Abstract
Key message
Domestication traits particularly fruit size and plant architecture and flowering are critical in transforming a progenitor’s wild stature into a super improved plant. The latest advancements in the CRISPR system, as well as its rapid adoption, are speeding up plant breeding.
Abstract
Solanaceae has a varied range of important crops, with a few model crops, such as tomato and, more recently, groundcherry, serving as a foundation for developing molecular techniques, genome editing tools, and establishing standards for other crops. Domestication traits in agricultural plants are quantified and widely adopted under modern plant breeding to improve small-fruited and bushy crop species like goji berry. The molecular mechanisms of the FW2.2, FW3.2, FW11.3, FAS/CLV3, LC/WUS, SP, SP5G, and CRISPR genome editing technology have been described in detail here. Furthermore, special focus has been placed on CRISPR gene editing achievements for revolutionizing Solanaceae breeding and changing the overall crop landscape. This review seeks to provide a thorough overview of the CRISPR technique’s ongoing advancements, particularly in Solanaceae, in terms of domesticated features, future prospects, and regulatory risks. We believe that this vigorous discussion will lead to a broader understanding of CRISPR gene editing as a tool for achieving key breeding goals in other Solanaceae minor crops with significant industrial value.
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Abbreviations
- CRISPR:
-
Clustered regularly interspaced palindromic repeats
- Cas9:
-
CRISPR associated nuclease 9
- FW:
-
Fruit weight
- LC:
-
Locule number
- WUS:
-
Wuschel
- FAS:
-
Fasciated
- CLV:
-
Clavata
- ZFN:
-
Zinc finger nuclease
- TALEN:
-
Transcription activator like effector nucleases
- IM:
-
Inflorescence meristem
- FM:
-
Floral meristem
- CNR:
-
Cell number regulator
- PLAC8:
-
Placenta specific 8
- CYP78A:
-
Cytochrome P450 class A78
- CSR:
-
Cell size regulator
- SNP:
-
Single nucleotide polymorphism
- AG:
-
Agamous
- NIL:
-
Near isogenic lines
- WT:
-
Wild type
- SP :
-
Self Pruning
- SAM:
-
Shoot apical meristem
- CEN:
-
Centroradialis
- TFL1:
-
Terminal flowers
- SFT:
-
Single flower truss
- SP5G :
-
Self Pruning 5 Gene
- SlER:
-
Solanum lycopersicum ERECTA
- PAM:
-
Protospacer adjacent motif
- Cpf1:
-
CRISPR Prevotella and Francisella 1
- DSB:
-
Double strand break
- Sp :
-
Streptococcus pyogenes
- NHEJ:
-
Non-homologous end joining
- HDR:
-
Homology directed repair
- uORF:
-
Upstream open reading frame
- dORF:
-
Downstream open reading frame
- InDel:
-
Insertion/deletion
- CSHL:
-
Cold spring harbor laboratory
- Fast-TrACC:
-
Fast treated Agrobacterium co-culture
- DR:
-
Developmental regulators
- MULT:
-
Multiflora
- CycB:
-
Lycopene beta cyclase
- Ko:
-
Knock out
- Ki:
-
Knock in
- TCM:
-
Traditional Chinese medicine
References
Amaya I, Ratcliffe OJ, Bradley DJ (1999) Expression of CENTRORADIALIS (CEN) and CEN-like genes in tobacco reveals a conserved mechanism controlling phase change in diverse species. Plant Cell 11:1405–1417. https://doi.org/10.1105/tpc.11.8.1405
Anastasiou E, Kenz S, Gerstung M, MacLean D, Timmer J, Fleck C et al (2007) Control of plant organ size by KLUH/CYP78A5-dependent intercellular signaling. Develop Cell 13:843–856. https://doi.org/10.1016/j.devcel.2007.10.001
Andersson M, Turesson H, Nicolia A, Falt AS, Samuelsson M, Hofvander P (2017) Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPRCas9 expression in protoplasts. Plant Cell Rep 36:117–128. https://doi.org/10.1007/s00299-016-2062-3
Anzalone AV, Koblan LW, Liu DR (2020) Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol 38(7):1–21. https://doi.org/10.1038/s41587-020-0561-9
Arora L, Narula A (2017) Gene editing and crop improvement using CRISPR-Cas9 system. Front Plant Sci 8:1932. https://doi.org/10.3389/fpls.2017.01932
