Fang Y, Zeng L, Xu J et al. 2015. A rare allele of GS2 enhances grain size and grain yield in rice. Mol. Plant 8:1455–65
    [Google Scholar]
  47. 47. 
    Huang BE, Verbyla KL, Verbyla AP, Raghavan C, Singh VK et al. 2015. MAGIC populations in crops: current status and future prospects. Theor. Appl. Genet. 128:999–1017
    [Google Scholar]
  48. 48. 
    Huang C, Chen Q, Xu G, Xu D, Tian J, Tian F. 2016. Identification and fine mapping of quantitative trait loci for the number of vascular bundle in maize stem. J. Integr. Plant Biol. 58:81–90
    [Google Scholar]
  49. 49. 
    Huang C, Sun H, Xu D, Chen Q, Liang Y et al. 2018. ZmCCT9 enhances maize adaptation to higher latitudes. PNAS 115:E334–41
    [Google Scholar]
  50. 50. 
    Huang J, Lu G, Liu L, Raihan MS, Xu J et al. 2020. The kernel size-related quantitative trait locus qKW9 encodes a pentatricopeptide repeat protein that affects photosynthesis and grain filling. Plant Physiol 183:1696–709
    [Google Scholar]
  51. 51. 
    Huang X, Han B. 2014. Natural variations and genome-wide association studies in crop plants. Annu. Rev. Plant Biol. 65:531–51Presents an overview of sequencing-based genotyping, GWAS, and subsequent innovations to crop breeding.
    [Google Scholar]
  52. 52. 
    Huang X, Kurata N, Wei X, Wang ZX, Wang A et al. 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–501
    [Google Scholar]
  53. 53. 
    Huang X, Qian Q, Liu Z, Sun H, He S et al. 2009. Natural variation at the DEP1 locus enhances grain yield in rice. Nat. Genet. 41:494–97
    [Google Scholar]
  54. 54. 
    Huang X, Yang S, Gong J, Zhao Q, Feng Q et al. 2016. Genomic architecture of heterosis for yield traits in rice. Nature 537:629–33
    [Google Scholar]
  55. 55. 
    Huang Y, Zhao S, Fu Y, Sun H, Ma X et al. 2018. Variation in the regulatory region of FZP causes increases in secondary inflorescence branching and grain yield in rice domestication. Plant J 96:716–33
    [Google Scholar]
  56. 56. 
    Hung HY, Shannon LM, Tian F, Bradbury PJ, Chen C et al. 2012. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. PNAS 109:E1913–21
    [Google Scholar]
  57. 57. 
    Jähne F, Hahn V, Würschum T, Leiser WL. 2020. Speed breeding short-day crops by LED-controlled light schemes. Theor. Appl. Genet. 133:2335–42
    [Google Scholar]
  58. 58. 
    Jia H, Li M, Li W, Liu L, Jian Y et al. 2020. A serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield. Nat. Commun. 11:988
    [Google Scholar]
  59. 59. 
    Jiao Y, Wang Y, Xue D, Wang J, Yan M et al. 2010. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat. Genet. 42:541–44Provides a great example of pleiotropy and an excellent breeding target (see also 103, 113, 172–174, and 205).
    [Google Scholar]
  60. 60. 
    Jin J, Huang W, Gao J, Yang J, Shi M et al. 2008. Genetic control of rice plant architecture under domestication. Nat. Genet. 40:1365–69
    [Google Scholar]
  61. 61. 
    Jin M, Liu X, Jia W, Liu H, Li W et al. 2018. ZmCOL3, a CCT gene represses flowering in maize by interfering with the circadian clock and activating expression of ZmCCT. J. Integr. Plant Biol. 60:465–80
    [Google Scholar]
  62. 62. 
    Khan AW, Garg V, Roorkiwal M, Golicz AA, Edwards D, Varshney RK. 2020. Super-pangenome by integrating the wild side of a species for accelerated crop improvement. Trends Plant Sci 25:148–58
    [Google Scholar]
  63. 63. 
    Khanday I, Skinner DJ, Yang B, Mercier R, Sundaresan V. 2019. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature 565:91–95
    [Google Scholar]
  64. 64. 
    Khush GS. 1995. Breaking the yield frontier of rice. GeoJournal 35:329–32
    [Google Scholar]
  65. 65. 
    Kim Y, Zhang D. 2018. Molecular control of male fertility for crop hybrid breeding. Trends Plant Sci 23:53–65
    [Google Scholar]
  66. 66. 
    Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T et al. 2002. Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43:1096–105
    [Google Scholar]
  67. 67. 
    Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H et al. 2007. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. PNAS 104:1424–29
    [Google Scholar]
  68. 68. 
    Kong D, Wang B, Wang H. 2020. UPA2 and ZmRAVL1: promising targets of genetic improvement of maize plant architecture. J. Integr. Plant Biol. 62:394–97
    [Google Scholar]
  69. 69. 
    Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y et al. 2006. An SNP caused loss of seed shattering during rice domestication. Science 312:1392–96
    [Google Scholar]
  70. 70. 
    Koppolu R, Schnurbusch T. 2019. Developmental pathways for shaping spike inflorescence architecture in barley and wheat. J. Integr. Plant Biol. 61:278–95
    [Google Scholar]
  71. 71. 
    Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J et al. 2009. A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–63
    [Google Scholar]
  72. 72. 
    Kuang Y, Li S, Ren B, Yan F, Spetz C et al. 2020. Base-editing-mediated artificial evolution of OsALS1 in planta to develop novel herbicide-tolerant rice germplasms. Mol. Plant 13:565–72A pioneer study to accelerate crop breeding with directed evolution of target genes by functional screening saturation mutations induced by CRISPR-based base editors (see also 79).
    [Google Scholar]
  73. 73. 
    Kubis A, Bareven A. 2019. Synthetic biology approaches for improving photosynthesis. J. Exp. Bot. 70:1425–33
    [Google Scholar]
  74. 74. 
    Kwon CT, Heo J, Lemmon ZH, Capua Y, Hutton SF et al. 2020. Rapid customization of Solanaceae fruit crops for urban agriculture. Nat. Biotechnol. 38:182–88
    [Google Scholar]
  75. 75. 
    Labios L. 2020. Marrying molecular farming and advanced manufacturing to develop a COVID-19 vaccine UC San Diego News Center. Press Release April 20. https://ucsdnews.ucsd.edu/pressrelease/marrying-molecular-farming-and-advanced-manufacturing-to-develop-a-covid-19-vaccine
  76. 76. 
    Larsson SJ, Lipka AE, Buckler ES. 2013. Lessons from Dwarf8 on the strengths and weaknesses of structured association mapping. PLOS Genet 9:e1003246
    [Google Scholar]
  77. 77. 
    Lemmon ZH, Reem NT, Dalrymple J, Soyk S, Swartwood KE et al. 2018. Rapid improvement of domestication traits in an orphan crop by genome editing. Nat. Plants 4:766–70Demonstrates the prospect of fast de novo domestication from wild or orphan crops with genome editing toward the creation of ideal crops (see also 84 and 212).
    [Google Scholar]
  78. 78. 
    Lesley JW. 1948. Plant breeding methods and current problems in developing improved varieties of tomatoes. Econ. Bot. 2:100–10
    [Google Scholar]
  79. 79. 
    Li C, Zhang R, Meng X, Chen S, Zong Y et al. 2020. Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors. Nat. Biotechnol. 38:875–82
    [Google Scholar]
  80. 80. 
    Li C, Zhou A, Sang T. 2006. Rice domestication by reducing shattering. Science 311:1936–39
    [Google Scholar]
  81. 81. 
    Li J, Yuan Y, Lu Z, Yang L, Gao R et al. 2012. Glabrous Rice 1, encoding a homeodomain protein, regulates trichome development in rice. Rice 5:32
    [Google Scholar]
  82. 82. 
    Li MW, Liu W, Lam HM, Gendron JM. 2019. Characterization of two growth period QTLs reveals modification of PRR3 genes during soybean domestication. Plant Cell Physiol 60:407–20
    [Google Scholar]
  83. 83. 
    Li S, Tian Y, Wu K, Ye Y, Yu J et al. 2018. Modulating plant growth–metabolism coordination for sustainable agriculture. Nature 560:595–600
    [Google Scholar]
  84. 84. 
    Li T, Yang X, Yu Y, Si X, Zhai X et al. 2018. Domestication of wild tomato is accelerated by genome editing. Nat. Biotechnol. 36:1160–63
    [Google Scholar]
  85. 85. 
    Li W, Deng Y, Ning Y, He Z, Wang G. 2020. Exploiting broad-spectrum disease resistance in crops: from molecular dissection to breeding. Annu. Rev. Plant Biol. 71:575–603
    [Google Scholar]
  86. 86. 
