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Qu Y, Fernie AR, Liu J, Yan J. Doubled haploid technology and synthetic apomixis: Recent advances and applications in future crop breeding. MOLECULAR PLANT 2024; 17:1005-1018. [PMID: 38877700 DOI: 10.1016/j.molp.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/19/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Doubled haploid (DH) technology and synthetic apomixis approaches can considerably shorten breeding cycles and enhance breeding efficiency. Compared with traditional breeding methods, DH technology offers the advantage of rapidly generating inbred lines, while synthetic apomixis can effectively fix hybrid vigor. In this review, we focus on (i) recent advances in identifying and characterizing genes responsible for haploid induction (HI), (ii) the molecular mechanisms of HI, (iii) spontaneous haploid genome doubling, and (iv) crop synthetic apomixis. We also discuss the challenges and potential solutions for future crop breeding programs utilizing DH technology and synthetic apomixis. Finally, we provide our perspectives about how to integrate DH and synthetic apomixis for precision breeding and de novo domestication.
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Affiliation(s)
- Yanzhi Qu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max- Planck- Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Jie Liu
- Yazhouwan National Laboratory, Sanya 572024, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Yazhouwan National Laboratory, Sanya 572024, China.
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2
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Clonal gametes enable polyploid genome design. Nat Genet 2024; 56:1045-1046. [PMID: 38773244 DOI: 10.1038/s41588-024-01751-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
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3
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Hojsgaard D, Nagel M, Feingold SE, Massa GA, Bradshaw JE. New Frontiers in Potato Breeding: Tinkering with Reproductive Genes and Apomixis. Biomolecules 2024; 14:614. [PMID: 38927018 PMCID: PMC11202281 DOI: 10.3390/biom14060614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Potato is the most important non-cereal crop worldwide, and, yet, genetic gains in potato have been traditionally delayed by the crop's biology, mostly the genetic heterozygosity of autotetraploid cultivars and the intricacies of the reproductive system. Novel site-directed genetic modification techniques provide opportunities for designing climate-smart cultivars, but they also pose new possibilities (and challenges) for breeding potato. As potato species show a remarkable reproductive diversity, and their ovules have a propensity to develop apomixis-like phenotypes, tinkering with reproductive genes in potato is opening new frontiers in potato breeding. Developing diploid varieties instead of tetraploid ones has been proposed as an alternative way to fill the gap in genetic gain, that is being achieved by using gene-edited self-compatible genotypes and inbred lines to exploit hybrid seed technology. In a similar way, modulating the formation of unreduced gametes and synthesizing apomixis in diploid or tetraploid potatoes may help to reinforce the transition to a diploid hybrid crop or enhance introgression schemes and fix highly heterozygous genotypes in tetraploid varieties. In any case, the induction of apomixis-like phenotypes will shorten the time and costs of developing new varieties by allowing the multi-generational propagation through true seeds. In this review, we summarize the current knowledge on potato reproductive phenotypes and underlying genes, discuss the advantages and disadvantages of using potato's natural variability to modulate reproductive steps during seed formation, and consider strategies to synthesize apomixis. However, before we can fully modulate the reproductive phenotypes, we need to understand the genetic basis of such diversity. Finally, we visualize an active, central role for genebanks in this endeavor by phenotyping properly genotyped genebank accessions and new introductions to provide scientists and breeders with reliable data and resources for developing innovations to exploit market opportunities.
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Affiliation(s)
- Diego Hojsgaard
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany;
| | - Manuela Nagel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany;
| | - Sergio E. Feingold
- Laboratorio de Agrobiotecnología, EEA Balcarce-IPADS (UEDD INTA–CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA), Balcarce B7620, Argentina; (S.E.F.); (G.A.M.)
| | - Gabriela A. Massa
- Laboratorio de Agrobiotecnología, EEA Balcarce-IPADS (UEDD INTA–CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA), Balcarce B7620, Argentina; (S.E.F.); (G.A.M.)
