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Gianguzzi V, Di Gristina E, Barone G, Sottile F, Domina G. Seed germination and vegetative and in vitro propagation of Hieracium lucidum subsp. lucidum ( Asteraceae), a critically endangered endemic taxon of the Sicilian flora. PeerJ 2024; 12:e16839. [PMID: 38348103 PMCID: PMC10860557 DOI: 10.7717/peerj.16839] [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: 09/07/2023] [Accepted: 01/05/2024] [Indexed: 02/15/2024] Open
Abstract
Hieracium lucidum subsp. lucidum is a critically endangered endemic taxa of the Sicilian flora. It is a relict of the Tertiary period surviving on the cliffs of Monte Gallo (NW-Sicily). This research focused on finding the best protocols for seed germination and vegetative and in vitro propagation to contribute to ex situ conservation. Seed germination tests were carried out using constant temperatures of 15 °C, 20 °C and 25 °C in continuous darkness and an alternating temperature of 30/15 °C (16 h/8 h, light/dark). The seeds had no dormancy, and a high germination capacity (70-95%) was obtained at all tested thermoperiods. The possibility of vegetative propagation of the taxon was evaluated through the rooting capacity of stem cuttings treated or not treated with indole-3-butyric acid (IBA). All cuttings were treated with IBA rooted within 2 months, while only 50% of the untreated cuttings were rooted within a longer time. An efficient protocol for rapid in vitro propagation from leaf portions was developed. The response of explants was tested on hormone-free Murashige and Skoog (MS) basal medium and MS enriched with different types of cytokinins: 6-Benzylaminopurine (BAP) and meta-Topolin (mT) in combination with naphthaleneacetic acid (NAA) and 2,4-Dichlorophenoxyacetic acid (2,4-D) at the same concentration. The combination of mT (2 mg L-1) and 2,4-D (1 mg L-1) in the medium was the most effective and showed the highest percentage of callus induction and the mean number of regenerated shoots. The maximum rate of root regeneration and the maximum number and length of roots were obtained on hormone-free MS and MS enriched with IBA at concentrations of 1 mg L-1. From the results obtained, it can be concluded that H. lucidum subsp. lucidum can be successfully propagated using one of the tested techniques, subject to the availability of the material for reproduction.
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Affiliation(s)
- Valeria Gianguzzi
- Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Palermo, Italy
| | - Emilio Di Gristina
- Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Palermo, Italy
| | - Giulio Barone
- Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Palermo, Italy
- NBFC, National Biodiversity Future Center, University of Palermo, Palermo, Italy
| | | | - Gianniantonio Domina
- Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Palermo, Italy
- NBFC, National Biodiversity Future Center, University of Palermo, Palermo, Italy
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2
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Bicknell R, Gaillard M, Catanach A, McGee R, Erasmuson S, Fulton B, Winefield C. Genetic mapping of the LOSS OF PARTHENOGENESIS locus in Pilosella piloselloides and the evolution of apomixis in the Lactuceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1239191. [PMID: 37692427 PMCID: PMC10485273 DOI: 10.3389/fpls.2023.1239191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023]
Abstract
Pilosella piloselloides var. praealta (syn. P. praealta; Hieracium praealtum) is a versatile model used to study gametophytic apomixis. In this system apomixis is controlled by three loci: one that controls the avoidance of meiosis (LOA), one that controls the avoidance of fertilization (LOP) and a third that controls autonomous endosperm formation (AutE). Using a unique polyhaploid mapping approach the LOP locus was mapped to a 654 kb genomic interval syntenic to linkage group 8 of Lactuca sativa. Polyhaploids form through the gametophytic action of a dominant determinant at LOP, so the mapped region represents both a functional and a physical domain for LOP in P. piloselloides. Allele sequence divergence (ASD) analysis of the PARTHENOGENESIS (PAR) gene within the LOP locus revealed that dominant PAR alleles in Pilosella remain highly similar across the genus, whilst the recessive alleles are more divergent. A previous report noted that dominant PAR alleles in both Pilosella and Taraxacum are modified by the presence of a class II transposable element (TE) in the promoter of the gene. This observation was confirmed and further extended to the related genus Hieracium. Sufficient differences were noted in the structure and location of the TE elements to conclude that TE insertional events had occurred independently in the three genera. Measures of allele crossover amongst the polyhaploids revealed that P. piloselloides is an autopolyploid species with tetrasomic inheritance. It was also noted that the dominant determinant of LOP in P. piloselloides could transmit via a diploid gamete (pollen or egg) but not via a haploid gamete. Using this information, a model is presented of how gametophytic apomixis may have evolved in several members of the Lactuceae, a tribe of the Asteraceae.
