Harnessing apomixis: natural mechanisms and synthetic innovations for advancing crop and forage breeding

Abstract

Apomixis, a reproductive mechanism that enables clonal seed production, generates progeny genetically identical to the maternal parent. In plant breeding, sexual reproduction can enhance traits through genetic recombination and hybrid vigor, yet trait segregation significantly raises breeding costs and complexity. Although apomixis occurs naturally across various plant species, it remains notably absent in major crops like rice and maize. Significant progress has been made in identifying the genes that govern this process. Recent breakthroughs in synthetic apomixis provide promising pathways for crop improvement. This review offers a comprehensive analysis of natural apomixis and its genetic regulators, with a focus on recent advances in synthetic apomictic systems. We also explore the current state and potential of apomixis in forage breeding, especially in addressing challenges related to self-incompatibility, polyploidy, and genomic complexity in forage species. Finally, we discuss the challenges in applying apomixis to forage breeding and future directions for this research.

Acknowledgments

We sincerely thank Professor Elvira Hörandl from the University of Göttingen for invaluable assistance in providing data on natural apomixis. The authors declare no conflicts of interest and affirm their agreement with the content of this manuscript. This work was funded by the National Key Research and Development Program, grant number 2022YFF1003203, and the Strategic Priority Research Program of the Chinese Academy of Sciences, grant number XDA26030202.

Author contributions

S.C. planned and designed the study. S.H. and S.C. developed the graphs and drafted the manuscript. X.H. and L.T. assisted in materials visualization. K.W. provided critical support during the manuscript revision process.

Data availability

Data sharing is not applicable to this article as no new data were created or analyzed in this study.

Conflict of interest statement

None declared.

References

[1] Cornish MA, Hayward MD, Lawrence MJ. Self-incompatibility in ryegrass. Heredity. 1979; 43:95-106

[2] Chen S, Jia J, Cheng L. et al. Transcriptomic analysis reveals a comprehensive calcium-and Phytohormone-dominated sig-naling response in Leymus chinensis self-incompatibility. Int J Mol Sci. 2019; 20:2356

[3] Cropano C, Manzanares C, Yates S. et al. Identification of candi-date genes for self-compatibility in perennial ryegrass (Lolium perenne L.). Front Plant Sci. 2021; 12:707901

[4] Li, Liu S, Wang Y. et al. Transcriptomic analysis of self-incompatibility in alfalfa. Plants (Basel). 2024; 13:13

[5] Chen ZJ. Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci. 2010; 15:57-71

[6] Hochholdinger F, Baldauf JA. Heterosis in plants. Curr Biol. 2018;28:R1089-92

[7] Parajuli A, Yu L-X, Peel M. et al. Self-incompatibility, Inbreeding Depression, and Potential to Develop Inbred Lines in Alfalfa. In: YU L-X, KOLE C,eds. The Alfalfa Genome. Springer International Publishing: Cham, 2021,255-69

[8] Wang Y, Underwood CJ. Apomixis. Curr Biol. 2023;33:R293-5

[9] Hojsgaard D, Greilhuber J, Pellino M. et al. Emergence of apospory and bypass of meiosis via apomixis after sex-ual hybridisation and polyploidisation. New Phytol. 2014a; 204: 1000-12

[10] Hojsgaard D, Pullaiah T.Apomixis in Angiosperms: Mechanisms, Occurrences, and Biotechnology. Boca Raton: CRC Press; 2023:

[11] Koltunow AM. Apomixis: embryo sacs and embryos formed without meiosis or fertilization in ovules. Plant Cell. 1993; 5: 1425-37

[12] Nogler GA. Gametophytic Apomixis. In: Johri BM,ed. Embryology of Angiosperms. Springer Berlin Heidelberg: Berlin, Heidelberg, 1984,475-518

[13] Calzada J-PV, Crane CF, Stelly DM. Apomixis-the asexual revo-lution. Science. 1996; 274:1322-3

[14] Liu Q, Han D, Tian S. et al. Fixing hybrid vigor by synthetic apomixis: a dream come true. Seed Biol. 2023; 2:1-3