    Li X, Li X, Fridman E, Tesso TT, Yu J 2015. Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis. PNAS 112:11823–28
    [Google Scholar]
  87. 87. 
    Li Y, Guan R, Liu Z, Ma Y, Wang L et al. 2008. Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor. Appl. Genet. 117:857–71
    [Google Scholar]
  88. 88. 
    Liang Y, Liu Q, Wang X, Huang C, Xu G et al. 2019. ZmMADS69 functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory module and contributes to maize flowering time adaptation. New Phytol 221:2335–47
    [Google Scholar]
  89. 89. 
    Liang Z, Qiu Y, Schnable JC. 2020. Genome–phenome wide association in maize and Arabidopsis identifies a common molecular and evolutionary signature. Mol. Plant 13:907–22
    [Google Scholar]
  90. 90. 
    Lin T, Zhu G, Zhang J, Xu X, Yu Q et al. 2014. Genomic analyses provide insights into the history of tomato breeding. Nat. Genet. 46:1220–26
    [Google Scholar]
  91. 91. 
    Lin Z, Li X, Shannon LM, Yeh CT, Wang ML et al. 2012. Parallel domestication of the Shattering1 genes in cereals. Nat. Genet. 44:720–24
    [Google Scholar]
  92. 92. 
    Liu H, Wang Q, Chen M, Ding Y, Yang X et al. 2020. Genome-wide identification and analysis of heterotic loci in three maize hybrids. Plant Biotechnol. J. 18:185–94
    [Google Scholar]
  93. 93. 
    Liu HJ, Jian L, Xu J, Zhang Q, Zhang M et al. 2020. High-throughput CRISPR/Cas9 mutagenesis streamlines trait gene identification in maize. Plant Cell 32:1397–413
    [Google Scholar]
  94. 94. 
    Liu HJ, Luo X, Niu L, Xiao Y, Chen L et al. 2017. Distant eQTLs and non-coding sequences play critical roles in regulating gene expression and quantitative trait variation in maize. Mol. Plant 10:414–26
    [Google Scholar]
  95. 95. 
    Liu HJ, Wang X, Xiao Y, Luo J, Qiao F et al. 2020. CUBIC: an atlas of genetic architecture promises directed maize improvement. Genome Biol 21:20
    [Google Scholar]
  96. 96. 
    Liu HJ, Yan J 2019. Crop genome-wide association study: a harvest of biological relevance. Plant J 97:8–18
    [Google Scholar]
  97. 97. 
    Liu L, Du Y, Shen X, Li M, Sun W et al. 2015. KRN4 controls quantitative variation in maize kernel row number. PLOS Genet 11:e1005670
    [Google Scholar]
  98. 98. 
    Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS. 2012. Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLOS ONE 7:e36406
    [Google Scholar]
  99. 99. 
    Liu T, Liu H, Zhang H, Xing Y. 2013. Validation and characterization of Ghd7.1, a major quantitative trait locus with pleiotropic effects on spikelets per panicle, plant height, and heading date in rice (Oryza sativa L.). J. Integr. Plant Biol. 55:917–27
    [Google Scholar]
  100. 100. 
    Liu Y, Du H, Li P, Shen Y, Peng H et al. 2020. Pan-genome of wild and cultivated soybeans. Cell 182:162–76.e13
    [Google Scholar]
  101. 101. 
    Lu S, Dong L, Fang C, Liu S, Kong L et al. 2020. Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nat. Genet. 52:428–36
    [Google Scholar]
  102. 102. 
    Lu S, Zhao X, Hu Y, Liu S, Nan H et al. 2017. Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield. Nat. Genet. 49:773–79
    [Google Scholar]
  103. 103. 
    Lu Z, Yu H, Xiong G, Wang J, Jiao Y et al. 2013. Genome-wide binding analysis of the transcription activator Ideal Plant Architecture1 reveals a complex network regulating rice plant architecture. Plant Cell 25:3743–59
    [Google Scholar]
  104. 104. 
    Luo C, Li X, Zhang Q, Yan J. 2019. Single gametophyte sequencing reveals that crossover events differ between sexes in maize. Nat. Commun. 10:785
    [Google Scholar]
  105. 105. 
    Lye ZN, Purugganan MD. 2019. Copy number variation in domestication. Trends Plant Sci 24:352–65
    [Google Scholar]
  106. 106. 
    Mackay TFC, Stone EA, Ayroles JF. 2009. The genetics of quantitative traits: challenges and prospects. Nat. Rev. Genet. 10:565–77
    [Google Scholar]
  107. 107. 