Avila CM, Nadal S, Moreno MT, Torres AM (2006) Development of a simple PCR-based marker for the determination of growth habit in Vicia faba L. using a candidate gene approach. Mol Breed 17:185–190. https://doi.org/10.1007/s11032-005-40754
Barrero LS, Tanksley SD (2004) Evaluating the genetic basis of multiple locule fruit in a broad cross section of tomato cultivars. Theor Appl Genet 109:669–679. https://doi.org/10.1007/s00122-004-1676-y
Bolotin A, Ouinquis B, Sorokin A, Ehrlich SD (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiol 151:2551–2561. https://doi.org/10.1099/mic.0.28048-0
Bradley D, Carpenter R, Copsey L, Vincent C, Rothstein S, Coen E (1996) Control of inflorescence architecture in Antirrhinum. Nature 379:791–797. https://doi.org/10.1038/379791a0
Bradley D, Ratcliffe OJ, Vincent C, Carpenter R, Coen ES (1997) Inflorescence commitment and architecture in Arabidopsis. Science 275:80–83. https://doi.org/10.1126/science.275.5296.80
Brooks C, Nekrasov V, Lippman ZB, Van Eck J (2014) Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPRassociated9 system. Plant Physiol 166:1292–1297. https://doi.org/10.1104/pp.114.247577
Callaway E (2018) CRISPR plants now subject to tough GM laws in European Union. Nature 560:16. https://doi.org/10.1038/d41586-018-05814-6
Cao K, Cui L, Zhou X, Ye L, Zou Z, Deng S (2016) Four tomato FLOWERING LOCUS T-like proteins act antagonistically to regulate floral initiation. Front Plant Sci 6:1213. https://doi.org/10.3389/fpls.2015.01213
Cardi T, D’Agostino N, Tripodi P (2017) Genetic transformation and genomic resources for next-generation precise genome engineering in vegetable crops. Front Plant Sci 8:241. https://doi.org/10.3389/fpls.2017.00241
Carmel-Goren L, Liu YS, Lifschitz E, Zamir D (2003) The SELFPRUNING gene family in tomato. Plant Mol Biol 52:1215–1222. https://doi.org/10.1023/B:PLAN.0000004333.96451.11
Carroll D (2011) Genome engineering with zinc-finger nucleases. Genetics 188:773–782. https://doi.org/10.1534/genetics.111.131433
Cermak T, Baltes NJ, Cegan R, Zhang Y, Voytas DF (2015) High frequency, precise modification of the tomato genome. Genome Biol 16:232. https://doi.org/10.1186/s13059-015-0796-9
Chakrabarti M, Zhang NA, Sauvage C, Muños S, Blanca J, Cañizares J, Causse M (2013) A cytochrome P450 regulates a domestication trait in cultivated tomato. Proc Nat Acad Sci USA 110(42):17125–17130. https://doi.org/10.1073/pnas.1307313110
Che G, Gu R, Zhao J, Liu X, Song X, Zi H et al (2020) Gene regulatory network controlling carpel number variation in cucumber. Develop. https://doi.org/10.1242/dev.184788
Chen F, Song Y, Li X, Chen J, Mo L, Zhang X, Zhang L (2019) Genome sequences of horticultural plants: past, present, and future. Hort Res 6(1):1–23. https://doi.org/10.1038/s41438-019-0195-6
Chu YH, Jang JC, Huang Z, van der Knaap E (2019) Tomato locule number and fruit size controlled by natural alleles of lc and fas. Plant Direct 3(7):e00142. https://doi.org/10.1002/pld3.142
Clark SE (2001) Cell signalling at the shoot meristem. Nat Rev Mol Cell Biol 2:276–284. https://doi.org/10.1038/35067079
Cong B, Liu J, Tanksley SD (2002) Natural alleles at a tomato fruit size quantitative trait locus differ by heterochronic regulatory mutations. Proc Nat Acad Sci USA 99:13606–13611. https://doi.org/10.1073/pnas.172520999
Cong B, Barrero LS, Tanksley SD (2008) Regulatory change in YABBY like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat Genet 40:800–804. https://doi.org/10.1038/ng.144
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823. https://doi.org/10.1126/science.1231143
De Maagd RA, Loonen A, Chouaref J, Pelé A, Meijer-Dekens F, Fransz P, Bai Y (2020) CRISPR/Cas inactivation of RECQ4 increases homeologous crossovers in an interspecific tomato hybrid. Plant Biotech J 18(3):805–813. https://doi.org/10.1111/pbi.13248
Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321. https://doi.org/10.1016/j.cell.2006.12.006
Doudna JA, Charpentier E (2014) The new frontier of genome engineering with CRISPR-Cas9. Science 346:1258096. https://doi.org/10.1126/science.1258096