[15] Heidemann B, Primetis E, Zahn IE. et al. To infinity and beyond: recent progress, bottlenecks, and potential of clonal seeds by apomixis. Plant J. 2025; 121:e70054

[16] Huang Y, Liang Y, Xie Y. et al. Efficient haploid induction via egg cell expression of dandelion PARTHENOGENESIS in foxtail millet (Setaria italica). Plant Biotechnol J. 2024; 22:1797-9

[17] Khanday I, Skinner D, Yang B. et al. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature. 2019; 565:91-5

[18] Song M, Wang W, Ji C. et al. Simultaneous production of high-frequency synthetic apomixis with high fertility and improved agronomic traits in hybrid rice. Mol Plant. 2024b; 17:4-7

[19] Vernet A, Meynard D, Lian Q. et al. High-frequency synthetic apomixis in hybrid rice. Nat Commun. 2022; 13:7963

[20] Wang C, Liu Q, Shen Y. et al. Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes. Nat Biotechnol. 2019; 37:283-6

[21] Wei X, Liu C, Chen X. et al. Synthetic apomixis with normal hybrid rice seed production. Mol Plant. 2023; 16:489-92

[22] Xie E, Li Y, Tang D. et al. A strategy for generating rice apomixis by gene editing. J Integr Plant Biol. 2019; 61:911-6

[23] Goeckeritz CZ, Zheng X, Harkess A. et al. Widespread applica-tion of apomixis in agriculture requires further study of natural apomicts. iScience. 2024; 27:110720

[24] Hojsgaard D, Klatt S, Baier R. et al. Taxonomy and biogeography of Apomixis in angiosperms and associated biodiversity char-acteristics. Crit Rev Plant Sci. 2014b; 33:414-27

[25] Hand ML, Koltunow AM. The genetic control of apomixis: asex-ual seed formation. Genetics. 2014; 197:441-50

[26] Ozias-Akins P, van Dijk PJ. Mendelian genetics of apomixis in plants. Annu Rev Genet. 2007; 41:509-37

[27] Fei X, Shi J, Liu Y. et al. The steps from sexual reproduction to apomixis. Planta. 2019; 249:1715-30

[28] Carman JG. Asynchronous expression of duplicate genes in angiosperms may cause apomixis, bispory, tetraspory, and polyembryony. Biol J Linn Soc. 1997; 61:51-94

[29] Majeský L’, Krahulec F, Vašut RJ. How apomictic taxa are treated in current taxonomy: a review. Taxon. 2017; 66:1017-40

[30] Hörandl E, Diego H, Ana C. et al. Apomixis in systematics, evolu-tion and Phylogenetics of angiosperms: current developments and prospects. Crit Rev Plant Sci. 2024;1-43

[31] Curk F, Ollitrault F, Garcia-Lor A. et al. Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers. Ann Bot. 2016; 117:565-83

[32] Yin PP, Tang LP, Zhang XS. et al. Options for engineering Apomixis in plants. Front Plant Sci. 2022; 13:864987

[33] Higgins J, Tomaszewska P, Pellny TK. et al. Diverged subpop-ulations in tropical Urochloa (Brachiaria) forage species indi-cate a role for facultative apomixis and varying ploidy in their population structure and evolution. Ann Bot. 2022; 130: 657-69

[34] Xu Y, Jia H, Tan C. et al. Apomixis: genetic basis and controlling genes. Hortic Res. 2022;9:uhac150

[35] Li S-Z, Wang J, Jia S-G. et al. Synthetic apomixis: from genetic basis to agricultural application. Seed Biol. 2023; 2:0

[36] Zhou L, Han J, Chen Y. et al. Bivalent formation 1, a plant-conserved gene, encodes an OmpH/coiled-coil motif-containing protein required for meiotic recombination in rice. JExp Bot. 2017; 68:2163-74

[37] Ji J, Tang D, Shen Y. et al. P31comet, a member of the synaptone-mal complex, participates in meiotic DSB formation in rice. Proc Natl Acad Sci USA. 2016; 113:10577-82

