Abstract
Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.
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Abe, A., Kosugi, S., Yoshida, K., Natsume, S., Takagi, H., Kanzaki, H., Matsumura, H., Yoshida, K., Mitsuoka, C., Tamiru, M., et al. (2012). Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30, 174–178.
Aflitos, S., Schijlen, E., de Jong, H., de Ridder, D., Smit, S., Finkers, R., Wang, J., Zhang, G., Li, N., Mao, L., et al. (2014). Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80, 136–148.
Alonge, M., Wang, X., Benoit, M., Soyk, S., Pereira, L., Zhang, L., Suresh, H., Ramakrishnan, S., Maumus, F., Ciren, D., et al. (2020). Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell 182, 145–161.e23.
Alseekh, S., Tohge, T., Wendenberg, R., Scossa, F., Omranian, N., Li, J., Kleessen, S., Giavalisco, P., Pleban, T., Mueller-Roeber, B., et al. (2015). Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. Plant Cell 27, 485–512.
Amano, M., Mochizuki, A., Kawagoe, Y., Iwahori, K., Niwa, K., Svoboda, J., Maeda, T., and Imura, Y. (2013). High-resolution mapping of zym, a recessive gene for Zucchini yellow mosaic virus resistance in cucumber. Theor Appl Genet 126, 2983–2993.
Arango, J., Jourdan, M., Geoffriau, E., Beyer, P., and Welsch, R. (2014). Carotene hydroxylase activity determines the levels of both α-carotene and total carotenoids in orange carrots. Plant Cell 26, 2223–2233.
Azpeitia, E., Tichtinsky, G., Le Masson, M., Serrano-Mislata, A., Lucas, J., Gregis, V., Gimenez, C., Prunet, N., Farcot, E., Kater, M.M., et al. (2021). Cauliflower fractal forms arise from perturbations of floral gene networks. Science 373, 192–197.
Barchi, L., Pietrella, M., Venturini, L., Minio, A., Toppino, L., Acquadro, A., Andolfo, G., Aprea, G., Avanzato, C., Bassolino, L., et al. (2019). A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution. Sci Rep 9, 11769.
Barrera-Redondo, J., Ibarra-Laclette, E., Vázquez-Lobo, A., Gutiérrez-Guerrero, Y.T., Sánchez de la Vega, G., Piñero, D., Montes-Hernández, S., Lira-Saade, R., and Eguiarte, L.E. (2019). The genome of Cucurbita argyrosperma (silver-seed gourd) reveals faster rates of protein-coding gene and long noncoding RNA turnover and neofunctionalization within Cucurbita. Mol Plant 12, 506–520.
Barry, C.S., and Giovannoni, J.J. (2006). Ripening in the tomato Green-ripe mutant is inhibited by ectopic expression of a protein that disrupts ethylene signaling. Proc Natl Acad Sci USA 103, 7923–7928.
Bauchet, G., Grenier, S., Samson, N., Segura, V., Kende, A., Beekwilder, J., Cankar, K., Gallois, J.L., Gricourt, J., Bonnet, J., et al. (2017). Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement. New Phytol 215, 624–641.
Berg, J.A., Hermans, F.W.K., Beenders, F., Lou, L., Vriezen, W.H., Visser, R.G.F., Bai, Y., and Schouten, H.J. (2020). Analysis of QTL dm4.1 for downy mildew resistance in cucumber reveals multiple subqtl: A novel RLK as candidate gene for the most important subQTL. Front Plant Sci 11, 569876.
Bhattarai, G., Shi, A., Feng, C., Dhillon, B., Mou, B., and Correll, J.C. (2020). Genome wide association studies in multiple spinach breeding populations refine downy mildew race 13 resistance genes. Front Plant Sci 11, 563187.
Boissot, N., Thomas, S., Sauvion, N., Marchal, C., Pavis, C., and Dogimont, C. (2010). Mapping and validation of QTLs for resistance to aphids and whiteflies in melon. Theor Appl Genet 121, 9–20.
Bolger, A., Scossa, F., Bolger, M.E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S., Sørensen, I., Lichtenstein, G., et al. (2014). The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 46, 1034–1038.
Borovsky, Y., Monsonego, N., Mohan, V., Shabtai, S., Kamara, I., Faigenboim, A., Hill, T., Chen, S., Stoffel, K., Van Deynze, A., et al. (2019). The zinc-finger transcription factor CcLOL1 controls chloroplast development and immature pepper fruit color in Capsicum chinense and its function is conserved in tomato. Plant J 99, 41–55.
Boualem, A., Fergany, M., Fernandez, R., Troadec, C., Martin, A., Morin, H., Sari, M.A., Collin, F., Flowers, J.M., Pitrat, M., et al. (2008). A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons. Science 321, 836–838.
Boualem, A., Troadec, C., Camps, C., Lemhemdi, A., Morin, H., Sari, M. A., Fraenkel-Zagouri, R., Kovalski, I., Dogimont, C., Perl-Treves, R., et al. (2015). A cucurbit androecy gene reveals how unisexual flowers develop and dioecy emerges. Science 350, 688–691.
Brotman, Y., Normantovich, M., Goldenberg, Z., Zvirin, Z., Kovalski, I., Stovbun, N., Doniger, T., Bolger, A.M., Troadec, C., Bendahmane, A., et al. (2013). Dual resistance of melon to Fusarium oxysporum races 0 and 2 and to Papaya ring-spot virus is controlled by a pair of head-to-head-oriented NB-LRR genes of unusual architecture. Mol Plant 6, 235–238.
Busta, L., Yim, W.C., LaBrant, E.W., Wang, P., Grimes, L., Malyszka, K., Cushman, J.C., Santos, P., Kosma, D.K., and Cahoon, E.B. (2018). Identification of genes encoding enzymes catalyzing the early steps of carrot polyacetylene biosynthesis. Plant Physiol 178, 1507–1521.
Cai, C., Wang, X., Liu, B., Wu, J., Liang, J., Cui, Y., Cheng, F., and Wang, X. (2017). Brassica rapa genome 2.0: A reference upgrade through sequence re-assembly and gene re-annotation. Mol Plant 10, 649–651.
Cai, X., Chang, L., Zhang, T., Chen, H., Zhang, L., Lin, R., Liang, J., Wu, J., Freeling, M., and Wang, X. (2021a). Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa. Genome Biol 22, 166.
Cai, X., Sun, X., Xu, C., Sun, H., Wang, X., Ge, C., Zhang, Z., Wang, Q., Fei, Z., Jiao, C., et al. (2021b). Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits. Nat Commun 12, 7246.
Cárdenas, P.D., Sonawane, P.D., Pollier, J., Vanden Bossche, R., Dewangan, V., Weithorn, E., Tal, L., Meir, S., Rogachev, I., Malitsky, S., et al. (2016). GAME9 regulates the biosynthesis of steroidal alkaloids and upstream isoprenoids in the plant mevalonate pathway. Nat Commun 7, 10654.
Catanzariti, A.M., Do, H.T.T., Bru, P., Sain, M., Thatcher, L.F., Rep, M., and Jones, D.A. (2017). The tomato I gene for Fusarium wilt resistance encodes an atypical leucine-rich repeat receptor-like protein whose function is nevertheless dependent on SOBIR1 and SERK3/BAK1. Plant J 89, 1195–1209.
Catanzariti, A.M., Lim, G.T.T., and Jones, D.A. (2015). The tomato I-3 gene: a novel gene for resistance to Fusarium wilt disease. New Phytol 207, 106–118.
Chakrabarti, M., Zhang, N., Sauvage, C., Muños, S., Blanca, J., Cañizares, J., Diez, M.J., Schneider, R., Mazourek, M., McClead, J., et al. (2013). A cytochrome P450 regulates a domestication trait in cultivated tomato. Proc Natl Acad Sci USA 110, 17125–17130.
Chalhoub, B., Denoeud, F., Liu, S., Parkin, I.A.P., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., et al. (2014). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345, 950–953.
Chen, C., Cui, Q., Huang, S., Wang, S., Liu, X., Lu, X., Chen, H., and Tian, Y. (2018). An EMS mutant library for cucumber. J Integr Agr 17, 1612–1619.
Chen, R., Chang, L., Cai, X., Wu, J., Liang, J., Lin, R., Song, Y., and Wang, X. (2021). Development of indel markers for Brassica rapa based on a high-resolution melting curve. Hortic Plant J 7, 31–37.
