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Kessler M, Aros-Mualin D. The power of independent generations in plants. THE NEW PHYTOLOGIST 2024. [PMID: 39329429 DOI: 10.1111/nph.20162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Affiliation(s)
- Michael Kessler
- Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Daniela Aros-Mualin
- Department of Botany and Plant Pathology, Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
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2
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Bureš P, Del Guacchio E, Šmerda J, Özcan M, Blizňáková P, Vavrinec M, Michálková E, Veselý P, Veselá K, Zedek F. Intergeneric hybrid origin of the invasive tetraploid Cirsium vulgare. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:749-763. [PMID: 38704835 DOI: 10.1111/plb.13653] [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: 10/25/2023] [Accepted: 04/09/2024] [Indexed: 05/07/2024]
Abstract
The invasive tetraploid Cirsium vulgare hybridizes with both Cirsium and Lophiolepis. Its conflicted position in molecular phylogenies, and its peculiar combination of morphological, anatomical, and genomic features that are alternatively shared with representatives of Cirsium or Lophiolepis, strongly suggest its intergeneric hybrid origin. Genetic relationships of C. vulgare (8 samples) with genus Lophiolepis (11 species) and other representatives of genus Cirsium (12 species) were evaluated using restriction site-associated DNA sequencing (RADseq) and examined using analytical and imaging approaches, such as NeighborNet, Heatmap, and STRUCTURE, to identify nuclear genomes admixture. Estimation of the intensity of spontaneous hybridization within and between Cirsium and Lophiolepis was based on herbarium revisions and published data for all reported hybrids pertinent to taxa currently included in Cirsium or Lophiolepis. The genome of any examined Cirsium species is more similar to C. vulgare than to any Lophiolepis species, and vice versa. The nuclear genome of the tetraploid C. vulgare is composed of two equivalent parts, each attributable either to Lophiolepis or to Cirsium; the organellar RADseq data clustered C. vulgare with the genus Cirsium. Spontaneous hybridization between Cirsium and Lophiolepis is significantly less intensive than within these genera. Our analyses provide compelling evidence that the invasive species C. vulgare has an allotetraploid intergeneric origin, with the maternal parent from Cirsium and the paternal from Lophiolepis. For the purpose of delimiting monophyletic genera, we propose keeping Lophiolepis separate from Cirsium and segregating C. vulgare into the hybridogenous genus Ascalea.
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Affiliation(s)
- P Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - E Del Guacchio
- Department of Biology, University of Naples Federico II, Naples, Italy
- Botanical Garden, University of Naples Federico II, Naples, Italy
| | - J Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - M Özcan
- Faculty of Forestry, Department of Forest Engineering, Artvin Coruh University, Artvin, Türkiye
| | - P Blizňáková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - M Vavrinec
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - E Michálková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - P Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - K Veselá
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - F Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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Han M, Qie Q, Liu M, Meng H, Wu T, Yang Y, Niu L, Sun G, Wang Y. Clonal growth characteristics and diversity patterns of different Clintonia udensis (Liliaceae) diploid and tetraploid cytotypes in the Hualongshan Mountains. Sci Rep 2024; 14:15509. [PMID: 38969683 PMCID: PMC11226640 DOI: 10.1038/s41598-024-66067-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
Polyploidization plays an important role in plant evolution and biodiversity. However, intraspecific polyploidy compared to interspecific polyploidy received less attention. Clintonia udensis (Liliaceae) possess diploid (2n = 2x = 14) and autotetraploid (2n = 4x = 28) cytotypes. In the Hualongshan Mountains, the autotetraploids grew on the northern slope, while the diploids grew on the southern slopes. The clonal growth characteristics and clonal architecture were measured and analyzed by field observations and morphological methods. The diversity level and differentiation patterns for two different cytotypes were investigated using SSR markers. The results showed that the clonal growth parameters, such as the bud numbers of each rhizome node and the ratio of rhizome branches in the autotetraploids were higher than those in the diploids. Both the diploids and autotetraploids appeared phalanx clonal architectures with short internodes between ramets. However, the ramets or genets of the diploids had a relatively scattered distribution, while those of the autotetraploids were relatively clumping. The diploids and autotetraploids all allocated more biomass to their vegetative growth. The diploids had a higher allocation to reproductive organs than that of autotetraploids, which indicated that the tetraploids invested more resources in clonal reproduction than diploids. The clone diversity and genetic diversity of the autotetraploids were higher than that of the diploids. Significant genetic differentiation between two different cytotypes was observed (P < 0.01). During establishment and evolution, C. udensis autotetraploids employed more clumping phalanx clonal architecture and exhibited more genetic variation than the diploids.
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Affiliation(s)
- Mian Han
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Qiyang Qie
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Meilan Liu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Huiqin Meng
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Tiantian Wu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Yadi Yang
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Lingling Niu
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China
| | - Genlou Sun
- Department of Botany, Saint Mary's University, Halifax, NS B3H 3C3, Canada.
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Taiyuan, 030031, China.
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4
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Vanrell MA, Novaes LR, Afonso A, Arroyo J, Simón-Porcar V. Ecological correlates of population genetics in Linum suffruticosum, an heterostylous polyploid and taxonomic complex endemic to the Western Mediterranean Basin. AOB PLANTS 2024; 16:plae027. [PMID: 39005727 PMCID: PMC11244263 DOI: 10.1093/aobpla/plae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 05/20/2024] [Indexed: 07/16/2024]
Abstract
Linum suffruticosum s.l. is a taxonomic complex widespread in the Western Mediterranean basin. The complex is characterized by a high phenotypic and cytogenetic diversity, and by a unique three-dimensional heterostyly system that makes it an obligate outcrosser. We studied the patterns of genetic diversity and structure of populations throughout the entire distribution of L. suffruticosum s.l. with microsatellite markers. We analysed their relationships with various biological and ecological variables, including the morph ratio and sex organ reciprocity of populations measured with a novel multi-dimensional method. Populations consistently showed an approximate 1:1 morph ratio with high sex organ reciprocity and high genetic diversity. We found high genetic differentiation of populations, showing a pattern of isolation by distance. The Rif mountains in NW Africa were the most important genetic barrier. The taxonomic treatment within the group was not related to the genetic differentiation of populations, but to their environmental differentiation. Genetic diversity was unrelated to latitude, elevation, population size, niche suitability or breeding system. However, there was a clear influence of ploidy level on the genetic diversity of populations, and a seeming centre-periphery pattern in its distribution. Our results suggest that polyploidization events, high outcrossing rates, isolation by distance and important geographical barriers to gene flow have played major roles in the microevolutionary history of this species complex.
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Affiliation(s)
- Maria Antònia Vanrell
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Letícia R Novaes
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Ana Afonso
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Juan Arroyo
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012 Seville, Spain
| | - Violeta Simón-Porcar
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, 41012 Seville, Spain
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Choi TY, Son DC, Oh A, Lee SR. Unveiling a potential threat to forest ecosystems: molecular diagnosis of Alliaria petiolata, a newly introduced alien plant in Korea. FRONTIERS IN PLANT SCIENCE 2024; 15:1395676. [PMID: 39011305 PMCID: PMC11246967 DOI: 10.3389/fpls.2024.1395676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Identifying stages of a species invasion in a new habitat (i.e., colonization, establishment, and landscape spread) and their primary determinants in biological invasion warrants attention, as it provides vital insights for preventing non-native species from becoming pervasive invaders. However, delineating invasion stages and their associated factors can pose significant challenges due to the ambiguous distinctions between these stages. Alliaria petiolata, one of the most noxious weeds in woodland habitats, has recently been introduced to Korea and observed in a few distant locations. Although the plant's spread has been relatively slow thus far, rapid spread is highly likely in the future, given the high invasive potential reported elsewhere. We indirectly diagnose the current status of A. petiolata invasion in Korea through the assessment of genetic diversity and phylogenetic inferences using genome-wide molecular markers and cytological data. We analyzed 86 individual samples collected from two native and six introduced populations, employing 1,172 SNPs. Our analysis estimated within- and among-population genetic diversity and included two clustering analyses. Furthermore, we investigated potential gene flow and reticulation events among the sampled populations. Our data unraveled that Korean garlic mustard exhibits a hexaploid ploidy level with two distinct chromosome numbers, 2n = 36 and 42. The extent of genetic diversity measured in Korean populations was comparable to that of native populations. Using genome-wide SNP data, we identified three distinct clusters with minor gene flow, while failing to detect indications of reticulation among Korean populations. Based on the multifaceted analyses, our study provides valuable insights into the colonization process and stressed the importance of closely monitoring A. petiolata populations in Korea.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, Republic of Korea
| | - Ami Oh
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
| | - Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
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6
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Touchette L, Godbout J, Lamothe M, Porth I, Isabel N. A cryptic syngameon within Betula shrubs revealed: Implications for conservation in changing subarctic environments. Evol Appl 2024; 17:e13689. [PMID: 38633131 PMCID: PMC11022622 DOI: 10.1111/eva.13689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 02/06/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Arctic and subarctic ecosystems are rapidly transforming due to global warming, emphasizing the need to understand the genetic diversity and adaptive strategies of northern plant species for effective conservation. This study focuses on Betula glandulosa, a native North American tundra shrub known as dwarf birch, which demonstrates an apparent capacity to adapt to changing climate conditions. To address the taxonomic challenges associated with shrub birches and logistical complexities of sampling in the northernmost areas where species' ranges overlap, we adopted a multicriteria approach. Incorporating molecular data, ploidy level assessment and leaf morphology, we aimed to distinguish B. glandulosa individuals from other shrub birch species sampled. Our results revealed three distinct species and their hybrids within the 537 collected samples, suggesting the existence of a shrub birch syngameon, a reproductive network of interconnected species. Additionally, we identified two discrete genetic clusters within the core species, B. glandulosa, that likely correspond to two different glacial lineages. A comparison between the nuclear and chloroplast SNP data emphasizes a long history of gene exchange between different birch species and genetic clusters. Furthermore, our results highlight the significance of incorporating interfertile congeneric species in conservation strategies and underscores the need for a holistic approach to conservation in the context of climate change, considering the complex dynamics of species interactions. While further research will be needed to describe this shrub birches syngameon and its constituents, this study is a first step in recognizing its existence and disseminating awareness among ecologists and conservation practitioners. This biological phenomenon, which offers evolutionary flexibility and resilience beyond what its constituent species can achieve individually, may have significant ecological implications.
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Affiliation(s)
- Lyne Touchette
- Department of Wood and Forest SciencesUniversité LavalQuebecQuebecCanada
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
| | - Julie Godbout
- Ministère des Ressources naturelles et des Forêts, Direction de la recherche forestièreQuébecQuébecCanada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
| | - Ilga Porth
- Department of Wood and Forest SciencesUniversité LavalQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest ServiceLaurentian Forestry CentreQuebecQuebecCanada
- Centre for Forest ResearchUniversité LavalQuebecQuebecCanada
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Lopes JML, Nascimento LSDQ, Souza VC, de Matos EM, Fortini EA, Grazul RM, Santos MO, Soltis DE, Soltis PS, Otoni WC, Viccini LF. Water stress modulates terpene biosynthesis and morphophysiology at different ploidal levels in Lippia alba (Mill.) N. E. Brown (Verbenaceae). PROTOPLASMA 2024; 261:227-243. [PMID: 37665420 DOI: 10.1007/s00709-023-01890-2] [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: 02/27/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Monoterpenes are the main component in essential oils of Lippia alba. In this species, the chemical composition of essential oils varies with genome size: citral (geraniol and neral) is dominant in diploids and tetraploids, and linalool in triploids. Because environmental stress impacts various metabolic pathways, we hypothesized that stress responses in L. alba could alter the relationship between genome size and essential oil composition. Water stress affects the flowering, production, and reproduction of plants. Here, we evaluated the effect of water stress on morphophysiology, essential oil production, and the expression of genes related to monoterpene synthesis in diploid, triploid, and tetraploid accessions of L. alba cultivated in vitro for 40 days. First, using transcriptome data, we performed de novo gene assembly and identified orthologous genes using phylogenetic and clustering-based approaches. The expression of candidate genes related to terpene biosynthesis was estimated by real-time quantitative PCR. Next, we assessed the expression of these genes under water stress conditions, whereby 1% PEG-4000 was added to MS medium. Water stress modulated L. alba morphophysiology at all ploidal levels. Gene expression and essential oil production were affected in triploid accessions. Polyploid accessions showed greater growth and metabolic tolerance under stress compared to diploids. These results confirm the complex regulation of metabolic pathways such as the production of essential oils in polyploid genomes. In addition, they highlight aspects of genotype and environment interactions, which may be important for the conservation of tropical biodiversity.
