| [1] |
Udall JA, Wendel JF. 2006. Polyploidy and crop improvement. |
| [2] |
Levin DA. 2004. The role of chromosomal change in plant evolution by Donald A. Levin. |
| [3] |
Shewry PR. 2009. Wheat. |
| [4] |
Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, et al. 2014. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. |
| [5] |
International Wheat Genome Sequencing Consortium (IWGSC). 2014. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. |
| [6] |
Schiessl SV, Katche E, Ihien E, Chawla HS, Mason AS. 2019. The role of genomic structural variation in the genetic improvement of polyploid crops. |
| [7] |
Schiavinato M, Marcet-Houben M, Dohm JC, Gabaldón T, Himmelbauer H. 2020. Parental origin of the allotetraploid tobacco Nicotiana benthamiana. |
| [8] |
Ding M, Chen ZJ. 2018. Epigenetic perspectives on the evolution and domestication of polyploid plant and crops. |
| [9] |
Madani H, Escrich A, Hosseini B, Sanchez-Muñoz R, Khojasteh A, et al. 2021. Effect of polyploidy induction on natural metabolite production in medicinal plants. |
| [10] |
Sattler MC, Carvalho CR, Clarindo WR. 2016. The polyploidy and its key role in plant breeding. |
| [11] |
Ramsey J, Schemske DW. 2002. Neopolyploidy in flowering plants. |
| [12] |
Baker HG. 1973. Chromosomal evolution in higher plants. G. Ledyard Stebbins. |
| [13] |
Van de Peer Y, Mizrachi E, Marchal K. 2017. The evolutionary significance of polyploidy. |
| [14] |
Schaart JG, van de Wiel CCM, Smulders MJM. 2021. Genome editing of polyploid crops: prospects, achievements and bottlenecks. |
| [15] |
Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, et al. 2017. Uncovering hidden variation in polyploid wheat. |
| [16] |
Weeks DP. 2017. Gene editing in polyploid crops: wheat, camelina, canola, potato, cotton, peanut, sugar cane, and citrus. |
| [17] |
Van Montagu M, Schell J, Holsters M, De Greve H, Leemans J, et al. 1981. Transfer, maintenance and expression of genes introduced into plant cells via the Ti plasmid. In Molecular Biology, Pathogenicity, and Ecology of Bacterial Plasmids, eds. Levy SB, Clowes RC, Koenig EL. Boston, MA: Springer. pp. 477−86 doi: 10.1007/978-1-4684-3983-0_46 |
| [18] |
Singh S, Chaudhary R, Deshmukh R, Tiwari S. 2023. Opportunities and challenges with CRISPR-Cas mediated homologous recombination based precise editing in plants and animals. |
| [19] |
Puchta H, Dujon B, Hohn B. 1993. Homologous recombination in plant cells is enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease. |
| [20] |
Stoddard BL. 2005. Homing endonuclease structure and function. |
| [21] |
Hoy MA. 2019. Transposable-element vectors and other methods to genetically modify Drosophila and other insects. In Insect Molecular Genetics. ed. Hoy MA. Amsterdam: Elsevier. pp. 315−44 doi: 10.1016/b978-0-12-815230-0.00008-x |
| [22] |
Arnould S, Perez C, Cabaniols JP, Smith J, Gouble A, et al. 2007. Engineered I-CreI derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells. |
| [23] |
Danilo B, Montes É, Archambeau H, Lodé M, Rousseau-Gueutin M, et al. 2022. I-SceI and customized meganucleases-mediated genome editing in tomato and oilseed rape. |
| [24] |
Dujon B. 1980. Sequence of the intron and flanking exons of the mitochondrial 21S rRNA gene of yeast strains having different alleles at the ω and rib-1 loci. |
| [25] |
Youssef D, Nihou A, Partier A, Tassy C, Paul W, et al. 2018. Induction of targeted deletions in transgenic bread wheat (Triticum aestivum L.) using customized meganuclease. |
| [26] |
Kim YG, Cha J, Chandrasegaran S. 1996. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. |
| [27] |
Tröder SE, Zevnik B. 2022. History of genome editing: from meganucleases to CRISPR. |
| [28] |
Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, et al. 2009. High-frequency modification of plant genes using engineered zinc-finger nucleases. |
| [29] |
Ran Y, Patron N, Kay P, Wong D, Buchanan M, et al. 2018. Zinc finger nuclease-mediated precision genome editing of an endogenous gene in hexaploid bread wheat (Triticum aestivum) using a DNA repair template. |
