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Dias S, Souza RC, Vasconcelos EV, Vasconcelos S, da Silva Oliveira AR, do Vale Martins L, de Oliveira Bustamante F, da Costa VA, Souza G, da Costa AF, Benko-Iseppon AM, Knytl M, Brasileiro-Vidal AC. Cytomolecular diversity among Vigna Savi (Leguminosae) subgenera. PROTOPLASMA 2024:10.1007/s00709-024-01944-z. [PMID: 38467939 DOI: 10.1007/s00709-024-01944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
The genus Vigna (Leguminosae) comprises about 150 species grouped into five subgenera. The present study aimed to improve the understanding of karyotype diversity and evolution in Vigna, using new and previously published data through different cytogenetic and DNA content approaches. In the Vigna subgenera, we observed a random distribution of rDNA patterns. The 35S rDNA varied in position, from terminal to proximal, and in number, ranging from one (V. aconitifolia, V. subg. Ceratotropis) to seven pairs (V. unguiculata subsp. unguiculata, V. subg. Vigna). On the other hand, the number of 5S rDNA was conserved (one or two pairs), except for V. radiata (V. subg. Ceratotropis), which had three pairs. Genome size was relatively conserved within the genus, ranging from 1C = 0.43 to 0.70 pg in V. oblongifolia and V. unguiculata subsp. unguiculata, respectively, both belonging to V. subg. Vigna. However, we observed a positive correlation between DNA content and the number of 35S rDNA sites. In addition, data from chromosome-specific BAC-FISH suggest that the ancestral 35S rDNA locus is conserved on chromosome 6 within Vigna. Considering the rapid diversification in the number and position of rDNA sites, such conservation is surprising and suggests that additional sites may have spread out from this ancestral locus.
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Affiliation(s)
- Sibelle Dias
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Rosilda Cintra Souza
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | | | | | - Lívia do Vale Martins
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Campus Amilcar Ferreira Sobral, Universidade Federal Do Piauí, Floriano, PI, Brazil
| | - Fernanda de Oliveira Bustamante
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade Do Estado de Minas Gerais - Unidade Divinópolis, Divinópolis, MG, Brazil
| | - Victor Alves da Costa
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Gustavo Souza
- Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Martin Knytl
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4K1, Canada
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843, Czech Republic
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Ho WK, Tanzi AS, Sang F, Tsoutsoura N, Shah N, Moore C, Bhosale R, Wright V, Massawe F, Mayes S. A genomic toolkit for winged bean Psophocarpus tetragonolobus. Nat Commun 2024; 15:1901. [PMID: 38429275 PMCID: PMC10907731 DOI: 10.1038/s41467-024-45048-x] [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: 02/13/2022] [Accepted: 01/12/2024] [Indexed: 03/03/2024] Open
Abstract
A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed 'the soybean for the tropics'. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.
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Affiliation(s)
- Wai Kuan Ho
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Alberto Stefano Tanzi
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Fei Sang
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Niki Tsoutsoura
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Niraj Shah
- Digital and Technology Services, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Christopher Moore
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Rahul Bhosale
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Victoria Wright
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Festo Massawe
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Sean Mayes
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
- International Centre for Research in the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India.
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Záveská E, Šída O, Leong-Škorničková J, Chumová Z, Trávníček P, Newman MF, Poulsen AD, Böhmová A, Chudáčková H, Fér T. Testing the large genome constraint hypothesis in tropical rhizomatous herbs: life strategies, plant traits and habitat preferences in gingers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1223-1238. [PMID: 37991980 DOI: 10.1111/tpj.16559] [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: 02/08/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Plant species with large genomes tend to be excluded from climatically more extreme environments with a shorter growing season. Species that occupy such environments are assumed to be under natural selection for more rapid growth and smaller genome size (GS). However, evidence for this is available only for temperate organisms. Here, we study the evolution of GS in two subfamilies of the tropical family Zingiberaceae to find out whether species with larger genomes are confined to environments where the vegetative season is longer. We tested our hypothesis on 337 ginger species from regions with contrasting climates by correlating their GS with an array of plant traits and environmental variables. We revealed 16-fold variation in GS which was tightly related to shoot seasonality. Negative correlations of GS with latitude, temperature and precipitation emerged in the subfamily Zingiberoidae, demonstrating that species with larger GS are excluded from areas with a shorter growing season. In the subfamily Alpinioideae, GS turned out to be correlated with the type of stem and light requirements and its members cope with seasonality mainly by adaptation to shady and moist habitats. The Ornstein-Uhlenbeck models suggested that evolution in regions with humid climates favoured larger GS than in drier regions. Our results indicate that climate seasonality exerts an upper constraint on GS not only in temperate regions but also in the tropics, unless species with large genomes find alternative ways to escape from that constraint.