[38] Miao C, Tang D, Zhang H. et al. Central region component1, a novel synaptonemal complex component, is essential for meiotic recombination initiation in rice. Plant Cell. 2013; 25: 2998-3009

[39] Ravi M, Marimuthu MP, Siddiqi I. Gamete formation without meiosis in Arabidopsis. Nature. 2008; 451:1121-4

[40] Marimuthu MP, Jolivet S, Ravi M. et al. Synthetic clonal repro-duction through seeds. Science. 2011; 331:876

[41] Zhang C, Song Y, Cheng ZH. et al. The Arabidopsis thaliana DSB formation (AtDFO) gene is required for meiotic double-strand break formation. Plant J. 2012; 72:271-81

[42] Chen HW, Yeh HY, Chang CC. et al. Biochemical characteriza-tion of the meiosis-essential yet evolutionarily divergent topoi-somerase VIB-like protein MTOPVIB from Arabidopsis thaliana. Nucleic Acids Res. 2024; 52:4541-55

[43] Steckenborn S, Cuacos M, Ayoub MA. et al. The meiotic topoi-somerase VI B subunit (MTOPVIB) is essential for meiotic DNA double-strand break formation in barley (Hordeum vulgare L.). Plant Reprod. 2023; 36:1-15

[44] Jing JL, Zhang T, Kao YH. et al. ZmMTOPVIB enables DNA double-Strand break formation and bipolar spindle assembly during maize meiosis. Plant Physiol. 2020; 184:1811-22

[45] Xue Z, Liu C, Shi W. et al. OsMTOPVIB is required for meiotic bipolar spindle assembly. Proc Natl Acad Sci USA. 2019; 116: 15967-72

[46] Nonomura K, Nakano M, Fukuda T. et al. The novel gene HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 of rice encodes a putative coiled-coil protein required for homologous chromosome pairing in MEIOSIS. Plant Cell. 2004; 16:1008-20

[47] Huang Y, Meng X, Rao Y. et al. OsWUS-driven synthetic apomixis in hybrid rice. Plant Commun. 2025; 6:101136

[48] Mieulet D, Jolivet S, Rivard M. et al. Turning rice meiosis into mitosis. Cell Res. 2016; 26:1242-54

[49] Shi W, Ji J, Xue Z. et al. PRD1, a homologous recombination initiation factor, is involved in spindle assembly in rice meiosis. New Phytol. 2021; 230:585-600

[50] Wang Y, Wang Y, Zang J. et al. ZmPRD1 is essential for double-strand break formation, but is not required for bipolar spindle assembly during maize meiosis. JExp Bot. 2022b; 73:3386-400

[51] De Muyt A, Pereira L, Vezon D. et al. A high throughput genetic screen identifies new early meiotic recombination functions in Arabidopsis thaliana. PLoS Genet. 2009; 5:e1000654

[52] Wang C, Qu S, Zhang J. et al. OsPRD2 is essential for double-strand break formation, but not spindle assembly during rice meiosis. Front Plant Sci. 2022a; 13:1122202

[53] Wang Y, Li SY, Wang YZ. et al. ZmASY1 interacts with ZmPRD3 and is crucial for meiotic double-strand break formation in maize. New Phytol. 2023; 237:454-70

[54] Wu Z, Ji J, Tang D. et al. OsSDS is essential for DSB formation in rice meiosis. Front Plant Sci. 2015; 6:21

[55] Grelon M, Vezon D, Gendrot G. et al. AtSPO11-1 is necessary for efficient meiotic recombination in plants. EMBO J. 2001; 20: 589-600

[56] d’Erfurth I, Jolivet S, Froger N. et al. Turning meiosis into mitosis. PLoS Biol. 2009; 7:e1000124

[57] d’Erfurth I, Cromer L, Jolivet S. et al. The cyclin-a CYCA1;2/TAM is required for the meiosis I to meiosis II transition and coop-erates with OSD1 for the prophase to first meiotic division transition. PLoS Genet. 2010; 6:e1000989