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Affiliation(s)
- Juliana Mainenti Leal Lopes
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
- School of Life Science and Environment, Department of Genetic and Biotechnology, University of Trás-Os-Montes and Alto Douro, 5001-801, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1649-004, Lisbon, Portugal
| | | | - Vinicius Carius Souza
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Elyabe Monteiro de Matos
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Evandro Alexandre Fortini
- Laboratory of Plant Tissue Culture (LCTII), Department of Plant Biology/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs S/N, Campus Universitário, Viçosa, MG, 36570-000, Brazil
| | | | - Marcelo Oliveira Santos
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Wagner Campos Otoni
- Laboratory of Plant Tissue Culture (LCTII), Department of Plant Biology/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs S/N, Campus Universitário, Viçosa, MG, 36570-000, Brazil
| | - Lyderson Facio Viccini
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil.
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Wefferling KM, Castro M, Castro S, Holmlund H, Loureiro J, Rothfels CJ, Schuettpelz E. Polyploid goldback and silverback ferns (Pentagramma) occupy a wider, colder, and wetter bioclimatic niche than diploid counterparts. AMERICAN JOURNAL OF BOTANY 2024; 111:e16305. [PMID: 38517199 DOI: 10.1002/ajb2.16305] [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: 08/22/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 03/23/2024]
Abstract
PREMISE The western North American fern genus Pentagramma (Pteridaceae) is characterized by complex patterns of ploidy variation, an understanding of which is critical to comprehending both the evolutionary processes within the genus and its current diversity. METHODS We undertook a cytogeographic study across the range of the genus, using a combination of chromosome counts and flow cytometry to infer ploidy level. Bioclimatic variables and elevation were used to compare niches. RESULTS We found that diploids and tetraploids are common and widespread, and triploids are rare and sporadic; in contrast with genome size inferences in earlier studies, no hexaploids were found. Diploids and tetraploids show different geographic ranges: only tetraploids were found in the northernmost portion of the range (Washington, Oregon, and British Columbia) and only diploids were found in the Sierra Nevada of California. Diploid, triploid, and tetraploid cytotypes were found to co-occur in relatively few localities: in the southern (San Diego County, California) and desert Southwest (Arizona) parts of the range, and along the Pacific Coast of California. CONCLUSIONS Tetraploids occupy a wider bioclimatic niche than diploids both within P. triangularis and at the genus-wide scale. It is unknown whether the wider niche of tetraploids is due to their expansion upon the diploid niche, if diploids have contracted their niche due to competition or changing abiotic conditions, or if this wider niche occupancy is due to multiple origins of tetraploids.
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Affiliation(s)
- Keir M Wefferling
- Department of Biology, Gary A. Fewless Herbarium, Cofrin Center for Biodiversity, University of Wisconsin-Green Bay, Green Bay, 54311, Wisconsin, USA
| | - Mariana Castro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Sílvia Castro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Helen Holmlund
- Natural Science Division, Pepperdine University, Malibu, 90263, California, USA
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | - Carl J Rothfels
- Department of Biology, Ecology Center, and Intermountain Herbarium, Utah State University, Logan, 84322, Utah, USA
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, 20560, DC, USA
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Yadav S, Ross EM, Wei X, Liu S, Nguyen LT, Powell O, Hickey LT, Deomano E, Atkin F, Voss-Fels KP, Hayes BJ. Use of continuous genotypes for genomic prediction in sugarcane. THE PLANT GENOME 2024; 17:e20417. [PMID: 38066702 DOI: 10.1002/tpg2.20417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 03/22/2024]
Abstract
Genomic selection in sugarcane faces challenges due to limited genomic tools and high genomic complexity, particularly because of its high and variable ploidy. The classification of genotypes for single nucleotide polymorphisms (SNPs) becomes difficult due to the wide range of possible allele dosages. Previous genomic studies in sugarcane used pseudo-diploid genotyping, grouping all heterozygotes into a single class. In this study, we investigate the use of continuous genotypes as a proxy for allele-dosage in genomic prediction models. The hypothesis is that continuous genotypes could better reflect allele dosage at SNPs linked to mutations affecting target traits, resulting in phenotypic variation. The dataset included genotypes of 1318 clones at 58K SNP markers, with about 26K markers filtered using standard quality controls. Predictions for tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and fiber content (Fiber) were made using parametric, non-parametric, and Bayesian methods. Continuous genotypes increased accuracy by 5%-7% for CCS and Fiber. The pseudo-diploid parametrization performed better for TCH. Reproducing kernel Hilbert spaces model with Gaussian kernel and AK4 (arc-cosine kernel with hidden layer 4) kernel outperformed other methods for TCH and CCS, suggesting that non-additive effects might influence these traits. The prevalence of low-dosage markers in the study may have limited the benefits of approximating allele-dosage information with continuous genotypes in genomic prediction models. Continuous genotypes simplify genomic prediction in polyploid crops, allowing additional markers to be used without adhering to pseudo-diploid inheritance. The approach can particularly benefit high ploidy species or emerging crops with unknown ploidy.
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Affiliation(s)
- Seema Yadav
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Xianming Wei
- Sugar Research Australia, Mackay, Queensland, Australia
| | - Shouye Liu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Loan To Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Owen Powell
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
| | - Emily Deomano
- Sugar Research Australia, Indooroopilly, Queensland, Australia
| | - Felicity Atkin
- Sugar Research Australia, Meringa Gordonvale, Queensland, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
- Department of Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia
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10
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Qian ZH, Li W, Wang QF, Liang SC, Wu S, Li ZZ, Chen JM. The chromosome-level genome of the submerged plant Cryptocoryne crispatula provides insights into the terrestrial-freshwater transition in Araceae. DNA Res 2024; 31:dsae003. [PMID: 38245835 PMCID: PMC10873505 DOI: 10.1093/dnares/dsae003] [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: 11/14/2023] [Revised: 12/27/2023] [Accepted: 01/18/2024] [Indexed: 01/22/2024] Open
Abstract
Plant terrestrialization (i.e. the transition to a terrestrial environment) is a significant evolutionary event that has been intensively studied. While certain plant lineages, particularly in angiosperms, have re-adapted to freshwater habitats after colonizing terrene, however, the molecular mechanism of the terrestrial-freshwater (T-F) transition remains limited. Here, the basal monocot Araceae was selected as the study object to explore the T-F transition adaptation mechanism by comparative genomic analysis. Our findings revealed that the substitution rates significantly increased in the lineage of freshwater Araceae, which may promote their adaptation to the freshwater habitat. Additionally, 20 gene sets across all four freshwater species displayed signs of positive selection contributing to tissue development and defense responses in freshwater plants. Comparative synteny analysis showed that genes specific to submerged plants were enriched in cellular respiration and photosynthesis. In contrast, floating plants were involved in regulating gene expression, suggesting that gene and genome duplications may provide the original material for plants to adapt to the freshwater environment. Our study provides valuable insights into the genomic aspects of the transition from terrestrial to aquatic environments in Araceae, laying the groundwork for future research in the angiosperm.
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Affiliation(s)
- Zhi-Hao Qian
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qing-Feng Wang
- Plant Diversity Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Shi-Chu Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China
| | - Shuang Wu
- Guangxi Association for Science and Technology, Nanning 530023, China
| | - Zhi-Zhong Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jin-Ming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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11
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Yoo MJ, Koh J, Boatwright JL, Soltis DE, Soltis PS, Barbazuk WB, Chen S. Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1191-1205. [PMID: 37997015 DOI: 10.1111/tpj.16553] [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: 08/10/2023] [Revised: 10/02/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. Here, we compared the leaf transcriptomes of recently formed natural allotetraploids (Tragopogon mirus and T. miscellus) and their diploid parents (T. porrifolius X T. dubius and T. pratensis X T. dubius, respectively). Analysis of 35 400 expressed loci showed a significantly higher level of transcriptomic additivity compared to old polyploids; only 22% were non-additively expressed in the polyploids, with 5.9% exhibiting transgressive expression (lower or higher expression in the polyploids than in the diploid parents). Among approximately 7400 common orthologous regions (COREs), most loci in both allopolyploids exhibited expression patterns that were vertically inherited from their diploid parents. However, 18% and 20.3% of the loci showed novel expression bias patterns in T. mirus and T. miscellus, respectively. The expression changes of 1500 COREs were explained by cis-regulatory divergence (the condition in which the two parental subgenomes do not interact) between the diploid parents, whereas only about 423 and 461 of the gene expression changes represent trans-effects (the two parental subgenomes interact) in T. mirus and T. miscellus, respectively. The low degree of both non-additivity and trans-effects on gene expression may present the ongoing evolutionary processes of the newly formed Tragopogon polyploids (~80-90 years).
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, New York, 13699, USA
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, USA
| | - J Lucas Boatwright
- Plant and Environmental Science Department, Clemson University, Clemson, South Carolina, 29634, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Pamela S Soltis
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, Mississippi, 38677, USA
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12
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da Cunha TB, de Sousa SM, Reis AC, de Matos EM, Viccini LF. Synthetic Tetraploid of Oncidium crispum Lodd. (Orchidaceae). Methods Mol Biol 2024; 2827:267-278. [PMID: 38985276 DOI: 10.1007/978-1-0716-3954-2_18] [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] [Indexed: 07/11/2024]
Abstract
In ornamental plants, artificial polyploidization has enabled the creation of new cultivars. Due to their high commercial value in the international flower market and their ornamental characteristics, such as the shape, size, color, and durability of their flower, orchids have received great attention in studies of artificial polyploidization. Here we described the protocol used for polyploid induction in Oncidium crispum, an epiphyte species native of southeastern Brazil, of great ornamental interest and widely sold in flower shops. The species stands out for having inflorescence with large flowers, brown in color with yellow spots. In addition, O. crispum has great potential for use in genetic improvement programs since the species is widely used in interspecific crosses. Closed capsules containing mature O. crispum seeds were subjected to running sterilized water for 10 min and then to a 1.5% sodium hypochlorite solution for 10 min. Small portions of seeds were introduced into 50 mL of water-soluble fertilizer with macro- and micronutrients (B>M) plus 0.7% agar. Explants originating from seeds previously in vitro germinated were submitted to 0.05% and 0.1% of colchicine for 4 days and 8 days. Flow cytometry and chromosome counts confirmed that the protocol successfully produced synthetic polyploid plants.