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Affiliation(s)
- E Záveská
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - O Šída
- Department of Botany, National Museum in Prague, Prague, Czech Republic
| | - J Leong-Škorničková
- The Herbarium, Singapore Botanic Gardens, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Z Chumová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - P Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - M F Newman
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - A D Poulsen
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - A Böhmová
- Department of Botany, National Museum in Prague, Prague, Czech Republic
- Department of Botany, Charles University, Prague, Czech Republic
| | - H Chudáčková
- Department of Botany, Charles University, Prague, Czech Republic
| | - T Fér
- Department of Botany, Charles University, Prague, Czech Republic
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Gálvez-Galván A, Garrido-Ramos MA, Prieto P. Bread wheat satellitome: a complex scenario in a huge genome. PLANT MOLECULAR BIOLOGY 2024; 114:8. [PMID: 38291213 PMCID: PMC10827815 DOI: 10.1007/s11103-023-01404-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/01/2023] [Indexed: 02/01/2024]
Abstract
In bread wheat (Triticum aestivum L.), chromosome associations during meiosis are extremely regulated and initiate at the telomeres and subtelomeres, which are enriched in satellite DNA (satDNA). We present the study and characterization of the bread wheat satellitome to shed light on the molecular organization of wheat subtelomeres. Our results revealed that the 2.53% of bread wheat genome is composed by satDNA and subtelomeres are particularly enriched in such DNA sequences. Thirty-four satellite DNA (21 for the first time in this work) have been identified, analyzed and cytogenetically validated. Many of the satDNAs were specifically found at particular subtelomeric chromosome regions revealing the asymmetry in subtelomere organisation among the wheat subgenomes, which might play a role in proper homologous recognition and pairing during meiosis. An integrated physical map of the wheat satellitome was also constructed. To the best of our knowledge, our results show that the combination of both cytogenetics and genome research allowed the first comprehensive analysis of the wheat satellitome, shedding light on the complex wheat genome organization, especially on the polymorphic nature of subtelomeres and their putative implication in chromosome recognition and pairing during meiosis.
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Affiliation(s)
- Ana Gálvez-Galván
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda. Menéndez Pidal, Campus Alameda del Obispo S/N, 14004, Córdoba, Spain
| | - Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain.
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda. Menéndez Pidal, Campus Alameda del Obispo S/N, 14004, Córdoba, Spain.
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Maybery-Reupert K, Isenegger D, Hayden M, Cogan N. Development of genomic resources for Rhodes grass ( Chloris gayana), draft genome and annotated variant discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1239290. [PMID: 37731974 PMCID: PMC10507473 DOI: 10.3389/fpls.2023.1239290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023]
Abstract
Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid.
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Affiliation(s)
- Kellie Maybery-Reupert
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Daniel Isenegger
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Pyšek P, Lučanová M, Dawson W, Essl F, Kreft H, Leitch IJ, Lenzner B, Meyerson LA, Pergl J, van Kleunen M, Weigelt P, Winter M, Guo WY. Small genome size and variation in ploidy levels support the naturalization of vascular plants but constrain their invasive spread. THE NEW PHYTOLOGIST 2023; 239:2389-2403. [PMID: 37438886 DOI: 10.1111/nph.19135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
Karyological characteristics are among the traits underpinning the invasion success of vascular plants. Using 11 049 species, we tested the effects of genome size and ploidy levels on plant naturalization (species forming self-sustaining populations where they are not native) and invasion (naturalized species spreading rapidly and having environmental impact). The probability that a species naturalized anywhere in the world decreased with increasing monoploid genome size (DNA content of a single chromosome set). Naturalized or invasive species with intermediate monoploid genomes were reported from many regions, but those with either small or large genomes occurred in fewer regions. By contrast, large holoploid genome sizes (DNA content of the unreplicated gametic nucleus) constrained naturalization but favoured invasion. We suggest that a small genome is an advantage during naturalization, being linked to traits favouring adaptation to local conditions, but for invasive spread, traits associated with a large holoploid genome, where the impact of polyploidy may act, facilitate long-distance dispersal and competition with other species.
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Affiliation(s)
- Petr Pyšek
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, CZ-128 44, Czech Republic
| | - Magdalena Lučanová
- Department of Evolutionary Biology of Plants, Institute of Botany, Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-370 05, Czech Republic
| | - Wayne Dawson
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Franz Essl
- Division of Bioinvasions, Global Change & Macroecology, Department of Botany and Biodiversity Research, University of Vienna, Wien, 1030, Austria
| | - Holger Kreft
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, Göttingen, 37077, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Büsgenweg 1, Göttingen, D-37077, Germany
- Campus-Institute Data Science, Goldschmidtstraße 1, Göttingen, 37077, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Bernd Lenzner
- Division of Bioinvasions, Global Change & Macroecology, Department of Botany and Biodiversity Research, University of Vienna, Wien, 1030, Austria
| | - Laura A Meyerson
- University of Rhode Island, Natural Resources Science, 9 East Alumni Avenue, Kingston, 02881, RI, USA
| | - Jan Pergl
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, D-78464, Germany
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Patrick Weigelt
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, Göttingen, 37077, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Büsgenweg 1, Göttingen, D-37077, Germany
- Campus-Institute Data Science, Goldschmidtstraße 1, Göttingen, 37077, Germany
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig, 04103, Germany
| | - Wen-Yong Guo
- Research Centre for Global Change and Complex Ecosystems, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
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Talhinhas P, Carvalho R, Tavares S, Ribeiro T, Azinheira H, Ramos AP, Silva MDC, Monteiro M, Loureiro J, Morais-Cecílio L. Diploid Nuclei Occur throughout the Life Cycles of Pucciniales Fungi. Microbiol Spectr 2023; 11:e0153223. [PMID: 37289058 PMCID: PMC10433954 DOI: 10.1128/spectrum.01532-23] [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: 04/11/2023] [Accepted: 05/14/2023] [Indexed: 06/09/2023] Open
Abstract
Within Eukaryotes, fungi are the typical representatives of haplontic life cycles. Basidiomycota fungi are dikaryotic in extensive parts of their life cycle, but diploid nuclei are known to form only in basidia. Among Basidiomycota, the Pucciniales are notorious for presenting the most complex life cycles, with high host specialization, and for their expanded genomes. Using cytogenomic (flow cytometry and cell sorting on propidium iodide-stained nuclei) and cytogenetic (FISH with rDNA probe) approaches, we report the widespread occurrence of replicating haploid and diploid nuclei (i.e., 1C, 2C and a small proportion of 4C nuclei) in diverse life cycle stages (pycnial, aecial, uredinial, and telial) of all 35 Pucciniales species analyzed, but not in sister taxa. These results suggest that the Pucciniales life cycle is distinct from any cycle known, i.e., neither haplontic, diplontic nor haplodiplontic, corroborating patchy and disregarded previous evidence. However, the biological basis and significance of this phenomenon remain undisclosed. IMPORTANCE Within Eukaryotes, fungi are the typical representatives of haplontic life cycles, contrasting with plants and animals. As such, fungi thus contain haploid nuclei throughout their life cycles, with sexual reproduction generating a single diploid cell upon karyogamy that immediately undergoes meiosis, thus resuming the haploid cycle. In this work, using cytogenetic and cytogenomic tools, we demonstrate that a vast group of fungi presents diploid nuclei throughout their life cycles, along with haploid nuclei, and that both types of nuclei replicate. Moreover, haploid nuclei are absent from urediniospores. The phenomenon appears to be transversal to the organisms in the order Pucciniales (rust fungi) and it does not occur in neighboring taxa, but a biological explanation or function for it remains elusive.