    Manning K, Tor M, Poole M, Hong Y, Thompson AJ et al. 2006. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat. Genet. 38:948–52
    [Google Scholar]
  108. 108. 
    Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW et al. 1993. Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262:1432–36
    [Google Scholar]
  109. 109. 
    Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler ES, Doebley J 2002. A single domestication for maize shown by multilocus microsatellite genotyping. PNAS 99:6080–84
    [Google Scholar]
  110. 110. 
    McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H et al. 2009. Genetic properties of the maize nested association mapping population. Science 325:737–40
    [Google Scholar]
  111. 111. 
    Messeguer J, Fogher C, Guiderdoni E, Marfa V, Catala MM et al. 2001. Field assessments of gene flow from transgenic to cultivated rice (Oryza sativa L.) using a herbicide resistance gene as tracer marker. Theor. Appl. Genet. 103:1151–59
    [Google Scholar]
  112. 112. 
    Mickelbart MV, Hasegawa PM, Baileyserres J. 2015. Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat. Rev. Genet. 16:237–51
    [Google Scholar]
  113. 113. 
    Miura K, Ikeda M, Matsubara A, Song XJ, Ito M et al. 2010. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat. Genet. 42:545–49
    [Google Scholar]
  114. 114. 
    Morishima H, Barbier P. 1990. Mating system and genetic structure of natural populations in wild rice Oryza rufipogon. Plant Species Biol 5:31–39
    [Google Scholar]
  115. 115. 
    Mu Q, Huang Z, Chakrabarti M, Illaberenguer E, Liu X et al. 2017. Fruit weight is controlled by Cell Size Regulator encoding a novel protein that is expressed in maturing tomato fruits. PLOS Genet 13:e1006930
    [Google Scholar]
  116. 116. 
    Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z et al. 2009. Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 21:2194–202
    [Google Scholar]
  117. 117. 
    Nakamura S, Abe F, Kawahigashi H, Nakazono K, Tagiri A et al. 2011. A wheat homolog of MOTHER OF FT AND TFL1 acts in the regulation of germination. Plant Cell 23:3215–29
    [Google Scholar]
  118. 118. 
    Nakamura S, Pourkheirandish M, Morishige H, Kubo Y, Nakamura M et al. 2016. Mitogen-Activated Protein Kinase Kinase 3 regulates seed dormancy in barley. Curr. Biol. 26:775–81
    [Google Scholar]
  119. 119. 
    Ning Y, Liu W, Wang G. 2017. Balancing immunity and yield in crop plants. Trends Plant Sci 22:1069–79
    [Google Scholar]
  120. 120. 
    Ogisotanaka E, Matsubara K, Yamamoto S, Nonoue Y, Wu J et al. 2013. Natural variation of the RICE FLOWERING LOCUS T 1 contributes to flowering time divergence in rice. PLOS ONE 8:e75959
    [Google Scholar]
  121. 121. 
    Oliva R, Ji C, Atienzagrande G, Huguettapia JC, Perezquintero AL et al. 2019. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat. Biotechnol. 37:1344–50
    [Google Scholar]
  122. 122. 
    Ouyang Y, Zhang Q. 2013. Understanding reproductive isolation based on the rice model. Annu. Rev. Plant Biol. 64:111–35
    [Google Scholar]
  123. 123. 
    Paixao JFR, Gillet F, Ribeiro TP, Bournaud C, Lourencotessutti IT et al. 2019. Improved drought stress tolerance in Arabidopsis by CRISPR/dCas9 fusion with a histone acetyltransferase. Sci. Rep. 9:8080
    [Google Scholar]
  124. 124. 
    Pan Q, Xu Y, Li K, Peng Y, Zhan W et al. 2017. The genetic basis of plant architecture in 10 maize recombinant inbred line populations. Plant Physiol 175:858–73
    [Google Scholar]
  125. 125. 
    Papanatsiou M, Petersen J, Henderson L, Wang Y, Christie JM, Blatt MR. 2019. Optogenetic manipulation of stomatal kinetics improves carbon assimilation, water use, and growth. Science 363:1456–59
    [Google Scholar]
  126. 126. 
    Papikian A, Liu W, Gallegobartolome J, Jacobsen SE. 2019. Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems. Nat. Commun. 10:729
    [Google Scholar]
  127. 127. 
    Peiffer JA, Romay MC, Gore MA, Flintgarcia S, Zhang Z et al. 2014. The genetic architecture of maize height. Genetics 196:1337–56
    [Google Scholar]
  128. 128. 