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Affiliation(s)
- Thalita Bordignon da Cunha
- Departamento de Biologia, Laboratório de Genética e Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Saulo Marçal de Sousa
- Departamento de Biologia, Laboratório de Genética e Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Aryane Campos Reis
- Departamento de Biologia, Laboratório de Genética e Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Elyabe Monteiro de Matos
- Departamento de Biologia, Laboratório de Genética e Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Lyderson Facio Viccini
- Departamento de Biologia, Laboratório de Genética e Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil.
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13
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Gruet C, Alaoui M, Gerin F, Prigent-Combaret C, Börner A, Muller D, Moënne-Loccoz Y. Genomic content of wheat has a higher influence than plant domestication status on the ability to interact with Pseudomonas plant growth-promoting rhizobacteria. PLANT, CELL & ENVIRONMENT 2023; 46:3933-3948. [PMID: 37614118 DOI: 10.1111/pce.14698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Plant evolutionary history has had profound effects on belowground traits, which is likely to have impacted the ability to interact with microorganisms, but consequences on root colonization and gene expression by plant growth-promoting rhizobacteria (PGPR) remain poorly understood. Here, we tested the hypothesis that wheat genomic content and domestication are key factors determining the capacity for PGPR interaction. Thus, 331 wheat representatives from eight Triticum or Aegilops species were inoculated under standardized conditions with the generalist PGPR Pseudomonas ogarae F113, using an autofluorescent reporter system for monitoring F113 colonization and expression of phl genes coding for the auxinic inducing signal 2,4-diacetylphloroglucinol. The interaction with P. ogarae F113 was influenced by ploidy level, presence of genomes AA, BB, DD, and domestication. While root colonization was higher for hexaploid and tetraploid species, and phl expression level higher for hexaploid wheat, the diploid Ae. tauschii displayed higher phl induction rate (i.e., expression:colonisation ratio) on roots. However, a better potential of interaction with F113 (i.e., under non-stress gnotobiotic conditions) did not translate, after seed inoculation, into better performance of wheat landraces in non-sterile soil under drought. Overall, results showed that domestication and especially plant genomic content modulate the PGPR interaction potential of wheats.
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Affiliation(s)
- Cécile Gruet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Maroua Alaoui
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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14
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Yew CL, Tsuchimatsu T, Shimizu-Inatsugi R, Yasuda S, Hatakeyama M, Kakui H, Ohta T, Suwabe K, Watanabe M, Takayama S, Shimizu KK. Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility. Nat Commun 2023; 14:7618. [PMID: 38030610 PMCID: PMC10687001 DOI: 10.1038/s41467-023-43275-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Abstract
The evolutionary transition to self-compatibility facilitates polyploid speciation. In Arabidopsis relatives, the self-incompatibility system is characterized by epigenetic dominance modifiers, among which small RNAs suppress the expression of a recessive SCR/SP11 haplogroup. Although the contribution of dominance to polyploid self-compatibility is speculated, little functional evidence has been reported. Here we employ transgenic techniques to the allotetraploid plant A. kamchatica. We find that when the dominant SCR-B is repaired by removing a transposable element insertion, self-incompatibility is restored. This suggests that SCR was responsible for the evolution of self-compatibility. By contrast, the reconstruction of recessive SCR-D cannot restore self-incompatibility. These data indicate that the insertion in SCR-B conferred dominant self-compatibility to A. kamchatica. Dominant self-compatibility supports the prediction that dominant mutations increasing selfing rate can pass through Haldane's sieve against recessive mutations. The dominance regulation between subgenomes inherited from progenitors contrasts with previous studies on novel epigenetic mutations at polyploidization termed genome shock.
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Grants
- JPMJCR16O3 MEXT | JST | Core Research for Evolutional Science and Technology (CREST)
- 310030_212551, 31003A_182318, 31003A_159767, 31003A_140917, 310030_212674 Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
- 310030_212674 Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
- grant numbers 16H06469, 16K21727, 22H02316, 22K21352, 22H05172 and 22H05179 MEXT | Japan Society for the Promotion of Science (JSPS)
- Postdoctoral fellowship, 22K21352, 16H06467 and 17H05833 MEXT | Japan Society for the Promotion of Science (JSPS)
- 21H02162, 22H05172 and 22H05179 MEXT | Japan Society for the Promotion of Science (JSPS)
- 21H04711 and 21H05030 MEXT | Japan Society for the Promotion of Science (JSPS)
- URPP Evolutoin in Action, Global Strategy and Partnerships Funding Scheme Universität Zürich (University of Zurich)
- URPP Evolutoini in Action Universität Zürich (University of Zurich)
- fellowship European Molecular Biology Organization (EMBO)
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Affiliation(s)
- Chow-Lih Yew
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Takashi Tsuchimatsu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
- Department of Biological Sciences, University of Tokyo, Tokyo, 113-0033, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Shinsuke Yasuda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
- Functional Genomics Center Zurich, 8057, Zurich, Switzerland
| | - Hiroyuki Kakui
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan
- Institute for Sustainable Agro-ecosystem Services, Graduate School of Agricultural and Life Sciences, University of Tokyo, Nishitokyo, 188-0002, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Takuma Ohta
- Graduate School of Bioresources, Mie University, Tsu, 514-0102, Japan
| | - Keita Suwabe
- Graduate School of Bioresources, Mie University, Tsu, 514-0102, Japan
| | - Masao Watanabe
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Seiji Takayama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zurich, Switzerland.
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan.
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15
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Leung K, van de Zande L, Beukeboom LW. Effects of polyploidization and their evolutionary implications are revealed by heritable polyploidy in the haplodiploid wasp Nasonia vitripennis. PLoS One 2023; 18:e0288278. [PMID: 37917617 PMCID: PMC10621845 DOI: 10.1371/journal.pone.0288278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/23/2023] [Indexed: 11/04/2023] Open
Abstract
Recurrent polyploidization occurred in the evolutionary history of most Eukaryota. However, how neopolyploid detriment (sterility, gigantism, gene dosage imbalances) has been overcome and even been bridged to evolutionary advantage (gene network diversification, mass radiation, range expansion) is largely unknown, particularly for animals. We used the parasitoid wasp Nasonia vitripennis, a rare insect system with heritable polyploidy, to begin addressing this knowledge gap. In Hymenoptera the sexes have different ploidies (haploid males, diploid females) and neopolyploids (diploid males, triploid females) occur for various species. Although such polyploids are usually sterile, those of N. vitripennis are reproductively capable and can even establish stable polyploid lines. To assess the effects of polyploidization, we compared a long-established polyploid line, the Whiting polyploid line (WPL) and a newly generated transformer knockdown line (tKDL) for fitness traits, absolute gene expression, and cell size and number. WPL polyploids have high male fitness and low female fecundity, while tKDL polyploids have poor male mate competition ability and high fertility. WPL has larger cells and cell number reduction, but the tKDL does not differ in this respect. Expression analyses of two housekeeping genes indicated that gene dosage is linked to sex irrespective of ploidy. Our study suggests that polyploid phenotypic variation may explain why some polyploid lineages thrive and others die out; a commonly proposed but difficult-to-test hypothesis. This documentation of diploid males (tKDL) with impaired competitive mating ability; triploid females with high fitness variation; and hymenopteran sexual dosage compensation (despite the lack of sex chromosomes) all challenges general assumptions on hymenopteran biology. We conclude that polyploidization is dependent on the duplicated genome characteristics and that genomes of different lines are unequally suited to survive diploidization. These results demonstrate the utility of N. vitripennis for delineating mechanisms of animal polyploid evolution, analogous to more advanced polyploid plant models.
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Affiliation(s)
- Kelley Leung
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Leo W. Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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16
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Halabi K, Shafir A, Mayrose I. PloiDB: the plant ploidy database. THE NEW PHYTOLOGIST 2023; 240:918-927. [PMID: 37337836 DOI: 10.1111/nph.19057] [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: 02/22/2023] [Accepted: 05/16/2023] [Indexed: 06/21/2023]
Abstract
See also the Commentary on this article by Spoelhof et al., 240: 909–911.
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Affiliation(s)
- Keren Halabi
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, 69978, Israel
| | - Anat Shafir
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, 69978, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv-Yafo, 69978, Israel
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17
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Gajdošová Z, Svitok M, Cetlová V, Mártonfiová L, Kučera J, Kolarčik V, Hurdu BI, Sîrbu IM, Turisová I, Turis P, Slovák M. Incidence and evolutionary relevance of autotriploid cytotypes in a relict member of the genus Daphne (Thymelaeaceae). AOB PLANTS 2023; 15:plad056. [PMID: 37899980 PMCID: PMC10601019 DOI: 10.1093/aobpla/plad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/09/2023] [Indexed: 10/31/2023]
Abstract
Odd ploidy-level cytotypes in sexually reproducing species are considered a dead end due to absent or reduced fertility. If sterility is only partial, however, their contribution to the population gene pool can be augmented by longevity and clonal growth. To test this, we investigated the cytotype origin and spatial pattern, and pollen viability in three relict shrub species of the genus Daphne (Thymelaeaceae Juss.) in central Europe. Daphne cneorum subsp. cneorum is a widespread European species that has a broad ecological amplitude, whereas D. cneorum subsp. arbusculoides and D. arbuscula are narrow endemics of the western Pannonian Plain and the Western Carpathians, respectively. Our study confirmed that all three taxa are diploid. However, of more than a thousand analysed individuals of D. cneorum subsp. cneorum, five in four different populations were triploid. Our data indicate that these triploids most likely originate from recurrent autopolyploidization events caused by the fusion of reduced and unreduced gametes. High pollen viability was observed in all three taxa and in both diploid and triploid cytotypes, ranging from 65 to 100 %. Our study highlights the significant role of odd ploidy-level cytotypes in interploidy gene flow, calling for more research into their reproduction, genetic variability, and overall fitness. Interestingly, while the endemic D. arbuscula differs from D. cneorum based on genetic and genome size data, D. cneorum subsp. arbusculoides was indistinguishable from D. cneorum subsp. cneorum. However, our study reveals that the subspecies differ in the number of flowers per inflorescence. This is the first comprehensive cytogeographic study of this intriguing genus at a regional scale, and in spite of its karyological stability, it contributes to our understanding of genomic evolution in plant species with a wide ecological amplitude.
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Affiliation(s)
- Zuzana Gajdošová
- Department of Evolution and Systematics, Institute of Botany, Plant Sciences and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
| | - Marek Svitok
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, Ul. T. G. Masaryka 24, SK-960 01 Zvolen, Slovak Republic
- Department of Forest Ecology, Czech University of Life Sciences Prague, CZ-16 521 Suchdol, Praha 6, Czech Republic
| | - Veronika Cetlová
- Department of Evolution and Systematics, Institute of Botany, Plant Sciences and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
| | - Lenka Mártonfiová
- Botanical Garden of Pavol Jozef Šafárik University in Košice, Mánesova 23, SK-043 52 Košice, Slovak Republic
| | - Jaromír Kučera
- Department of Evolution and Systematics, Institute of Botany, Plant Sciences and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
| | - Vladislav Kolarčik
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, SK-041 54 Košice, Slovak Republic
| | - Bogdan-Iuliu Hurdu
- Department of Taxonomy and Evolution, Institute of Biological Research, 48 Republicii St., R-400015 Cluj-Napoca, Romania
| | - Ioana-Minodora Sîrbu
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91–95, R-050095Bucharest, Romania
| | - Ingrid Turisová
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University in Banská Bystrica, Tajovského 40, SK-974 01 Banská Bystrica, Slovak Republic
| | - Peter Turis
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University in Banská Bystrica, Tajovského 40, SK-974 01 Banská Bystrica, Slovak Republic
| | - Marek Slovák
- Department of Evolution and Systematics, Institute of Botany, Plant Sciences and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Praha, Czech Republic
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18
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Lake TA, Briscoe Runquist RD, Flagel LE, Moeller DA. Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge. Evol Appl 2023; 16:1680-1696. [PMID: 38020872 PMCID: PMC10660801 DOI: 10.1111/eva.13593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/05/2023] [Accepted: 08/25/2023] [Indexed: 12/01/2023] Open
Abstract
Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500 km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from the early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.