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Affiliation(s)
- Ross Bicknell
- Department of Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Christchurch, New Zealand
| | - Marion Gaillard
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Andrew Catanach
- Department of Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Christchurch, New Zealand
| | - Robert McGee
- Department of Plant Science, McGill University, Lincoln, QC, Canada
| | - Sylvia Erasmuson
- Department of Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Christchurch, New Zealand
| | - Beatrice Fulton
- Department of Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Christchurch, New Zealand
| | - Christopher Winefield
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Canterbury, New Zealand
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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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Loureiro J, Čertner M, Lučanová M, Sliwinska E, Kolář F, Doležel J, Garcia S, Castro S, Galbraith DW. The Use of Flow Cytometry for Estimating Genome Sizes and DNA Ploidy Levels in Plants. Methods Mol Biol 2023; 2672:25-64. [PMID: 37335468 DOI: 10.1007/978-1-0716-3226-0_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Flow cytometry has emerged as a uniquely flexible, accurate, and widely applicable technology for the analysis of plant cells. One of its most important applications centers on the measurement of nuclear DNA contents. This chapter describes the essential features of this measurement, outlining the overall methods and strategies, but going on to provide a wealth of technical details to ensure the most accurate and reproducible results. The chapter is aimed to be equally accessible to experienced plant cytometrists as well as those newly entering the field. Besides providing a step-by-step guide for estimating genome sizes and DNA-ploidy levels from fresh tissues, special attention is paid to the use of seeds and desiccated tissues for such purposes. Methodological aspects regarding field sampling, transport, and storage of plant material are also given in detail. Finally, troubleshooting information for the most common problems that may arise during the application of these methods is provided.
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Affiliation(s)
- João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Magdalena Lučanová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Bydgoszcz, Poland
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC, Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - David W Galbraith
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA
- Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Kaifeng, China
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Fehrer J, Bertrand YJK, Hartmann M, Caklová P, Josefiová J, Bräutigam S, Chrtek J. A Multigene Phylogeny of Native American Hawkweeds ( Hieracium Subgen. Chionoracium, Cichorieae, Asteraceae): Origin, Speciation Patterns, and Migration Routes. PLANTS (BASEL, SWITZERLAND) 2022; 11:2584. [PMID: 36235450 PMCID: PMC9571344 DOI: 10.3390/plants11192584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Native American hawkweeds are mainly mountainous species that are distributed all over the New World. They are severely understudied with respect to their origin, colonization of the vast distribution area, and species relationships. Here, we attempt to reconstruct the evolutionary history of the group by applying seven molecular markers (plastid, nuclear ribosomal and low-copy genes). Phylogenetic analyses revealed that Chionoracium is a subgenus of the mainly Eurasian genus Hieracium, which originated from eastern European hawkweeds about 1.58-2.24 million years ago. Plastid DNA suggested a single origin of all Chionoracium species. They colonized the New World via Beringia and formed several distinct lineages in North America. Via one Central American lineage, the group colonized South America and radiated into more than a hundred species within about 0.8 million years, long after the closure of the Isthmus of Panama and the most recent uplift of the Andes. Despite some incongruences shown by different markers, most of them revealed the same crown groups of closely related taxa, which were, however, largely in conflict with traditional sectional classifications. We provide a basic framework for further elucidation of speciation patterns. A thorough taxonomic revision of Hieracium subgen. Chionoracium is recommended.