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Affiliation(s)
- Pedro Talhinhas
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Rita Carvalho
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Sílvia Tavares
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Copenhagen, Denmark
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Teresa Ribeiro
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Helena Azinheira
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Ana Paula Ramos
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- LPVVA, Laboratório de Patologia Vegetal “Veríssimo de Almeida”, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Maria do Céu Silva
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | | | - João Loureiro
- CFE-Centre for Functional Ecology and Terra Associated Laboratory, Departamento de Ciências da Vida, Universidade de Coimbra, Coimbra, Portugal
| | - Leonor Morais-Cecílio
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
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Kim HT, Park SH, Kim JS. Dynamic hybridization between two spleenworts, Asplenium incisum and Asplenium ruprechtii in Korea. FRONTIERS IN PLANT SCIENCE 2023; 14:1116040. [PMID: 37476173 PMCID: PMC10354290 DOI: 10.3389/fpls.2023.1116040] [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: 12/05/2022] [Accepted: 05/31/2023] [Indexed: 07/22/2023]
Abstract
Natural hybridization between Asplenium incisum and A. ruprechtii has been observed in Northeast Asia and its allotetraploid species, A. castaneoviride, was reported. However, the hybridization process between the parental species and the origin of the allotetraploid taxon remains obscure. Additionally, the systematic affinities of the recently described hybrid A. bimixtum, considered to have originated from the hybridization of A. ruprechtii, A. trichomanes, and A. incisum, is unresolved owing to its similarity to A. castaneoviride. The goals of this study were to (1) investigate the hybridization between A. ruprechtii and A. incisum; (2) verify the origin of A. castaneoviride occurring in Korea, whether it independently arose from 2x sterile hybrids; and (3) elucidate the reliability of identifying A. bimixtum. Three genotypes, A. incisum, A. ruprechtii, and their hybrid, were identified based on the nuclear gene pgiC sequence and finally divided them into six types by ploidy levels: diploid A. incisum, A. ruprechtii, and four hybrid types (diploid A. × castaneoviride, triploid A. × castaneoviride, allotetraploid A. castaneoviride, and A. bimixtum). In the analyses of plastid DNA, all hybrids had an A. ruprechtii-type rbcL gene. In addition, the four plastomes of A. ruprechtii and the hybrids had high pairwise sequence identities greater than 98.48%. They increased up to 99.88% when a large deletion of A. x castaneoriviride (2x) collected from Buramsan populations was ignored. Notably, this large deletion was also found in triploid A. × castaneoviride and allotetraploid A. castaneoviride in the same populations. Sequence data of the nuclear and plastid genes showed that hybridization is unidirectional, and A. ruprechtii is the maternal parent. The large deletion of rpoC2-rps2 commonly found in the different ploidy hybrids of the Buramsan population suggests that the allotetraploid A. castaneoviride can be created independently from sterile hybrids. We assume that both polyploidization driving allopolyploidy and minority cytotype exclusion took place independently in the population, since A castaenoviride co-occurs with A. ruprechtii in small populations. Furthermore, it was also observed that an enlarged noncoding region in fern organelle (ENRIFO) of the plastome was found in the genus Asplenium.