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Affiliation(s)
- Thomas A. Lake
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | | | - Lex E. Flagel
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
- GencoveLong Island CityNew YorkUSA
| | - David A. Moeller
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
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19
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Walczyk AM, Hersch-Green EI. Genome-material costs and functional trade-offs in the autopolyploid Solidago gigantea (giant goldenrod) series. AMERICAN JOURNAL OF BOTANY 2023; 110:e16218. [PMID: 37551707 DOI: 10.1002/ajb2.16218] [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: 03/23/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 08/09/2023]
Abstract
PREMISE Increased genome-material costs of N and P atoms inherent to organisms with larger genomes have been proposed to limit growth under nutrient scarcities and to promote growth under nutrient enrichments. Such responsiveness may reflect a nutrient-dependent diploid versus polyploid advantage that could have vast ecological and evolutionary implications, but direct evidence that material costs increase with ploidy level and/or influence cytotype-dependent growth, metabolic, and/or resource-use trade-offs is limited. METHODS We grew diploid, autotetraploid, and autohexaploid Solidago gigantea plants with one of four ambient or enriched N:P ratios and measured traits related to material costs, primary and secondary metabolism, and resource-use. RESULTS Relative to diploids, polyploids invested more N and P into cells, and tetraploids grew more with N enrichments, suggesting that material costs increase with ploidy level. Polyploids also generally exhibited strategies that could minimize material-cost constraints over both long (reduced monoploid genome size) and short (more extreme transcriptome downsizing, reduced photosynthesis rates and terpene concentrations, enhanced N-use efficiencies) evolutionary time periods. Furthermore, polyploids had lower transpiration rates but higher water-use efficiencies than diploids, both of which were more pronounced under nutrient-limiting conditions. CONCLUSIONS N and P material costs increase with ploidy level, but material-cost constraints might be lessened by resource allocation/investment mechanisms that can also alter ecological dynamics and selection. Our results enhance mechanistic understanding of how global increases in nutrients might provide a release from material-cost constraints in polyploids that could impact ploidy (or genome-size)-specific performances, cytogeographic patterning, and multispecies community structuring.
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Affiliation(s)
- Angela M Walczyk
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Biology Department, Gustavus Adolphus College, 800 West College Avenue, St. Peter, MN, 56082, USA
| | - Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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Katche EI, Schierholt A, Schiessl SV, He F, Lv Z, Batley J, Becker HC, Mason AS. Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid Brassica napus. G3 (BETHESDA, MD.) 2023; 13:jkad136. [PMID: 37313757 PMCID: PMC10411605 DOI: 10.1093/g3journal/jkad136] [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: 04/24/2023] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/15/2023]
Abstract
Established allopolyploids are known to be genomically stable and fertile. However, in contrast, most newly resynthesized allopolyploids are infertile and meiotically unstable. Identifying the genetic factors responsible for genome stability in newly formed allopolyploid is key to understanding how 2 genomes come together to form a species. One hypothesis is that established allopolyploids may have inherited specific alleles from their diploid progenitors which conferred meiotic stability. Resynthesized Brassica napus lines are often unstable and infertile, unlike B. napus cultivars. We tested this hypothesis by characterizing 41 resynthesized B. napus lines produced by crosses between 8 Brassica rapa and 8 Brassica oleracea lines for copy number variation resulting from nonhomologous recombination events and fertility. We resequenced 8 B. rapa and 5 B. oleracea parent accessions and analyzed 19 resynthesized lines for allelic variation in a list of meiosis gene homologs. SNP genotyping was performed using the Illumina Infinium Brassica 60K array for 3 individuals per line. Self-pollinated seed set and genome stability (number of copy number variants) were significantly affected by the interaction between both B. rapa and B. oleracea parental genotypes. We identified 13 putative meiosis gene candidates which were significantly associated with frequency of copy number variants and which contained putatively harmful mutations in meiosis gene haplotypes for further investigation. Our results support the hypothesis that allelic variants inherited from parental genotypes affect genome stability and fertility in resynthesized rapeseed.
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Affiliation(s)
- Elizabeth Ihien Katche
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Antje Schierholt
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Sarah-Veronica Schiessl
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main D-60325, Germany
| | - Fei He
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
| | - Zhenling Lv
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Heiko C Becker
- Department of Crop Sciences, Division of Plant Breeding Methodology, Georg-August University Göttingen, Göttingen 37073, Germany
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Bonn 53115, Germany
- Department of Plant Breeding, Justus Liebig University, Giessen 35392, Germany
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21
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Mata JK, Martin SL, Smith TW. Global biodiversity data suggest allopolyploid plants do not occupy larger ranges or harsher conditions compared with their progenitors. Ecol Evol 2023; 13:e10231. [PMID: 37600489 PMCID: PMC10433117 DOI: 10.1002/ece3.10231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 08/22/2023] Open
Abstract
Understanding the factors determining species' geographical and environmental range is a central question in evolution and ecology, and key for developing conservation and management practices. Shortly after the discovery of polyploidy, just over 100 years ago, it was suggested that polyploids generally have greater range sizes and occur in more extreme conditions than their diploid congeners. This suggestion is now widely accepted in the literature and is attributed to polyploids having an increased capacity for genetic diversity that increases their potential for adaptation and invasiveness. However, the data supporting this idea are mixed. Here, we compare the niche of allopolyploid plants to their progenitor species to determine whether allopolyploidization is associated with increased geographic range or extreme environmental tolerance. Our analysis includes 123 allopolyploid species that exist as only one known ploidy level, with at least one known progenitor species, and at least 50 records in the Global Biodiversity Information Facility (GBIF) database. We used GBIF occurrence data and range modeling tools to quantify the geographic and environmental distribution of these allopolyploids relative to their progenitors. We find no indication that allopolyploid plants occupy more extreme conditions or larger geographic ranges than their progenitors. Data evaluated here generally indicate no significant difference in range between allopolyploids and progenitors, and where significant differences do occur, the progenitors are more likely to exist in extreme conditions. We concluded that the evidence from these data indicate allopolyploidization does not result in larger or more extreme ranges. Thus, allopolyploidization does not have a consistent effect on species distribution, and we conclude it is more likely the content of an allopolyploid's genome rather than polyploidy per se that determines the potential for invasiveness.
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22
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Cohen JI, Turgman-Cohen S. The Conservation Genetics of Iris lacustris (Dwarf Lake Iris), a Great Lakes Endemic. PLANTS (BASEL, SWITZERLAND) 2023; 12:2557. [PMID: 37447118 DOI: 10.3390/plants12132557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/26/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
Iris lacustris, a northern Great Lakes endemic, is a rare species known from 165 occurrences across Lakes Michigan and Huron in the United States and Canada. Due to multiple factors, including habitat loss, lack of seed dispersal, patterns of reproduction, and forest succession, the species is threatened. Early population genetic studies using isozymes and allozymes recovered no to limited genetic variation within the species. To better explore genetic variation across the geographic range of I. lacustris and to identify units for conservation, we used tunable Genotyping-by-Sequencing (tGBS) with 171 individuals across 24 populations from Michigan and Wisconsin, and because the species is polyploid, we filtered the single nucleotide polymorphism (SNP) matrices using polyRAD to recognize diploid and tetraploid loci. Based on multiple population genetic approaches, we resolved three to four population clusters that are geographically structured across the range of the species. The species migrated from west to east across its geographic range, and minimal genetic exchange has occurred among populations. Four units for conservation are recognized, but nine adaptive units were identified, providing evidence for local adaptation across the geographic range of the species. Population genetic analyses with all, diploid, and tetraploid loci recovered similar results, which suggests that methods may be robust to variation in ploidy level.
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Affiliation(s)
- James Isaac Cohen
- Department of Botany and Plant Ecology, Weber State University, 1415 Edvalson St., Dept. 2504, Ogden, UT 84408-2504, USA
| | - Salomon Turgman-Cohen
- E.S. Witchger School of Engineering, Marian University, 3200 Cold Spring Road, Indianapolis, IN 46222-1997, USA
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23
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Beshera KA, Harris PM, Michael SK. Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia. Zootaxa 2023; 5301:182-198. [PMID: 37518566 DOI: 10.11646/zootaxa.5301.2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Indexed: 08/01/2023]
Abstract
The Lake Tana Labeobarbus species flock represents one of the world's most famous examples of lacustrine species radiations. Previous studies of this group have resulted in the description of at least 15 species based on their differences in functional morphology and definition of two clades (lacustrine and riverine spawning clades) based on life history traits. A total of 166 fish representing 14 Labeobarbus species were genotyped using 10 lineage-specific hexaploid microsatellite loci. Six of these loci were developed for this study based on DNA sequence contigs derived from a microsatellite-enriched genomic library of Labeobarbus intermedius from Lake Tana; the remaining four loci were obtained from a previous study. The genotypes of the 10 loci were analyzed to examine genetic diversity and population structure within Lake Tana Labeobarbus. Overall mean allelic richness (NA) was 17.6 alleles per locus and observed (Ho) and expected (He) heterozygosities were 0.84 ± 0.14 and 0.73 ± 0.09, respectively, across all Lake Tana Labeobarbus samples examined. Our analyses reveal that there is little genetic differentiation among species (FST = 0.020-0.099; only 10 of 91 species comparisons were significant), but moderate differentiation (FST = 0.11, p < 0.05) between lacustrine and riverine spawning populations. Relative to previous phylogenetic hypotheses, our phenetic analysis employing the R-based Analysis of Phylogenetics and Evolution (APE) program seems to perform marginally better in revealing lineages within Lake Tana Labeobarbus. Herein, our results are compared to a previous microsatellite-based study of the same populations.
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Affiliation(s)
- Kebede A Beshera
- Department of Biological Sciences and Chemistry; Southern University and Agricultural & Mechanical College; 801 Harding Blvd; Baton Rouge; LA 70807; USA.
| | - Phillip M Harris
- Biodiversity and Systematics; Department of Biological Sciences; The University of Alabama; Tuscaloosa; AL 35487-0345; USA.
| | - Semhar K Michael
- Department of Mathematics and Statistics; South Dakota State University; Box 2225; Brookings; SD.
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24
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Chembrammal R, Thoppil JE. B-Chromosomes in a Mixoploid Karyotype of Strobilanthes virendrakumarana. CYTOL GENET+ 2023. [DOI: 10.3103/s0095452723020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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25
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Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex. BIOLOGY 2023; 12:biology12030418. [PMID: 36979110 PMCID: PMC10045763 DOI: 10.3390/biology12030418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with complex morphological patterns. In such TCGs, mosaic-like character combinations and conflicts of morphological data with molecular phylogenies present a major problem for species classification. Here, we used the large polyploid apomictic European Ranunculus auricomus complex to study relationships among five diploid sexual progenitor species and 75 polyploid apomictic derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal and stem leaves, receptacles), genomic data (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed genomic clusters correspond to morphological groupings based on basal leaves and concatenated traits, and morphological groups were best resolved with RAD-Seq data; (2) described apomictic taxa usually overlap within trait morphospace except for those taxa at the space edges; (3) apomictic phenotypes are highly influenced by parental subgenome composition and to a lesser extent by climatic factors; and (4) allopolyploid apomictic taxa, compared to their sexual progenitor, resemble a mosaic of ecological and morphological intermediate to transgressive biotypes. The joint evaluation of phylogenomic, phenotypic, reproductive, and ecological data supports a revision of purely descriptive, subjective traditional morphological classifications.