[58] Wang Y, Fuentes RR, van Rengs WMJ. et al. Harnessing clonal gametes in hybrid crops to engineer polyploid genomes. Nat Genet. 2024; 56:1075-9

[59] Stacey NJ, Kuromori T, Azumi Y. et al. Arabidopsis SPO11-2 functions with SPO11-1 in meiotic recombination. Plant J. 2006; 48:206-16

[60] Fayos I, Meunier AC, Vernet A. et al. Assessment of the roles of SPO11-2 and SPO11-4 in meiosis in rice using CRISPR/Cas9 mutagenesis. JExp Bot. 2020; 71:7046-58

[61] Li M, Li S, He Y. et al. ZmSPO11-2 is critical for meiotic recom-bination in maize. Chromosom Res. 2022; 30:415-28

[62] Zhan J. RDR6 is essential for double-Strand break formation during male meiosis in Rice. Plant Cell. 2020; 32:3053-4

[63] Cifuentes M, Jolivet S, Cromer L. et al. TDM1 regulation deter-mines the number of meiotic divisions. PLoS Genet. 2016; 12: e1005856

[64] Shao T, Tang D, Wang K. et al. OsREC8 is essential for chromatid cohesion and metaphase I monopolar orientation in rice meio-sis. Plant Physiol. 2011; 156:1386-96

[65] Song M, Li F, Chen Z. et al. Engineering high-frequency apomixis with normal seed production in hybrid rice. iScience. 2024a; 27:111479

[66] Ross KJ, Fransz P, Armstrong SJ. et al. Cytological characteri-zation of four meiotic mutants of Arabidopsis isolated from T-DNA-transformed lines. Chromosom Res. 1997; 5:551-9

[67] Ravi M, Chan SW. Haploid plants produced by centromere-mediated genome elimination. Nature. 2010; 464:615-8

[68] Lv J, Yu K, Wei J. et al. Generation of paternal haploids in wheat by genome editing of the centromeric histone CENH3. Nat Biotechnol. 2020; 38:1397-401

[69] Wang N, Gent JI, Dawe RK. Haploid induction by a maize cenh3 null mutant. Sci Adv. 2021;7:eabe2299

[70] Yao L, Zhang Y, Liu C. et al. OsMATL mutation induces haploid seed formation in indica rice. Nat Plants. 2018; 4:530-3

[71] Gilles LM, Khaled A, Laffaire JB. et al. Loss of pollen-specific phospholipase NOT LIKE DAD triggers gynogenesis in maize. EMBO J. 2017; 36:707-17

[72] Kelliher T, Starr D, Richbourg L. et al. MATRILINEAL, a sperm-specific phospholipase, triggers maize haploid induc-tion. Nature. 2017; 542:105-9

[73] Liu C, Li X, Meng D. et al. A 4-bp insertion at ZmPLA1 encoding a putative phospholipase a generates haploid induction in maize. Mol Plant. 2017; 10:520-2

[74] Li Y, Lin Z, Yue Y. et al. Loss-of-function alleles of ZmPLD3 cause haploid induction in maize. Nat Plants. 2021; 7:1579-88

[75] Jiang C, Sun J, Li R. et al. A reactive oxygen species burst causes haploid induction in maize. Mol Plant. 2022; 15:943-55

[76] Jang JH, Seo HS, Widiez T. et al. Loss-of-function of gynoecium-expressed phospholipase pPLAIIγ triggers maternal haploid induction in Arabidopsis. New Phytol. 2023; 238:1813-24

[77] Sun Y, Hou L, Li C. et al. Maternal haploid induction in maize via mutation of gamete expression protein 1. Plant Biotechnol J. 2025; 23:2595-607

[78] Mao Y, Nakel T, Erbasol Serbes I. et al. ECS1 and ECS2 suppress polyspermy and the formation of haploid plants by promoting double fertilization. Elife. 2023; 12:e85832

[79] Zhang X, Shi C, Li S. et al. A female in vivo haploid-induction system via mutagenesis of egg cell-specific peptidases. Mol Plant. 2023; 16:471-80