Cheng, F., Sun, R., Hou, X., Zheng, H., Zhang, F., Zhang, Y., Liu, B., Liang, J., Zhuang, M., Liu, Y., et al. (2016). Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet 48, 1218–1224.
Cheng, F., Wu, J., and Wang, X. (2014). Genome triplication drove the diversification of Brassica plants. Hortic Res 1, 14024.
Choe, S., Choi, B., Kang, J.H., and Seo, J.K. (2021). Tolerance to tomato yellow leaf curl virus in transgenic tomato overexpressing a cellulose synthase-like gene. Plant Biotechnol J 19, 657–659.
Cui, H., Fan, C., Ding, Z., Wang, X., Tang, L., Bi, Y., Luan, F., and Gao, P. (2022). CmPMRl and CmPMrs are responsible for resistance to powdery mildew caused by Podosphaera xanthii race 1 in melon. Theor Appl Genet 135, 1209–1222.
de Jonge, R., Peter van Esse, H., Maruthachalam, K., Bolton, M.D., Santhanam, P., Saber, M.K., Zhang, Z., Usami, T., Lievens, B., Subbarao, K.V., et al. (2012). Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing. Proc Natl Acad Sci USA 109, 5110–5115.
Debernardi, J.M., Tricoli, D.M., Ercoli, M.F., Hayta, S., Ronald, P., Palatnik, J.F., and Dubcovsky, J. (2020). A GRF-GIF chimeric protein improves the regeneration efficiency of transgenic plants. Nat Biotechnol 38, 1274–1279.
Della Coletta, R., Qiu, Y., Ou, S., Hufford, M.B., and Hirsch, C.N. (2021). How the pan-genome is changing crop genomics and improvement. Genome Biol 22, 3.
Deng, H., Chen, Y., Liu, Z., Liu, Z., Shu, P., Wang, R., Hao, Y., Su, D., Pirrello, J., Liu, Y., et al. (2022a). SlERF.F12 modulates the transition to ripening in tomato fruit by recruiting the co-repressor Topless and histone deacetylases to repress key ripening genes. Plant Cell 34, 1250–1272.
Deng, Y., Liu, S., Zhang, Y., Tan, J., Li, X., Chu, X., Xu, B., Tian, Y., Sun, Y., Li, B., et al. (2022b). A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding. Mol Plant 15, 1268–1284.
Dohm, J.C., Minoche, A.E., Holtgräwe, D., Capella-Gutiérrez, S., Zakrzewski, F., Tafer, H., Rupp, O., Sörensen, T.R., Stracke, R., Reinhardt, R., et al. (2014). The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505, 546–549.
Dorn, K.M., Fankhauser, J.D., Wyse, D.L., and Marks, M.D. (2015). A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop. DNA Res 22, 121–131.
Du, M., Zhao, J., Tzeng, D.T.W., Liu, Y., Deng, L., Yang, T., Zhai, Q., Wu, F., Huang, Z., Zhou, M., et al. (2017). MYC2 orchestrates a hierarchical transcriptional cascade that regulates jasmonate-mediated plant immunity in tomato. Plant Cell 29, 1883–1906.
Fekih, R., Takagi, H., Tamiru, M., Abe, A., Natsume, S., Yaegashi, H., Sharma, S., Sharma, S., Kanzaki, H., Matsumura, H., et al. (2013). MutMap+: genetic mapping and mutant identification without crossing in rice. PLoS ONE 8, e68529.
Feng, Q., Xiao, L., He, Y., Liu, M., Wang, J., Tian, S., Zhang, X., and Yuan, L. (2021). Highly efficient, genotype-independent transformation and gene editing in watermelon (Citrullus lanatus) using a chimeric ClGRF4-GIF1 gene. Integrative Plant Biol 63, 2038–2042.
Finkers, R., van Kaauwen, M., Ament, K., Burger-Meijer, K., Egging, R., Huits, H., Kodde, L., Kroon, L., Shigyo, M., Sato, S., et al. (2021). Insights from the first genome assembly of Onion (Allium cepa). G3 (Bethesda) 11, jkab243.
Franks, S.J., Kane, N.C., O’Hara, N.B., Tittes, S., and Rest, J.S. (2016). Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools. Mol Ecol 25, 3622–3631.
Fridman, E., Carrari, F., Liu, Y.S., Fernie, A.R., and Zamir, D. (2004). Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science 305, 1786–1789.
Galpaz, N., Burger, Y., Lavee, T., Tzuri, G., Sherman, A., Melamed, T., Eshed, R., Meir, A., Portnoy, V., Bar, E., et al. (2013). Genetic and chemical characterization of an EMS induced mutation in Cucumis melo CRTISO gene. Arch Biochem Biophys 539, 117–125.
Galpaz, N., Gonda, I., Shem-Tov, D., Barad, O., Tzuri, G., Lev, S., Fei, Z., Xu, Y., Mao, L., Jiao, C., et al. (2018). Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based highresolution QTL and eQTL mapping. Plant J 94, 169–191.
Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D.M., Burzynski-Chang, E.A., Fish, T.L., Stromberg, K.A., Sacks, G.L., et al. (2019). The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat Genet 51, 1044–1051.
Gao, L., Zhao, W., Qu, H., Wang, Q., and Zhao, L. (2016). The yellow-fruited tomato 1 (yft1) mutant has altered fruit carotenoid accumulation and reduced ethylene production as a result of a genetic lesion in ETHYLENE INSENSITIVE2. Theor Appl Genet 129, 717–728.
Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M., Mir, G., González, V.M., Hénaff, E., Câmara, F., Cozzuto, L., Lowy, E., et al. (2012). The genome of melon (Cucumis melo L.). Proc Natl Acad Sci USA 109, 11872–11877.
Giner, A., Pascual, L., Bourgeois, M., Gyetvai, G., Rios, P., Picó, B., Troadec, C., Bendahmane, A., Garcia-Mas, J., and Martín-Hernández, A.M. (2017). A mutation in the melon Vacuolar Protein Sorting 41prevents systemic infection of Cucumber mosaic virus. Sci Rep 7, 10471.
Gonzalez-Cendales, Y., Catanzariti, A.M., Baker, B., Mcgrath, D.J., and Jones, D.A. (2016). Identification of I-7 expands the repertoire of genes for resistance to Fusarium wilt in tomato to three resistance gene classes. Mol Plant Pathol 17, 448–463.
Guo, G., Wang, S., Liu, J., Pan, B., Diao, W., Ge, W., Gao, C., and Snyder, J.C. (2017). Rapid identification of QTLs underlying resistance to Cucumber mosaic virus in pepper (Capsicum frutescens). Theor Appl Genet 130, 41–52.
Guo, G., Zhang, G., Pan, B., Diao, W., Liu, J., Ge, W., Gao, C., Zhang, Y., Jiang, C., and Wang, S. (2019a). Development and application of indel markers for Capsicum spp. based on whole-genome re-sequencing. Sci Rep 9, 3691.
Guo, L., Qiu, J., Han, Z., Ye, Z., Chen, C., Liu, C., Xin, X., Ye, C.Y., Wang, Y.Y., Xie, H., et al. (2015). A host plant genome (Zizania latifolia) after a century-long endophyte infection. Plant J 83, 600–609.
Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W.J., Zhang, H., Zheng, Y., Mao, L., Ren, Y., Wang, Z., et al. (2013). The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45, 51–58.
Guo, S., Zhao, S., Sun, H., Wang, X., Wu, S., Lin, T., Ren, Y., Gao, L., Deng, Y., Zhang, J., et al. (2019b). Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nat Genet 51, 1616–1623.
Harkess, A., Zhou, J., Xu, C., Bowers, J.E., Van der Hulst, R., Ayyampalayam, S., Mercati, F., Riccardi, P., McKain, M.R., Kakrana, A., et al. (2017). The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nat Commun 8, 1279.
Hatakeyama, K., Niwa, T., Kato, T., Ohara, T., Kakizaki, T., and Matsumoto, S. (2017). The tandem repeated organization of NB-LRR genes in the clubroot-resistant CRb locus in Brassica rapa L. Mol Genet Genomics 292, 397–405.
Hatakeyama, K., Suwabe, K., Tomita, R.N., Kato, T., Nunome, T., Fukuoka, H., and Matsumoto, S. (2013). Identification and characterization of Crr1a, a gene for resistance to clubroot disease (Plasmodiophora brassicae Woronin) in Brassica rapa L. PLoS ONE 8, e54745.