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce B7620, Argentina
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Binmöller L, Volkert C, Kiefer C, Zühl L, Slawinska MW, Loreth A, Nauerth BH, Ibberson D, Martinez R, Mandakova TM, Zipper R, Schmidt A. Differential expression and evolutionary diversification of RNA helicases in Boechera sexual and apomictic reproduction. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2451-2469. [PMID: 38263359 DOI: 10.1093/jxb/erae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/22/2024] [Indexed: 01/25/2024]
Abstract
In higher plants, sexual reproduction is characterized by meiosis of the first cells of the germlines, and double fertilization of the egg and central cell after gametogenesis. In contrast, in apomicts of the genus Boechera, meiosis is omitted or altered and only the central cell requires fertilization, while the embryo forms parthenogenetically from the egg cell. To deepen the understanding of the transcriptional basis underlying these differences, we applied RNA-seq to compare expression in reproductive tissues of different Boechera accessions. This confirmed previous evidence of an enrichment of RNA helicases in plant germlines. Furthermore, few RNA helicases were differentially expressed in female reproductive ovule tissues harboring mature gametophytes from apomictic and sexual accessions. For some of these genes, we further found evidence for a complex recent evolutionary history. This included a homolog of Arabidopsis thaliana FASCIATED STEM4 (FAS4). In contrast to AtFAS4, which is a single-copy gene, FAS4 is represented by three homologs in Boechera, suggesting a potential for subfunctionalization to modulate reproductive development. To gain first insights into functional roles of FAS4, we studied Arabidopsis lines carrying mutant alleles. This identified the crucial importance of AtFAS4 for reproduction, as we observed developmental defects and arrest during male and female gametogenesis.
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Affiliation(s)
- Laura Binmöller
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Christopher Volkert
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Christiane Kiefer
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Luise Zühl
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Magdalena W Slawinska
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Anna Loreth
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Berit H Nauerth
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany
| | - Rafael Martinez
- Centre for Organismal Studies Heidelberg, Department of Developmental Biology, Heidelberg University, Im Neuenheimer Feld 230, D-69120, Heidelberg, Germany
| | - Terezie M Mandakova
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Reinhard Zipper
- Institute of Biology, Plant Evolutionary Biology, University of Hohenheim, Garbenstrasse 30, D-70599 Stuttgart, Germany
| | - Anja Schmidt
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
- Institute of Biology, Plant Evolutionary Biology, University of Hohenheim, Garbenstrasse 30, D-70599 Stuttgart, Germany
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5
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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 Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 15:1308059. [PMID: 38476690 PMCID: PMC10929715 DOI: 10.3389/fpls.2024.1308059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/31/2024] [Indexed: 03/14/2024]
Abstract
Introduction Among candidate genes underlying the control components of apomixis, APOLLO is known for its strong linkage to apomeiosis in the genus Boechera. The gene has "apo alleles," which are characterized by a set of linked apomixis-specific polymorphisms, and "sex alleles." All apomictic Boechera genotypes are heterozygous for the apo/sex alleles, whereas all sexual genotypes are homozygous for sex alleles. Methods In this study, native and synthetic APOLLO promoters were characterized by detecting the expression level of the β-glucuronidase (GUS) gene in Arabidopsis. Results Comparing various flower developmental stages in transgenic lines containing different constructs with 2-kb native transgenic lines revealed that changes to the APOLLO promoter causes shifts in tissue and developmental stage specificity of GUS expression. Importantly, several apomixis-specific polymorphisms in the 5'UTR change the timing and location of GUS activity from somatic to reproductive tissues. Discussion These synthetic data simulate a plausible evolutionary process, whereby apomixis-specific gene activity can be achieved.