Engqvist MKM, Rabe KS (2019) Applications of protein engineering and directed evolution in plant research. Plant Physiol 179:907–917. https://doi.org/10.1104/pp.18.01534
Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang DL et al (2014) Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas induced gene modifications in Arabidopsis. Proc Nat Acad Sci USA 111:4632–4637. https://doi.org/10.1073/pnas.1400822111
Fernie AR, Yan J (2019) De novo domestication: an alternative route toward new crops for the future. Mol Plant 12:615–631. https://doi.org/10.1016/j.molp.2019.03.016
Frary A, Nesbitt TC, Frary A, Grandillo S, van Der 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. https://doi.org/10.1126/science.289.5476.85
Gelvin SB (2010) Plant proteins involved in Agrobacterium-mediated genetic transformation. Annu Rev Phytopathol 48:45–68. https://doi.org/10.1146/annurev-phyto-080508-081852
Giovannoni J, Nguyen C, Ampofo B, Zhong S, Fei Z (2017) The epigenome and transcriptional dynamics of fruit ripening. Annu Rev Plant Biol 68:61–84. https://doi.org/10.1146/annurev-arplant-042916-040906
Gonzalo MJ, Brewer MT, Anderson C, Sullivan D, Gray S, van der Knaap E (2009) Tomato fruit shape analysis using morphometric and morphology attributes implemented in Tomato Analyzer software Program. J Am Soc Hort Sci 134(1):77–87. https://doi.org/10.21273/JASHS.134.1.77
Guo M, Simmons CR (2011) Cell number counts–the fw2.2 and CNR genes and implications for controlling plant fruit and organ size. Plant Sci 181:1–7. https://doi.org/10.1016/j.plantsci.2011.03.010
Guo M, Rupe MA, Dieter JA, Zou J, Spielbauer D, Duncan KE et al (2010) Cell Number Regulator1 affects plant and organ size in maize: implications for crop yield enhancement and heterosis. Plant Cell 22(4):1057–1073. https://doi.org/10.1105/tpc.109.073676
Hayut SF, Bessudo CM, Levy AA (2017) Targeted recombination between homologous chromosomes for precise breeding in tomato. Nat Commun 8:15605. https://doi.org/10.1038/ncomms15605
Heidmann I, de Lange B, Lambalk J, Angenent GC, Boutilier K (2011) Efficient sweet pepper transformation mediated by the BABY BOOM transcription factor. Plant Cell Rep 30:1107–1115. https://doi.org/10.1007/s00299-011-1018-x
Huang Z, van Der Knaap E (2011) Tomato fruit weight 11.3 maps close to fasciated on the bottom of chromosome 11. Theor Appl Genet 123:465–474. https://doi.org/10.1007/s00122-011-1599-3
Hurd RG (1973) Long-day effects on growth and flower initiation of tomato plants in low light. Ann Appl Biol 73:221–228. https://doi.org/10.1111/j.1744-7348.1973.tb01328.x
Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Toki S (2015) CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochem Biophy Res Commun 467:76–82. https://doi.org/10.1016/j.bbrc.2015.09.117
Jin J, Huang W, Gao JP, Yang J, Shi M, Zhu MZ, Lin HX (2008) Genetic control of rice plant architecture under domestication. Nat Genet 40(11):1365–1369. https://doi.org/10.1038/ng.247
Jusiak B, Cleto S, Perez-Piñera P, Lu TK (2016) Engineering synthetic gene circuits in living cells with CRISPR technology. Trends Biotechnol 34:535–547. https://doi.org/10.1016/j.tibtech.2015.12.014
Karkute SG, Singh AK, Gupta OP, Singh PM, Singh B (2017) CRISPR/Cas9 mediated genome engineering for improvement of horticultural crops. Front Plant Sci 8:1635. https://doi.org/10.3389/fpls.2017.01635
Khan MZ, Zaidi SSA, Amin I, Mansoor S (2019) A CRISPR way for fast-forward crop domestication. Trends Plant Sci 24(4):293–296. https://doi.org/10.1016/j.tplants.2019.01.011
Klap C, Yeshayahou E, Bolger AM, Arazi T, Gupta SK, Shabtai S et al (2017) Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function. Plant Biotechnol J 15:634–647. https://doi.org/10.1111/pbi.12662
Knott GJ, Doudna JA (2018) CRISPR-Cas guides the future of genetic engineering. Science 361:866–869. https://doi.org/10.1126/science.aat5011