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Affiliation(s)
- Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | - Yann J. K. Bertrand
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | - Matthias Hartmann
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
- Department of Geobotany & Botanical Garden, Institute of Biology, Martin Luther University Halle-Wittenberg, 06108 Halle (Saale), Germany
- Thünen Institute of Biodiversity, Bundesallee 65, 38116 Braunschweig, Germany
| | - Petra Caklová
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | - Jiřina Josefiová
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | | | - Jindřich Chrtek
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, 12801 Prague, Czech Republic
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6
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Fairbanks DJ. Demystifying the mythical Mendel: a biographical review. Heredity (Edinb) 2022; 129:4-11. [PMID: 35414696 DOI: 10.1038/s41437-022-00526-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/10/2022] [Indexed: 11/09/2022] Open
Abstract
Gregor Mendel is widely recognised as the founder of genetics. His experiments led him to devise an enduring theory, often distilled into what are now known as the principles of segregation and independent assortment. Although he clearly articulated these principles, his theory is considerably richer, encompassing the nature of fertilisation, the role of hybridisation in evolution, and aspects often considered as exceptions or extensions, such as pleiotropy, incomplete dominance, and epistasis. In an admirable attempt to formulate a more expansive theory, he researched hybridisation in at least twenty plant genera, intentionally choosing some species whose inheritance he knew would deviate from the patterns he observed in the garden pea (Pisum sativum). Regrettably, he published the results of only a few of these additional experiments; evidence of them is largely confined to letters he wrote to Carl von Nägeli. Because most original documentation is lost or destroyed, scholars have attempted to reconstruct his history and achievements from fragmentary evidence, a situation that has led to unfortunate omissions, errors, and speculations. These range from historical uncertainties, such as what motivated his experiments, to unfounded suppositions regarding his discoveries, including assertions that he never articulated the principles ascribed to him, staunchly opposed Darwinism, fictitiously recounted experiments, and falsified data to better accord with his theory. In this review, I have integrated historical and scientific evidence within a biographical framework to dispel misconceptions and provide a clearer and more complete view of who Mendel was and what he accomplished.
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Sailer C, Tiberi S, Schmid B, Stöcklin J, Grossniklaus U. Apomixis and genetic background affect distinct traits in Hieracium pilosella L. grown under competition. BMC Biol 2021; 19:177. [PMID: 34454477 PMCID: PMC8403437 DOI: 10.1186/s12915-021-01117-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Apomixis, the asexual reproduction through seeds, occurs in over 40 plant families and avoids the hidden cost of sex. Apomictic plants are thought to have an advantage in sparse populations and when colonizing new areas but may have a disadvantage in changing environments because they propagate via fixed genotypes. In this study, we separated the influences of different genetic backgrounds (potentially reflecting local adaptation) from those of the mode of reproduction, i.e., sexual vs. apomictic, on nine fitness-related traits in Hieracium pilosella L. We aimed to test whether apomixis per se may provide a fitness advantage in different competitive environments in a common garden setting. RESULTS To separate the effects of genetic background from those of reproductive mode, we generated five families of apomictic and sexual full siblings by crossing two paternal with four maternal parents. Under competition, apomictic plants showed reproductive assurance (probability of seeding, fertility), while offspring of sexual plants with the same genetic background had a higher germination rate. Sexual plants grew better (biomass) than apomictic plants in the presence of grass as a competitor but apomictic plants spread further vegetatively (maximum stolon length) when their competitors were sexual plants of the same species. Furthermore, genetic background as represented by the five full-sibling families influenced maximum stolon length, the number of seeds, and total fitness. Under competition with grass, genetic background influenced fecundity, the number of seeds, and germination rate. CONCLUSIONS Our results suggest that both the mode of reproduction as well as the genetic background affect the success of H. pilosella in competitive environments. Total fitness, the most relevant trait for adaptation, was only affected by the genetic background. However, we also show for the first time that apomixis per se has effects on fitness-related traits that are not confounded by-and thus independent of-the genetic background.