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Affiliation(s)
- Hyoung Tae Kim
- Department of Ecological and Environmental System, Kyungpook National University, Sangju, Republic of Korea
| | - Sang Hee Park
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jung Sung Kim
- Department of Forest Science, Chungbuk National University, Cheongju, Republic of Korea
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Hutang GR, Tong Y, Zhu XG, Gao LZ. Genome size variation and polyploidy prevalence in the genus Eragrostis are associated with the global dispersal in arid area. FRONTIERS IN PLANT SCIENCE 2023; 14:1066925. [PMID: 36993864 PMCID: PMC10040770 DOI: 10.3389/fpls.2023.1066925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Biologists have long debated the drivers of the genome size evolution and variation ever since Darwin. Assumptions for the adaptive or maladaptive consequences of the associations between genome sizes and environmental factors have been proposed, but the significance of these hypotheses remains controversial. Eragrostis is a large genus in the grass family and is often used as crop or forage during the dry seasons. The wide range and complex ploidy levels make Eragrostis an excellent model for investigating how the genome size variation and evolution is associated with environmental factors and how these changes can ben interpreted. METHODS We reconstructed the Eragrostis phylogeny and estimated genome sizes through flow cytometric analyses. Phylogenetic comparative analyses were performed to explore how genome size variation and evolution is related to their climatic niches and geographical ranges. The genome size evolution and environmental factors were examined using different models to study the phylogenetic signal, mode and tempo throughout evolutionary history. RESULTS Our results support the monophyly of Eragrostis. The genome sizes in Eragrostis ranged from ~0.66 pg to ~3.80 pg. We found that a moderate phylogenetic conservatism existed in terms of the genome sizes but was absent from environmental factors. In addition, phylogeny-based associations revealed close correlations between genome sizes and precipitation-related variables, indicating that the genome size variation mainly caused by polyploidization may have evolved as an adaptation to various environments in the genus Eragrostis. CONCLUSION This is the first study to take a global perspective on the genome size variation and evolution in the genus Eragrostis. Our results suggest that the adaptation and conservatism are manifested in the genome size variation, allowing the arid species of Eragrostis to spread the xeric area throughout the world.
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Affiliation(s)
- Ge-Ran Hutang
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Tong
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xun-Ge Zhu
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Zhi Gao
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, College of Tropical Crops, Hainan University, Haikou, China
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10
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Shi M, Wang Y, Olvera-Vazquez SG, Iñiguez JC, Thein MS, Watanabe KN. Comparison of Chayote ( Sechium edule (Jacq.) Sw.) Accessions from Mexico, Japan, and Myanmar Using Reproductive Characters and Microsatellite Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:476. [PMID: 36771559 PMCID: PMC9919900 DOI: 10.3390/plants12030476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Promoting neglected and underutilized crop species is a possible solution to deal with the complex challenges of global food security. Chayote is a Neglected and Underutilized Cucurbit Species (NUCuS), which is recognized as a fruit vegetable in Latin America and is widely grown in Asia and Africa. However, basic biological knowledge about the crop is insufficient in scientific sources, especially outside of its center of origin. In this study, limited observations on reproductive characters were conducted, differentiating accessions from Mexico, Japan, and Myanmar. Cytological evaluation among Mexican and Japanese accessions showed that the relative nuclear DNA content is 1.55 ± 0.05 pg, the estimated genome size is 1511 at 2C/Mbp, and the observed mitotic chromosomal number is 2n = 28. The genetic diversity of 21 chayote accessions was also examined using six microsatellite markers. A global low genetic heterozygosity (Ho = 0.286 and He = 0.408) and three genetic groups were detected. The results established the basis to provide insights into chayote arrival history in Asia by looking at the crop's reproductive morphology, cytology, and genetic diversity status outside its origin center. This could help in developing sustainable utilization and conservation programs for chayote.
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Affiliation(s)
- Miao Shi
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Yihang Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Sergio Gabriel Olvera-Vazquez
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
- GQE-Le Moulon, INRAe et University Paris-Saclay, Bâtiment Bréguet, 3 Rue Joliot Curie 2e ét, 91190 Gif-sur-Yvette, France
| | - Jorge Cadena Iñiguez
- Colegio de Postgraduados, Campus San Luis Potosí, Salias de Hidalgo, San Luis Potosí 78622, Mexico
| | - Min San Thein
- Department of Agricultural Research, Ministry of Agriculture, Livestock and Irrigation, Yezin, Myanmar
| | - Kazuo N. Watanabe
- Tsukuba Plant Innovation Research Center, Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
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11
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Nikolova M, Aneva I, Zhelev P, Semerdjieva I, Zheljazkov VD, Vladimirov V, Stoyanov S, Berkov S, Yankova-Tsvetkova E. Metabolic Profiles, Genetic Diversity, and Genome Size of Bulgarian Population of Alkanna tinctoria. PLANTS (BASEL, SWITZERLAND) 2022; 12:111. [PMID: 36616241 PMCID: PMC9823991 DOI: 10.3390/plants12010111] [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: 11/22/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Alkanna tinctoria (L.) Tausch Boraginaceae is a medicinal plant whose root is used for its antimicrobial and anti-inflammatory properties. A. tinctoria roots have been subject to numerous studies. However, the aerial parts have been explored less. The objective of the present study was to compare the chemical profile of aerial parts and roots as well as the total alkannin content in roots of 11 populations of the species from different floristic regions of Bulgaria. Methanolic extracts from 22 samples were analyzed by GC/MS. Phenolic, fatty, and organic acids, sterols, polyols, fatty alcohols, and sugars were identified. Ononitol (4-O-methyl-myo-inositol) was found as the main compound in the aerial parts. The total alkannin content in the roots was evaluated by the spectrophotometric method and compared with that of the commercial product. Populations with high alkannin content and rich in other bioactive compounds were identified. A relatively low genetic diversity in the studied populations was observed. The present study is the first comprehensive study on metabolite profiles and genetic diversity of the Bulgarian populations of A. tinctoria. The occurrence of ononitol in the aerial parts of the species is reported for the first time, as well as the phenolic acid profiles of the species in both aerial parts and roots. The results showed that aerial parts of the plant are also promising for use as a source of valuable biologically active substances.