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26
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Gruet C, Abrouk D, Börner A, Muller D, Moënne-Loccoz Y. Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere. PLANT, CELL & ENVIRONMENT 2023; 46:1018-1032. [PMID: 36494920 DOI: 10.1111/pce.14508] [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: 08/07/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB {SS} (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by quantitative polymerase chain reaction their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions.
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Affiliation(s)
- Cécile Gruet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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27
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Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora × cambivora. IMA Fungus 2023; 14:4. [PMID: 36823663 PMCID: PMC9951538 DOI: 10.1186/s43008-023-00109-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023] Open
Abstract
Invasive, exotic plant pathogens pose a major threat to native and agricultural ecosystems. Phytophthora × cambivora is an invasive, destructive pathogen of forest and fruit trees causing severe damage worldwide to chestnuts (Castanea), apricots, peaches, plums, almonds and cherries (Prunus), apples (Malus), oaks (Quercus), and beech (Fagus). It was one of the first damaging invasive Phytophthora species to be introduced to Europe and North America, although its origin is unknown. We determined its population genetic history in Europe, North and South America, Australia and East Asia (mainly Japan) using genotyping-by-sequencing. Populations in Europe and Australia appear clonal, those in North America are highly clonal yet show some degree of sexual reproduction, and those in East Asia are partially sexual. Two clonal lineages, each of opposite mating type, and a hybrid lineage derived from these two lineages, dominated the populations in Europe and were predominantly found on fagaceous forest hosts (Castanea, Quercus, Fagus). Isolates from fruit trees (Prunus and Malus) belonged to a separate lineage found in Australia, North America, Europe and East Asia, indicating the disease on fruit trees could be caused by a distinct lineage of P. × cambivora, which may potentially be a separate sister species and has likely been moved with live plants. The highest genetic diversity was found in Japan, suggesting that East Asia is the centre of origin of the pathogen. Further surveys in unsampled, temperate regions of East Asia are needed to more precisely identify the location and range of the centre of diversity.
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28
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Liu C, Wang YG. Does one subgenome become dominant in the formation and evolution of a polyploid? ANNALS OF BOTANY 2023; 131:11-16. [PMID: 35291007 PMCID: PMC9904339 DOI: 10.1093/aob/mcac024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/15/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Polyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution. SCOPE In addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered. CONCLUSIONS Contrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.
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Affiliation(s)
| | - You-Gan Wang
- Science and Engineering Facility, Queensland University of Technology, Brisbane, Queensland, Australia
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29
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Sader MA, Costa LA, Souza G, Urdampilleta JD, Simon J, Vaio M. South American Plant Chromosome Numbers Databases: The Information We Have and the Information We Lack on the Most Plant-Diverse Continent. Methods Mol Biol 2023; 2703:211-225. [PMID: 37646948 DOI: 10.1007/978-1-0716-3389-2_16] [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] [Indexed: 09/01/2023]
Abstract
Chromosome numbers have been used in plant taxonomy, and they are still fundamental for taxon delimitation and genome evolution studies. South America is one of the most diverse continents in terms of plant species and there is a considerable number of species not yet analyzed. Accumulated knowledge about plant chromosome numbers has been compiled from online databases, and here we present an overview. The CCDB is one of the largest plant cytological databases and includes data for around 18% of known vascular plants in the world. In this work, we review the information contained in CCDB and in three databases with exclusive information for South America. At present, the three existing databases comprise information on around 1800 plant taxa related to specific regions, countries, or biomes. Efforts are necessary to expand cytological knowledge and to collect all the available information in a plant chromosome database for this continent.
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Affiliation(s)
- Mariela A Sader
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Universidad de Córdoba - CONICET, Córdoba, Argentina
| | - Lucas A Costa
- Laboratorio de Citogenética Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Brazil
| | - Gustavo Souza
- Laboratorio de Citogenética Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Brazil
| | - Juan D Urdampilleta
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Universidad de Córdoba - CONICET, Córdoba, Argentina
| | - Joan Simon
- BioC (GReB, IRBio) - Laboratori de Botànica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Magdalena Vaio
- Laboratorio de Evolución y Domesticación de las Plantas, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay.
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30
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Clo J, Kolář F. Inbreeding depression in polyploid species: a meta-analysis. Biol Lett 2022; 18:20220477. [PMID: 36514955 PMCID: PMC9748776 DOI: 10.1098/rsbl.2022.0477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022] Open
Abstract
Whole-genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects, the resulting morphological and fitness consequences and how they affect the survival of polyploid lineages are intensively studied. Another important factor may also determine the probability of establishment and success of polyploid lineages: inbreeding depression. Inbreeding depression is expected to play an important role in the establishment of neopolyploid lineages, their capacity to colonize new environments, and in the simultaneous evolution of ploidy and other life-history traits such as self-fertilization. Both theoretically and empirically, there is no consensus on the consequences of polyploidy on inbreeding depression. In this meta-analysis, we investigated the effect of polyploidy on the evolution of inbreeding depression, by performing a meta-analysis within angiosperm species. The main results of our study are that the consequences of polyploidy on inbreeding depression are complex and depend on the time since polyploidization. We found that young polyploid lineages have a much lower amount of inbreeding depression than their diploid relatives and their established counterparts. Natural polyploid lineages are intermediate and have a higher amount of inbreeding depression than synthetic neopolyploids, and a smaller amount than diploids, suggesting that the negative effect of polyploidy on inbreeding depression decreases with time since polyploidization.
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Affiliation(s)
- Josselin Clo
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01 Prague, Czech Republic
| | - Filip Kolář
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
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31
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Li S, Moller CA, Mitchell NG, Martin DG, Sacks EJ, Saikia S, Labonte NR, Baldwin BS, Morrison JI, Ferguson JN, Leakey ADB, Ainsworth EA. The leaf economics spectrum of triploid and tetraploid C 4 grass Miscanthus x giganteus. PLANT, CELL & ENVIRONMENT 2022; 45:3462-3475. [PMID: 36098093 PMCID: PMC9825850 DOI: 10.1111/pce.14433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
The leaf economics spectrum (LES) describes multivariate correlations in leaf structural, physiological and chemical traits, originally based on diverse C3 species grown under natural ecosystems. However, the specific contribution of C4 species to the global LES is studied less widely. C4 species have a CO2 concentrating mechanism which drives high rates of photosynthesis and improves resource use efficiency, thus potentially pushing them towards the edge of the LES. Here, we measured foliage morphology, structure, photosynthesis, and nutrient content for hundreds of genotypes of the C4 grass Miscanthus× giganteus grown in two common gardens over two seasons. We show substantial trait variations across M.× giganteus genotypes and robust genotypic trait relationships. Compared to the global LES, M.× giganteus genotypes had higher photosynthetic rates, lower stomatal conductance, and less nitrogen content, indicating greater water and photosynthetic nitrogen use efficiency in the C4 species. Additionally, tetraploid genotypes produced thicker leaves with greater leaf mass per area and lower leaf density than triploid genotypes. By expanding the LES relationships across C3 species to include C4 crops, these findings highlight that M.× giganteus occupies the boundary of the global LES and suggest the potential for ploidy to alter LES traits.
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Affiliation(s)
- Shuai Li
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Institute for Sustainability, Energy, and EnvironmentUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Christopher A. Moller
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Global Change and Photosynthesis Research Unit, USDA ARSUrbanaIllinoisUSA
| | - Noah G. Mitchell
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Global Change and Photosynthesis Research Unit, USDA ARSUrbanaIllinoisUSA
| | - Duncan G. Martin
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Erik J. Sacks
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Sampurna Saikia
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Nicholas R. Labonte
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Brian S. Baldwin
- Department of Plant and Soil SciencesMississippi State UniversityStarkvilleMississippiUSA
| | - Jesse I. Morrison
- Department of Plant and Soil SciencesMississippi State UniversityStarkvilleMississippiUSA
| | - John N. Ferguson
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Andrew D. B. Leakey
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Elizabeth A. Ainsworth
- Center for Advanced Bioenergy and Bioproducts InnovationUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignIllinoisUrbanaUSA
- Global Change and Photosynthesis Research Unit, USDA ARSUrbanaIllinoisUSA
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
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32
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Liu S, Wang X, Li Q, Peng W, Zhang Z, Chu P, Guo S, Fan Y, Lyu S. AtGCS promoter-driven clustered regularly interspaced short palindromic repeats/Cas9 highly efficiently generates homozygous/biallelic mutations in the transformed roots by Agrobacterium rhizogenes-mediated transformation. FRONTIERS IN PLANT SCIENCE 2022; 13:952428. [PMID: 36330262 PMCID: PMC9623429 DOI: 10.3389/fpls.2022.952428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/22/2022] [Indexed: 06/01/2023]
Abstract
Agrobacterium rhizogenes-mediated (ARM) transformation is an efficient and powerful tool to generate transgenic roots to study root-related biology. For loss-of-function studies, transgenic-root-induced indel mutations by CRISPR/Cas9 only with homozygous/biallelic mutagenesis can exhibit mutant phenotype(s) (excluding recessive traits). However, a low frequency of homozygous mutants was produced by a constitutive promoter to drive Cas9 expression. Here, we identified a highly efficient Arabidopsis thaliana gamma-glutamylcysteine synthetase promoter, termed AtGCSpro, with strong activity in the region where the root meristem will initiate and in the whole roots in broad eudicots species. AtGCSpro achieved higher homozygous/biallelic mutation efficiency than the most widely used CaMV 35S promoter in driving Cas9 expression in soybean, Lotus japonicus, and tomato roots. Using the pAtGCSpro-Cas9 system, the average homozygous/biallelic mutation frequency is 1.7-fold and 8.3-fold higher than the p2 × 35Spro-Cas9 system for single and two target site(s) in the genome, respectively. Our results demonstrate the advantage of the pAtGCSpro-Cas9 system used in ARM transformation, especially its great potential in diploids with multiple-copy genes targeted mutations and polyploid plants with multiplex genome editing. AtGCSpro is conservatively active in various eudicots species, suggesting that AtGCSpro might be applied in a wide range of dicots species.
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Affiliation(s)
| | | | | | | | | | | | | | - Yinglun Fan
- *Correspondence: Yinglun Fan, ; Shanhua Lyu, ;
| | - Shanhua Lyu
- *Correspondence: Yinglun Fan, ; Shanhua Lyu, ;
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Akagi T, Jung K, Masuda K, Shimizu KK. Polyploidy before and after domestication of crop species. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102255. [PMID: 35870416 DOI: 10.1016/j.pbi.2022.102255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/01/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species.
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Affiliation(s)
- Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
| | - Katharina Jung
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland
| | - Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zürich, Switzerland; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan.