Hendelman, A., Zebell, S., Rodriguez-Leal, D., Dukler, N., Robitaille, G., Wu, X., Kostyun, J., Tal, L., Wang, P., Bartlett, M.E., et al. (2021). Conserved pleiotropy of an ancient plant homeobox gene uncovered by cis-regulatory dissection. Cell 184, 1724–1739.e16.
Hirakawa, H., Shirasawa, K., Miyatake, K., Nunome, T., Negoro, S., Ohyama, A., Yamaguchi, H., Sato, S., Isobe, S., Tabata, S., et al. (2014). Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. DNA Res 21, 649–660.
Hosmani, P.S., Flores-Gonzalez, M., van de Geest, H., Maumus, F., Bakker, L.V., Schijlen, E., van Haarst, J., Cordewener, J., Sanchez-Perez, G., Peters, S., et al. (2019). An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. bioRxiv, 767764.
Hu, B., Li, D., Liu, X., Qi, J., Gao, D., Zhao, S., Huang, S., Sun, J., and Yang, L. (2017). Engineering non-transgenic gynoecious cucumber using an improved transformation protocol and optimized CRISPR/Cas9 system. Mol Plant 10, 1575–1578.
Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W.J., Wang, X., Xie, B., Ni, P., et al. (2009). The genome of the cucumber, Cucumis sativus L. Nat Genet 41, 1275–1281.
Huang, Y., Cao, H.S., Yang, L., Chen, C., Shabala, L., Xiong, M., Niu, M. L., Liu, J., Zheng, Z.H., Zhou, L.J., et al. (2019). Tissue-specific respiratory burst oxidase homolog-dependent H2O2 signaling to the plasma membrane H+-ATPase confers potassium uptake and salinity tolerance in Cucurbitaceae. J Exp Bot 70, 5879–5893.
Hulse-Kemp, A.M., Maheshwari, S., Stoffel, K., Hill, T.A., Jaffe, D., Williams, S.R., Weisenfeld, N., Ramakrishnan, S., Kumar, V., Shah, P., et al. (2018). Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. Hortic Res 5, 4.
Iorizzo, M., Ellison, S., Senalik, D., Zeng, P., Satapoomin, P., Huang, J., Bowman, M., Iovene, M., Sanseverino, W., Cavagnaro, P., et al. (2016). A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet 48, 657–666.
Itkin, M., Heinig, U., Tzfadia, O., Bhide, A.J., Shinde, B., Cardenas, P.D., Bocobza, S.E., Unger, T., Malitsky, S., Finkers, R., et al. (2013). Biosynthesis of antinutritional alkaloids in solanaceous crops is mediated by clustered genes. Science 341, 175–179.
Itkin, M., Rogachev, I., Alkan, N., Rosenberg, T., Malitsky, S., Masini, L., Meir, S., Iijima, Y., Aoki, K., de Vos, R., et al. (2011). GLYCOALKALOID METABOLISM1 is required for steroidal alkaloid glycosylation and prevention of phytotoxicity in tomato. Plant Cell 23, 4507–4525.
Jang, S.J., Jeong, H.B., Jung, A., Kang, M.Y., Kim, S., Ha, S.H., Kwon, J. K., and Kang, B.C. (2020). Phytoene synthase 2 can compensate for the absence of PSY1 in the control of color in Capsicum fruit. J Exp Bot 71, 3417–3427.
Jang, Y.J., Seo, M., Hersh, C.P., Rhee, S.J., Kim, Y., and Lee, G.P. (2019). An evolutionarily conserved non-synonymous SNP in a leucine-rich repeat domain determines anthracnose resistance in watermelon. Theor Appl Genet 132, 473–488.
Jeong, H.B., Jang, S.J., Kang, M.Y., Kim, S., Kwon, J.K., and Kang, B.C. (2020). Candidate gene analysis reveals that the fruit color locus c1 corresponds to PRR2 in pepper (Capsicum frutescens). Front Plant Sci 11, 399.
Jiang, F., and Doudna, J.A. (2017). CRISPR-Cas9 structures and mechanisms. Annu Rev Biophys 46, 505–529.
Jin, M., Lee, S.S., Ke, L., Kim, J.S., Seo, M.S., Sohn, S.H., Park, B.S., and Bonnema, G. (2014). Identification and mapping of a novel dominant resistance gene, TuRB07 to Turnip mosaic virus in Brassica rapa. Theor Appl Genet 127, 509–519.
Kasianov, A.S., Klepikova, A.V., Kulakovskiy, I.V., Gerasimov, E.S., Fedotova, A.V., Besedina, E.G., Kondrashov, A.S., Logacheva, M.D., and Penin, A.A. (2017). High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution. Plant J 91, 278–291.
Khan, A.W., Garg, V., Roorkiwal, M., Golicz, A.A., Edwards, D., and Varshney, R.K. (2020). Super-pangenome by integrating the wild side of a species for accelerated crop improvement. Trends Plant Sci 25, 148–158.
Kim, O.R., Cho, M.C., Kim, B.D., and Huh, J.H. (2010). A splicing mutation in the gene encoding phytoene synthase causes orange coloration in Habanero pepper fruits. Mol Cells 30, 569–574.
Kim, S., Park, J., Yeom, S.I., Kim, Y.M., Seo, E., Kim, K.T., Kim, M.S., Lee, J.M., Cheong, K., Shin, H.S., et al. (2017a). New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 18, 210.
Kim, S., Park, M., Yeom, S.I., Kim, Y.M., Lee, J.M., Lee, H.A., Seo, E., Choi, J., Cheong, K., Kim, K.T., et al. (2014). Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46, 270–278.
Kim, S.B., Kang, W.H., Huy, H.N., Yeom, S.I., An, J.T., Kim, S., Kang, M. Y., Kim, H.J., Jo, Y.D., Ha, Y., et al. (2017b). Divergent evolution of multiple virus-resistance genes from a progenitor in Capsicum spp. New Phytol 213, 886–899.
Kitashiba, H., Li, F., Hirakawa, H., Kawanabe, T., Zou, Z., Hasegawa, Y., Tonosaki, K., Shirasawa, S., Fukushima, A., Yokoi, S., et al. (2014). Draft sequences of the radish (Raphanus sativus L.) genome. DNA Res 21, 481–490.
Klee, H.J., and Giovannoni, J.J. (2011). Genetics and control of tomato fruit ripening and quality attributes. Annu Rev Genet 45, 41–59.
Komatsu, H., Abdellatif, I.M.Y., Yuan, S., Ono, M., Nonaka, S., Ezura, H., Ariizumi, T., and Miura, K. (2020). Genome editing in PDS genes of tomatoes by non-selection method and of Nicotiana benthamiana by one single guide RNA to edit two orthologs. Plant Biotechnol 37, 213–221.
Kourelis, J., and van der Hoorn, R.A.L. (2018). Defended to the nines: 25 years of resistance gene cloning identifies nine mechanisms for R protein function. Plant Cell 30, 285–299.
Krieger, U., Lippman, Z.B., and Zamir, D. (2010). The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato. Nat Genet 42, 459–463.
Kwon, C.T., Heo, J., Lemmon, Z.H., Capua, Y., Hutton, S.F., Van Eck, J., Park, S.J., and Lippman, Z.B. (2020). Rapid customization of Solanaceae fruit crops for urban agriculture. Nat Biotechnol 38, 182–188.
Lapidot, M., Karniel, U., Gelbart, D., Fogel, D., Evenor, D., Kutsher, Y., Makhbash, Z., Nahon, S., Shlomo, H., Chen, L., et al. (2015). A novel route controlling begomovirus resistance by the messenger RNA surveillance factor pelota. PLoS Genet 11, e1005538.
Lee, S.Y., Jang, S.J., Jeong, H.B., Lee, S.Y., Venkatesh, J., Lee, J.H., Kwon, J.K., and Kang, B.C. (2021). A mutation in Zeaxanthin epoxidase contributes to orange coloration and alters carotenoid contents in pepper fruit (Capsicum annuum). Plant J 106, 1692–1707.
Lefebvre, V., Kuntz, M., Camara, B., and Palloix, A. (1998). The capsanthin-capsorubin synthase gene: a candidate gene for the y locus controlling the red fruit colour in pepper. Plant Mol Biol 36, 785–789.