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Affiliation(s)
- Milena Nikolova
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Ina Aneva
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Petar Zhelev
- Department of Dendrology, University of Forestry, 1797 Sofia, Bulgaria
| | - Ivanka Semerdjieva
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Department of Botany and Agrometeorology, Agricultural University, Mendeleev 12, 4000 Plovdiv, Bulgaria
| | - Valtcho D. Zheljazkov
- Department of Crop and Soil Science, Oregon State University, 3050 SW Campus Way, 109 Crop Science, Building, Corvallis, OR 97331, USA
| | - Vladimir Vladimirov
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Botanical Garden, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Stoyan Stoyanov
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Strahil Berkov
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Elina Yankova-Tsvetkova
- Department of Plant and Fungal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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12
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Orooji F, Mirzaghaderi G, Kuo YT, Fuchs J. Variation in the Number and Position of rDNA Loci Contributes to the Diversification and Speciation in Nigella (Ranunculaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:917310. [PMID: 35812971 PMCID: PMC9261981 DOI: 10.3389/fpls.2022.917310] [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: 04/11/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Nigella is a small genus belonging to the Ranunculaceae family which is presumably originated and distributed in Aegean and the adjacent Western-Irano-Turanian region. Comparative repeat analysis of N. sativa, N. damascena and N. bucharica was performed using low-pass Illumina genomic reads followed by karyotyping and FISH mapping of seven Nigella species using the in silico identified repeats and ribosomal DNA (rDNA) probes. High- and moderate-copy repeat sequences occupy 57.52, 59.01, and 64.73% of N. sativa, N. damascena and N. bucharica genomes, respectively. Roughly, half of the genomes are retrotransposons (class I transposons), while DNA transposons (class II transposons) contributed to only about 2% of the genomes. The analyzed Nigella species possess large genomes of about 7.4 to 12.4 Gbp/1C. Only two satellite repeats in N. sativa, one in N. damascena and four in N. bucharica were identified, which were mostly (peri)centromeric and represented about 1% of each genome. A high variation in number and position of 45S rDNA loci were found among Nigella species. Interestingly, in N. hispanica, each chromosome revealed at least one 45S rDNA site and one of them occurs in hemizygous condition. Based on the chromosome numbers, genome size and (peri)centromeric satellites, three karyotype groups were observed: Two with 2n = 2x = 12 and a karyotype formula of 10m + 2t (including N. sativa, N. arvensis, N. hispanica as the first group and N. damascena and N. orientalis as the second group) and a more distant group with 2n = 2x = 14 and a karyotype formula of 8m + 2st + 4t (including N. integrifolia and N. bucharica). These karyotype groups agreed with the phylogenetic analysis using ITS and rbcL sequences. We conclude that variation in (peri)centromeric sequences, number and localization of rDNA sites as well as chromosome number (dysploidy) are involved in the diversification of the genus Nigella.
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Affiliation(s)
- Fatemeh Orooji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Yi-Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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13
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Notartomaso S, Boccella S, Antenucci N, Ricciardi F, Fazio F, Liberatore F, Scarselli P, Scioli M, Mascio G, Bruno V, Battaglia G, Nicoletti F, Maione S, Luongo L. Analgesic Activity of Cinnabarinic Acid in Models of Inflammatory and Neuropathic Pain. Front Mol Neurosci 2022; 15:892870. [PMID: 35721314 PMCID: PMC9204652 DOI: 10.3389/fnmol.2022.892870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/05/2022] [Indexed: 12/02/2022] Open
Abstract
Cinnabarinic acid (CA) is a trace kynurenine metabolite, which activates both type-4 metabotropic glutamate (mGlu4) and arylic hydrocarbon (Ah) receptors. We examined the action of CA in models of inflammatory and neuropathic pain moving from the evidence that mGlu4 receptors are involved in the regulation of pain thresholds. Systemic administration of low doses of CA (0.125 and 0.25 mg/kg, i.p.) reduced nocifensive behaviour in the second phase of the formalin test. CA-induced analgesia was abrogated in mGlu4 receptor knockout mice, but was unaffected by treatment with the Ah receptor antagonist, CH223191 (1 mg/Kg, s.c.). Acute injection of low doses of CA (0.25 mg/kg, i.p.) also caused analgesia in mice subjected to Chronic Constriction Injury (CCI) of the sciatic nerve. Electrophysiological recording showed no effect of CA on spinal cord nociceptive neurons and a trend to a lowering effect on the frequency and duration of excitation of the rostral ventromedial medulla (RVM) ON cells in CCI mice. However, local application of CH223191 or the group-III mGlu receptor antagonist, MSOP disclosed a substantial lowering and enhancing effect of CA on both populations of neurons, respectively. When repeatedly administered to CCI mice, CA retained the analgesic activity only when combined with CH223191. Repeated administration of CA plus CH223191 restrained the activity of both spinal nociceptive neurons and RVM ON cells, in full agreement with the analgesic activity. These findings suggest that CA is involved in the regulation of pain transmission, and its overall effect depends on the recruitment of mGlu4 and Ah receptors.