    Peng J, Richards DE, Hartley NM, Murphy G, Devos KM et al. 1999.. ‘ Green revolution’ genes encode mutant gibberellin response modulators. Nature 400:256–61
    [Google Scholar]
  129. 129. 
    Pourkheirandish M, Hensel G, Kilian B, Senthil N, Chen G et al. 2015. Evolution of the grain dispersal system in barley. Cell 162:527–39
    [Google Scholar]
  130. 130. 
    Ramsay L, Comadran J, Druka A, Marshall D, Thomas WTB 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]
  131. 131. 
    Ray JD, Kilen TC, Abel CA, Paris RL. 2003. Soybean natural cross-pollination rates under field conditions. Environ. Biosaf. Res. 2:133–38
    [Google Scholar]
  132. 132. 
    Rick CM, Holle M, Thorp RW. 1978. Rates of cross-pollination in Lycopersicon pimpinellifolium: impact of genetic variation in floral characters. Plant Syst. Evol. 129:31–44
    [Google Scholar]
  133. 133. 
    Ruan B, Shang L, Zhang B, Hu J, Wang Y et al. 2020. Natural variation in the promoter of TGW2 determines grain width and weight in rice. New Phytol 227:629–40
    [Google Scholar]
  134. 134. 
    Sakuma S, Golan G, Guo Z, Ogawa T, Tagiri A et al. 2019. Unleashing floret fertility in wheat through the mutation of a homeobox gene. PNAS 116:5182–87
    [Google Scholar]
  135. 135. 
    Salvi S, Sponza G, Morgante M, Tomes DT, Niu X et al. 2007. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. PNAS 104:11376–81
    [Google Scholar]
  136. 136. 
    Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A et al. 2002. Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701–2
    [Google Scholar]
  137. 137. 
    Sato K, Yamane M, Yamaji N, Kanamori H, Tagiri A et al. 2016. Alanine aminotransferase controls seed dormancy in barley. Nat. Commun. 7:11625
    [Google Scholar]
  138. 138. 
    Sazonovs A, Barrett JC. 2018. Rare-variant studies to complement genome-wide association studies. Annu. Rev. Genom. Hum. Genet. 19:97–112
    [Google Scholar]
  139. 139. 
    Schaefer RJ, Michno JM, Jeffers J, Hoekenga O, Dilkes B et al. 2018. Integrating coexpression networks with GWAS to prioritize causal genes in maize. Plant Cell 30:2922–42
    [Google Scholar]
  140. 140. 
    Schaid DJ, Chen W, Larson NB. 2018. From genome-wide associations to candidate causal variants by statistical fine-mapping. Nat. Rev. Genet. 19:491–504Introduces the influencing factors and statistical approaches to fine-map functional genetic variants.
    [Google Scholar]
  141. 141. 
    Sey NYA, Hu B, Mah W, Fauni H, McAfee JC et al. 2020. A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles. Nat. Neurosci. 23:583–93
    [Google Scholar]
  142. 142. 
    Shen B, Wang L, Lin X, Yao Z, Xu H et al. 2019. Engineering a new chloroplastic photorespiratory bypass to increase photosynthetic efficiency and productivity in rice. Mol. Plant 12:199–214
    [Google Scholar]
  143. 143. 
    Singh BD, Singh AK. 2015. Mapping populations. Marker-Assisted Plant Breeding: Principles and Practices125–50 New Delhi: Springer India
    [Google Scholar]
  144. 144. 
    Solovieff N, Cotsapas C, Lee PH, Purcell SM, Smoller JW. 2013. Pleiotropy in complex traits: challenges and strategies. Nat. Rev. Genet. 14:483–95
    [Google Scholar]
  145. 145. 
    South PF, Cavanagh AP, Liu HW, Ort DR. 2019. Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field. Science 363:eaat9077
    [Google Scholar]
  146. 146. 
    Soyk S, Lemmon ZH, Oved M, Fisher J, Liberatore KL et al. 2017. Bypassing negative epistasis on yield in tomato imposed by a domestication gene. Cell 169:1142–55.e12
    [Google Scholar]
  147. 147. 
    Soyk S, Lemmon ZH, Sedlazeck FJ, Jimenezgomez JM, Alonge M et al. 2019. Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat. Plants 5:471–79
    [Google Scholar]
  148. 148. 
    Studer AJ, Wang H, Doebley JF. 2017. Selection during maize domestication targeted a gene network controlling plant and inflorescence architecture. Genetics 207:755–65
    [Google Scholar]
  149. 149. 