| [30] |
DeFrancesco L. 2011. Move over ZFNs. |
| [31] |
Carroll D. 2011. Genome engineering with zinc-finger nucleases. |
| [32] |
Hansen K, Coussens MJ, Sago J, Subramanian S, Gjoka M, et al. 2012. Genome editing with CompoZr custom zinc finger nucleases (ZFNs). |
| [33] |
Li T, Huang S, Jiang WZ, Wright D, Spalding MH, et al. 2011. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. |
| [34] |
Zaman QU, Li C, Cheng H, Hu Q. 2019. Genome editing opens a new era of genetic improvement in polyploid crops. |
| [35] |
Wang Q, Ma X, Qian S, Zhou X, Sun K, et al. 2015. Rescue of a plant negative-strand RNA virus from cloned cDNA: insights into enveloped plant virus movement and morphogenesis. |
| [36] |
Clasen BM, Stoddard TJ, Luo S, Demorest ZL, Li J, et al. 2016. Improving cold storage and processing traits in potato through targeted gene knockout. |
| [37] |
Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, et al. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. |
| [38] |
Chen K, Wang Y, Zhang R, Zhang H, Gao C. 2019. CRISPR/Cas genome editing and precision plant breeding in agriculture. |
| [39] |
Abe F, Haque E, Hisano H, Tanaka T, Kamiya Y, et al. 2019. Genome-edited triple-recessive mutation alters seed dormancy in wheat. |
| [40] |
Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, et al. 2014. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. |
| [41] |
Li S, Lin D, Zhang Y, Deng M, Chen Y, et al. 2022. Genome-edited powdery mildew resistance in wheat without growth penalties. |
| [42] |
Qiu Y, Li X, Fan M, Tang H, Zhang S, et al. 2025. Modification of starch traits in commercial wheat through TaWaxy gene editing. |
| [43] |
Bi W, Liu J, Li Y, He Z, Chen Y, et al. 2024. CRISPR/Cas9-guided editing of a novel susceptibility gene in potato improves Phytophthora resistance without growth penalty. |
| [44] |
Ramasamy M, Rajkumar MS, Bedre R, Irigoyen S, Berg-Falloure K, et al. 2024. Genome editing of NPR3 confers potato resistance to Candidatus Liberibacter spp. |
| [45] |
Arshad R, Razzaq T, Ahmad B, Hou T, Li C, et al. 2025. Banana breeding by genome design. |
| [46] |
Song Z, Li W, Lai X, Chen H, Wang L, et al. 2024. MaC2H2-IDD regulates fruit softening and involved in softening disorder induced by cold stress in banana. |
| [47] |
Chen Y, Fu M, Li H, Wang L, Liu R, et al. 2021. High-oleic acid content, nontransgenic allotetraploid cotton (Gossypium hirsutum L.) generated by knockout of GhFAD2 genes with CRISPR/Cas9 system. |
| [48] |
López-Casado G, Sánchez-Raya C, Ric-Varas PD, Paniagua C, Blanco-Portales R, et al. 2023. CRISPR/Cas9 editing of the polygalacturonase FaPG1 gene improves strawberry fruit firmness. |
| [49] |
Brant EJ, Eid A, Kannan B, Baloglu MC, Altpeter F. 2024. The extent of multiallelic, co-editing of LIGULELESS1 in highly polyploid sugarcane tunes leaf inclination angle and enables selection of the ideotype for biomass yield. |
| [50] |
Wang F, Liang S, Wang G, Hu T, Fu C, et al. 2024. CRISPR–Cas9-mediated construction of a cotton CDPK mutant library for identification of insect-resistance genes. |
| [51] |
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, et al. 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. |
| [52] |
Li J, Manghwar H, Sun L, Wang P, Wang G, et al. 2019. Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants. |
| [53] |
Anzalone AV, Koblan LW, Liu DR. 2020. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. |
| [54] |
Li B, Sun C, Li J, Gao C. 2024. Targeted genome-modification tools and their advanced applications in crop breeding. |
| [55] |
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. |
| [56] |
Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. 2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. |
| [57] |
Zhang R, Liu J, Chai Z, Chen S, Bai Y, et al. 2019. Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing. |
| [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. |
| [59] |