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Affiliation(s)
- Christian Sailer
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich, University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Current address: Institute of Biomedical Informatics, Graz University of Technology, Streymayergasse 16, 8010, Graz, Austria
| | - Simone Tiberi
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Bernhard Schmid
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich, University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Department of Geography, University of Zurich, Winterthurerstrasse 190, 8075, Zurich, Switzerland
| | - Jürg Stöcklin
- Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich, University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.,Institute of Botany, University of Basel, Schönbeinstrasse 6, 4056, Basel, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland. .,Zurich-Basel Plant Science Center, University of Zurich, ETH Zurich, University of Basel, Tannenstrasse 1, 8092, Zurich, Switzerland.
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Mráz P, Mrázová V. Greater reproductive assurance of asexual plant compared with sexual relative in a low-density sympatric population: Experimental evidence for pollen limitation. J Evol Biol 2021; 34:1503-1509. [PMID: 34331325 DOI: 10.1111/jeb.13910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/07/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022]
Abstract
High reproductive assurance is regarded as a key advantage of uniparentally reproducing organisms for establishing a new population. This demographic benefit should especially be relevant for plants with autonomous apomixis, that is those which produce seeds completely independently from mates and pollinators. Indeed, many autonomous apomicts occupy larger distributional ranges when compared to their sexual relatives, showing geographical parthenogenesis patterns. However, uniparental reproduction advantage has only rarely been quantified in natural populations and results provided a mixed support, partly because allopatric sexual and asexual populations were exposed to different environmental and pollination conditions causing considerable between-population variation in the level of reproductive assurance. Here, we compared the level and stability of reproductive assurance between sexual self-incompatible and asexual autonomously apomictic plants of Hieracium alpinum (Asteraceae) cultivated in a sympatric low-density population with two levels of spatial clumping of sexual plants. Overall, we found that the realized seed set (i.e. proportion of well-developed seeds per capitulum) of asexuals was ca. 3 times greater than that of sexuals (83% vs. 27%), whereas the variance of this trait expressed as coefficient of variation was ca. 4 times smaller in asexuals compared with sexuals (19% vs. 83%). Solitary sexual plants had more than 2 times lower realized seed set when compared to clumps composed of two spatially close (20-30 cm) sexual plants (13% vs. 34%). Our study provides experimental evidence for benefit of uniparental reproduction of asexuals in a sympatric situation when the availability of mates is limited. This, together with unpredictability of pollinator environment could provide autonomous apomicts with an ultimate demographic superiority during colonization reflected in geographical parthenogenesis observed in this species.
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Affiliation(s)
- Patrik Mráz
- Herbarium Collections and Department of Botany, Charles University, Praha, Czechia
| | - Viera Mrázová
- Herbarium Collections and Department of Botany, Charles University, Praha, Czechia
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Astuti G, Barone G, Di Gristina E, Domina G, Giacò A, Orsenigo S, Peruzzi L. Chromosome numbers for the Italian flora: 11. ITALIAN BOTANIST 2021. [DOI: 10.3897/italianbotanist.11.70173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this contribution, new chromosome data obtained on material collected in Italy are presented. It includes counts for Centaurea aegusae, Hieracium racemosum subsp. lucanum, H. australe subsp. australe, Lysimachia arvensis subsp. arvensis, Micromeria graeca subsp. graeca, and M. graeca subsp. consentina.