[80] Conner JA, Podio M, Ozias-Akins P. Haploid embryo production in rice and maize induced by PsASGR-BBML transgenes. Plant Reprod. 2017; 30:41-52

[81] Conner JA, Mookkan M, Huo H. et al. A parthenogenesis gene of apomict origin elicits embryo formation from unfertilized eggs in a sexual plant. Proc Natl Acad Sci USA. 2015; 112:11205-10

[82] Zhang Z, Conner J, Guo Y. et al. Haploidy in tobacco induced by PsASGR-BBML transgenes via parthenogenesis. Genes (Basel). 2020; 11:11

[83] Skinner DJ, Mallari MD, Zafar K. et al. Efficient parthenogenesis via egg cell expression of maize BABY BOOM 1: a step toward synthetic apomixis. Plant Physiol. 2023; 193:2278-81

[84] Underwood CJ, Vijverberg K, Rigola D. et al. A PARTHENOGENE-SIS allele from apomictic dandelion can induce egg cell division without fertilization in lettuce. Nat Genet. 2022; 54:84-93

[85] Che L, Tang D, Wang K. et al. OsAM1 is required for leptotene-zygotene transition in rice. Cell Res. 2011; 21:654-65

[86] Pawlowski WP, Wang CJ, Golubovskaya IN. et al. Maize AMEI-OTIC1 is essential for multiple early meiotic processes and likely required for the initiation of meiosis. Proc Natl Acad Sci USA. 2009; 106:3603-8

[87] Honari M, Ashnest JR, Sharbel TF. Sex-versus apomixis-specific polymorphisms in the 5’UTR of APOLLO from Boechera shift gene expression from somatic to reproductive tissues in Ara-bidopsis. Front Plant Sci. 2024; 15:1308059

[88] Underwood CJ, Mercier R. Engineering Apomixis: clonal seeds approaching the fields. Annu Rev Plant Biol. 2022; 73:201-25

[89] Yu H, Wang M, Tang D. et al. OsSPO11-1 is essential for both homologous chromosome pairing and crossover formation in rice. Chromosoma. 2010; 119:625-36

[90] Zhao Y, Ren L, Zhao T. et al. SCC3 is an axial element essen-tial for homologous chromosome pairing and synapsis. Elife. 2024; 13:13

[91] Zhang T, Zhao S-H, He Y. ZmTDM1 encodes a tetratricopeptide repeat domain protein and is required for meiotic exit in maize. Plant J. 2024; 117:1517-27

[92] Marimuthu MPA, Maruthachalam R, Bondada R. et al. Epige-netically mismatched parental centromeres trigger genome elimination in hybrids. Sci Adv. 2021;7:eabk1151

[93] Qu Y, Fernie AR, Liu J. et al. Doubled haploid technology and synthetic apomixis: recent advances and applications in future crop breeding. Mol Plant. 2024; 17:1005-18

[94] Sugi N, Calhau ARM, Jacquier NMA. et al. The peri-germ cell membrane: poorly characterized but key interface for plant reproduction. Nat Plants. 2024; 10:1607-9

[95] Boutilier K, Offringa R, Sharma VK. et al. Ectopic expression of BABY BOOM triggers a conversion from vegetative to embry-onic growth. Plant Cell. 2002; 14:1737-49

[96] Liu Q, Han D, Cheng D. et al. AtRKD5 inhibits the parthenogenic potential mediated by AtBBM. J Integr Plant Biol. 2024; 66: 1517-31

[97] Xiong J, Yajie J, Shenlin Y. et al. In vivo haploid induction via parthenogenesis gene ToPAR in Rice. Rice Sci. 2025; 32: 273-6

[98] Lu Z, Shao G, Xiong J. et al. MONOCULM 3, an ortholog of WUSCHEL in rice, is required for tiller bud formation. J Genet Genomics. 2015; 42:71-8

[99] Zuo J, Niu QW, Frugis G. et al. The WUSCHEL gene pro-motes vegetative-to-embryonic transition in Arabidopsis. Plant J. 2002; 30:349-59