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Affiliation(s)
- Maryam Honari
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
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6
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Liang R, Gao C. Creating one-line hybrid crops by synthetic apomixis. MOLECULAR PLANT 2024; 17:16-18. [PMID: 38105558 DOI: 10.1016/j.molp.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Affiliation(s)
- Ronghong Liang
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Caixia Gao
- New Cornerstone Science Laboratory, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Puchta H, Houben A. Plant chromosome engineering - past, present and future. THE NEW PHYTOLOGIST 2024; 241:541-552. [PMID: 37984056 DOI: 10.1111/nph.19414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
Spontaneous chromosomal rearrangements (CRs) play an essential role in speciation, genome evolution and crop domestication. To be able to use the potential of CRs for breeding, plant chromosome engineering was initiated by fragmenting chromosomes by X-ray irradiation. With the rise of the CRISPR/Cas system, it became possible to induce double-strand breaks (DSBs) in a highly efficient manner at will at any chromosomal position. This has enabled a completely new level of predesigned chromosome engineering. The genetic linkage between specific genes can be broken by inducing chromosomal translocations. Natural inversions, which suppress genetic exchange, can be reverted for breeding. In addition, various approaches for constructing minichromosomes by downsizing regular standard A or supernumerary B chromosomes, which could serve as future vectors in plant biotechnology, have been developed. Recently, a functional synthetic centromere could be constructed. Also, different ways of genome haploidization have been set up, some based on centromere manipulations. In the future, we expect to see even more complex rearrangements, which can be combined with previously developed engineering technologies such as recombinases. Chromosome engineering might help to redefine genetic linkage groups, change the number of chromosomes, stack beneficial genes on mini cargo chromosomes, or set up genetic isolation to avoid outcrossing.
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Affiliation(s)
- Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences (JKIP) - Molecular Biology, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
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8
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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9
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Skinner DJ, Mallari MD, Zafar K, Cho MJ, Sundaresan V. Efficient parthenogenesis via egg cell expression of maize BABY BOOM 1: a step toward synthetic apomixis. PLANT PHYSIOLOGY 2023; 193:2278-2281. [PMID: 37610248 DOI: 10.1093/plphys/kiad461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/01/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
The maize BABY BOOM 1 gene, when ectopically expressed in egg cells, induces parthenogenetic haploid progeny at high frequency, suggesting a promising route for producing clonal hybrid seeds in maize.
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Affiliation(s)
- Debra J Skinner
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Michelle D Mallari
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Kashaf Zafar
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Myeong-Je Cho
- Plant Genomics and Transformation Facility, Innovative Genomics Institute, University of California, Berkeley 94704, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, CA 95616, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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10
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Tonosaki K, Kinoshita T. Polycomb repression of the asexual embryo. NATURE PLANTS 2023; 9:1783-1784. [PMID: 37814023 DOI: 10.1038/s41477-023-01537-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
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11
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Mahlandt A, Singh DK, Mercier R. Engineering apomixis in crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:131. [PMID: 37199785 DOI: 10.1007/s00122-023-04357-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/04/2023] [Indexed: 05/19/2023]
Abstract
Apomixis is an asexual mode of reproduction through seeds where progeny are clones of the mother plants. Naturally apomictic modes of reproduction are found in hundreds of plant genera distributed across more than 30 plant families, but are absent in major crop plants. Apomixis has the potential to be a breakthrough technology by allowing the propagation through seed of any genotype, including F1 hybrids. Here, we have summarized the recent progress toward synthetic apomixis, where combining targeted modifications of both the meiosis and fertilization processes leads to the production of clonal seeds at high frequencies. Despite some remaining challenges, the technology has approached a level of maturity that allows its consideration for application in the field.
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Affiliation(s)
- Alexander Mahlandt
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Dipesh Kumar Singh
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, Germany.
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12
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Abstract
Wang and Underwood introduce apomixis in plants.
