New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation

Literature Cited

1. 1. 

   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 182:1145–61.e23
   [Google Scholar]
2. 2. 

   Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW et al. 2019. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:7785149–57
   [Google Scholar]
3. 3. 

   Bateson W, Saunders ER, Punnett RC 1906. Further experiments on inheritance in sweet peas and stocks: preliminary account. Proc. R. Soc. B 77:517236–38
   [Google Scholar]
4. 4. 

   Bernard RL. 1972. Two genes affecting stem termination in soybeans. Crop Sci 12:2235–39
   [Google Scholar]
5. 5. 

   Birchler JA, Veitia RA. 2012. Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. PNAS 109:3714746–53
   [Google Scholar]
6. 6. 

   Birchler JA, Yao H, Chudalayandi S, Vaiman D, Veitia RA 2010. Heterosis. Plant Cell 22:72105–12
   [Google Scholar]
7. 7. 

   Blackman BK, Strasburg JL, Raduski AR, Michaels SD, Rieseberg LH 2010. The role of recently derived FT paralogs in sunflower domestication. Curr. Biol. 20:7629–35
   [Google Scholar]
8. 8. 

   Boden SA, Cavanagh C, Cullis BR, Ramm K, Greenwood J et al. 2015. Ppd-1 is a key regulator of inflorescence architecture and paired spikelet development in wheat. Nat. Plants 1:214016
   [Google Scholar]
9. 9. 

   Bomblies K, Lempe J, Epple P, Warthmann N, Lanz C et al. 2007. Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLOS Biol 5:9e236
   [Google Scholar]
10. 10. 

    Bomblies K, Weigel D. 2007. Hybrid necrosis: autoimmunity as a potential gene-flow barrier in plant species. Nat. Rev. Genet. 8:5382–93
    [Google Scholar]
11. 11. 

    Campbell BW, Hoyle JW, Bucciarelli B, Stec AO, Samac DA et al. 2019. Functional analysis and development of a CRISPR/Cas9 allelic series for a CPR5 ortholog necessary for proper growth of soybean trichomes. Sci. Rep. 9:114757
    [Google Scholar]
12. 12. 

    Cao Y, Lim E, Xu M, Weng J-K, Marelli B 2020. Precision delivery of multiscale payloads to tissue‐specific targets in plants. Adv. Sci. 7:131903551
    [Google Scholar]
13. 13. 

    Chae E, Bomblies K, Kim S-T, Karelina D, Zaidem M et al. 2014. Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis. Cell 159:61341–51
    [Google Scholar]
14. 14. 

    Chen C, Chen H, Lin Y-S, Shen J-B, Shan J-X et al. 2014. A two-locus interaction causes interspecific hybrid weakness in rice. Nat. Commun. 5:13357
    [Google Scholar]
15. 15. 

    Chen K, Wang Y, Zhang R, Zhang H, Gao C 2019. CRISPR/Cas genome editing and precision plant breeding in agriculture. Annu. Rev. Plant Biol. 70:667–97
    [Google Scholar]
16. 16. 

    Chu Y-H, Jang J-C, Huang Z, van der Knaap E 2019. Tomato locule number and fruit size controlled by natural alleles of lc and fas. . Plant Direct 3:7e00142
    [Google Scholar]
17. 17. 

    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. 44:121388–92
    [Google Scholar]
18. 18. 

    Costanzo M, Kuzmin E, van Leeuwen J, Mair B, Moffat J et al. 2019. Global genetic networks and the genotype-to-phenotype relationship. Cell 177:185–100
    [Google Scholar]
19. 19. 

    Cunningham FJ, Goh NS, Demirer GS, Matos JL, Landry MP 2018. Nanoparticle-mediated delivery towards advancing plant genetic engineering. Trends Biotechnol 36:9882–97
    [Google Scholar]
20. 20. 

    Diss G, Ascencio D, DeLuna A, Landry CR 2014. Molecular mechanisms of paralogous compensation and the robustness of cellular networks. J. Exp. Zool. Part B Mol. Dev. Evol. 322:7488–99
    [Google Scholar]
21. 21. 