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10
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Fehrer J, Slavíková R, Paštová L, Josefiová J, Mráz P, Chrtek J, Bertrand YJK. Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae). FRONTIERS IN PLANT SCIENCE 2021; 12:647375. [PMID: 33777082 PMCID: PMC7994888 DOI: 10.3389/fpls.2021.647375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 05/14/2023]
Abstract
Molecular evolution of ribosomal DNA can be highly dynamic. Hundreds to thousands of copies in the genome are subject to concerted evolution, which homogenizes sequence variants to different degrees. If well homogenized, sequences are suitable for phylogeny reconstruction; if not, sequence polymorphism has to be handled appropriately. Here we investigate non-coding rDNA sequences (ITS/ETS, 5S-NTS) along with the chromosomal organization of their respective loci (45S and 5S rDNA) in diploids of the Hieraciinae. The subtribe consists of genera Hieracium, Pilosella, Andryala, and Hispidella and has a complex evolutionary history characterized by ancient intergeneric hybridization, allele sharing among species, and incomplete lineage sorting. Direct or cloned Sanger sequences and phased alleles derived from Illumina genome sequencing were subjected to phylogenetic analyses. Patterns of homogenization and tree topologies based on the three regions were compared. In contrast to most other plant groups, 5S-NTS sequences were generally better homogenized than ITS and ETS sequences. A novel case of ancient intergeneric hybridization between Hispidella and Hieracium was inferred, and some further incongruences between the trees were found, suggesting independent evolution of these regions. In some species, homogenization of ITS/ETS and 5S-NTS sequences proceeded in different directions although the 5S rDNA locus always occurred on the same chromosome with one 45S rDNA locus. The ancestral rDNA organization in the Hieraciinae comprised 4 loci of 45S rDNA in terminal positions and 2 loci of 5S rDNA in interstitial positions per diploid genome. In Hieracium, some deviations from this general pattern were found (3, 6, or 7 loci of 45S rDNA; three loci of 5S rDNA). Some of these deviations concerned intraspecific variation, and most of them occurred at the tips of the tree or independently in different lineages. This indicates that the organization of rDNA loci is more dynamic than the evolution of sequences contained in them and that locus number is therefore largely unsuitable to inform about species relationships in Hieracium. No consistent differences in the degree of sequence homogenization and the number of 45S rDNA loci were found, suggesting interlocus concerted evolution.
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Affiliation(s)
- Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- *Correspondence: Judith Fehrer,
| | - Renáta Slavíková
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | | | - Jiřina Josefiová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Patrik Mráz
- Department of Botany, Charles University, Prague, Czechia
| | - Jindřich Chrtek
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Charles University, Prague, Czechia
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11
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Zagorski D, Hartmann M, Bertrand YJK, Paštová L, Slavíková R, Josefiová J, Fehrer J. Characterization and Dynamics of Repeatomes in Closely Related Species of Hieracium (Asteraceae) and Their Synthetic and Apomictic Hybrids. FRONTIERS IN PLANT SCIENCE 2020; 11:591053. [PMID: 33224172 PMCID: PMC7667050 DOI: 10.3389/fpls.2020.591053] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/09/2020] [Indexed: 05/05/2023]
Abstract
The repetitive content of the plant genome (repeatome) often represents its largest fraction and is frequently correlated with its size. Transposable elements (TEs), the main component of the repeatome, are an important driver in the genome diversification due to their fast-evolving nature. Hybridization and polyploidization events are hypothesized to induce massive bursts of TEs resulting, among other effects, in an increase of copy number and genome size. Little is known about the repeatome dynamics following hybridization and polyploidization in plants that reproduce by apomixis (asexual reproduction via seeds). To address this, we analyzed the repeatomes of two diploid parental species, Hieracium intybaceum and H. prenanthoides (sexual), their diploid F1 synthetic and their natural triploid hybrids (H. pallidiflorum and H. picroides, apomictic). Using low-coverage next-generation sequencing (NGS) and a graph-based clustering approach, we detected high overall similarity across all major repeatome categories between the parental species, despite their large phylogenetic distance. Medium and highly abundant repetitive elements comprise ∼70% of Hieracium genomes; most prevalent were Ty3/Gypsy chromovirus Tekay and Ty1/Copia Maximus-SIRE elements. No TE bursts were detected, neither in synthetic nor in natural hybrids, as TE abundance generally followed theoretical expectations based on parental genome dosage. Slight over- and under-representation of TE cluster abundances reflected individual differences in genome size. However, in comparative analyses, apomicts displayed an overabundance of pararetrovirus clusters not observed in synthetic hybrids. Substantial deviations were detected in rDNAs and satellite repeats, but these patterns were sample specific. rDNA and satellite repeats (three of them were newly developed as cytogenetic markers) were localized on chromosomes by fluorescence in situ hybridization (FISH). In a few cases, low-abundant repeats (5S rDNA and certain satellites) showed some discrepancy between NGS data and FISH results, which is due partly to the bias of low-coverage sequencing and partly to low amounts of the satellite repeats or their sequence divergence. Overall, satellite DNA (including rDNA) was markedly affected by hybridization, but independent of the ploidy or reproductive mode of the progeny, whereas bursts of TEs did not play an important role in the evolutionary history of Hieracium.