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Affiliation(s)
- Yazhong Wang
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Charles J Underwood
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
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13
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Liu C, He Z, Zhang Y, Hu F, Li M, Liu Q, Huang Y, Wang J, Zhang W, Wang C, Wang K. Synthetic apomixis enables stable transgenerational transmission of heterotic phenotypes in hybrid rice. PLANT COMMUNICATIONS 2023; 4:100470. [PMID: 36325606 PMCID: PMC10030361 DOI: 10.1016/j.xplc.2022.100470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/28/2022] [Accepted: 10/29/2022] [Indexed: 05/04/2023]
Abstract
In hybrid plants, heterosis often produces large, vigorous plants with high yields; however, hybrid seeds are generated by costly and laborious crosses of inbred parents. Apomixis, in which a plant produces a clone of itself via asexual reproduction through seeds, may produce another revolution in plant biology. Recently, synthetic apomixis enabled clonal reproduction of F1 hybrids through seeds in rice (Oryza sativa), but the inheritance of the synthetic apomixis trait and superior heterotic phenotypes across generations remained unclear. Here, we propagated clonal plants to the T4 generation and investigated their genetic and molecular stability at each generation. By analyzing agronomic traits, as well as the genome, methylome, transcriptome, and allele-specific transcriptome, we showed that the descendant clonal plants remained stable. Unexpectedly, in addition to normal clonal seeds, the plants also produced a few aneuploids that had eliminated large genomic segments in each generation. Despite the identification of rare aneuploids, the observation that the synthetic apomixis trait is stably transmitted through multiple generations helps confirm the feasibility of using apomixis in the future.
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Affiliation(s)
- Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Zexue He
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Yan Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Fengyue Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Mengqi Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Qing Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yong Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Jian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China.
| | - Chun Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Hainan Yazhou Bay Seed Lab, Sanya, Hainan 572025, China.
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14
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Wei X, Liu C, Chen X, Lu H, Wang J, Yang S, Wang K. Synthetic apomixis with normal hybrid rice seed production. MOLECULAR PLANT 2023; 16:489-492. [PMID: 36609144 DOI: 10.1016/j.molp.2023.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Affiliation(s)
- Xin Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Xi Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Hongwei Lu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Jian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Shenlin Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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15
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Takasaki H, Ikeda M, Hasegawa R, Zhang Y, Sakamoto S, Maruyama D, Mitsuda N, Kinoshita T, Ohme-Takagi M. Elongation of Siliques Without Pollination 3 Regulates Nutrient Flow Necessary for Embryogenesis. PLANT & CELL PHYSIOLOGY 2023; 64:117-123. [PMID: 36264192 DOI: 10.1093/pcp/pcac151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Apomixis, defined as the transfer of maternal germplasm to offspring without fertilization, enables the fixation of F1-useful traits, providing advantages in crop breeding. However, most apomictic plants require pollination to produce the endosperm. The endosperm is essential for embryogenesis, and its development is suppressed until fertilization. We show that the expression of a chimeric repressor of the Elongation of Siliques without Pollination 3 (ESP3) gene (Pro35S:ESP3-SRDX) induces ovule enlargement without fertilization in Arabidopsis thaliana. The ESP3 gene encodes a protein similar to the flowering Wageningen homeodomain transcription factor containing a StAR-related lipid transfer domain. However, ESP3 lacks the homeobox-encoding region. Genes related to the cell cycle and sugar metabolism were upregulated in unfertilized Pro35S:ESP3-SRDX ovules similar to those in fertilized seeds, while those related to autophagy were downregulated similar to those in fertilized seeds. Unfertilized Pro35S:ESP3-SRDX ovules partially nourished embryos when only the egg was fertilized, accumulating hexoses without central cell proliferation. ESP3 may regulate nutrient flow during seed development, and ESP3-SRDX could be a useful tool for complete apomixis that does not require pseudo-fertilization.