Li, D., Qian, J., Li, W., Jiang, Y., Gan, G., Li, W., Chen, R., Yu, N., Li, Y., Wu, Y., et al. (2019a). Genome sequence and analysis of the eggplant (Solanum melongena L.). bioRxiv, 824540.
Li, H., Wang, S., Chai, S., Yang, Z., Zhang, Q., Xin, H., Xu, Y., Lin, S., Chen, X., Yao, Z., et al. (2022). Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nat Commun 13, 682.
Li, P., Su, T., Zhao, X., Wang, W., Zhang, D., Yu, Y., Bayer, P.E., Edwards, D., Yu, S., and Zhang, F. (2021). Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson. Plant Biotechnol J 19, 966–976.
Li, Q., Li, H., Huang, W., Xu, Y., Zhou, Q., Wang, S., Ruan, J., Huang, S., and Zhang, Z. (2019b). A chromosome-scale genome assembly of cucumber (Cucumis sativus L.). Gigascience 8.
Li, R., Sun, S., Wang, H., Wang, K., Yu, H., Zhou, Z., Xin, P., Chu, J., Zhao, T., Wang, H., et al. (2020a). FIS1 encodes a GA2-oxidase that regulates fruit firmness in tomato. Nat Commun 11, 5844.
Li, T., Yang, X., Yu, Y., Si, X., Zhai, X., Zhang, H., Dong, W., Gao, C., and Xu, C. (2018). Domestication of wild tomato is accelerated by genome editing. Nat Biotechnol 36, 1160–1163.
Li, X., Tieman, D., Liu, Z., Chen, K., and Klee, H.J. (2020b). Identification of a lipase gene with a role in tomato fruit short-chain fatty acid-derived flavor volatiles by genome-wide association. Plant J 104, 631–644.
Li, Y., Liu, G.F., Ma, L.M., Liu, T.K., Zhang, C.W., Xiao, D., Zheng, H.K., Chen, F., and Hou, X.L. (2020c). A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. Hortic Res 7, 212.
Li, Z., Zhang, Z., Yan, P., Huang, S., Fei, Z., and Lin, K. (2011). RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics 12, 540.
Liang, Q., Deng, H., Li, Y., Liu, Z., Shu, P., Fu, R., Zhang, Y., Pirrello, J., Zhang, Y., Grierson, D., et al. (2020). Like Heterochromatin Protein 1b represses fruit ripening via regulating the H3K27me3 levels in ripening-related genes in tomato. New Phytol 227, 485–497.
Liao, Y., Wang, J., Zhu, Z., Liu, Y., Chen, J., Zhou, Y., Liu, F., Lei, J., Gaut, B.S., Cao, B., et al. (2022). The 3D architecture of the pepper genome and its relationship to function and evolution. Nat Commun 13, 3479.
Lim, J.H., Park, C.J., Huh, S.U., Choi, L.M., Lee, G.J., Kim, Y.J., and Paek, K.H. (2011). Capsicum annuum WRKYb transcription factor that binds to the CaPR-10 promoter functions as a positive regulator in innate immunity upon TMV infection. Biochem Biophys Res Commun 411, 613–619.
Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., Zhang, Z., Lun, Y., Li, S., Wang, X., et al. (2014). Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46, 1220–1226.
Lippman, Z., and Tanksley, S.D. (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., Wang, Y., Zhai, W., Deng, J., Wang, H., Cui, Y., Cheng, F., Wang, X., and Wu, J. (2013). Development of InDel markers for Brassica rapa based on whole-genome re-sequencing. Theor Appl Genet 126, 231–239.
Liu, J., Li, J., Wang, H., and Yan, J. (2020). Application of deep learning in genomics. Sci China Life Sci 63, 1860–1878.
Liu, S., Liu, Y., Yang, X., Tong, C., Edwards, D., Parkin, I.A.P., Zhao, M., Ma, J., Yu, J., Huang, S., et al. (2014). The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun 5, 3930.
Liu, X., Chen, J., and Zhang, X. (2021). Genetic regulation of shoot architecture in cucumber. Hortic Res 8, 143.
Liu, Y., and Tian, Z. (2020). From one linear genome to a graph-based pan-genome: a new era for genomics. Sci China Life Sci 63, 1938–1941.
Lonardi, S., Muñoz-Amatriaín, M., Liang, Q., Shu, S., Wanamaker, S.I., Lo, S., Tanskanen, J., Schulman, A.H., Zhu, T., Luo, M.C., et al. (2019). The genome of cowpea (Vigna unguiculata [L.] Walp.). Plant J 98, 767–782.
Lu, Y., Liu, M., Zhao J., Wang, Y., Luo, S., Xuan, S., Dai, S., Wang, C., and Shen, S. (2014). Construction of one mutant library and research on phenotypic variation of M2 population leaves in Chinese cabbage. Acta Horticult Sin 41, 1609–1619.
Lv, H., Fang, Z., Yang, L., Zhang, Y., Wang, Q., Liu, Y., Zhuang, M., Yang, Y., Xie, B., Liu, B., et al. (2014). Mapping and analysis of a novel candidate Fusarium wilt resistance gene FOC1 in Brassica oleracea. BMC Genomics 15, 1094.
Ma, C., Liu, M., Li, Q., Si, J., Ren, X., and Song, H. (2019). Efficient BoPDS gene editing in cabbage by the CRISPR/Cas9 system. Hortic Plant J 5, 164–169.
Manning, K., Tör, M., Poole, M., Hong, Y., Thompson, A.J., King, G.J., Giovannoni, J.J., and Seymour, G.B. (2006). A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38, 948–952.
Mao, Z., Zhu, P., Liu, F., Huang, Y., Ling, J., Chen, G., Yang, Y., Feng, D., and Xie, B. (2015). Cloning and functional analyses of pepper CaRKNR involved in Meloidogyne incognita resistance. Euphytica 205, 903–913.
Martel, C., Vrebalov, J., Tafelmeyer, P., and Giovannoni, J.J. (2011). The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-dependent manner. Plant Physiol 157, 1568–1579.
Martin, A., Troadec, C., Boualem, A., Rajab, M., Fernandez, R., Morin, H., Pitrat, M., Dogimont, C., and Bendahmane, A. (2009). A transposon-induced epigenetic change leads to sex determination in melon. Nature 461, 1135–1138.
Matsumura, H., Hsiao, M.C., Toyoda, A., Taniai, N., Tarora, K., Urasaki, N., Anand, S.S., Dhillon, N.P.S., Schafleitner, R., and Lee, C.R. (2019). Long-read bitter gourd genome and the genomic architecture of domestication. bioRxiv, 822411.
Matsuo, S., Miyatake, K., Endo, M., Urashimo, S., Kawanishi, T., Negoro, S., Shimakoshi, S., and Fukuoka, H. (2020). Loss of function of the Pad-1 aminotransferase gene, which is involved in auxin homeostasis, induces parthenocarpy in Solanaceae plants. Proc Natl Acad Sci USA 117, 12784–12790.
Menda, N., Semel, Y., Peled, D., Eshed, Y., and Zamir, D. (2004). In silico screening of a saturated mutation library of tomato. Plant J 38, 861–872.
Ming, R., VanBuren, R., Liu, Y., Yang, M., Han, Y., Li, L.T., Zhang, Q., Kim, M.J., Schatz, M.C., Campbell, M., et al. (2013). Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol 14, R41.
Montero-Pau, J., Blanca, J., Bombarely, A., Ziarsolo, P., Esteras, C., Martí-Gómez, C., Ferriol, M., Gómez, P., Jamilena, M., Mueller, L., et al. (2018). De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus. Plant Biotechnol J 16, 1161–1171.
Mou, S., Liu, Z., Gao, F., Yang, S., Su, M., Shen, L., Wu, Y., and He, S. (2017). CaHDZ27, a homeodomain-leucine zipper I protein, positively regulates the resistance to Ralstonia solanacearum infection in pepper. Mol Plant Microbe Interact 30, 960–973.
Muños, S., Ranc, N., Botton, E., Bérard, A., Rolland, S., Duffé, P., Carretero, Y., Le Paslier, M.C., Delalande, C., Bouzayen, M., et al. (2011). Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. Plant Physiol 156, 2244–2254.
Nadakuduti, S.S., Holdsworth, W.L., Klein, C.L., and Barry, C.S. (2014). KNOX genes influence a gradient of fruit chloroplast development through regulation of GOLDEN2-LIKE expression in tomato. Plant J 78, 1022–1033.