Gaillochet C, Peña Fernández A, Goossens V, D'Halluin K, Drozdzecki A, et al. 2023. Systematic optimization of Cas12a base editors in wheat and maize using the ITER platform. |
| [60] |
Zong Y, Wang Y, Li C, Zhang R, Chen K, et al. 2017. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. |
| [61] |
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. |
| [62] |
Veillet F, Kermarrec MP, Chauvin L, Chauvin JE, Nogué F. 2020. CRISPR-induced indels and base editing using the Staphylococcus aureus Cas9 in potato. |
| [63] |
Perroud PF, Guyon-Debast A, Veillet F, Kermarrec MP, Chauvin L, et al. 2022. Prime Editing in the model plant Physcomitrium patens and its potential in the tetraploid potato. |
| [64] |
Lin Q, Zong Y, Xue C, Wang S, Jin S, et al. 2020. Prime genome editing in rice and wheat. |
| [65] |
Vats S, Kumar J, Sonah H, Zhang F, Deshmukh R. 2024. Prime editing in plants: prospects and challenges. |
| [66] |
Ni P, Zhao Y, Zhou X, Liu Z, Huang Z, et al. 2023. Efficient and versatile multiplex prime editing in hexaploid wheat. |
| [67] |
Sánchez-León S, Gil-Humanes J, Ozuna CV, Giménez MJ, Sousa C, et al. 2018. Low-gluten, nontransgenic wheat engineered with CRISPR/Cas9. |
| [68] |
Chang Y, Tang H, Wang S, Li X, Huang P, et al. 2024. Efficient induction and rapid identification of haploid grains in tetraploid wheat by editing genes TtMTL and pyramiding anthocyanin markers. |
| [69] |
D'Halluin K, Vanderstraeten C, Van Hulle J, Rosolowska J, Van Den Brande I, et al. 2013. Targeted molecular trait stacking in cotton through targeted double-strand break induction. |
| [70] |
Jøhansen IE, Liu Y, Jorgensen B, Bennett EP, Andreasson E, et al. 2019. High efficacy full allelic CRISPR/Cas9 gene editing in tetraploid potato. |
| [71] |
Ly DNP, Iqbal S, Fosu-Nyarko J, Milroy S, Jones MGK. 2023. Multiplex CRISPR-Cas9 gene-editing can deliver potato cultivars with reduced browning and acrylamide. |
| [72] |
Decima Oneto CA, Massa GA, Echarte L, Rey Burusco MF, Gonzalez MN, et al. 2025. CRISPR/Cas9 editing of CBP80 enhances drought tolerance in potato (Solanum tuberosum). |
| [73] |
Ahmad N, Fatima S, Mehmood MA, Zaman QU, Atif RM, et al. 2023. Targeted genome editing in polyploids: lessons from Brassica. |
| [74] |
Grewal S, Yang CY, Scholefield D, Ashling S, Ghosh S, et al. 2024. Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii. |
| [75] |
Zhang Z, Zhang J, Kang L, Qiu X, Xu S, et al. 2024. Structural variation discovery in wheat using PacBio high-fidelity sequencing. |
| [76] |
Wang M, Tu L, Yuan D, Zhu D, Shen C, et al. 2019. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. |
| [77] |
Li B, Yang Q, Yang L, Zhou X, Deng L, et al. 2023. A gap-free reference genome reveals structural variations associated with flowering time in rapeseed (Brassica napus). |
| [78] |
Sakthivel SK, Vennapusa AR, Melmaiee K. 2025. Enhancing quality and climate resilient traits in vegetatively propagated polyploids: transgenic and genome editing advancements, challenges and future directions. |
| [79] |
Selma S, Gianoglio S, Uranga M, Vázquez-Vilar M, Espinosa-Ruiz A, et al. 2022. Potato virus X-delivered CRISPR activation programs lead to strong endogenous gene induction and transient metabolic reprogramming in Nicotiana benthamiana. |
| [80] |
Tiwari JK, Buckseth T, Challam C, Zinta R, Bhatia N, et al. 2022. CRISPR/Cas genome editing in potato: current status and future perspectives. |
| [81] |
Cao X, Xie H, Song M, Lu J, Ma P, et al. 2023. Cut−dip−budding delivery system enables genetic modifications in plants without tissue culture. |
| [82] |
Qiao JH, Zang Y, Gao Q, Liu S, Zhang XW, et al. 2025. Transgene- and tissue culture-free heritable genome editing using RNA virus-based delivery in wheat. |
| [83] |
Wolter F, Schindele P, Puchta H. 2019. Plant breeding at the speed of light: the power of CRISPR/Cas to generate directed genetic diversity at multiple sites. |
| [84] |
Bai M, Lin W, Peng C, Song P, Kuang H, et al. 2024. Expressing a human RNA demethylase as an assister improves gene-editing efficiency in plants. |