    Dixit A, Parnas O, Li B, Chen J, Fulco CP et al. 2016. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167:71853–66.e17
    [Google Scholar]
22. 22. 

    Doebley JF, Gaut BS, Smith BD 2006. The molecular genetics of crop domestication. Cell 127:71309–21
    [Google Scholar]
23. 23. 

    Doebley JF, Stec A, Hubbard L 1997. The evolution of apical dominance in maize. Nature 386:6624485–88
    [Google Scholar]
24. 24. 

    Fisher RA. 1919. The correlation between relatives on the supposition of Mendelian inheritance. Trans. R. Soc. Edinburgh 52:2399–433
    [Google Scholar]
25. 25. 

    Fray RG, Grierson D. 1993. Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression. Plant Mol. Biol. 22:4589–602
    [Google Scholar]
26. 26. 

    Galli M, Gallavotti A. 2016. Expanding the regulatory network for meristem size in plants. Trends Genet 32:6372–83
    [Google Scholar]
27. 27. 

    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. 51:61044–51
    [Google Scholar]
28. 28. 

    Garcia AAF, Wang S, Melchinger AE, Zeng Z-B 2008. Quantitative trait loci mapping and the genetic basis of heterosis in maize and rice. Genetics 180:31707–24
    [Google Scholar]
29. 29. 

    Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH et al. 2017. Programmable base editing of A·T to G·C in genomic DNA without DNA cleavage. Nature 551:7681464–71
    [Google Scholar]
30. 30. 

    Hermsen JGT. 1963. The genetic basis of hybrid necrosis in wheat. Genetica 33:245–87
    [Google Scholar]
31. 31. 

    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. 41:4494–97
    [Google Scholar]
32. 32. 

    Huang X, Yang S, Gong J, Zhao Q, Feng Q et al. 2016. Genomic architecture of heterosis for yield traits in rice. Nature 537:7622629–33
    [Google Scholar]
33. 33. 

    Hufford MB, Berny Mier y Teran JC, Gepts P 2019. Crop biodiversity: an unfinished magnum opus of nature. Annu. Rev. Plant Biol. 70:727–51
    [Google Scholar]
34. 34. 

    Isaacson T, Ronen G, Zamir D, Hirschberg J 2002. Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of β-carotene and xanthophylls in plants. Plant Cell 14:2333–42
    [Google Scholar]
35. 35. 

    Iwata H, Gaston A, Remay A, Thouroude T, Jeauffre J et al. 2012. The TFL1 homologue KSN is a regulator of continuous flowering in rose and strawberry. Plant J 69:1116–25
    [Google Scholar]
36. 36. 

    Jacobs TB, Zhang N, Patel D, Martin GB 2017. Generation of a collection of mutant tomato lines using pooled CRISPR libraries. Plant Physiol 174:42023–37
    [Google Scholar]
37. 37. 

    Jaeger KE, Pullen N, Lamzin S, Morris RJ, Wigge PA 2013. Interlocking feedback loops govern the dynamic behavior of the floral transition in Arabidopsis. . Plant Cell 25:3820–33
    [Google Scholar]
38. 38. 

    Je BI, Gruel J, Lee YK, Bommert P, Arevalo ED et al. 2016. Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits. Nat. Genet. 48:7785–91
    [Google Scholar]
39. 39. 

    Jenkins JA, Mackinney G. 1953. Inheritance of carotenoid differences in the tomato hybrid yellow x tangerine. Genetics 38:2107–16
    [Google Scholar]
40. 40. 

    Jenkins JA, Mackinney G. 1955. Carotenoids of the apricot tomato and its hybrids with yellow and tangerine. Genetics 40:5715–20
    [Google Scholar]
41. 41. 

    Jeuken MJW, Zhang NW, McHale LK, Pelgrom K, den Boer E et al. 2009. Rin4 causes hybrid necrosis and race-specific resistance in an interspecific lettuce hybrid. Plant Cell 21:103368–78
    [Google Scholar]
42. 42. 