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12
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Scheben A, Hojsgaard D. Can We Use Gene-Editing to Induce Apomixis in Sexual Plants? Genes (Basel) 2020; 11:E781. [PMID: 32664641 PMCID: PMC7397034 DOI: 10.3390/genes11070781] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/12/2022] Open
Abstract
Apomixis, the asexual formation of seeds, is a potentially valuable agricultural trait. Inducing apomixis in sexual crop plants would, for example, allow breeders to fix heterosis in hybrid seeds and rapidly generate doubled haploid crop lines. Molecular models explain the emergence of functional apomixis, i.e., apomeiosis + parthenogenesis + endosperm development, as resulting from a combination of genetic or epigenetic changes that coordinate altered molecular and developmental steps to form clonal seeds. Apomixis-like features and synthetic clonal seeds have been induced with limited success in the sexual plants rice and maize by using gene editing to mutate genes related to meiosis and fertility or via egg-cell specific expression of embryogenesis genes. Inducing functional apomixis and increasing the penetrance of apomictic seed production will be important for commercial deployment of the trait. Optimizing the induction of apomixis with gene editing strategies that use known targets as well as identifying alternative targets will be possible by better understanding natural genetic variation in apomictic species. With the growing availability of genomic data and precise gene editing tools, we are making substantial progress towards engineering apomictic crops.
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Affiliation(s)
- Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA;
| | - Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Untere Karspuele 2, 37073 Goettingen, Germany
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Chrtek J, Mráz P, Belyayev A, Paštová L, Mrázová V, Caklová P, Josefiová J, Zagorski D, Hartmann M, Jandová M, Pinc J, Fehrer J. Evolutionary history and genetic diversity of apomictic allopolyploids in Hieracium s.str.: morphological versus genomic features. AMERICAN JOURNAL OF BOTANY 2020; 107:66-90. [PMID: 31903548 DOI: 10.1002/ajb2.1413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 11/13/2019] [Indexed: 05/02/2023]
Abstract
PREMISE The origin of allopolyploids is believed to shape their evolutionary potential, ecology, and geographical ranges. Morphologically distinct apomictic types sharing the same parental species belong to the most challenging groups of polyploids. We evaluated the origins and variation of two triploid taxa (Hieracium pallidiflorum, H. picroides) presumably derived from the same diploid parental pair (H. intybaceum, H. prenanthoides). METHODS We used a suite of approaches ranging from morphological, phylogenetic (three unlinked molecular markers), and cytogenetic analyses (in situ hybridization) to genome size screening and genome skimming. RESULTS Genotyping proved the expected parentage of all analyzed accessions of H. pallidiflorum and H. picroides and revealed that nearly all of them originated independently. Genome sizes and genome dosage largely corresponded to morphology, whereas the maternal origin of the allopolyploids had no discernable effect. Polyploid accessions of both parental species usually contained genetic material from other species. Given the phylogenetic distance of the parents, their chromosomes appeared only weakly differentiated in genomic in situ hybridization (GISH), as well as in overall comparisons of the repetitive fraction of their genomes. Furthermore, the repeatome of a phylogenetically more closely related species (H. umbellatum) differed significantly more. CONCLUSIONS We proved (1) multiple origins of hybridogeneous apomicts from the same diploid parental taxa, and (2) allopolyploid origins of polyploid accessions of the parental species. We also showed that the evolutionary dynamics of very fast evolving markers such as satellite DNA or transposable elements does not necessarily follow patterns of speciation.
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Affiliation(s)
- Jindřich Chrtek
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Patrik Mráz
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Alexander Belyayev
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Ladislava Paštová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Viera Mrázová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Petra Caklová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Jiřina Josefiová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Danijela Zagorski
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Matthias Hartmann
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Michaela Jandová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Jan Pinc
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Judith Fehrer
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
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