Nazar, R.N., Xu, X., Kurosky, A., and Robb, J. (2018). Antagonistic function of the Ve R-genes in tomato. Plant Mol Biol 98, 67–79.
Nguyen, C.V., Vrebalov, J.T., Gapper, N.E., Zheng, Y., Zhong, S., Fei, Z., and Giovannoni, J.J. (2014). Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening. Plant Cell 26, 585–601.
Nie, J., He, H., Peng, J., Yang, X., Bie, B., Zhao, J., Wang, Y., Si, L., Pan, J. S., and Cai, R. (2015a). Identification and fine mapping of pm5.1: a recessive gene for powdery mildew resistance in cucumber (Cucumis sativus L.). Mol Breed 35, 7.
Nie, J., Wang, Y., He, H., Guo, C., Zhu, W., Pan, J., Li, D., Lian, H., Pan, J., and Cai, R. (2015b). Loss-of-function mutations in CsMLO1 confer durable powdery mildew resistance in cucumber (Cucumis sativus L.). Front Plant Sci 6, 1155.
Osorio, S., Alba, R., Damasceno, C.M.B., Lopez-Casado, G., Lohse, M., Zanor, M.I., Tohge, T., Usadel, B., Rose, J.K.C., Fei, Z., et al. (2011). Systems biology of tomato fruit development: combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions. Plant Physiol 157, 405–425.
Ou, L., Li, D., Lv, J., Chen, W., Zhang, Z., Li, X., Yang, B., Zhou, S., Yang, S., Li, W., et al. (2018). Pan-genome of cultivated pepper (Capsicum) and its use in gene presence-absence variation analyses. New Phytol 220, 360–363.
Oumouloud, A., Mokhtari, M., Chikh-Rouhou, H., Arnedo-Andrés, M.S., González-Torres, R., and Álvarez, J.M. (2012). Characterization of the Fusarium wilt resistance Fom-2 gene in melon. Mol Breed 30, 325–334.
Park, S.J., Jiang, K., Tal, L., Yichie, Y., Gar, O., Zamir, D., Eshed, Y., and Lippman, Z.B. (2014). Optimization of crop productivity in tomato using induced mutations in the florigen pathway. Nat Genet 46, 1337–1342.
Pecrix, Y., Staton, S.E., Sallet, E., Lelandais-Brière, C., Moreau, S., Carrère, S., Blein, T., Jardinaud, M.F., Latrasse, D., Zouine, M., et al. (2018). Whole-genome landscape of Medicago truncatula symbiotic genes. Nat Plants 4, 1017–1025.
Powell, A.L.T., Nguyen, C.V., Hill, T., Cheng, K.L.L., Figueroa-Balderas, R., Aktas, H., Ashrafi, H., Pons, C., Fernández-Muñoz, R., Vicente, A., et al. (2012). Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336, 1711–1715.
Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., Zeng, P., Wang, S., Shang, Y., Gu, X., et al. (2013). A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45, 1510–1515.
Qian, W., Zhang, S., Zhang, S., Li, F., Zhang, H., Wu, J., Wang, X., Walsh, J.A., and Sun, R. (2013). Mapping and candidate-gene screening of the novel Turnip mosaic virus resistance gene retr02 in Chinese cabbage (Brassica rapa L.). Theor Appl Genet 126, 179–188.
Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., Cheng, J., Zhao, S., Xu, M., Luo, Y., et al. (2014). Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci USA 111, 5135–5140.
Razali, R., Bougouffa, S., Morton, M.J.L., Lightfoot, D.J., Alam, I., Essack, M., Arold, S.T., Kamau, A.A., Schmöckel, S.M., Pailles, Y., et al. (2018). The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance. Front Plant Sci 9, 1402.
Rehrig, W.Z., Ashrafi, H., Hill, T., Prince, J., and Van Deynze, A. (2014). CaDMR1 cosegregates with QTL Pc5.1 for resistance to Phytophthora capsici in pepper (Capsicum annuum). Plant Genome 7, plantgenome2014.2003.0011.
Ren, R., Xu, J., Zhang, M., Liu, G., Yao, X., Zhu, L., and Hou, Q. (2020a). Identification and molecular mapping of a gummy stem blight resistance gene in wild watermelon (Citrullus amarus) germplasm PI 189225. Plant Dis 104, 16–24.
Ren, Y., Li, M., Guo, S., Sun, H., Zhao, J., Zhang, J., Liu, G., He, H., Tian, S., Yu, Y., et al. (2021). Evolutionary gain of oligosaccharide hydrolysis and sugar transport enhanced carbohydrate partitioning in sweet watermelon fruits. Plant Cell 33, 1554–1573.
Ren, Y., Sun, H., Zong, M., Guo, S., Ren, Z., Zhao, J., Li, M., Zhang, J., Tian, S., Wang, J., et al. (2020b). Localization shift of a sugar transporter contributes to phloem unloading in sweet watermelons. New Phytol 227, 1858–1871.
Ren, Y., Zhang, Z., Liu, J., Staub, J.E., Han, Y., Cheng, Z., Li, X., Lu, J., Miao, H., Kang, H., et al. (2009). An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE 4, e5795.
Reyes-Chin-Wo, S., Wang, Z., Yang, X., Kozik, A., Arikit, S., Song, C., Xia, L., Froenicke, L., Lavelle, D.O., Truco, M.J., et al. (2017). Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun 8, 14953.
Ruggieri, V., Alexiou, K.G., Morata, J., Argyris, J., Pujol, M., Yano, R., Nonaka, S., Ezura, H., Latrasse, D., Boualem, A., et al. (2018). An improved assembly and annotation of the melon (Cucumis melo L.) reference genome. Sci Rep 8, 8088.
Schmidt, M.H.W., Vogel, A., Denton, A.K., Istace, B., Wormit, A., van de Geest, H., Bolger, M.E., Alseekh, S., Maß, J., Pfaff, C., et al. (2017). De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant Cell 29, 2336–2348.
Schmutz, J., McClean, P.E., Mamidi, S., Wu, G.A., Cannon, S.B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., et al. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46, 707–713.
Shan, N., Gan, Z., Nie, J., Liu, H., Wang, Z., and Sui, X. (2020). Comprehensive characterization of fruit volatiles and nutritional quality of three cucumber (Cucumis sativus L.) genotypes from different geographic groups after bagging treatment. Foods 9, 294.
Shang, Y., Ma, Y., Zhou, Y., Zhang, H., Duan, L., Chen, H., Zeng, J., Zhou, Q., Wang, S., Gu, W., et al. (2014). Biosynthesis, regulation, and domestication of bitterness in cucumber. Science 346, 1084–1088.
Shen, J., Tieman, D., Jones, J.B., Taylor, M.G., Schmelz, E., Huffaker, A., Bies, D., Chen, K., and Klee, H.J. (2014). A 13-lipoxygenase, TomloxC, is essential for synthesis of C5 flavour volatiles in tomato. J Exp Bot 65, 419–428.
Shen, J., Zhang, Y., Ge, D., Wang, Z., Song, W., Gu, R., Che, G., Cheng, Z., Liu, R., and Zhang, X. (2019). CsBRC1 inhibits axillary bud outgrowth by directly repressing the auxin efflux carrier CsPIN3 in cucumber. Proc Natl Acad Sci USA 116, 17105–17114.
Shimizu, M., Pu, Z., Kawanabe, T., Kitashiba, H., Matsumoto, S., Ebe, Y., Sano, M., Funaki, T., Fukai, E., Fujimoto, R., et al. (2015). Map-based cloning of a candidate gene conferring Fusarium yellows resistance in Brassica oleracea. Theor Appl Genet 128, 119–130.
Shopan, J., Mou, H., Zhang, L., Zhang, C., Ma, W., Walsh, J.A., Hu, Z., Yang, J., and Zhang, M. (2017). Eukaryotic translation initiation factor 2B-beta (eIF2Bβ), a new class of plant virus resistance gene. Plant J 90, 929–940.
Slotte, T., Hazzouri, K.M., Ågren, J.A., Koenig, D., Maumus, F., Guo, Y.L., Steige, K., Platts, A.E., Escobar, J.S., Newman, L.K., et al. (2013). The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45, 831–835.
Song, X., Wang, J., Li, N., Yu, J., Meng, F., Wei, C., Liu, C., Chen, W., Nie, F., Zhang, Z., et al. (2019). Deciphering the high-quality genome sequence of coriander that causes controversial feelings. Plant Biotechnol J 18, 1444–1456.