    Jiang K, Liberatore KL, Park SJ, Alvarez JP, Lippman ZB 2013. Tomato yield heterosis is triggered by a dosage sensitivity of the florigen pathway that fine-tunes shoot architecture. PLOS Genet 9:12e1004043
    [Google Scholar]
43. 43. 

    Jiang Y, Schmidt RH, Zhao Y, Reif JC 2017. A quantitative genetic framework highlights the role of epistatic effects for grain-yield heterosis in bread wheat. Nat. Genet. 49:121741–46
    [Google Scholar]
44. 44. 

    Kachanovsky DE, Filler S, Isaacson T, Hirschberg J 2012. Epistasis in tomato color mutations involves regulation of phytoene synthase 1 expression by cis-carotenoids. PNAS 109:4619021–26
    [Google Scholar]
45. 45. 

    Kempin S, Savidge B, Yanofsky M 1995. Molecular basis of the cauliflower phenotype in Arabidopsis. Science 267:5197522–25
    [Google Scholar]
46. 46. 

    Klee HJ, Giovannoni JJ. 2011. Genetics and control of tomato fruit ripening and quality attributes. Annu. Rev. Genet. 45:41–59
    [Google Scholar]
47. 47. 

    Krieger U, Lippman ZB, Zamir D 2010. The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato. Nat. Genet. 42:5459–63
    [Google Scholar]
48. 48. 

    Krüger J, Thomas CM, Golstein C, Dixon MS, Smoker M et al. 2002. A tomato cysteine protease required for Cf-2-dependent disease resistance and suppression of autonecrosis. Science 296:5568744–47
    [Google Scholar]
49. 49. 

    Kuzmin E, VanderSluis B, Wang W, Tan G, Deshpande R et al. 2018. Systematic analysis of complex genetic interactions. Science 360:6386eaao1729
    [Google Scholar]
50. 50. 

    Kwak M, Velasco D, Gepts P 2008. Mapping homologous sequences for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris). J. Hered. 99:3283–91
    [Google Scholar]
51. 51. 

    Kwon C-T, Heo J, Lemmon ZH, Capua Y, Hutton SF et al. 2020. Rapid customization of Solanaceae fruit crops for urban agriculture. Nat. Biotechnol. 38:2182–88
    [Google Scholar]
52. 52. 

    Kyozuka J, Tokunaga H, Yoshida A 2014. Control of grass inflorescence form by the fine-tuning of meristem phase change. Curr. Opin. Plant Biol. 17:1110–15
    [Google Scholar]
53. 53. 

    Lan T-H, Paterson AH. 2000. Comparative mapping of quantitative trait loci sculpting the curd of Brassica oleracea. . Genetics 155:41927–54
    [Google Scholar]
54. 54. 

    Lauter N, Doebley J. 2002. Genetic variation for phenotypically invariant traits detected in teosinte: implications for the evolution of novel forms. Genetics 160:1333–42
    [Google Scholar]
55. 55. 

    Lee J, Lee I. 2010. Regulation and function of SOC1, a flowering pathway integrator. J. Exp. Bot. 61:92247–54
    [Google Scholar]
56. 56. 

    Lemmon ZH, Park SJ, Jiang K, Van Eck J, Schatz MC, Lippman ZB 2016. The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation. Genome Res 26:121676–86
    [Google Scholar]
57. 57. 

    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 4:10766–70
    [Google Scholar]
58. 58. 

    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. 38:7875–82
    [Google Scholar]
59. 59. 

    Li T, Yang X, Yu Y, Si X, Zhai X et al. 2018. Domestication of wild tomato is accelerated by genome editing. Nat. Biotechnol. 36:121160–63
    [Google Scholar]
60. 60. 

    Li Y, Zhou G, Ma J, Jiang W, Jin L et al. 2014. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol. 32:101045–52
    [Google Scholar]
61. 61. 

    Lifschitz E, Ayre BG, Eshed Y 2014. Florigen and anti-florigen—a systemic mechanism for coordinating growth and termination in flowering plants. Front. Plant Sci. 5:465
    [Google Scholar]
62. 62. 