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Affiliation(s)
- Hironori Takasaki
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570 Japan
| | - Miho Ikeda
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570 Japan
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji-cho, Fukui, 910-1195 Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8570 Japan
| | - Reika Hasegawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570 Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8570 Japan
| | - Yilin Zhang
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570 Japan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8570 Japan
| | - Daisuke Maruyama
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Toksuka-ku, Yokohama, Kanagawa, 244-0813 Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8570 Japan
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Toksuka-ku, Yokohama, Kanagawa, 244-0813 Japan
| | - Masaru Ohme-Takagi
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570 Japan
- Institute of Tropical Plant Science and Microbiology, National Cheng Kung University, No.1, University Road, Tainan City 701, Taiwan
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16
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Synthetic apomixis: the beginning of a new era. Curr Opin Biotechnol 2023; 79:102877. [PMID: 36628906 DOI: 10.1016/j.copbio.2022.102877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023]
Abstract
Apomixis is a process of asexual reproduction that enables plants to bypass meiosis and fertilization to generate clonal seeds that are identical to the maternal genotype. Apomixis has tremendous potential for breeding plants with desired characteristics, given its ability to fix any elite genotype. However, little is known about the origin and dynamics of natural apomictic plant systems. The introgression of apomixis-related genes from natural apomicts has achieved limited success. Therefore, synthetic apomixis, engineered to include apomeiosis, autonomous embryo formation, and autonomous endosperm development, has been proposed as a promising platform to effectuate apomixis in any crop. In this study, we have summarized recent advances in the understanding of synthetic apomixis and discussed the limitations of current synthetic apomixis systems and ways to overcome them.
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Shen K, Qu M, Zhao P. The Roads to Haploid Embryogenesis. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020243. [PMID: 36678955 PMCID: PMC9865920 DOI: 10.3390/plants12020243] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 05/31/2023]
Abstract
Although zygotic embryogenesis is usually studied in the field of seed biology, great attention has been paid to the methods used to generate haploid embryos due to their applications in crop breeding. These mainly include two methods for haploid embryogenesis: in vitro microspore embryogenesis and in vivo haploid embryogenesis. Although microspore culture systems and maize haploid induction systems were discovered in the 1960s, little is known about the molecular mechanisms underlying haploid formation. In recent years, major breakthroughs have been made in in vivo haploid induction systems, and several key factors, such as the matrilineal (MTL), baby boom (BBM), domain of unknown function 679 membrane protein (DMP), and egg cell-specific (ECS) that trigger in vivo haploid embryo production in both the crops and Arabidopsis models have been identified. The discovery of these haploid inducers indicates that haploid embryogenesis is highly related to gamete development, fertilization, and genome stability in ealry embryos. Here, based on recent efforts to identify key players in haploid embryogenesis and to understand its molecular mechanisms, we summarize the different paths to haploid embryogenesis, and we discuss the mechanisms of haploid generation and its potential applications in crop breeding. Although these haploid-inducing factors could assist egg cells in bypassing fertilization to initiate embryogenesis or trigger genome elimination in zygotes after fertilization to form haploid embryos, the fertilization of central cells to form endosperms is a prerequisite step for haploid formation. Deciphering the molecular and cellular mechanisms for haploid embryogenesis, increasing the haploid induction efficiency, and establishing haploid induction systems in other crops are critical for promoting the application of haploid technology in crop breeding, and these should be addressed in further studies.
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Affiliation(s)
- Kun Shen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mengxue Qu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Abstract
Introducing asexual reproduction through seeds - apomixis - into crop species could revolutionize agriculture by allowing F1 hybrids with enhanced yield and stability to be clonally propagated. Engineering synthetic apomixis has proven feasible in inbred rice through the inactivation of three genes (MiMe), which results in the conversion of meiosis into mitosis in a line ectopically expressing the BABYBOOM1 (BBM1) parthenogenetic trigger in egg cells. However, only 10-30% of the seeds are clonal. Here, we show that synthetic apomixis can be achieved in an F1 hybrid of rice by inducing MiMe mutations and egg cell expression of BBM1 in a single step. We generate hybrid plants that produce more than 95% of clonal seeds across multiple generations. Clonal apomictic plants maintain the phenotype of the F1 hybrid along successive generations. Our results demonstrate that there is no barrier to almost fully penetrant synthetic apomixis in an important crop species, rendering it compatible with use in agriculture.