    Studer AJ, Zhao Q, Ross-Ibarra J, Doebley J. 2011. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat. Genet. 43:1160–63
    [Google Scholar]
  150. 150. 
    Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H et al. 2010. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. PNAS 107:5792–97
    [Google Scholar]
  151. 151. 
    Sun H, Qian Q, Wu K, Luo J, Wang S et al. 2014. Heterotrimeric G proteins regulate nitrogen-use efficiency in rice. Nat. Genet. 46:652–56
    [Google Scholar]
  152. 152. 
    Sun J, Liu H, Liu J, Cheng S, Peng Y et al. 2019. CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes. Bioinformatics 35:2501–3
    [Google Scholar]
  153. 153. 
    Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S et al. 2013. QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–83
    [Google Scholar]
  154. 154. 
    Takahashi Y, Shomura A, Sasaki T, Yano M 2001. Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2. PNAS 98:7922–27
    [Google Scholar]
  155. 155. 
    Takeda T, Suwa Y, Suzuki M, Kitano H, Ueguchitanaka M et al. 2003. The OsTB1 gene negatively regulates lateral branching in rice. Plant J 33:513–20
    [Google Scholar]
  156. 156. 
    Tan L, Li X, Liu F, Sun X, Li C et al. 2008. Control of a key transition from prostrate to erect growth in rice domestication. Nat. Genet. 40:1360–64
    [Google Scholar]
  157. 157. 
    Tanksley SD, Nelson JC. 1996. Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor. Appl. Genet. 92:191–203
    [Google Scholar]
  158. 158. 
    Tao Y, Zhao X, Mace E, Henry R, Jordan D. 2019. Exploring and exploiting pan-genomics for crop improvement. Mol. Plant 12:156–69
    [Google Scholar]
  159. 159. 
    Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q et al. 2011. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43:159–62
    [Google Scholar]
  160. 160. 
    Tian J, Wang C, Xia J, Wu L, Xu G et al. 2019. Teosinte ligule allele narrows plant architecture and enhances high-density maize yields. Science 365:658–64Provides a classic example that a teosinte allele lost during domestication could significantly improve modern maize yields.
    [Google Scholar]
  161. 161. 
    Tieman D, Zhu G, Resende MF Jr., Lin T, Nguyen C et al. 2017. A chemical genetic roadmap to improved tomato flavor. Science 355:391–94
    [Google Scholar]
  162. 162. 
    Torada A, Koike M, Ogawa T, Takenouchi Y, Tadamura K et al. 2016. A causal gene for seed dormancy on wheat chromosome 4A encodes a MAP kinase kinase. Curr. Biol. 26:782–87
    [Google Scholar]
  163. 163. 
    Tuinstra MR, Ejeta G, Goldsbrough PB. 1997. Heterogeneous inbred family (HIF) analysis: a method for developing near-isogenic lines that differ at quantitative trait loci. Theor. Appl. Genet. 95:1005–11
    [Google Scholar]
  164. 164. 
    Turner A, Beales J, Faure S, Dunford RP, Laurie DA 2005. The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310:1031–34
    [Google Scholar]
  165. 165. 
    Vilhjálmsson BJ, Nordborg M. 2013. The nature of confounding in genome-wide association studies. Nat. Rev. Genet. 14:1–2Explains the true underlying sources of, and how to effectively address, the confounding in GWAS.
    [Google Scholar]
  166. 166. 
    Voichek Y, Weigel D. 2020. Identifying genetic variants underlying phenotypic variation in plants without complete genomes. Nat. Genet. 52:534–40
    [Google Scholar]
  167. 167. 
    Wang C, Liu Q, Shen Y, Hua Y, Wang J et al. 2019. Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes. Nat. Biotechnol. 37:283–86
    [Google Scholar]
  168. 168. 
    Wang C, Tang S, Zhan Q, Hou Q, Zhao Y et al. 2019. Dissecting a heterotic gene through GradedPool-Seq mapping informs a rice-improvement strategy. Nat. Commun. 10:2982
    [Google Scholar]
  169. 169. 
    Wang H, Sun S, Ge W, Zhao L, Hou B et al. 2020. Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat. Science 368:eaba5435
    [Google Scholar]
  170. 170. 
    Wang J, Lin Z, Zhang X, Liu H, Zhou L et al. 2019. krn1, a major quantitative trait locus for kernel row number in maize. New Phytol 223:1634–46
    [Google Scholar]
  171. 171. 