    Lifschitz E, Eshed Y. 2006. Universal florigenic signals triggered by FT homologues regulate growth and flowering cycles in perennial day-neutral tomato. J. Exp. Bot. 57:133405–14
    [Google Scholar]
63. 63. 

    Lin Q, Zong Y, Xue C, Wang S, Jin S et al. 2020. Prime genome editing in rice and wheat. Nat. Biotechnol. 38:582–85
    [Google Scholar]
64. 64. 

    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. 46:111220–26
    [Google Scholar]
65. 65. 

    Lippman ZB, Cohen O, Alvarez JP, Abu-Abied M, Pekker I et al. 2008. The making of a compound inflorescence in tomato and related nightshades. PLOS Biol 6:11e288
    [Google Scholar]
66. 66. 

    Liu B, Watanabe S, Uchiyama T, Kong F, Kanazawa A et al. 2010. The soybean stem growth habit gene Dt1 is an ortholog of Arabidopsis TERMINAL FLOWER1. . Plant Physiol 153:1198–210
    [Google Scholar]
67. 67. 

    Liu H-J, Jian L, Xu J, Zhang Q, Zhang M et al. 2020. High-throughput CRISPR/Cas9 mutagenesis streamlines trait gene identification in maize. Plant Cell 32:51397–413
    [Google Scholar]
68. 68. 

    MacArthur JW, Chiasson LP. 1947. Cytogenetic notes on tomato species and hybrids. Genetics 32:2165–77
    [Google Scholar]
69. 69. 

    Maher MF, Nasti RA, Vollbrecht M, Starker CG, Clark MD, Voytas DF 2020. Plant gene editing through de novo induction of meristems. Nat. Biotechnol. 38:184–89
    [Google Scholar]
70. 70. 

    Melchinger AE, Piepho H-P, Utz HF, Muminović J, Wegenast T et al. 2007. Genetic basis of heterosis for growth-related traits in Arabidopsis investigated by testcross progenies of near-isogenic lines reveals a significant role of epistasis. Genetics 177:31827–37
    [Google Scholar]
71. 71. 

    Moyers BT, Morrell PL, McKay JK 2018. Genetic costs of domestication and improvement. J. Hered. 109:2103–16
    [Google Scholar]
72. 72. 

    Müller NA, Zhang L, Koornneef M, Jiménez-Gómez JM 2018. Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication. PNAS 115:277135–40
    [Google Scholar]
73. 73. 

    Mullins MG, Bouquet A, Williams LE 1992. Biology of the Grapevine Cambridge, UK: Cambridge Univ. Press
74. 74. 

    Muños S, Ranc N, Botton E, Bérard A, Rolland S et al. 2011. Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. . Plant Physiol 156:42244–54
    [Google Scholar]
75. 75. 

    Norman TM, Horlbeck MA, Replogle JM, Ge AY, Xu A et al. 2019. Exploring genetic interaction manifolds constructed from rich single-cell phenotypes. Science 365:6455786–93
    [Google Scholar]
76. 76. 

    Park SJ, Eshed Y, Lippman ZB 2014. Meristem maturation and inflorescence architecture—lessons from the Solanaceae. Curr. Opin. Plant Biol. 17:170–77
    [Google Scholar]
77. 77. 

    Park SJ, Jiang K, Tal L, Yichie Y, Gar O et al. 2014. Optimization of crop productivity in tomato using induced mutations in the florigen pathway. Nat. Genet. 46:121337–42
    [Google Scholar]
78. 78. 

    Peralta IE, Spooner DM. 2005. Morphological characterization and relationships of wild tomatoes (Solanum L. Sect. Lycopersicon). A Festschrift for William G. D'Arcy R Keating, V Hollowell, T Croat 227–57 Chicago: Univ. Chicago Press
    [Google Scholar]
79. 79. 

    Phillips PC. 2008. Epistasis—the essential role of gene interactions in the structure and evolution of genetic systems. Nat. Rev. Genet. 9:11855–67
    [Google Scholar]
80. 80. 