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Paczesniak D, Pellino M, Goertzen R, Guenter D, Jahnke S, Fischbach A, Lovell JT, Sharbel TF. Seed size, endosperm and germination variation in sexual and apomictic Boechera. FRONTIERS IN PLANT SCIENCE 2022; 13:991531. [PMID: 36466233 PMCID: PMC9716183 DOI: 10.3389/fpls.2022.991531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Asexual reproduction results in offspring that are genetically identical to the mother. Among apomictic plants (reproducing asexually through seeds) many require paternal genetic contribution for proper endosperm development (pseudogamous endosperm). We examined phenotypic diversity in seed traits using a diverse panel of sexual and apomictic accessions from the genus Boechera. While genetic uniformity resulting from asexual reproduction is expected to reduce phenotypic diversity in seeds produced by apomictic individuals, pseudogamous endosperm, variable endosperm ploidy, and the deviations from 2:1 maternal:paternal genome ratio in endosperm can all contribute to increased phenotypic diversity among apomictic offspring. We characterized seed size variation in 64 diploid sexual and apomictic (diploid and triploid) Boechera lineages. In order to find out whether individual seed size was related to endosperm ploidy we performed individual seed measurements (projected area and mass) using the phenoSeeder robot system and flow cytometric seed screen. In order to test whether individual seed size had an effect on resulting fitness we performed a controlled growth experiment and recorded seedling life history traits (germination success, germination timing, and root growth rate). Seeds with triploid embryos were 33% larger than those with diploid embryos, but no average size difference was found between sexual and apomictic groups. We identified a maternal effect whereby chloroplast lineage 2 had 30% larger seeds than lineage 3, despite having broad and mostly overlapping geographic ranges. Apomictic seeds were not more uniform in size than sexual seeds, despite genetic uniformity of the maternal gametophyte in the former. Among specific embryo/endosperm ploidy combinations, seeds with tetraploid (automomous) endosperm were on average smaller, and the proportion of such seeds was highest in apomicts. Larger seeds germinated more quickly than small seeds, and lead to higher rates of root growth in young seedlings. Seed mass is under balancing selection in Boechera, and it is an important predictor of several traits, including germination probability and timing, root growth rates, and developmental abnormalities in apomictic accessions.
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Affiliation(s)
- Dorota Paczesniak
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
- Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Marco Pellino
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
- Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Richard Goertzen
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
| | - Devan Guenter
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
| | - Siegfried Jahnke
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Jülich, Germany
| | - Andreas Fischbach
- Forschungszentrum Jülich, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Jülich, Germany
| | - John T. Lovell
- Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Timothy F. Sharbel
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SK, Canada
- Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Ojosnegros S, Alvarez JM, Grossmann J, Gagliardini V, Quintanilla LG, Grossniklaus U, Fernández H. The Shared Proteome of the Apomictic Fern Dryopteris affinis ssp. affinis and Its Sexual Relative Dryopteris oreades. Int J Mol Sci 2022; 23:ijms232214027. [PMID: 36430514 PMCID: PMC9693225 DOI: 10.3390/ijms232214027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Ferns are a diverse evolutionary lineage, sister to the seed plants, which is of great ecological importance and has a high biotechnological potential. Fern gametophytes represent one of the simplest autotrophic, multicellular plant forms and show several experimental advantages, including a simple and space-efficient in vitro culture system. However, the molecular basis of fern growth and development has hardly been studied. Here, we report on a proteomic study that identified 417 proteins shared by gametophytes of the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative Dryopteris oreades. Most proteins are predicted to localize to the cytoplasm, the chloroplast, or the nucleus, and are linked to enzymatic, binding, and