Kwon CT, Heo J, Lemmon ZH, Capua Y, Hutton SF, Van Eck J, Lippman ZB (2020) Rapid customization of Solanaceae fruit crops for urban agriculture. Nat Biotechnol 38(2):182–188. https://doi.org/10.1038/s41587-019-0361-2
Lacroix B, Citovsky V (2016) A functional bacterium-to-plant DNA transfer machinery of Rhizobium etli. PLoS Pathog 12:e1005502. https://doi.org/10.1371/journal.ppat.1005502
Lemmon ZH, Reem NT, Dalrymple J, Soyk S, Swartwood KE, Rodríguez-Leal D et al (2018) Rapid improvement of domestication traits in an orphan crop by genome editing. Nat Plant 4(10):766–770. https://doi.org/10.1038/s41477-018-0259-x
Li T, Liu B, Spalding MH, Weeks DP, Yang B (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390–392. https://doi.org/10.1038/nbt.2199
Li T, Yang X, Yu Y, Si X, Zhai X, Zhang H et al (2018) Domestication of wild tomato is accelerated by genome editing. Nat Biotech 36(12):1160–1163. https://doi.org/10.1038/nbt.4273
Li C, Zhang R, Meng X, Chen S, Zong Y, Lu C, Gao C (2020) Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors. Nat Biotechnol 38(7):1–8. https://doi.org/10.1038/s41587-019-0393-7
Liang S, Jie C, Kai X, Wencai Y (2017) Origin of the domesticated horticultural species and molecular bases of fruit shape and size changes during the domestication, taking tomato as an example. Hort Plant J 3(3):125–132. https://doi.org/10.1016/j.hpj.2017.07.007
Lifschitz E, Eviatar T, Rozman A, Shalit A, Goldshmidt A, Amsellem Z, Eshed Y (2006) The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli. Proc Nat Acad Sci USA 103(16):6398–6403. https://doi.org/10.1073/pnas.0601620103
Lippman Z, Tanksley SD (2001) Dissecting the genetic pathway to extreme fruit size in tomato using a cross between the small-fruited wild species Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom. Genetics 158:413–422
Liu B, Watanabe S, Uchiyama T, Kong F, Kanazawa A, Xia Z, Masuta C (2010) The soybean stem growth habit gene Dt1 is an ortholog of Arabidopsis TERMINAL FLOWER1. Plant Physiol 153(1):198–210. https://doi.org/10.1104/pp.109.150607
Liu X, Kim YJ, Muller R, Yumul RE, Liu C, Pan Y et al (2011) AGAMOUS terminates floral stem cell maintenance in Arabidopsis by directly repressing WUSCHEL through recruitment of Polycomb Group proteins. Plant Cell 23:3654–3670. https://doi.org/10.1105/tpc.111.091538
Lohmann JU, Hong RL, Hobe M, Busch MA, Parcy F, Simon R et al (2001) A molecular link between stem cell regulation and floral patterning in Arabidopsis. Cell 105:793–803. https://doi.org/10.1016/S0092-8674(01)00384-1
Lowe K, Wu E, Wang N, Hoerster G, Hastings C, Cho MJ et al (2016) Morphogenic regulators Baby boom and Wuschel improve monocot transformation. Plant Cell 28:1998–2015. https://doi.org/10.1105/tpc.16.00124
MacArthur JW (1932) Inherited characters in tomato. I-the self pruning habit. J Hered 23:394–395
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(1):84–89. https://doi.org/10.1038/s41587-019-0337-2
Meyer RS, Purugganan MD (2013) Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet 14:840–852. https://doi.org/10.1038/nrg3605
Morineau C, Bellec Y, Tellier F, Gissot L, Kelemen Z, Nogué F, Faure JD (2017) Selective gene dosage by CRISPR-Cas9 genome editing in hexaploid Camelina sativa. Plant Biotechnol J 15:729–739. https://doi.org/10.1111/pbi.12671
Mu Q, Huang Z, Chakrabarti M, IllaBerenguer E, Liu X, Wang Y 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(8):e1006930. https://doi.org/10.1371/journal.pgen.1006930
Muños S, Ranc N, Botton E, Bérard A, Rolland S, Duffé P et al (2011) Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. Plant Physiol 156:2244–2254. https://doi.org/10.1104/pp.111.173997
Naito Y, Hino K, Bono H, Ui-Tei K (2015) CRISPR direct: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31:1120–1123. https://doi.org/10.1093/bioinformatics/btu743
Nekrasov V, Wang C, Win J, Lanz C, Weigel D, Kamoun S (2017) Rapid generation of a transgene free powdery mildew resistant tomato by genome deletion. Sci Rep 7:482. https://doi.org/10.1038/s41598-017-00578-x