Soyk, S., Müller, N.A., Park, S.J., Schmalenbach, I., Jiang, K., Hayama, R., Zhang, L., Van Eck, J., Jiménez-Gómez, J.M., and Lippman, Z.B. (2017). Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Nat Genet 49, 162–168.
Stam, R., Nosenko, T., Hörger, A.C., Stephan, W., Seidel, M., Kuhn, J.M. M., Haberer, G., and Tellier, A. (2019). The de novo reference genome and transcriptome assemblies of the wild tomato species Solanum chilense highlights birth and death of NLR genes between tomato species. G3 9, 3933–3941.
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313.
Stewart, C. Jr, Kang, B.C., Liu, K., Mazourek, M., Moore, S.L., Yoo, E.Y., Kim, B.D., Paran, I., and Jahn, M.M. (2005). The Pun1 gene for pungency in pepper encodes a putative acyltransferase. Plant J 42, 675–688.
Su, T., Li, P., Wang, H., Wang, W., Zhao, X., Yu, Y., Zhang, D., Yu, S., and Zhang, F. (2019). Natural variation in a calreticulin gene causes reduced resistance to Ca2+ deficiency-induced tipburn in Chinese cabbage (Brassica rapa ssp. pekinensis). Plant Cell Environ 42, 3044–3060.
Su, T., Wang, W., Li, P., Zhang, B., Li, P., Xin, X., Sun, H., Yu, Y., Zhang, D., Zhao, X., et al. (2018). A genomic variation map provides insights into the genetic basis of spring chinese cabbage (Brassica rapa ssp. pekinensis) selection. Mol Plant 11, 1360–1376.
Sun, C., Deng, L., Du, M., Zhao, J., Chen, Q., Huang, T., Jiang, H., Li, C. B., and Li, C. (2020a). A transcriptional network promotes anthocyanin biosynthesis in tomato flesh. Mol Plant 13, 42–58.
Sun, H., Wu, S., Zhang, G., Jiao, C., Guo, S., Ren, Y., Zhang, J., Zhang, H., Gong, G., Jia, Z., et al. (2017). Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes. Mol Plant 10, 1293–1306.
Sun, X., Zhu, S., Li, N., Cheng, Y., Zhao, J., Qiao, X., Lu, L., Liu, S., Wang, Y., Liu, C., et al. (2020b). A chromosome-level genome assembly of garlic (Allium sativum) provides insights into genome evolution and allicin biosynthesis. Mol Plant 13, 1328–1339.
Takagi, H., Uemura, A., Yaegashi, H., Tamiru, M., Abe, A., Mitsuoka, C., Utsushi, H., Natsume, S., Kanzaki, H., Matsumura, H., et al. (2013). MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii. New Phytol 200, 276–283.
Takei, H., Shirasawa, K., Kuwabara, K., Toyoda, A., Matsuzawa, Y., Iioka, S., and Ariizumi, T. (2021). De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme, by long-read sequencing. DNA Res 28, dsaa029.
Tang, D., Jia, Y., Zhang, J., Li, H., Cheng, L., Wang, P., Bao, Z., Liu, Z., Feng, S., Zhu, X., et al. (2022). Genome evolution and diversity of wild and cultivated potatoes. Nature 606, 535–541.
Tian, S., Jiang, L., Cui, X., Zhang, J., Guo, S., Li, M., Zhang, H., Ren, Y., Gong, G., Zong, M., et al. (2018). Engineering herbicide-resistant watermelon variety through CRISPR/Cas9-mediated base-editing. Plant Cell Rep 37, 1353–1356.
Tian, S., Jiang, L., Gao, Q., Zhang, J., Zong, M., Zhang, H., Ren, Y., Guo, S., Gong, G., Liu, F., et al. (2017). Efficient CRISPR/Cas9-based gene knockout in watermelon. Plant Cell Rep 36, 399–406.
Tian, Y., Zeng, Y., Zhang, J., Yang, C.G., Yan, L., Wang, X.J., Shi, C.Y., Xie, J., Dai, T.Y., Peng, L., et al. (2015). High quality reference genome of drumstick tree (Moringa oleifera Lam.), a potential perennial crop. Sci China Life Sci 58, 627–638.
Tieman, D., Zhu, G., Resende Jr., M.F.R., Lin, T., Nguyen, C., Bies, D., Rambla, J.L., Beltran, K.S.O., Taylor, M., Zhang, B., et al. (2017). A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394.
Tikunov, Y.M., Roohanitaziani, R., Meijer-Dekens, F., Molthoff, J., Paulo, J., Finkers, R., Capel, I., Carvajal Moreno, F., Maliepaard, C., Nijenhuis-de Vries, M., et al. (2020). The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit. Plant J 103, 1189–1204.
Tomás-Barberán, F.A., and Espín, J.C. (2001). Phenolic compounds and related enzymes as determinants of quality in fruits and vegetables. J Sci Food Agric 81, 853–876.
Tomato Genome Consortium, (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635–641.
Ueno, H., Matsumoto, E., Aruga, D., Kitagawa, S., Matsumura, H., and Hayashida, N. (2012). Molecular characterization of the CRa gene conferring clubroot resistance in Brassica rapa. Plant Mol Biol 80, 621–629.
Ueta, R., Abe, C., Watanabe, T., Sugano, S.S., Ishihara, R., Ezura, H., Osakabe, Y., and Osakabe, K. (2017). Rapid breeding of parthenocarpic tomato plants using CRISPR/Cas9. Sci Rep 7, 507.
Umer, M.J., Bin Safdar, L., Gebremeskel, H., Zhao, S., Yuan, P., Zhu, H., Kaseb, M.O., Anees, M., Lu, X., He, N., et al. (2020). Identification of key gene networks controlling organic acid and sugar metabolism during watermelon fruit development by integrating metabolic phenotypes and gene expression profiles. Hortic Res 7, 193.
Urasaki, N., Takagi, H., Natsume, S., Uemura, A., Taniai, N., Miyagi, N., Fukushima, M., Suzuki, S., Tarora, K., Tamaki, M., et al. (2017). Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions. DNA Res 24, 51–58.
Varshney, R.K., Chen, W., Li, Y., Bharti, A.K., Saxena, R.K., Schlueter, J. A., Donoghue, M.T.A., Azam, S., Fan, G., Whaley, A.M., et al. (2012). Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30, 83–89.
Varshney, R.K., Song, C., Saxena, R.K., Azam, S., Yu, S., Sharpe, A.G., Cannon, S., Baek, J., Rosen, B.D., Tar’an, B., et al. (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31, 240–246.
Verlaan, M.G., Hutton, S.F., Ibrahem, R.M., Kormelink, R., Visser, R.G.F., Scott, J.W., Edwards, J.D., and Bai, Y. (2013). The tomato yellow leaf curl virus resistance genes Ty-1 and Ty-3 are allelic and code for DFDGD-class RNA-dependent RNA polymerases. PLoS Genet 9, e1003399.
Vrebalov, J., Ruezinsky, D., Padmanabhan, V., White, R., Medrano, D., Drake, R., Schuch, W., and Giovannoni, J. (2002). A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296, 343–346.
Wang, J., Sun, P., Li, Y., Liu, Y., Yang, N., Yu, J., Ma, X., Sun, S., Xia, R., Liu, X., et al. (2018). An overlooked paleotetraploidization in Cucurbitaceae. Mol Biol Evol 35, 16–26.
Wang, P., Wang, L., Guo, J., Yang, W., and Shen, H. (2016). Molecular mapping of a gene conferring resistance to Phytophthora capsici Leonian race 2 in pepper line PI201234 (Capsicum annuum L.). Mol Breed 36, 66.
Wang, P., Xu, X., Zhao, G., He, Y., Hou, C., Kong, W., Zhang, J., Liu, S., Xu, Y., and Xu, Z. (2020a). Genetic mapping and candidate gene analysis for melon resistance to Phytophthora capsici. Sci Rep 10, 20456.
Wang, S., Yang, X., Xu, M., Lin, X., Lin, T., Qi, J., Shao, G., Tian, N., Yang, Q., Zhang, Z., et al. (2015). A rare SNP identified a TCP transcription factor essential for tendril development in cucumber. Mol Plant 8, 1795–1808.
Wang, X., Gao, L., Jiao, C., Stravoravdis, S., Hosmani, P.S., Saha, S., Zhang, J., Mainiero, S., Strickler, S.R., Catala, C., et al. (2020b). Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nat Commun 11, 5817.
Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S., Bai, Y., Mun, J.H., Bancroft, I., Cheng, F., et al. (2011). The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43, 1035–1039.
Wang, X., Aguirre, L., Rodriguez-Leal, D., Hendelman, A., Benoit, M., and Lippman, Z.B. (2021). Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. Nat Plants 7, 419–427.
Wang, Y., Fan, G., Liu, Y., Sun, F., Shi, C., Liu, X., Peng, J., Chen, W., Huang, X., Cheng, S., et al. (2013). The sacred lotus genome provides insights into the evolution of flowering plants. Plant J 76, 557–567.
Wang, Y., Tan, J., Wu, Z., VandenLangenberg, K., Wehner, T.C., Wen, C., Zheng, X., Owens, K., Thornton, A., Bang, H.H., et al. (2019). STAYGREEN, STAY HEALTHY: a loss-of-susceptibility mutation in the STAYGREEN gene provides durable, broad-spectrum disease resistances for over 50 years of US cucumber production. New Phytol 221, 415–430.
Wei, Q., Wang, J., Wang, W., Hu, T., Hu, H., and Bao, C. (2020). A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant. Hortic Res 7, 153.
Wei, T., van Treuren, R., Liu, X., Zhang, Z., Chen, J., Liu, Y., Dong, S., Sun, P., Yang, T., Lan, T., et al. (2021). Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce. Nat Genet 53, 752–760.
Wen, C., Mao, A., Dong, C., Liu, H., Yu, S., Guo, Y.D., Weng, Y., and Xu, Y. (2015). Fine genetic mapping of target leaf spot resistance gene cca-3 in cucumber, Cucumis sativus L. Theor Appl Genet 128, 2495–2506.
Wen, C., Zhao, W., Liu, W., Yang, L., Wang, Y., Liu, X., Xu, Y., Ren, H., Guo, Y., Li, C., et al. (2019). CsTFL1 inhibits determinate growth and terminal flower formation through interaction with CsNOT2a in cucumber (Cucumis sativus L.). Development 146, dev180166.
Wilkinson, J.Q., Lanahan, M.B., Yen, H.C., Giovannoni, J.J., and Klee, H.J. (1995). An ethylene-inducible component of signal transduction encoded by Never-ripe. Science 270, 1807–1809.
Witek, K., Jupe, F., Witek, A.I., Baker, D., Clark, M.D., and Jones, J.D.G. (2016). Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing. Nat Biotechnol 34, 656–660.
Witek, K., Lin, X., Karki, H.S., Jupe, F., Witek, A.I., Steuernagel, B., Stam, R., van Oosterhout, C., Fairhead, S., Heal, R., et al. (2021). A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. Nat Plants 7, 198–208.
Woycicki, R., Witkowicz, J., Gawronski, P., Dabrowska, J., Lomsadze, A., Pawelkowicz, M., Siedlecka, E., Yagi, K., Plader, W., Seroczynska, A., et al. (2011). The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One 6, e22728.
Wu, S., Shamimuzzaman, M., Sun, H., Salse, J., Sui, X., Wilder, A., Wu, Z., Levi, A., Xu, Y., Ling, K.S., et al. (2017). The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus. Plant J 92, 963–975.
Wu, S., Wang, X., Reddy, U., Sun, H., Bao, K., Gao, L., Mao, L., Patel, T., Ortiz, C., Abburi, V.L., et al. (2019). Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection. Plant Biotechnol J 17, 2246–2258.
Wu, Z., Liu, Z., Chang, S., and Zhao, Y. (2020). An EMS mutant library for carrot and genetic analysis of some mutants. Breed Sci 70, 540–546.
Xie, D., Xu, Y., Wang, J., Liu, W., Zhou, Q., Luo, S., Huang, W., He, X., Li, Q., Peng, Q., et al. (2019). The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype. Nat Commun 10, 5158.
Xin, T., Zhang, Z., Li, S., Zhang, S., Li, Q., Zhang, Z.H., Huang, S., and Yang, X. (2019). Genetic regulation of ethylene dosage for cucumber fruit elongation. Plant Cell 31, 1063–1076.
Xu, C., Jiao, C., Sun, H., Cai, X., Wang, X., Ge, C., Zheng, Y., Liu, W., Sun, X., Xu, Y., et al. (2017). Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nat Commun 8, 15275.
Xu, C., Liberatore, K.L., MacAlister, C.A., Huang, Z., Chu, Y.H., Jiang, K., Brooks, C., Ogawa-Ohnishi, M., Xiong, G., Pauly, M., et al. (2015). A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nat Genet 47, 784–792.
Xu, Z.S., Yang, Q.Q., Feng, K., and Xiong, A.S. (2019). Changing carrot color: insertions in DcMYB7 alter the regulation of anthocyanin biosynthesis and modification. Plant Physiol 181, 195–207.
Xu, Z.S., Yang, Q.Q., Feng, K., Yu, X., and Xiong, A.S. (2020). DcMYB113, a root-specific R2R3-MYB, conditions anthocyanin biosynthesis and modification in carrot. Plant Biotechnol J 18, 1585–1597.
Yamaguchi, H., Ohnishi, J., Saito, A., Ohyama, A., Nunome, T., Miyatake, K., and Fukuoka, H. (2018). An NB-LRR gene, TYNBS1, is responsible for resistance mediated by the Ty-2 Begomovirus resistance locus of tomato. Theor Appl Genet 131, 1345–1362.
Yang, J., Liu, D., Wang, X., Ji, C., Cheng, F., Liu, B., Hu, Z., Chen, S., Pental, D., Ju, Y., et al. (2016). The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet 48, 1225–1232.
Yang, J., Wang, Y., Shen, H., and Yang, W. (2014). In silico identification and experimental validation of insertion-deletion polymorphisms in tomato genome. DNA Res 21, 429–438.
Yang, K., Tian, Z., Chen, C., Luo, L., Zhao, B., Wang, Z., Yu, L., Li, Y., Sun, Y., Li, W., et al. (2015). Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication. Proc Natl Acad Sci USA 112, 13213–13218.
Yang, L., Koo, D.H., Li, Y., Zhang, X., Luan, F., Havey, M.J., Jiang, J., and Weng, Y. (2012). Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly. Plant J 71, 895–906.
Yang, Y., Zhu, G., Li, R., Yan, S., Fu, D., Zhu, B., Tian, H., Luo, Y., and Zhu, H. (2017). The RNA editing factor SlORRM4 is required for normal fruit ripening in tomato. Plant Physiol 175, 1690–1702.
Ye, J., Wang, X., Hu, T., Zhang, F., Wang, B., Li, C., Yang, T., Li, H., Lu, Y., Giovannoni, J.J., et al. (2017). An indel in the promoter of Al-ACTIVATED MALATE TRANSPORTER9 selected during tomato domestication determines fruit malate contents and aluminum tolerance. Plant Cell 29, 2249–2268.
Ye, J., Wang, X., Wang, W., Yu, H., Ai, G., Li, C., Sun, P., Wang, X., Li, H., Ouyang, B., et al. (2021). Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato. Plant Physiol 186, 2078–2092.
Young, N.D., Debellé, F., Oldroyd, G.E.D., Geurts, R., Cannon, S.B., Udvardi, M.K., Benedito, V.A., Mayer, K.F.X., Gouzy, J., Schoof, H., et al. (2011). The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480, 520–524.
Yu, H., and Li, J. (2022). Breeding future crops to feed the world through de novo domestication. Nat Commun 13, 1171.
Yu, H., Lin, T., Meng, X., Du, H., Zhang, J., Liu, G., Chen, M., Jing, Y., Kou, L., Li, X., et al. (2021). A route to de novo domestication of wild allotetraploid rice. Cell 184, 1156–1170.e14.
Yu, S., Su, T., Zhi, S., Zhang, F., Wang, W., Zhang, D., Zhao, X., and Yu, Y. (2016). Construction of a sequence-based bin map and mapping of QTLs for downy mildew resistance at four developmental stages in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Mol Breed 36, 44.
Yuan, Y., Ren, S., Liu, X., Su, L., Wu, Y., Zhang, W., Li, Y., Jiang, Y., Wang, H., Fu, R., et al. (2022). SlWRKY35 positively regulates carotenoid biosynthesis by activating the MEP pathway in tomato fruit. New Phytol 234, 164–178.