    Ping J, Liu Y, Sun L, Zhao M, Li Y et al. 2014. Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean. Plant Cell 26:72831–42
    [Google Scholar]
81. 81. 

    Pnueli L, Carmel-Goren L, Hareven D, Gutfinger T, Alvarez J et al. 1998. The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125:111979–89
    [Google Scholar]
82. 82. 

    Purugganan MD, Boyles AL, Suddith JI 2000. Variation and selection at the CAULIFLOWER floral homeotic gene accompanying the evolution of domesticated Brassica oleracea. . Genetics 155:2855–62
    [Google Scholar]
83. 83. 

    Ramsay L, Comadran J, Druka A, Marshall DF, 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 43:2169–72
    [Google Scholar]
84. 84. 

    Reynard GB. 1961. New source of the j2 gene governing jointless pedicel in tomato. Science 134:3496 2102. Erratum. 1962 Science 135:35091118
    [Google Scholar]
85. 85. 

    Rick CM. 1956. A new jointless gene from the Galapagos L pimpinellifolium TGC Rep. 6, Tomato Genet. Coop., Univ. Fla Gainesville, FL: https://tgc.ifas.ufl.edu/vol4/vol4.pdf
    [Google Scholar]
86. 86. 

    Rodríguez GR, Kim HJ, Van Der Knaap E 2013. Mapping of two suppressors of OVATE (sov) loci in tomato. Heredity 111:3256–64
    [Google Scholar]
87. 87. 

    Rodríguez GR, Muños S, Anderson C, Sim S-C, Michel A et al. 2011. Distribution of SUN, OVATE, LC, and FAS in the tomato germplasm and the relationship to fruit shape diversity. Plant Physiol 156:1275–85
    [Google Scholar]
88. 88. 

    Rodríguez-Leal D, Xu C, Kwon CT, Soyars C, Demesa-Arevalo E et al. 2019. Evolution of buffering in a genetic circuit controlling plant stem cell proliferation. Nat. Genet. 51:5786–92
    [Google Scholar]
89. 89. 

    Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB 2017. Engineering quantitative trait variation for crop improvement by genome editing. Cell 171:2470–80.e8
    [Google Scholar]
90. 90. 

    Sax K. 1923. The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. . Genetics 8:6552–60
    [Google Scholar]
91. 91. 

    Schmidt C, Pacher M, Puchta H 2019. Efficient induction of heritable inversions in plant genomes using the CRISPR/Cas system. Plant J 98:4577–89
    [Google Scholar]
92. 92. 

    Schnable PS, Springer NM. 2013. Progress toward understanding heterosis in crop plants. Annu. Rev. Plant Biol. 64:71–88
    [Google Scholar]
93. 93. 

    Schoof H, Lenhard M, Haecker A, Mayer KFX, Jürgens G, Laux T 2000. The stem cell population of Arabidopsis shoot meristems is maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell 100:6635–44
    [Google Scholar]
94. 94. 

    Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M et al. 2018. Accurate detection of complex structural variations using single-molecule sequencing. Nat. Methods 15:6461–68
    [Google Scholar]
95. 95. 

    Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T et al. 2017. Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nat. Biotechnol. 35:5441–43
    [Google Scholar]
96. 96. 

    Shull GH. 1908. The composition of a field of maize. J. Hered. os-4:1296–301
    [Google Scholar]
97. 97. 

    Shull GH. 1910. Hybridization methods in corn breeding. J. Hered. 1:298–107
    [Google Scholar]
98. 98. 

    Somssich M, Je BI, Simon R, Jackson D 2016. CLAVATA-WUSCHEL signaling in the shoot meristem. Development 143:183238–48
    [Google Scholar]
99. 99. 

    Soyars CL, James SR, Nimchuk ZL 2016. Ready, aim, shoot: stem cell regulation of the shoot apical meristem. Curr. Opin. Plant Biol. 29:163–68
    [Google Scholar]
100. 100. 

     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 169:61142–55.e12
     [Google Scholar]
101. 101. 

     Soyk S, Lemmon ZH, Sedlazeck FJ, Jiménez-Gómez JM, Alonge M et al. 2019. Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nat. Plants 5:5471–79
     [Google Scholar]
102. 102. 