Nemhauser JL, Torii KU (2016) Plant synthetic biology for molecular engineering of signaling and development. Nat Plants 2:16010. https://doi.org/10.1038/nplants.2016.10
O’Brien A, Bailey TL (2014) GT-Scan: identifying unique genomic targets. Bioinformatics 30:2673–2675. https://doi.org/10.1093/bioinformatics/btu354
Pan C, Ye L, Qin L, Liu X, He Y, Wang J et al (2016) CRISPR/Cas9- mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Sci Rep 6:24765. https://doi.org/10.1038/srep24765
Park SJ, Jiang K, Tal L, Yichie Y, Gar O, Zamir D et al (2014) Optimization of crop productivity in tomato using induced mutations in the florigen pathway. Nat Genet 46(12):1337–1342. https://doi.org/10.1038/ng.3131
Pnueli L, Carmel-Goren L, Hareven D, Gutfinger T, Alvarez J, Ganal M, Lifschitz E (1998) The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Develop 125(11):1979–1989
Prakash DP, Ramachandra YL, Hanur VS (2015) Factors affecting in vitro shoot regeneration in hypocotyls of brinjal (Solanum melongena L.) in the early steps of Agrobacterium-mediated transformation. J Hort Sci 10:136–142
Que Q, Chilton MDM, de Fontes CM, He C, Nuccio M, Zhu T, Wu Y, Chen JS, Shi L (2010) Trait stacking in transgenic crops: challenges and opportunities. GM Crops 1(4):220–229. https://doi.org/10.4161/gmcr.1.4.13439
Rehman F, Gong H, Li Z, Zeng S, Yang T, Ai P et al (2020) Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.). BMC Plant Biol 20:474. https://doi.org/10.1186/s12870-020-02567-1
Rodríguez GR, Muños S, Anderson C, Sim SC, Michel A, Causse M et al (2011) Distribution of SUN, OVATE, LC, and FAS in the tomato germplasm and the relationship to fruit shape diversity. Plant Physiol 156:275–285. https://doi.org/10.1104/pp.110.167577
Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB (2017) Engineering quantitative trait variation for crop improvement by genome editing. Cell 171(2):470–480. https://doi.org/10.1016/j.cell.2017.08.030
Salesse-Smith CE, Sharwood RE, Busch FA, Kromdijk J, Bardal V, Stern DB (2018) Overexpression of Rubisco subunits with RAF1 increases Rubisco content in maize. Nat Plants 4(10):802–810. https://doi.org/10.1038/s41477-018-0252-4
Scheben A, Wolter F, Batley J, Puchta H, Edwards D (2017) Towards CRISPR/Cas crops–bringing together genomics and genome editing. New Phytol 216:682–698. https://doi.org/10.1111/nph.14702
Shalit A, Rozman A, Goldshmidt A, Alvarez JP, Bowman JL, Eshed Y et al (2009) The flowering hormone florigen functions as a general systemic regulator of growth and termination. Proc Nat Acad Sci USA 106:8392–8397. https://doi.org/10.1073/pnas.0810810106
Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Gao C (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31(8):686–688. https://doi.org/10.1038/nbt.2650
Soyk S, Müller NA, Park SJ, Schmalenbach I, Jiang K, Hayama R et al (2017) Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Nat Genet 49(1):162–168. https://doi.org/10.1038/ng.3733
Sussex IM (1989) Developmental programming of the shoot meristem. Cell 56:225–229. https://doi.org/10.1016/0092-8674(89)90895-7
Tang X, Liu G, Zhou J, Ren Q, You Q, Tian L et al (2018) A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biol 19:84. https://doi.org/10.1186/s13059-018-1458-5
Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327:818–822. https://doi.org/10.1126/science.1183700
van der Knaap E, Chakrabarti M, Chu YH, Clevenger JP, Illa-Berenguer E, Huang Z et al (2014) What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape. Front Plant Sci 5:227. https://doi.org/10.3389/fpls.2014.00227
Van Eck J (2018) Genome editing and plant transformation of Solanaceous food crops. Curr Opi Biotechnol 49:35–41. https://doi.org/10.1016/j.copbio.2017.07.012
Varshney RK, Ribaut JM, Buckler ES, Tuberosa R, Rafalski JA, Langridge P (2012) Can genomics boost productivity of orphan crops? Nat Biotechnol 30(12):1172–1176. https://doi.org/10.1038/nbt.2440