    Wang J, Long X, Chern M, Chen X. 2020. Understanding the molecular mechanisms of trade-offs between plant growth and immunity. Sci. China Life Sci In press. https://doi.org/10.1007/s11427-020-1719-y
    [Crossref] [Google Scholar]
  172. 172. 
    Wang J, Yu H, Xiong G, Lu Z, Jiao Y et al. 2017. Tissue-specific ubiquitination by IPA1 INTERACTING PROTEIN1 modulates IPA1 protein levels to regulate plant architecture in rice. Plant Cell 29:697–707
    [Google Scholar]
  173. 173. 
    Wang J, Zhou L, Shi H, Chern M, Yu H et al. 2018. A single transcription factor promotes both yield and immunity in rice. Science 361:1026–28
    [Google Scholar]
  174. 174. 
    Wang L, Sun S, Jin J, Fu D, Yang X et al. 2015. Coordinated regulation of vegetative and reproductive branching in rice. PNAS 112:15504–9
    [Google Scholar]
  175. 175. 
    Wang M, Li W, Fang C, Xu F, Liu Y et al. 2018. Parallel selection on a dormancy gene during domestication of crops from multiple families. Nat. Genet. 50:1435–41
    [Google Scholar]
  176. 176. 
    Wang M, Yu Y, Haberer G, Marri PR, Fan C et al. 2014. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat. Genet. 46:982–88
    [Google Scholar]
  177. 177. 
    Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S et al. 2018. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557:43–49
    [Google Scholar]
  178. 178. 
    Wang X, Wang H, Liu S, Ferjani A, Li J et al. 2016. Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings. Nat. Genet. 48:1233–41
    [Google Scholar]
  179. 179. 
    Wang Y, Wang H, Wei L, Li S, Liu L, Wang X. 2020. Synthetic promoter design in Escherichia coli based on a deep generative network. Nucleic Acids Res 48:6403–12
    [Google Scholar]
  180. 180. 
    Watanabe S, Hideshima R, Xia Z, Tsubokura Y, Sato S et al. 2009. Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics 182:1251–62
    [Google Scholar]
  181. 181. 
    Watanabe S, Xia Z, Hideshima R, Tsubokura Y, Sato S et al. 2011. A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics 188:395–407
    [Google Scholar]
  182. 182. 
    Watson A, Ghosh S, Williams MJ, Cuddy WS, Simmonds J et al. 2018. Speed breeding is a powerful tool to accelerate crop research and breeding. Nat. Plants 4:23–29
    [Google Scholar]
  183. 183. 
    Wei X, Xu J, Guo H, Jiang L, Chen S et al. 2010. DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol 153:1747–58
    [Google Scholar]
  184. 184. 
    Wills DM, Whipple CJ, Takuno S, Kursel LE, Shannon LM et al. 2013. From many, one: genetic control of prolificacy during maize domestication. PLOS Genet 9:e1003604
    [Google Scholar]
  185. 185. 
    Wing RA, Purugganan MD, Zhang Q. 2018. The rice genome revolution: from an ancient grain to Green Super Rice. Nat. Rev. Genet. 19:505–17
    [Google Scholar]
  186. 186. 
    Wu W, Zheng X, Lu G, Zhong Z, Gao H et al. 2013. Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia. PNAS 110:2775–80
    [Google Scholar]
  187. 187. 
    Xia Z, Watanabe S, Yamada T, Tsubokura Y, Nakashima H et al. 2012. Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. PNAS 109:12852–53
    [Google Scholar]
  188. 188. 
    Xiao Y, Liu H, Wu L, Warburton M, Yan J 2017. Genome-wide association studies in maize: praise and stargaze. Mol. Plant 10:359–74
    [Google Scholar]
  189. 189. 
    Xiao Y, Tong H, Yang X, Xu S, Pan Q et al. 2016. Genome-wide dissection of the maize ear genetic architecture using multiple populations. New Phytol 210:1095–106
    [Google Scholar]
  190. 190. 
    Xu J, Chen G, Hermanson PJ, Xu Q, Sun C et al. 2019. Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize. Genome Biol 20:243
    [Google Scholar]
  191. 191. 
    Xu K, Xu X, Fukao T, Canlas PE, Maghirang-Rodriguez R et al. 2006. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–8
    [Google Scholar]
  192. 192. 
    Xu S. 2003. Theoretical basis of the Beavis effect. Genetics 165:2259–68
    [Google Scholar]
  193. 193. 