     Soyk S, Müller NA, Park SJ, Schmalenbach I, Jiang K et al. 2017. Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Nat. Genet. 49:1162–68
     [Google Scholar]
103. 103. 

     Stephenson AG. 1981. Flower and fruit abortion: proximate causes and ultimate functions. Annu. Rev. Ecol. Syst. 12:253–79
     [Google Scholar]
104. 104. 

     Stetter MG, Gates DJ, Mei W, Ross-Ibarra J 2017. How to make a domesticate. Curr. Biol. 27:17R896–900
     [Google Scholar]
105. 105. 

     Stitzer MC, Ross-Ibarra J. 2018. Maize domestication and gene interaction. New Phytol 220:2395–408
     [Google Scholar]
106. 106. 

     Swinnen G, Goossens A, Pauwels L 2016. Lessons from domestication: targeting cis-regulatory elements for crop improvement. Trends Plant Sci 21:6506–15
     [Google Scholar]
107. 107. 

     Taoka K, Ohki I, Tsuji H, Furuita K, Hayashi K et al. 2011. 14-3-3 proteins act as intracellular receptors for rice Hd3a florigen. Nature 476:7360332–35
     [Google Scholar]
108. 108. 

     Tomes ML, Quackenbush FW, Nelson OE, North B 1953. The inheritance of carotenoid pigment systems in the tomato. Genetics 38:2117–27
     [Google Scholar]
109. 109. 

     Torres Cleuren YN, Ewe CK, Chipman KC, Mears ER, Wood CG et al. 2019. Extensive intraspecies cryptic variation in an ancient embryonic gene regulatory network. eLife 8:e48220
     [Google Scholar]
110. 110. 

     van der Knaap E, Chakrabarti M, Chu YH, Clevenger JP, Illa-Berenguer E et al. 2014. What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape. Front. Plant Sci. 5:227
     [Google Scholar]
111. 111. 

     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 557:770343–49
     [Google Scholar]
112. 112. 

     Weller JL, Ortega R. 2015. Genetic control of flowering time in legumes. Front. Plant Sci. 6:207
     [Google Scholar]
113. 113. 

     Wittkopp PJ, Kalay G. 2012. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat. Rev. Genet. 13:159–69
     [Google Scholar]
114. 114. 

     Wu S, Zhang B, Keyhaninejad N, Rodríguez GR, Kim HJ et al. 2018. A common genetic mechanism underlies morphological diversity in fruits and other plant organs. Nat. Commun. 9:14734
     [Google Scholar]
115. 115. 

     Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E 2008. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319:58691527–30
     [Google Scholar]
116. 116. 

     Xu C, Liberatore KL, MacAlister CA, Huang Z, Chu Y-H et al. 2015. A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nat. Genet. 47:7784–92
     [Google Scholar]
117. 117. 

     Yamamoto E, Takashi T, Morinaka Y, Lin S, Wu J et al. 2010. Gain of deleterious function causes an autoimmune response and Bateson-Dobzhansky-Muller incompatibility in rice. Mol. Genet. Genom. 283:4305–15
     [Google Scholar]
118. 118. 

     Zhang C, Wang P, Tang D, Yang Z, Lu F et al. 2019. The genetic basis of inbreeding depression in potato. Nat. Genet. 51:3374–78
     [Google Scholar]
119. 119. 

     Zhang S, Jiao Z, Liu L, Wang K, Zhong D et al. 2018. Enhancer-promoter interaction of SELF PRUNING 5G shapes photoperiod adaptation. Plant Physiol 178:41631–42
     [Google Scholar]
120. 120. 

     Zong Y, Song Q, Li C, Jin S, Zhang D et al. 2018. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat. Biotechnol. 36:10950–53
     [Google Scholar]
121. 121. 

     Zsögön A, Čermák T, Naves ER, Notini MM, Edel KH et al. 2018. De novo domestication of wild tomato using genome editing. Nat. Biotechnol. 36:121211–16
     [Google Scholar]