[100] Ren H, Shankle K, Cho MJ. et al. Synergistic induction of fertilization-independent embryogenesis in rice egg cells by paternal-genome-expressed transcription factors. Nat Plants. 2024; 10:1892-9

[101] Zhong Y, Liu C, Qi X. et al. Mutation of ZmDMP enhances haploid induction in maize. Nat Plants. 2019; 5:575-80

[102] Qian H, Guo J, Shi H. Genetic manipulation of the genes for clonal seeds results in sterility in cotton. BMC Plant Biol. 2024; 24:946

[103] Wang J, Wang K, Yang W-C. et al. Simultaneous editing of SPO11-1, REC8 and OSD 1 yields aneutetraploid soybeans. Plant Biotechnol J. 2025

[104] Adema K, Schon MA, Nodine MD. et al. Lost in space: what single-cell RNA sequencing cannot tell you. Trends Plant Sci. 2024; 29:1018-28

[105] Bawa G,LiuZ,YuX. et al. Introducing single cell stereo-sequencing technology to transform the plant transcriptome landscape. Trends Plant Sci. 2024; 29:249-65

[106] da Costa Lima Moraes A, Mollinari M, Ferreira RCU. et al. Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis. Theor Appl Genet. 2023; 136:238

[107] Deo TG, Ferreira RCU, Lara LAC. et al. High-resolution linkage map with allele dosage allows the identification of regions gov-erning complex traits and Apospory in Guinea grass (Megath-yrsus maximus). Front Plant Sci. 2020; 11:15

[108] Dusi DMA, Alves ER, Cabral GB. et al.An exonuclease V homo-logue is expressed predominantly during early megasporogen-esis in apomictic Brachiaria brizantha. Planta. 2023; 258:5

[109] Koehler AD, Irsigler AST, Carneiro VTC. et al. SERK genes identification and expression analysis during somatic embryo-genesis and sporogenesis of sexual and apomictic Brachiaria brizantha (syn. Urochloa brizantha). Planta. 2020; 252:39

[110] Stokstad E. Unmixed blessing. Science. 2023; 380:684-7

[111] Peha H, Ren H, Skinner D. et al. Twin embryo formation by induced parthenogenesis. Plant Reprod. 2024; 38:3

[112] Koltunow AM, Grossniklaus U. Apomixis: a developmental per-spective. Annu Rev Plant Biol. 2003; 54:547-74

[113] Ul Haq SI, Zheng D, Feng N. et al. Progresses of CRISPR/Cas9 genome editing in forage crops. J Plant Physiol. 2022; 279: 153860

[114] Liu X, Zhang S, Jiang Y. et al. Use of CRISPR/Cas9-based gene editing to simultaneously mutate multiple homologous genes required for pollen development and male fertility in maize. Cells. 2022; 11:11

[115] Rusnak B, Clark FK, Vadde BVL. et al. What is a plant cell type in the age of single-cell biology? It’s complicated. Annu Rev Cell Dev Biol. 2024; 40:301-28

[116] Jia HH, Xu YT, Yin ZP. et al. Transcriptomes and DNA methy-lomes in apomictic cells delineate nucellar embryogenesis ini-tiation in citrus. DNA Res. 2021;28:dsab014

[117] Niccolò T, Anderson AW, Emidio A. Apomixis: oh, what a tangled web we have! Planta. 2023; 257:92

[118] Pasten MC, Carballo J, Gallardo J. et al. A combined transcrip-tome - miRNAome approach revealed that a kinesin gene is differentially targeted by a novel miRNA in an apomictic genotype of Eragrostis curvula. Front Plant Sci. 2022; 13:1012682

[119] Hanson AD, Voiniciuc C. Editorial overview: plant synthetic biology. Curr Opin Biotechnol. 2024; 90:103211

[120] Schmid MW, Schmidt A, Grossniklaus U. The female gameto-phyte: an emerging model for cell type-specific systems biology in plant development. Front Plant Sci. 2015; 6:907

[121] Farooq MA, Gao S, Hassan MA. et al. Artificial intelligence in plant breeding. Trends Genet. 2024; 40:891-908