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Affiliation(s)
- Serena Notartomaso
- Department of Molecular Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
| | - Serena Boccella
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - N. Antenucci
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Flavia Ricciardi
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Francesco Fazio
- Department of Psychiatry and Health Science, University of California, San Diego, La Jolla, CA, United States
| | - F. Liberatore
- Department of Molecular Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
| | - P. Scarselli
- Department of Molecular Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
| | - M. Scioli
- Department of Molecular Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
| | - Giada Mascio
- Department of Molecular Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
| | - V. Bruno
- Department of Molecular Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Giuseppe Battaglia
- Department of Molecular Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Ferdinando Nicoletti
- Department of Molecular Pathology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Sabatino Maione
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
| | - Livio Luongo
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Neuromed, Pozzilli, Italy
- *Correspondence: Livio Luongo,
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14
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Bell KL, Petit RA, Cutler A, Dobbs EK, Macpherson JM, Read TD, Burgess KS, Brosi BJ. Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures. Ecol Evol 2021; 11:16082-16098. [PMID: 34824813 PMCID: PMC8601920 DOI: 10.1002/ece3.8281] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular identification of mixed-species pollen samples has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via amplicon sequencing, but whole-genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per sample and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each sample using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k-mer identification method with reference libraries constructed from full-genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 amplicon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but diverged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS-based pollen identification is the lack of representation of plant diversity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed-species pollen samples.
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Affiliation(s)
- Karen L Bell
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: School of Biological Sciences University of Western Australia Perth Australia
- Present address: CSIRO Land & Water and CSIRO Health & Biosecurity Floreat WA Australia
| | - Robert A Petit
- Division of Infectious Diseases Department of Medicine Emory University Atlanta Georgia USA
| | - Anya Cutler
- Department of Environmental Sciences Emory University Atlanta Georgia USA
| | - Emily K Dobbs
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: Department of Biology Northern Kentucky University Highland Heights Kentucky USA
| | - J Michael Macpherson
- Department of Biology Chapman University Orange California USA
- Present address: 23andMe Mountain View California USA
| | - Timothy D Read
- Division of Infectious Diseases Department of Medicine Emory University Atlanta Georgia USA
| | - Kevin S Burgess
- Department of Biology Columbus State University Columbus Georgia USA
| | - Berry J Brosi
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: Department of Biology University of Washington Seattle Washington USA
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15
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Senderowicz M, Nowak T, Rojek-Jelonek M, Bisaga M, Papp L, Weiss-Schneeweiss H, Kolano B. Descending Dysploidy and Bidirectional Changes in Genome Size Accompanied Crepis (Asteraceae) Evolution. Genes (Basel) 2021; 12:1436. [PMID: 34573417 PMCID: PMC8472258 DOI: 10.3390/genes12091436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 02/05/2023] Open
Abstract
The evolution of the karyotype and genome size was examined in species of Crepis sensu lato. The phylogenetic relationships, inferred from the plastid and nrITS DNA sequences, were used as a framework to infer the patterns of karyotype evolution. Five different base chromosome numbers (x = 3, 4, 5, 6, and 11) were observed. A phylogenetic analysis of the evolution of the chromosome numbers allowed the inference of x = 6 as the ancestral state and the descending dysploidy as the major direction of the chromosome base number evolution. The derived base chromosome numbers (x = 5, 4, and 3) were found to have originated independently and recurrently in the different lineages of the genus. A few independent events of increases in karyotype asymmetry were inferred to have accompanied the karyotype evolution in Crepis. The genome sizes of 33 Crepis species differed seven-fold and the ancestral genome size was reconstructed to be 1C = 3.44 pg. Both decreases and increases in the genome size were inferred to have occurred within and between the lineages. The data suggest that, in addition to dysploidy, the amplification/elimination of various repetitive DNAs was likely involved in the genome and taxa differentiation in the genus.
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Affiliation(s)
- Magdalena Senderowicz
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
| | - Teresa Nowak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
| | - Magdalena Rojek-Jelonek
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
| | - Maciej Bisaga
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
| | - Laszlo Papp
- Eötvös Loránd University Botanical Garden, Illés u. 25, 1083 Budapest, Hungary;
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria;
| | - Bozena Kolano
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-007 Katowice, Poland; (M.S.); (T.N.); (M.R.-J.); (M.B.)
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16
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Temsch EM, Koutecký P, Urfus T, Šmarda P, Doležel J. Reference standards for flow cytometric estimation of absolute nuclear DNA content in plants. Cytometry A 2021; 101:710-724. [PMID: 34405937 PMCID: PMC9545105 DOI: 10.1002/cyto.a.24495] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 11/11/2022]
Abstract
The estimation of nuclear DNA content has been by far the most popular application of flow cytometry in plants. Because flow cytometry measures relative fluorescence intensities of nuclei stained by a DNA fluorochrome, ploidy determination, and estimation of the nuclear DNA content in absolute units both require comparison to a reference standard of known DNA content. This implies that the quality of the results obtained depends on the standard selection and use. Internal standardization, when the nuclei of an unknown sample and the reference standard are isolated, stained, and measured simultaneously, is mandatory for precise measurements. As DNA peaks representing G1/G0 nuclei of the sample and standard appear on the same histogram of fluorescence intensity, the quotient of their position on the fluorescence intensity axis provides the quotient of DNA amounts. For the estimation of DNA amounts in absolute units, a number of well‐established standards are now available to cover the range of known plant genome sizes. Since there are different standards in use, the standard and the genome size assigned to it has always to be reported. When none of the established standards fits, the introduction of a new standard species is needed. For this purpose, the regression line approach or simultaneous analysis of the candidate standard with several established standards should be prioritized. Moreover, the newly selected standard organism has to fulfill a number of requirements: it should be easy to identify and maintain, taxonomically unambiguous, globally available, with known genome size stability, lacking problematic metabolites, suitable for isolation of sufficient amounts of nuclei, and enabling measurements with low coefficients of variation of DNA peaks, hence suitable for the preparation of high quality samples.