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Han TS, Hu ZY, Du ZQ, Zheng QJ, Liu J, Mitchell-Olds T, Xing YW. Adaptive responses drive the success of polyploid yellowcresses ( Rorippa, Brassicaceae) in the Hengduan Mountains, a temperate biodiversity hotspot. PLANT DIVERSITY 2022; 44:455-467. [PMID: 36187546 PMCID: PMC9512641 DOI: 10.1016/j.pld.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 06/16/2023]
Abstract
Polyploids contribute substantially to plant evolution and biodiversity; however, the mechanisms by which they succeed are still unclear. According to the polyploid adaptation hypothesis, successful polyploids spread by repeated adaptive responses to new environments. Here, we tested this hypothesis using two tetraploid yellowcresses (Rorippa), the endemic Rorippa elata and the widespread Rorippa palustris, in the temperate biodiversity hotspot of the Hengduan Mountains. Speciation modes were resolved by phylogenetic modeling using 12 low-copy nuclear loci. Phylogeographical patterns were then examined using haplotypes phased from four plastid and ITS markers, coupled with historical niche reconstruction by ecological niche modeling. We inferred the time of hybrid origins for both species as the mid-Pleistocene, with shared glacial refugia within the southern Hengduan Mountains. Phylogeographic and ecological niche reconstruction indicated recurrent northward colonization by both species after speciation, possibly tracking denuded habitats created by glacial retreat during interglacial periods. Common garden experiment involving perennial R. elata conducted over two years revealed significant changes in fitness-related traits across source latitudes or altitudes, including latitudinal increases in survival rate and compactness of plant architecture, suggesting gradual adaptation during range expansion. These findings support the polyploid adaptation hypothesis and suggest that the spread of polyploids was aided by adaptive responses to environmental changes during the Pleistocene. Our results thus provide insight into the evolutionary success of polyploids in high-altitude environments.
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Affiliation(s)
- Ting-Shen Han
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Zheng-Yan Hu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Qiang Du
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan-Jing Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | | | - Yao-Wu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
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Vidal-Russell R, Tadey M, Urfusová R, Urfus T, Souto CP. Evolutionary importance of the relationship between cytogeography and climate: New insights on creosote bushes from North and South America. PLANT DIVERSITY 2022; 44:492-498. [PMID: 36187552 PMCID: PMC9512640 DOI: 10.1016/j.pld.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 06/16/2023]
Abstract
Relationships between genome size and environmental variables suggest that DNA content might be adaptive and of evolutionary importance in plants. The genus Larrea provides an interesting system to test this hypothesis, since it shows both intra- and interspecific variation in genome size. Larrea has an amphitropical distribution in North and South American deserts, where it is most speciose. Larrea tridentata in North America shows a gradient of increasing autopolyploidy; while three of the four studied South American species are diploids, Larrea divaricata, Larrea nitida, Larrea ameghinoi, and the fourth is an allopolyploid, Larrea cuneifolia. We downloaded available focal species' georeferenced records from seven data reservoirs. We used these records to extract biologically relevant environmental variables from WorldClim at 30 arc seconds scale, to have a broad characterization of the variable climatic conditions of both regions, and a climatic envelope for each species. We estimated relative DNA content index and relative monoploid genome values, by flow cytometry, of four most abundant Larrea species throughout their respective ranges. Then we winnow the bioclimatic dataset down to uncorrelated variables and sampled locales, to analyse the degree of association between both intra- and interspecific relative DNA content and climatic variables that are functionally relevant in arid environments using Pearson correlations, general linear and mixed effects models. Within the genus Larrea, relative DNA content increases with rising temperature and decreases with rising precipitation. At the intraspecific level, all four species show relative DNA content variation across climatic conditions. Larrea is a genus that shows genome size variation correlated with climate. Our results are also consistent with the hypothesis that extreme environmental pressures may have facilitated repeated whole genome duplication events in North America, while in South America, reticulate evolution, as allopolyploidization, and speciation might have been climate-dependent since the Oligocene.
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Affiliation(s)
- Romina Vidal-Russell
- Laboratorio Ecotono- INIBIOMA (CONICET-UNComahue), Quintral, 1250, Bariloche, Río Negro, Argentina
| | - Mariana Tadey
- Laboratorio Ecotono- INIBIOMA (CONICET-UNComahue), Quintral, 1250, Bariloche, Río Negro, Argentina
| | - Romana Urfusová
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00, Prague, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 00, Prague, Czech Republic
| | - Cintia Paola Souto
- Laboratorio Ecotono- INIBIOMA (CONICET-UNComahue), Quintral, 1250, Bariloche, Río Negro, Argentina
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Martínez-Fortún J, Phillips DW, Jones HD. Natural and artificial sources of genetic variation used in crop breeding: A baseline comparator for genome editing. Front Genome Ed 2022; 4:937853. [PMID: 36072906 PMCID: PMC9441798 DOI: 10.3389/fgeed.2022.937853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Traditional breeding has successfully selected beneficial traits for food, feed, and fibre crops over the last several thousand years. The last century has seen significant technological advancements particularly in marker assisted selection and the generation of induced genetic variation, including over the last few decades, through mutation breeding, genetic modification, and genome editing. While regulatory frameworks for traditional varietal development and for genetic modification with transgenes are broadly established, those for genome editing are lacking or are still evolving in many regions. In particular, the lack of "foreign" recombinant DNA in genome edited plants and that the resulting SNPs or INDELs are indistinguishable from those seen in traditional breeding has challenged development of new legislation. Where products of genome editing and other novel breeding technologies possess no transgenes and could have been generated via traditional methods, we argue that it is logical and proportionate to apply equivalent legislative oversight that already exists for traditional breeding and novel foods. This review analyses the types and the scale of spontaneous and induced genetic variation that can be selected during traditional plant breeding activities. It provides a base line from which to judge whether genetic changes brought about by techniques of genome editing or other reverse genetic methods are indeed comparable to those routinely found using traditional methods of plant breeding.
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Affiliation(s)
| | | | - Huw D. Jones
- IBERS, Aberystwyth University, Aberystwyth, United Kingdom
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Zhong Y, Liu Y, Wu W, Chen J, Sun C, Liu H, Shu J, Ebihara A, Yan Y, Zhou R, Schneider H. Genomic insights into genetic diploidization in the homosporous fern Adiantum nelumboides. Genome Biol Evol 2022; 14:evac127. [PMID: 35946426 PMCID: PMC9387920 DOI: 10.1093/gbe/evac127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Whole genome duplication has been recognized as a major process in speciation of land plants, especially in ferns. Whereas genome downsizing contributes greatly to the post-genome shock responses of polyploid flowering plants, diploidization of polyploid ferns diverges by maintaining most of the duplicated DNA and is thus expected to be dominated by genic processes. As a consequence, fern genomes provide excellent opportunities to study ecological speciation enforced by expansion of protein families via polyploidy. To test the key predictions of this hypothesis, we reported the de novo genome sequence of Adiantum nelumboides, a tetraploid homosporous fern. The obtained draft genome had a size of 6.27 Gb assembled into 11,767 scaffolds with the contig N50 of 1.37 Mb. Repetitive DNA sequences contributed with about 81.7%, a remarkably high proportion of the genome. With 69,568 the number of predicted protein-coding genes exceeded those reported in most other land plant genomes. Intragenomic synteny analyses recovered 443 blocks with the average block size of 1.29 Mb and the average gene content of 16 genes. The results are consistent with the hypothesis of high ancestral chromosome number, lack of substantial genome downsizing, and dominance of genic diploidization. As expected in the calciphilous plants, a notable number of detected genes were involved in calcium uptake and transport. In summary, the genome sequence of a tetraploid homosporous fern not only provides access to a genomic resource of a derived fern, but also supports the hypothesis of maintenance of high chromosome numbers and duplicated DNA in young polyploid ferns.
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Affiliation(s)
- Yan Zhong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - Wei Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jingfang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chenyu Sun
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hongmei Liu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Jiangping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, and the Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, and the Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
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Yang F, Wan H, Li J, Wang Q, Yang N, Zhu X, Liu Z, Yang Y, Ma W, Fan X, Yang W, Zhou Y. Pentaploidization Enriches the Genetic Diversity of Wheat by Enhancing the Recombination of AB Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:883868. [PMID: 35845672 PMCID: PMC9281561 DOI: 10.3389/fpls.2022.883868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Allohexaploidization and continuous introgression play a key role in the origin and evolution of bread wheat. The genetic bottleneck of bread wheat resulting from limited germplasms involved in the origin and modern breeding may be compensated by gene flow from tetraploid wheat through introgressive hybridization. The inter-ploidy hybridization between hexaploid and tetraploid wheat generates pentaploid hybrids first, which absorbed genetic variations both from hexaploid and tetraploid wheat and have great potential for re-evolution and improvement in bread wheat. Therefore, understanding the effects of the pentaploid hybrid is of apparent significance in our understanding of the historic introgression and in informing breeding. In the current study, two sets of F2 populations of synthetic pentaploid wheat (SPW1 and SPW2) and synthetic hexaploid wheat (SHW1 and SHW2) were created to analyze differences in recombination frequency (RF) of AB genomes and distorted segregation of polymorphic SNP markers through SNP genotyping. Results suggested that (1) the recombination of AB genomes in the SPW populations was about 3- to 4-fold higher than that in the SHW populations, resulting from the significantly (P < 0.01) increased RF between adjacent and linked SNP loci, especially the variations that occurred in a pericentromeric region which would further enrich genetic diversity; (2) the crosses of hexaploid × tetraploid wheat could be an efficient way to produce pentaploid derivatives than the crosses of tetraploid × hexaploid wheat according to the higher germination rate found in the former crosses; (3) the high proportion of distorted segregation loci that skewed in favor of the female parent genotype/allele in the SPW populations might associate with the fitness and survival of the offspring. Based on the presented data, we propose that pentaploid hybrids should increasingly be used in wheat breeding. In addition, the contribution of gene flow from tetraploid wheat to bread wheat mediated by pentaploid introgressive hybridization also was discussed in the re-evolution of bread wheat.
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Affiliation(s)
- Fan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Hongshen Wan
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jun Li
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qin Wang
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Ning Yang
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xinguo Zhu
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Zehou Liu
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yumin Yang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Wujun Ma
- Australia-China Joint Centre for Wheat Improvement, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wuyun Yang
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China (Ministry of Agriculture and Rural Affairs of P.R.C.), Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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Transcriptome Profiling Identifies Candidate Genes Contributing to Male and Female Gamete Development in Synthetic Brassica Allohexaploids. PLANTS 2022; 11:plants11121556. [PMID: 35736707 PMCID: PMC9228180 DOI: 10.3390/plants11121556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Polyploidy plays a crucial role in plant evolution and speciation. The development of male and female gametes is essential to the reproductive capacity of polyploids, but their gene expression pattern has not been fully explored in newly established polyploids. The present study aimed to reveal a detailed atlas of gene expression for gamete development in newly synthetic Brassica allohexaploids that are not naturally existing species. Comparative transcriptome profiling between developing anthers (staged from meiosis to mature pollen) and ovules (staged from meiosis to mature embryo sac) was performed using RNA-Seq analysis. A total of 8676, 9775 and 4553 upregulated differentially expressed genes (DEGs) were identified for the development of both gametes, for male-only, and for female-only gamete development, respectively, in the synthetic Brassica allohexaploids. By combining gene ontology (GO) biological process analysis and data from the published literature, we identified 37 candidate genes for DNA double-strand break formation, synapsis and the crossover of homologous recombination during male and female meiosis and 51 candidate genes for tapetum development, sporopollenin biosynthesis and pollen wall development in male gamete development. Furthermore, 23 candidate genes for mitotic progression, nuclear positioning and cell specification and development were enriched in female gamete development. This study lays a good foundation for revealing the molecular regulation of genes related to male and female gamete development in Brassica allohexaploids and provides more resourceful genetic information on the reproductive biology of Brassica polyploid breeding.