Zhang, C., Badri Anarjan, M., Win, K.T., Begum, S., and Lee, S. (2021a). QTL-seq analysis of powdery mildew resistance in a Korean cucumber inbred line. Theor Appl Genet 134, 435–451.
Zhang, C., Liu, L., Wang, X., Vossen, J., Li, G., Li, T., Zheng, Z., Gao, J., Guo, Y., Visser, R.G.F., et al. (2014). The Ph-3 gene from Solanum pimpinellifolium encodes CC-NBS-LRR protein conferring resistance to Phytophthora infestans. Theor Appl Genet 127, 1353–1364.
Zhang, H., Li, S., Yang, L., Cai, G., Chen, H., Gao, D., Lin, T., Cui, Q., Wang, D., Li, Z., et al. (2021b). Gain-of-function of the 1-aminocyclopropane-1-carboxylate synthase gene ACS1G induces female flower development in cucumber gynoecy. Plant Cell 33, 306–321.
Zhang, H., Li, X., Yu, H., Zhang, Y., Li, M., Wang, H., Wang, D., Wang, H., Fu, Q., Liu, M., et al. (2019). A high-quality melon genome assembly provides insights into genetic basis of fruit trait improvement. iScience 22, 16–27.
Zhang, J., Guo, S., Ji, G., Zhao, H., Sun, H., Ren, Y., Tian, S., Li, M., Gong, G., Zhang, H., et al. (2020a). A unique chromosome translocation disrupting ClWIP1 leads to gynoecy in watermelon. Plant J 101, 265–277.
Zhang, K., Wang, X., Zhu, W., Qin, X., Xu, J., Cheng, C., Lou, Q., Li, J., and Chen, J. (2018a). Complete resistance to powdery mildew and partial resistance to downy mildew in a Cucumis hystrix introgression line of cucumber were controlled by a co-localized locus. Theor Appl Genet 131, 2229–2243.
Zhang, L., Cai, X., Wu, J., Liu, M., Grob, S., Cheng, F., Liang, J., Cai, C., Liu, Z., Liu, B., et al. (2018b). Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. Hortic Res 5, 50.
Zhang, L., Huang, J., Su, S., Wei, X., Yang, L., Zhao, H., Yu, J., Wang, J., Hui, J., Hao, S., et al. (2021c). FERONIA receptor kinase-regulated reactive oxygen species mediate self-incompatibility in Brassica rapa. Curr Biol 31, 3004–3016.e4.
Zhang, L., Su, W., Tao, R., Zhang, W., Chen, J., Wu, P., Yan, C., Jia, Y., Larkin, R.M., Lavelle, D., et al. (2017). RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis. Nat Commun 8, 2264.
Zhang, X., Feng, C., Wang, M., Li, T., Liu, X., and Jiang, J. (2021d). Plasma membrane-localized SlSWEET7a and SlSWEET14 regulate sugar transport and storage in tomato fruits. Hortic Res 8, 186.
Zhang, X., Liu, T., Wang, J., Wang, P., Qiu, Y., Zhao, W., Pang, S., Li, X., Wang, H., Song, J., et al. (2021e). Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes. Mol Plant 14, 2032–2055.
Zhang, Y.L., Jia, Q.L., Li, D.W., Wang, J.E., Yin, Y.X., and Gong, Z.H. (2013). Characteristic of the pepper CaRGA2 gene in defense responses against Phytophthora capsici Leonian. Int J Mol Sci 14, 8985–9004.
Zhang, Z., Mao, L., Chen, H., Bu, F., Li, G., Sun, J., Li, S., Sun, H., Jiao, C., Blakely, R., et al. (2015). Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber. Plant Cell 27, 1595–1604.
Zhang, Z., Wang, B., Wang, S., Lin, T., Yang, L., Zhao, Z., Zhang, Z., Huang, S., and Yang, X. (2020b). Genome-wide target mapping shows histone deacetylase complex1 regulates cell proliferation in cucumber fruit. Plant Physiol 182, 167–184.
Zhao, G., Lian, Q., Zhang, Z., Fu, Q., He, Y., Ma, S., Ruggieri, V., Monforte, A.J., Wang, P., Julca, I., et al. (2019a). A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits. Nat Genet 51, 1607–1615.
Zhao, J., Jiang, L., Che, G., Pan, Y., Li, Y., Hou, Y., Zhao, W., Zhong, Y., Ding, L., Yan, S., et al. (2019b). A functional allele of CsFUL1 regulates fruit length through repressing CsSUP and inhibiting auxin transport in cucumber. Plant Cell 31, 1289–1307.
Zhao, W., Li, Y., Fan, S., Wen, T., Wang, M., Zhang, L., and Zhao, L. (2021). The transcription factor WRKY32 affects tomato fruit colour by regulating YELLOW FRUITED-TOMATO 1, a core component of ethylene signal transduction. J Exp Bot 72, 4269–4282.
Zheng, Z., Nonomura, T., Appiano, M., Pavan, S., Matsuda, Y., Toyoda, H., Wolters, A.M.A., Visser, R.G.F., and Bai, Y. (2013). Loss of function in Mlo orthologs reduces susceptibility of pepper and tomato to powdery mildew disease caused by Leveillula taurica. PLoS ONE 8, e70723.
Zhi, X., Shu, J., Zheng, Z., Li, T., Sun, X., Bai, J., Cui, Y., Wang, X., Huang, Z., Guo, Y., et al. (2020). Fine mapping of the Ph-2 gene conferring resistance to late blight (Phytophthora infestans) in tomato. Plant Dis 105, 851–858.
Zhong, Y., Chen, B., Wang, D., Zhu, X., Li, M., Zhang, J., Chen, M., Wang, M., Riksen, T., Liu, J., et al. (2022). In vivo maternal haploid induction in tomato. Plant Biotechnol J 20, 250–252.
Zhou, Y., Ma, Y., Zeng, J., Duan, L., Xue, X., Wang, H., Lin, T., Liu, Z., Zeng, K., Zhong, Y., et al. (2016). Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae. Nat Plants 2, 1–8.
Zhou, Y., Zhang, Z., Bao, Z., Li, H., Lyu, Y., Zan, Y., Wu, Y., Cheng, L., Fang, Y., Wu, K., et al. (2022). Graph pangenome captures missing heritability and empowers tomato breeding. Nature 606, 527–534.
Zhu, G., Wang, S., Huang, Z., Zhang, S., Liao, Q., Zhang, C., Lin, T., Qin, M., Peng, M., Yang, C., et al. (2018). Rewiring of the fruit metabolome in tomato breeding. Cell 172, 249–261.e12.
Zhu, Z., Sun, B., Cai, W., Zhou, X., Mao, Y., Chen, C., Wei, J., Cao, B., Chen, C., Chen, G., et al. (2019). Natural variations in the MYB transcription factor MYB31 determine the evolution of extremely pungent peppers. New Phytol 223, 922–938.
Zsögön, A., Čermák, T., Naves, E.R., Notini, M.M., Edel, K.H., Weinl, S., Freschi, L., Voytas, D.F., Kudla, J., and Peres, L.E.P. (2018). De novo domestication of wild tomato using genome editing. Nat Biotechnol 36, 1211–1216.
Acknowledgements
This work was supported by the National Natural Science Foundation of China (31991180, 31922076, 32130093), the National Key Research and Development Program of China (2019YFA0906200, 2021YFF1000100), the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202101), Guangdong Major Project of Basic and Applied Basic Research (2021B0301030004), the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District (RC201901-05) and Shenzhen Outstanding Talents Training Fund, the Shenzhen Science and Technology Program (KQTD2016113010482651), the “Taishan Scholar” Foundation of the People’s Government of Shandong Province, Yunnan Science Fund (202105AF150028, 202005AE160015). We apologize to any authors whose work may not have been cited owing to length restrictions. We gratefully acknowledge Dr. William J. Lucas (Department of Plant Biology, University of California, Davis, Dr. Kuipeng Xu (College of Horticulture, Qingdao Agricultural University), Dr. Shenhao Wang (College of Horticulture, Northwest A&F University), Mengzhuo Zhang (Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences) and Dr. Ling Ma (The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University) for their kind assistance in preparing this review article.
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Li, H., Yang, X., Shang, Y. et al. Vegetable biology and breeding in the genomics era. Sci. China Life Sci. 66, 226–250 (2023). https://doi.org/10.1007/s11427-022-2248-6
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DOI: https://doi.org/10.1007/s11427-022-2248-6