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Affiliation(s)
- Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
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17
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The complete chloroplast genome of Secale sylvestre (Poaceae: Triticeae). J Appl Genet 2021; 63:115-117. [PMID: 34392474 PMCID: PMC8755654 DOI: 10.1007/s13353-021-00656-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/19/2021] [Accepted: 07/27/2021] [Indexed: 11/17/2022]
Abstract
Secale sylvestre is a wild species of rye, morphologically distinct from domestic species. To draw comparisons between species based on molecular features, it is important to have high-quality sequences, especially in the case of organellar genomes. For such reason, the complete chloroplast genome of Secale sylvestre Host introd. no. 6047 will provide useful data for ecological, agricultural, and phylogenetic purposes. Here we present the complete, annotated chloroplast genome sequence of Secale sylvestre Host introd. no. 6047. The genome is 137116 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number (MW557517).
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18
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Galbraith DW. Validation of crowd-sourced plant genome size measurements. Cytometry A 2021; 101:703-706. [PMID: 34363316 DOI: 10.1002/cyto.a.24493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/11/2022]
Affiliation(s)
- David W Galbraith
- BIO5 Institute, Arizona Cancer Center, and Department of Biomedical Engineering, University of Arizona, School of Plant Sciences, Tucson, Arizona, USA
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19
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Tomaszewska P, Pellny TK, Hernández LM, Mitchell RAC, Castiblanco V, de Vega JJ, Schwarzacher T, Heslop-Harrison P(J. Flow Cytometry-Based Determination of Ploidy from Dried Leaf Specimens in Genomically Complex Collections of the Tropical Forage Grass Urochloa s. l. Genes (Basel) 2021; 12:957. [PMID: 34201593 PMCID: PMC8306847 DOI: 10.3390/genes12070957] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 01/31/2023] Open
Abstract
Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. We aimed to develop an optimized approach to determine ploidy of germplasm collection of this tropical forage grass group using dried leaf material, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Our methods enable robust identification of ploidy levels (coefficient of variation of G0/G1 peaks, CV, typically <5%). Ploidy of some 348 forage grass accessions (ploidy range from 2x to 9x), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes are used in the current breeding programs at CIAT and EMBRAPA: the 'brizantha' and 'humidicola' agamic complexes are variable, with multiple ploidy levels. Some U. brizantha accessions have odd level of ploidy (5x), and the relative differences in fluorescence values of the peak positions between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed aneuploidy.
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Affiliation(s)
- Paulina Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (T.S.); (P.H.-H.)
| | - Till K. Pellny
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; (T.K.P.); (R.A.C.M.)
| | - Luis M. Hernández
- International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia; (L.M.H.); (V.C.)
| | | | - Valheria Castiblanco
- International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia; (L.M.H.); (V.C.)
| | - José J. de Vega
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK;
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (T.S.); (P.H.-H.)
| | - Pat (J.S.) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK; (T.S.); (P.H.-H.)
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Puhl LE, Crossa J, Munilla S, Pérez-Rodríguez P, Cantet RJC. Additive genetic variance and covariance between relatives in synthetic wheat crosses with variable parental ploidy levels. Genetics 2021; 217:iyaa048. [PMID: 33724416 PMCID: PMC8045691 DOI: 10.1093/genetics/iyaa048] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/17/2020] [Indexed: 12/04/2022] Open
Abstract
Cultivated bread wheat (Triticum aestivum L.) is an allohexaploid species resulting from the natural hybridization and chromosome doubling of allotetraploid durum wheat (T. turgidum) and a diploid goatgrass Aegilops tauschii Coss (Ae. tauschii). Synthetic hexaploid wheat (SHW) was developed through the interspecific hybridization of Ae. tauschii and T. turgidum, and then crossed to T. aestivum to produce synthetic hexaploid wheat derivatives (SHWDs). Owing to this founding variability, one may infer that the genetic variances of native wild populations vs improved wheat may vary due to their differential origin and evolutionary history. In this study, we partitioned the additive variance of SHW and SHWD with respect to their breed origin by fitting a hierarchical Bayesian model with heterogeneous covariance structure for breeding values to estimate variance components for each breed category, and segregation variance. Two data sets were used to test the proposed hierarchical Bayesian model, one from a multi-year multi-location field trial of SHWD and the other comprising the two species of SHW. For the SHWD, the Bayesian estimates of additive variances of grain yield from each breed category were similar for T. turgidum and Ae. tauschii, but smaller for T. aestivum. Segregation variances between Ae. tauschii-T. aestivum and T. turgidum-T. aestivum populations explained a sizable proportion of the phenotypic variance. Bayesian additive variance components and the Best Linear Unbiased Predictors (BLUPs) estimated by two well-known software programs were similar for multi-breed origin and for the sum of the breeding values by origin for both data sets. Our results support the suitability of models with heterogeneous additive genetic variances to predict breeding values in wheat crosses with variable ploidy levels.