    Xue W, Xing Y, Weng X, Zhao Y, Tang W 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]
  194. 194. 
    Yan L, Fu D, Li C, Blechl AE, Tranquilli G et al. 2006. The wheat and barley vernalization gene VRN3 is an orthologue of FT. PNAS 103:19581–86
    [Google Scholar]
  195. 195. 
    Yan L, Loukoianov A, Blechl AE, Tranquilli G, Ramakrishna W et al. 2004. The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–44
    [Google Scholar]
  196. 196. 
    Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J 2003. Positional cloning of the wheat vernalization gene VRN1. PNAS 100:6263–68
    [Google Scholar]
  197. 197. 
    Yan WH, Wang P, Chen HX, Zhou HJ, Li QP et al. 2011. A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol. Plant 4:319–30
    [Google Scholar]
  198. 198. 
    Yang CJ, Kursel LE, Studer AJ, Bartlett ME, Whipple CJ, Doebley J. 2016. A gene for genetic background in Zea Mays: fine-mapping enhancer of teosinte branched1.2 to a YABBY class transcription factor. Genetics 204:1573–85
    [Google Scholar]
  199. 199. 
    Yang N, Liu J, Gao Q, Gui S, Chen L et al. 2019. Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nat. Genet. 51:1052–59
    [Google Scholar]
  200. 200. 
    Yang Q, He Y, Kabahuma M, Chaya T, Kelly A et al. 2017. A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens. Nat. Genet. 49:1364–72
    [Google Scholar]
  201. 201. 
    Yang Q, Li Z, Li W, Ku L, Wang C et al. 2013. CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize. PNAS 110:16969–74
    [Google Scholar]
  202. 202. 
    Yu J, Holland JB, McMullen MD, Buckler ES. 2008. Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–51
    [Google Scholar]
  203. 203. 
    Yu X, Zhao Z, Zheng X, Zhou J, Kong W et al. 2018. A selfish genetic element confers non-Mendelian inheritance in rice. Science 360:1130–32
    [Google Scholar]
  204. 204. 
    Zhang H, Wang X, Pan Q, Li P, Liu Y et al. 2019. QTG-seq accelerates QTL fine mapping through QTL partitioning and whole-genome sequencing of bulked segregant samples. Mol. Plant 12:426–37
    [Google Scholar]
  205. 205. 
    Zhang L, Yu H, Ma B, Liu G, Wang J et al. 2017. A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice. Nat. Commun. 8:14789
    [Google Scholar]
  206. 206. 
    Zhang Y, Lubberstedt T, Xu M. 2013. The genetic and molecular basis of plant resistance to pathogens. J. Genet. Genom. 40:23–35
    [Google Scholar]
  207. 207. 
    Zhang Z, Li J, Tang Z, Sun X, Zhang H et al. 2018. Gnp4/LAX2, a RAWUL protein, interferes with the OsIAA3–OsARF25 interaction to regulate grain length via the auxin signaling pathway in rice. J. Exp. Bot. 69:4723–37
    [Google Scholar]
  208. 208. 
    Zhao Y, Xie P, Guan P, Wang Y, Li Y et al. 2019. Btr1-A induces grain shattering and affects spike morphology and yield-related traits in wheat. Plant Cell Physiol 60:1342–53
    [Google Scholar]
  209. 209. 
    Zhu G, Wang S, Huang Z, Zhang S, Liao Q et al. 2018. Rewiring of the fruit metabolome in tomato breeding. Cell 172:249–61.e12
    [Google Scholar]
  210. 210. 
    Zhu Q, Zeng D, Yu S, Cui C, Li J et al. 2018. From golden rice to aSTARice: bioengineering astaxanthin biosynthesis in rice endosperm. Mol. Plant 11:1440–48
    [Google Scholar]
  211. 211. 
    Zhu YJ, Fan YY, Wang K, Huang DR, Liu WZ et al. 2017. Rice Flowering Locus T 1 plays an important role in heading date influencing yield traits in rice. Sci. Rep. 7:4918
    [Google Scholar]
  212. 212. 
    Zsogon A, Cermak T, Naves ER, Notini MM, Edel KH et al. 2018. De novo domestication of wild tomato using genome editing. Nat. Biotechnol. 36:1211–16
    [Google Scholar]
/content/journals/10.1146/annurev-arplant-080720-090632
Loading
/content/journals/10.1146/annurev-arplant-080720-090632
Loading

Data & Media loading...

Supplemental Material

Supplementary Data

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error