Wang Y, Wang S, Zhao Y, Khan DM, Zheng J, Zhu S (2009) Genetic characterization of a new growth habit mutant in tomato (Solanum lycopersicum). Plant Mol Biol Rep 27(4):431. https://doi.org/10.1007/s11105-009-0095-2
Wang L, Li J, Zhao J, He C (2015) Evolutionary developmental genetics of fruit morphological variation within the Solanaceae. Front Plant Sci 6:248. https://doi.org/10.3389/fpls.2015.00248
Wang T, Zhang H, Zhu H (2019) CRISPR technology is revolutionizing the improvement of tomato and other fruit crops. Hort Res 6(1):1–13. https://doi.org/10.1038/s41438-019-0159-x
Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S (2011) A modular cloning system for standardized assembly of multigene constructs. PLoS ONE 6(2):e16765. https://doi.org/10.1371/journal.pone.0016765
Wersch S, Li X (2019) Stronger when together: clustering of plant NLR disease resistance genes. Trends Plant Sci 24:688–699. https://doi.org/10.1016/j.tplants.2019.05.005
Xie K, Zhang J, Yang Y (2014) Genome-wide prediction of highly specific guide RNA spacers for the CRISPR-Cas9 mediated genome editing in model plants and major crops. Mol Plant 7:923–926. https://doi.org/10.1093/mp/ssu009
Xu C, Liberatore KL, MacAlister CA, Huang Z, Chu YH, Jiang K et al (2015) A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nat Genet 47:784–792. https://doi.org/10.1038/ng.3309
Yanofsky MF, Ma H, Bowman JL, Drews GN, Feldmann KA, Meyerowitz EM (1990) The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346:35–39. https://doi.org/10.1038/346035a0
Yin K, Gao C, Qiu JL (2017) Progress and prospects in plant genome editing. Nat Plants 3(8):1–6. https://doi.org/10.1038/nplants.2017.107
Zhang N, Brewer MT, van der Knaap E (2012) Fine mapping of fw3.2 controlling fruit weight in tomato. Theor Appl Genet 125(2):273–284. https://doi.org/10.1007/s00122-012-1832-8
Zhang H, Si X, Ji X, Fan R, Liu J, Chen K, Gao C (2018a) Genome editing of upstream open reading frames enables translational control in plants. Nat Biotechnol 36(9):894–898. https://doi.org/10.1038/nbt.4202
Zhang S, Jiao Z, Liu L, Wang K, Zhong D, Li S, Cui X (2018b) Enhancer-promoter interaction of SELF PRUNING 5G shapes photoperiod adaptation. Plant Physiol 178(4):1631–1642. https://doi.org/10.1104/pp.18.01137
Zhang Y, Pribil M, Palmgren M, Gao C (2020) A CRISPR way for accelerating improvement of food crops. Nat Food 1:200–205. https://doi.org/10.1038/s43016-020-0051-8
Zsögön A, Čermák T, Naves ER, Notini MM, Edel KH, Weinl S et al (2018) De novo domestication of wild tomato using genome editing. Nat Biotechnol 36(12):1211–1216. https://doi.org/10.1038/nbt.4272
Acknowledgements
This work was supported by grants from Strategic and Priority Research Program of Chinese Academy of Sciences [XDA24030502], National Key R&D Program of China [2018YFD1000607]; the National Natural Science Foundation of China [31770334, 32170389]; Science and Technology Program of Guangzhou [201904010167]; Guangdong Provincial Special Fund For Modern Agriculture Industry Technology Innovation Teams, China [2020KJ148]. The funding organizations did not aid in designing the study and manuscript write up.
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FR, YW conceptualize the main theme; FR drafted the manuscript; FR, HG prepared scientific illustrations; YB, FR contributed in the concept of molecular mechanisms of genes; YW, SZ and HH reviewed the draft and suggested technical points to improve the manuscript. All authors read and approved for submission of revised version of the manuscript.
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Rehman, F., Gong, H., Bao, Y. et al. CRISPR gene editing of major domestication traits accelerating breeding for Solanaceae crops improvement. Plant Mol Biol 108, 157–173 (2022). https://doi.org/10.1007/s11103-021-01229-6
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DOI: https://doi.org/10.1007/s11103-021-01229-6