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A generalist-specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range. Proc Natl Acad Sci U S A 2022; 119:e2118879119. [PMID: 35377798 PMCID: PMC9169841 DOI: 10.1073/pnas.2118879119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Polyploidy, which occurs in roughly half of all flowering plants and an even higher percentage of grasses, is thought to be a major driver of adaptation. Higher numbers of copies of each gene in polyploid genomes can increase genetic diversity, which could drive shifts in habitat preference, adaptability, and fitness. To test the effects of increased ploidy, we compared genomic diversity, environmental niche, and fitness responses across climatic gradients between tetraploid and octoploid switchgrass. We found that the octoploids contained novel combinations of the ancestral tetraploid genetic diversity, which was linked to the expansion of switchgrass into unsuitable habitats for tetraploid populations. Our experiments revealed evidence of niche divergence, differential fitness, and a generalist–specialist trade-off between cytotypes. Polyploidy results from whole-genome duplication and is a unique form of heritable variation with pronounced evolutionary implications. Different ploidy levels, or cytotypes, can exist within a single species, and such systems provide an opportunity to assess how ploidy variation alters phenotypic novelty, adaptability, and fitness, which can, in turn, drive the development of unique ecological niches that promote the coexistence of multiple cytotypes. Switchgrass, Panicum virgatum, is a widespread, perennial C4 grass in North America with multiple naturally occurring cytotypes, primarily tetraploids (4×) and octoploids (8×). Using a combination of genomic, quantitative genetic, landscape, and niche modeling approaches, we detect divergent levels of genetic admixture, evidence of niche differentiation, and differential environmental sensitivity between switchgrass cytotypes. Taken together, these findings support a generalist (8×)–specialist (4×) trade-off. Our results indicate that the 8× represent a unique combination of genetic variation that has allowed the expansion of switchgrass’ ecological niche and thus putatively represents a valuable breeding resource.
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Parveen S, Singh N, Adit A, Kumaria S, Tandon R, Agarwal M, Jagannath A, Goel S. Contrasting Reproductive Strategies of Two Nymphaea Species Affect Existing Natural Genetic Diversity as Assessed by Microsatellite Markers: Implications for Conservation and Wetlands Restoration. FRONTIERS IN PLANT SCIENCE 2022; 13:773572. [PMID: 35371128 PMCID: PMC8965595 DOI: 10.3389/fpls.2022.773572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Nymphaea, commonly known as water lily, is the largest and most widely distributed genus in the order Nymphaeales. The importance of Nymphaea in wetland ecosystems and their increased vulnerability make them a great choice for conservation and management. In this work, we studied genetic diversity in a collection of 90 N. micrantha and 92 N. nouchali individuals from six different states of India, i.e., Assam, Manipur, Meghalaya, Maharashtra, Goa, and Kerala, using simple sequence repeat (SSR) markers developed by low throughput Illumina sequencing (10X coverage of genome) of N. micrantha. Nymphaea nouchali is native to India, whereas N. micrantha is suggested to be introduced to the country for its aesthetic and cultural values. The study revealed extensive polymorphism in N. nouchali, while in N. micrantha, no apparent genetic divergence was detected prompting us to investigate the reason(s) by studying the reproductive biology of the two species. The study revealed that N. micrantha predominantly reproduces asexually which has impacted the genetic diversity of the species to a great extent. This observation is of immense importance for a successful re-establishment of Nymphaea species during restoration programs of wetlands. The information generated on reproductive behaviors and their association with genotypic richness can help in strategizing genetic resource conservation, especially for species with limited distribution. The study has also generated 22,268 non-redundant microsatellite loci, out of which, 143 microsatellites were tested for polymorphism and polymorphic markers were tested for transferability in five other Nymphaea species, providing genomic resources for further studies on this important genus.
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Affiliation(s)
- Seema Parveen
- Department of Botany, University of Delhi, New Delhi, India
| | - Nutan Singh
- Department of Botany, North-Eastern Hill University, Shillong, India
| | - Arjun Adit
- Department of Botany, University of Delhi, New Delhi, India
| | - Suman Kumaria
- Department of Botany, North-Eastern Hill University, Shillong, India
| | - Rajesh Tandon
- Department of Botany, University of Delhi, New Delhi, India
| | - Manu Agarwal
- Department of Botany, University of Delhi, New Delhi, India
| | - Arun Jagannath
- Department of Botany, University of Delhi, New Delhi, India
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Oliveira W, Silva JLS, Cruz-Neto O, Oliveira MTP, Fernandes de Albuquerque I, Borges LA, Lopes AV. Higher frequency of legitimate pollinators and fruit set of autotetraploid trees of Libidibia ferrea (Leguminosae) compared to diploids in a mixed tropical urban population. JOURNAL OF PLANT RESEARCH 2022; 135:235-245. [PMID: 35150366 DOI: 10.1007/s10265-022-01373-0] [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: 10/12/2020] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
In mixed-ploidy populations, newly formed polyploids initially occur at low frequencies when compared to diploids. However, polyploidy may lead to morphological and phenological changes, which promote reproductive isolation and favor polyploid establishment and reproductive success. Additionally, previous studies have shown that polyploidy can confer some adaptive advantages to organisms in stressful environments. Here, we investigate variation in reproductive phenology, floral traits and reproductive success between diploid and autotetraploid trees of Libidibia ferrea (Mart. Ex Tul.) L.P. Queiroz (Leguminosae) in a mixed tropical urban population, a stressful environment. We assessed ploidy levels, flowering and fruiting phenology, flowering synchrony, floral and reproductive biology, pollination and fruit and seed set. We tested the hypothesis that autotetraploid individuals have a higher frequency of pollinators and higher fruit and seed set per inflorescence (as a proxy of reproductive success) than diploids in an urban green space. Libidibia ferrea is a good model to test our hypothesis because it is self-incompatible (i.e. relies on pollinators to set fruits). In the urban ecosystem studied, we found that diploids flowered for 6-7 months/year and autotetraploids for 3-5 months/year. Flowering synchrony was low between and within cytotypes and even though autotetraploids and diploids exhibited some overlap in flowering period, diploids flowered alone for 2-3 months. Autotetraploids had significantly more flowers per inflorescences, larger flowers and larger pollen grains (as expected for polyploids), but also a higher frequency of visits by legitimate pollinators including two exclusive ones, and higher fruit and seed set per inflorescence when compared to diploids, despite having a shorter flowering period. Our findings reveal some advantages for polyploids over their related diploids in a tropical urban green space. Also, our results highlight the need for more studies that seek to understand abiotic mechanisms affecting reproductive output of polyploids in urban ecosystems.
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Affiliation(s)
- Willams Oliveira
- Programa de Pós-Graduação em Biologia Vegetal, Centro de Biociências (CB), Universidade Federal de Pernambuco (UFPE), Recife, PE, 50372-970, Brazil
| | - Jéssica Luiza S Silva
- Departamento de Botânica, Centro de Biociências (CB), Universidade Federal de Pernambuco (UFPE), Recife, PE, 50372-970, Brazil
| | - Oswaldo Cruz-Neto
- Departamento de Botânica, Centro de Biociências (CB), Universidade Federal de Pernambuco (UFPE), Recife, PE, 50372-970, Brazil
| | - Marcela Tomaz P Oliveira
- Programa de Pós-Graduação em Biologia Vegetal, Centro de Biociências (CB), Universidade Federal de Pernambuco (UFPE), Recife, PE, 50372-970, Brazil
| | - Isabelle Fernandes de Albuquerque
- Programa de Pós-Graduação em Biologia Vegetal, Centro de Biociências (CB), Universidade Federal de Pernambuco (UFPE), Recife, PE, 50372-970, Brazil
| | - Laís Angélica Borges
- Departamento de Biociências, Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), João Pessoa, 58397-000, Brazil
| | - Ariadna Valentina Lopes
- Departamento de Botânica, Centro de Biociências (CB), Universidade Federal de Pernambuco (UFPE), Recife, PE, 50372-970, Brazil.
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43
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Batista LG, Mello VH, Souza AP, Margarido GRA. Genomic prediction with allele dosage information in highly polyploid species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:723-739. [PMID: 34800132 DOI: 10.1007/s00122-021-03994-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Including allele, dosage can improve genomic selection in highly polyploid species under higher frequency of different heterozygous genotypic classes and high dominance degree levels. Several studies have shown how to leverage allele dosage information to improve the accuracy of genomic selection models in autotetraploid. In this study, we expanded the methodology used for genomic selection in autotetraploid to higher (and mixed) ploidy levels. We adapted the models to build covariance matrices of both additive and digenic dominance effects that are subsequently used in genomic selection models. We applied these models using estimates of ploidy and allele dosage to sugarcane and sweet potato datasets and validated our results by also applying the models in simulated data. For the simulated datasets, including allele dosage information led up to 140% higher mean predictive abilities in comparison to using diploidized markers. Including dominance effects were highly advantageous when using diploidized markers, leading to mean predictive abilities which were up to 115% higher in comparison to only including additive effects. When the frequency of heterozygous genotypes in the population was low, such as in the sugarcane and sweet potato datasets, there was little advantage in including allele dosage information in the models. Overall, we show that including allele dosage can improve genomic selection in highly polyploid species under higher frequency of different heterozygous genotypic classes and high dominance degree levels.
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Affiliation(s)
- Lorena G Batista
- Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Victor H Mello
- Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Anete P Souza
- Center of Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Gabriel R A Margarido
- Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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44
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Chan JCS, Ooi MKJ, Guja LK. Polyploidy but Not Range Size Is Associated With Seed and Seedling Traits That Affect Performance of Pomaderris Species. FRONTIERS IN PLANT SCIENCE 2022; 12:779651. [PMID: 35095956 PMCID: PMC8793627 DOI: 10.3389/fpls.2021.779651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Ploidy and species range size or threat status have been linked to variation in phenotypic and phenological seed and seedling traits, including seed size, germination rate (speed) and seedling stature. There is surprisingly little known about the ecological outcomes of relationships between ploidy, key plant traits and the drivers of range size. Here we determined whether ploidy and range size in Pomaderris, a genus of shrubs that includes many threatened species, are associated with variation in seed and seedling traits that might limit the regeneration performance of obligate seeders in fire-prone systems. We experimentally quantified seed dormancy and germination processes using fire-related heat treatments and evaluated seedling performance under drought stress. We also examined the association of seed size with other seed and seedling traits. Polyploids had bigger seeds, a faster germination rate and larger and taller seedlings than diploids. There was a lack of any clear relationship between range size and seed or seedling traits. The ploidy effects observed for many traits are likely to be indirect and associated with the underlying seed size differences. These findings indicate that there is a higher potential competitive advantage in polyploid than diploid Pomaderris during regeneration, a critical stage in the post-fire environment. This insight to the regeneration phase may need to be considered when planning and prioritising management of threatened species.