structural activities. A subset of 145 proteins are involved in growth, reproduction, phytohormone signaling and biosynthesis, and gene expression, including homologs of SHEPHERD (SHD), HEAT SHOCK PROTEIN 90-5 (CR88), TRP4, BOBBER 1 (BOB1), FLAVONE 3'-O-METHYLTRANSFERASE 1 (OMT1), ZEAXANTHIN EPOXIDASE (ABA1), GLUTAMATE DESCARBOXYLASE 1 (GAD), and dsRNA-BINDING DOMAIN-LIKE SUPERFAMILY PROTEIN (HLY1). Nearly 25% of the annotated proteins are associated with responses to biotic and abiotic stimuli. As for biotic stress, the proteins PROTEIN SGT1 HOMOLOG B (SGT1B), SUPPRESSOR OF SA INSENSITIVE2 (SSI2), PHOSPHOLIPASE D ALPHA 1 (PLDALPHA1), SERINE/THREONINE-PROTEIN KINASE SRK2E (OST1), ACYL CARRIER PROTEIN 4 (ACP4), and NONHOST RESISTANCE TO P. S. PHASEOLICOLA1 (GLPK) are worth mentioning. Regarding abiotic stimuli, we found proteins associated with oxidative stress: SUPEROXIDE DISMUTASE[CU-ZN] 1 (CSD1), and GLUTATHIONE S-TRANSFERASE U19 (GSTU19), light intensity SERINE HYDROXYMETHYLTRANSFERASE 1 (SHM1) and UBIQUITIN-CONJUGATING ENZYME E2 35 (UBC35), salt and heavy metal stress included MITOCHONDRIAL PHOSPHATE CARRIER PROTEIN 3 (PHT3;1), as well as drought and thermotolerance: LEA7, DEAD-BOX ATP-DEPENDENT RNA HELICASE 38 (LOS4), and abundant heat-shock proteins and other chaperones. In addition, we identified interactomes using the STRING platform, revealing protein-protein associations obtained from co-expression, co-occurrence, text mining, homology, databases, and experimental datasets. By focusing on ferns, this proteomic study increases our knowledge on plant development and evolution, and may inspire future applications in crop species.
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Affiliation(s)
- Sara Ojosnegros
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
| | - José Manuel Alvarez
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
| | - Jonas Grossmann
- Functional Genomic Center Zurich, University and ETH Zurich, 8092 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8006 Zurich, Switzerland
| | - Luis G. Quintanilla
- Department of Biology and Geology, Physics and Inorganic Chemistry, University Rey Juan Carlos, 28933 Móstoles, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8006 Zurich, Switzerland
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
- Correspondence: ; Tel.: +34-985-104-811
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Paetzold C, Barke BH, Hörandl E. Evolution of Transcriptomes in Early-Generation Hybrids of the Apomictic Ranunculus auricomus Complex ( Ranunculaceae). Int J Mol Sci 2022; 23:ijms232213881. [PMID: 36430360 PMCID: PMC9697309 DOI: 10.3390/ijms232213881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
Hybridisation in plants may cause a shift from sexual to asexual seed formation (apomixis). Indeed, natural apomictic plants are usually hybrids, but it is still unclear how hybridisation could trigger the shift to apomixis. The genome evolution of older apomictic lineages is influenced by diverse processes such as polyploidy, mutation accumulation, and allelic sequence divergence. To disentangle the effects of hybridisation from these other factors, we analysed the transcriptomes of flowering buds from artificially produced, diploid F2 hybrids of the Ranunculus auricomus complex. The hybrids exhibited unreduced embryo sac formation (apospory) as one important component of apomixis, whereas their parental species were sexual. We revealed 2915 annotated single-copy genes that were mostly under purifying selection according to dN/dS ratios. However, pairwise comparisons revealed, after rigorous filtering, 79 genes under diversifying selection between hybrids and parents, whereby gene annotation assigned ten of them to reproductive processes. Four genes belong to the meiosis-sporogenesis phase (ASY1, APC1, MSP1, and XRI1) and represent, according to literature records, candidate genes for apospory. We conclude that hybridisation could combine novel (or existing) mutations in key developmental genes in certain hybrid lineages, and establish (together with altered gene expression profiles, as observed in other studies) a heritable regulatory mechanism for aposporous development.
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Affiliation(s)
- Claudia Paetzold
- Department of Botany and Molecular Evolution, Senckenberg Research Institute, 60325 Frankfurt am Main, Germany
| | - Birthe H. Barke
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Goettingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Goettingen, Germany
- Correspondence:
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