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Affiliation(s)
- Jason C. S. Chan
- Centre for Ecosystem Science, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mark K. J. Ooi
- Centre for Ecosystem Science, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Australian National Biodiversity Research, a joint venture between Parks Australia and CSIRO, Canberra, ACT, Australia
| | - Lydia K. Guja
- Centre for Australian National Biodiversity Research, a joint venture between Parks Australia and CSIRO, Canberra, ACT, Australia
- National Seed Bank, Australian National Botanic Gardens, Parks Australia, Canberra, ACT, Australia
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45
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Blasio F, Prieto P, Pradillo M, Naranjo T. Genomic and Meiotic Changes Accompanying Polyploidization. PLANTS (BASEL, SWITZERLAND) 2022; 11:125. [PMID: 35009128 PMCID: PMC8747196 DOI: 10.3390/plants11010125] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 05/04/2023]
Abstract
Hybridization and polyploidy have been considered as significant evolutionary forces in adaptation and speciation, especially among plants. Interspecific gene flow generates novel genetic variants adaptable to different environments, but it is also a gene introgression mechanism in crops to increase their agronomical yield. An estimate of 9% of interspecific hybridization has been reported although the frequency varies among taxa. Homoploid hybrid speciation is rare compared to allopolyploidy. Chromosome doubling after hybridization is the result of cellular defects produced mainly during meiosis. Unreduced gametes, which are formed at an average frequency of 2.52% across species, are the result of altered spindle organization or orientation, disturbed kinetochore functioning, abnormal cytokinesis, or loss of any meiotic division. Meiotic changes and their genetic basis, leading to the cytological diploidization of allopolyploids, are just beginning to be understood especially in wheat. However, the nature and mode of action of homoeologous recombination suppressor genes are poorly understood in other allopolyploids. The merger of two independent genomes causes a deep modification of their architecture, gene expression, and molecular interactions leading to the phenotype. We provide an overview of genomic changes and transcriptomic modifications that particularly occur at the early stages of allopolyploid formation.
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Affiliation(s)
- Francesco Blasio
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4048, 14080 Cordova, Spain;
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Tomás Naranjo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
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Jiang Y, Ju T, Neaves LE, Li J, Tan W, Huang Y, Liu Y, Mao K. Distinct Genetic Structure Reflects Ploidy Level Differentiation in Newly Discovered, Extremely Small Populations of Xanthocyparis vietnamensis from Southwestern China. Front Genet 2021; 12:733576. [PMID: 34790221 PMCID: PMC8591046 DOI: 10.3389/fgene.2021.733576] [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: 06/30/2021] [Accepted: 09/15/2021] [Indexed: 11/23/2022] Open
Abstract
Population genetic assessment is crucial for the conservation and management of threatened species. Xanthocyparis vietnamensis is an endangered species that is currently restricted to karst mountains in southwestern China and Vietnam. This rare conifer was first recorded in 2002 from northern Vietnam and then in 2013 from Guangxi, China, yet nothing is known about its genetic diversity nor ploidy level variation, although previous cytological study suggest that Vietnamese populations are tetraploids. There have been about 45 individuals found to date in Guangxi, China. Here, we genotyped 33 X. vietnamensis individuals using 20 newly developed, polymorphic microsatellite loci, to assess the genetic variability of its extremely small populations. The genetic diversity of X. vietnamensis (HE = 0.511) was lower than that of two other heliophile species, Calocedrus macrolepis and Fokienia hodginsii, which have similar distribution ranges. This is consistent with the signature of a genetic bottleneck detected in X. vietnamensis. Although the population genetic differentiation coefficient across loci is moderate (FST = 0.125), STRUCTURE analysis revealed two distinct genetic clusters, namely the northern and southern population groups; DAPC analysis grouped the southern populations together in one cluster separate from the northern populations; AMOVA analysis detected a significant genetic differentiation between the two population groups (FRT = 0.089, p < 0.05), and BARRIER analysis detected a genetic barrier between them. Moreover, we detected differentiation in ploidy level between northern and southern populations, sampled individuals from the former and the later are all diploid and tetraploid cytotypes with mean genome sizes of 26.08 and 48.02 pg/2C, respectively. We deduced that heterogeneous geomorphology and historical events (e.g., human deforestation, Quaternary climate oscillations) may have contributed to population fragmentation and small population size in X. vietnamensis. Considering both genetic and ploidy level differentiation, we propose that two different management units (northern and southern) should be considered and a combination of in situ and ex situ conservation measures should be employed to preserve populations of this endangered species in southwestern China in the light of our findings.
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Affiliation(s)
- Yuliang Jiang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Tsam Ju
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Linda E Neaves
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Weining Tan
- Administration of Mulun National Nature Reserve of Guangxi, Huanjiang, China
| | - Yusong Huang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, China
| | - Yan Liu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guangxi Institute of Botany, Guilin, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
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47
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Neither connectivity nor genetic diversity matter in the conservation of a rare fern and a moss on insular erratic boulders. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01414-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractErratic boulders provide habitat for rock-dwelling species and contribute to the biodiversity of landscapes. In the calcareous Swiss lowlands, siliceous erratic boulders are exclusive habitat islands for the regionally critically endangered fern Asplenium septentrionale, about 20 bryophyte species and numerous lichens. Focusing on island biogeographical processes, we analysed the conservation genomics of A. septentrionale and the moss Hedwigia ciliata on insular erratic boulders in the Swiss lowlands and the adjacent “mainland” in siliceous mountains. We genotyped both species using double digest restriction associated DNA sequencing (ddRAD). For the tetraploid A. septentrionale, abundant identical multilocus genotypes within populations suggested prevalent intragametophytic selfing, and six out of eight boulder populations consisting of a single multilocus genotype each indicated single spore founder events. The genetic structure of A. septentrionale mainland populations coincided with Pleistocene glacial refugia. Four genetic lineages of H. ciliata were identified, and populations consisting of a single multilocus genotype were less common than in A. septentrionale. For both taxa, multilocus genotype diversity on boulders was lower than in mainland populations. The absence of common genetic groups among boulder populations, and the absence of isolation by distance patterns, suggested colonisation of boulders through independent long-distance dispersal events. Successful boulder colonisation of A. septentrionale seems to be rare, while colonisation by H. ciliata appears to be more frequent. We conclude that pivotal principles of conservation biology, such as connectivity and genetic diversity, are of less importance for the studied cryptogams on insular erratic boulders because of long-distance dispersal, intragametophytic selfing and polyploidy.
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48
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Subedi M, Neff E, Davis TM. Developing Chenopodium ficifolium as a potential B genome diploid model system for genetic characterization and improvement of allotetraploid quinoa (Chenopodium quinoa). BMC PLANT BIOLOGY 2021; 21:490. [PMID: 34696717 PMCID: PMC8543794 DOI: 10.1186/s12870-021-03270-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Quinoa (Chenopodium quinoa) is a high-value grain known for its excellent nutritional balance. It is an allotetraploid species (AABB, 2n = 4x = 36) formed by the hybridization between AA and BB genome diploid (2n = 2x = 18) species. This study reports genetic studies in Chenopodium ficifolium as a potential B genome diploid model system to simplify the genetic studies of quinoa including gene identification and marker-assisted breeding. RESULTS Portsmouth, New Hampshire and Quebec City, Quebec accessions of C. ficifolium were used to develop an F2 population segregating for agronomically relevant traits including flowering time, plant height, the number of branches, branch angle, and internode length. Marker-trait associations were identified for the FLOWERING LOCUS T-LIKE 1 (FTL1) marker gene, where the alternate alleles (A1/A2) were segregating among the F2 generation plants in association with flowering time, plant height, and the number of branches. There was a strong correlation of the flowering time trait with both plant height and the number of branches. Thus, a possible multifaceted functional role for FTL1 may be considered. The parental Portsmouth and Quebec City accessions were homozygous for the alternate FTL1 alleles, which were found to be substantially diverged. SNPs were identified in the FTL1 coding sequence that could have some functional significance in relation to the observed trait variation. CONCLUSION These results draw further attention to the possible functional roles of the FTL1 locus in Chenopodium and justify continued exploration of C. ficifolium as a potential diploid model system for the genetic study of quinoa. We expect our findings to aid in quinoa breeding as well as to any studies related to the Chenopodium genus.
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Affiliation(s)
- Madhav Subedi
- Department of Biological Sciences, University of New Hampshire, Durham, USA.
| | - Erin Neff
- Department of Biological Sciences, University of New Hampshire, Durham, USA
| | - Thomas M Davis
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, USA
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49
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Karunarathne P, Hojsgaard D. Single Independent Autopolyploidization Events From Distinct Diploid Gene Pools and Residual Sexuality Support Range Expansion of Locally Adapted Tetraploid Genotypes in a South American Grass. Front Genet 2021; 12:736088. [PMID: 34671384 PMCID: PMC8520906 DOI: 10.3389/fgene.2021.736088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/07/2021] [Indexed: 12/02/2022] Open
Abstract
Polyploidy plays a major role in plant evolution. The establishment of new polyploids is often a consequence of a single or few successful polyploidization events occurring within a species’ evolutionary trajectory. New polyploid lineages can play different roles in plant diversification and go through several evolutionary stages influenced by biotic and abiotic constraints and characterized by extensive genetic changes. The study of such changes has been crucial for understanding polyploid evolution. Here, we use the multiploid-species Paspalum intermedium to study population-level genetic and morphological variation and ecological differentiation in polyploids. Using flow cytometry, amplified fragment length polymorphism (AFLP) genetic markers, environmental variables, and morphological data, we assessed variations in ploidy, reproductive modes, and the genetic composition in 35 natural populations of P. intermedium along a latitudinal gradient in South America. Our analyses show that apomictic auto-tetraploids are of multiple independent origin. While overall genetic variation was higher in diploids, both diploids and tetraploids showed significant variation within and among populations. The spatial distribution of genetic variation provides evidence for a primary origin of the contact zone between diploids and tetraploids and further supports the hypothesis of geographic displacement between cytotypes. In addition, a strong link between the ecological differentiation of cytotypes and spatial distribution of genetic variation was observed. Overall, the results indicate that polyploidization in P. intermedium is a recurrent phenomenon associated to a shift in reproductive mode and that multiple polyploid lineages from genetically divergent diploids contributed to the successful establishment of local polyploid populations and dispersal into new environments.
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Affiliation(s)
- Piyal Karunarathne
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.,Georg-August University School of Science, University of Goettingen, Goettingen, Germany.,Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.,Taxonomy & Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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50
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Suissa JS, Kinosian SP, Schafran PW, Bolin JF, Taylor WC, Zimmer EA. Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex. Mol Phylogenet Evol 2021; 166:107332. [PMID: 34687842 DOI: 10.1016/j.ympev.2021.107332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Abstract
Polyploidy and hybridization are important processes in seed-free plant evolution. However, a major gap lies in our understanding of how these processes affect the evolutionary history of high-ploidy systems. The heterosporous lycophyte genus Isoëtes is a lineage with many putative hybrids and high-level polyploid taxa (ranging from tetraploid to dodecaploid). Here, we use a complex of western North American Isoëtes, to understand the role of hybridization and high-level polyploidy in generating and maintaining novel diversity. To uncover these processes, we use restriction-site associated DNA sequencing (RADseq), multiple alleles of a single low-copy nuclear marker, whole plastomes, cytology (genome size estimates and chromosome counts), and reproductive status (fertile or sterile). With this dataset, we show that hybridization occurs easily between species in this complex and is bidirectional between identical, but not different, cytotypes. Furthermore, we show that fertile allopolyploids appear to have formed repeatedly from sterile homoploid and interploid hybrids. We propose that low prezygotic reproductive barriers and a high frequency of whole-genome duplication allow for high-level polyploid systems to generate novel lineages, and that these mechanisms may be important in shaping extant Isoëtes diversity.
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Affiliation(s)
- Jacob S Suissa
- The Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; The Arnold Arboretum of Harvard University, Boston, MA, USA; Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Sylvia P Kinosian
- Department of Biology & Ecology Center, Utah State University, Logan, UT, USA
| | - Peter W Schafran
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Boyce Thompson Institute, Ithaca, NY, USA
| | - Jay F Bolin
- Department of Biology, Catawba College, Salisbury, NC, USA
| | - W Carl Taylor
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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