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Affiliation(s)
- L E Puhl
- Departamento de Métodos Cuantitativos y Sistemas de Información, Facultad de Agronomía, Universidad de Buenos Aires, 1417 Ciudad Autónoma de Buenos Aires, Argentina
| | - J Crossa
- Biometrics and Statistics Unit. International Maize and Wheat Improvement Center (CIMMYT), Carretera México -Veracruz, Km 45, Col. El Batán, CP 56237, Texcoco, Edo. de México, México
- Departamento de Estadística, Colegio de Postgraduados, Montecillo, Edo. de México, CP. 56230, México
| | - S Munilla
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires. Instituto de Investigaciones en Producción Animal (INPA), Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Ciudad Autónoma de Buenos Aires, Argentina
| | - P Pérez-Rodríguez
- Departamento de Estadística, Colegio de Postgraduados, Montecillo, Edo. de México, CP. 56230, México
| | - R J C Cantet
- Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires. Instituto de Investigaciones en Producción Animal (INPA), Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Ciudad Autónoma de Buenos Aires, Argentina
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Lunkova NF, Zhukovskaya NV, Ivanov VB. Relationship of the Holoploid DNA Content with the Life Form and Duration of Plants’ Life Cycle. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420060041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Antonova EV, Fuchs J, Röder MS. Influence of Chronic Man-made Pollution on Bromus inermis Genome Size. RUSS J ECOL+ 2020. [DOI: 10.1134/s1067413620040025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Molecular genetic analysis of spring wheat core collection using genetic diversity, population structure, and linkage disequilibrium. BMC Genomics 2020; 21:434. [PMID: 32586286 PMCID: PMC7318758 DOI: 10.1186/s12864-020-06835-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/16/2020] [Indexed: 12/20/2022] Open
Abstract
Background Wheat (Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is very important to understand the genetic diversity among global wheat genotypes. Also, understanding the genetic diversity is useful in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. Results To understand the genetic diversity in wheat, a set of 103 spring wheat genotypes which represented five different continents were used. These genotypes were genotyped using 36,720 genotyping-by-sequencing derived SNPs (GBS-SNPs) which were well distributed across wheat chromosomes. The tested 103-wheat genotypes contained three different subpopulations based on population structure, principle coordinate, and kinship analyses. A significant variation was found within and among the subpopulations based on the AMOVA. Subpopulation 1 was found to be the more diverse subpopulation based on the different allelic patterns (Na, Ne, I, h, and uh). No high linkage disequilibrium was found between the 36,720 SNPs. However, based on the genomic level, D genome was found to have the highest LD compared with the two other genomes A and B. The ratio between the number of significant LD/number of non-significant LD suggested that chromosomes 2D, 5A, and 7B are the highest LD chromosomes in their genomes with a value of 0.08, 0.07, and 0.05, respectively. Based on the LD decay, the D genome was found to be the lowest genome with the highest number of haplotype blocks on chromosome 2D. Conclusion The recent study concluded that the 103-spring wheat genotypes and their GBS-SNP markers are very appropriate for GWAS studies and QTL-mapping. The core collection comprises three different subpopulations. Genotypes in subpopulation 1 are the most diverse genotypes and could be used in future breeding programs if they have desired traits. The distribution of LD hotspots across the genome was investigated which provides useful information on the genomic regions that includes interesting genes.
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Rahman M, Baten A, Mauleon R, King GJ, Liu L, Barkla BJ. Identification, characterization and epitope mapping of proteins encoded by putative allergenic napin genes from Brassica rapa. Clin Exp Allergy 2020; 50:848-868. [PMID: 32306538 DOI: 10.1111/cea.13612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/25/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Brassica rapeseed crops contain high concentrations of oil in the seed. The remaining meal, following oil extraction, has a high protein content, but is of low value due to the presence of high amounts of napin seed storage proteins. These 2S albumin-like proteins are difficult to digest and have been identified as major allergens in humans. OBJECTIVE To comprehensively characterize the napin gene (NG) family in Brassica rapa and to gain an understanding of the structural basis of allergenicity of the expressed proteins. METHODS To identify candidate napin genes in B rapa, 2S albumin-like napin genes of Arabidopsis thaliana were used as query sequences to search for similarity against the B rapa var. pekinensis Chiifu-401 v2 and the var. trilocularis R-o-18 v1.5 genomes. Multiple sequence alignment (MSA) and epitope modelling was carried out to determine structural and evolutionary relationships of NGs and their potential allergenicity. RESULTS Four candidate napin genes in R-o-18 and ten in Chiifu-401 were identified with high sequence similarity to A thaliana napin genes. Multiple sequence alignment revealed strong conservation among the candidate genes. An epitope survey indicated high conservation of allergenic epitope motifs with known 2S albumin-like allergens. CONCLUSION Napin is thought to be responsible for a high prevalence of food allergies. Characterization of the napin gene family in B rapa will give important insight into the protein structure, and epitope modelling will help to advance studies into allergenicity including the development of precise diagnostic screenings and therapies for this potential food allergy as well as the possible manipulation of napin levels in the seed by gene editing technology.
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Affiliation(s)
- Mahmudur Rahman
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Abdul Baten
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.,Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
| | - Ramil Mauleon
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
| | - Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
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Pellicer J, Leitch IJ. The Plant DNA C-values database (release 7.1): an updated online repository of plant genome size data for comparative studies. THE NEW PHYTOLOGIST 2020; 226:301-305. [PMID: 31608445 DOI: 10.1111/nph.16261] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/08/2019] [Indexed: 05/07/2023]
Affiliation(s)
- Jaume Pellicer
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
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Barrington DS, Patel NR, Southgate MW. Inferring the impacts of evolutionary history and ecological constraints on spore size and shape in the ferns. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11339. [PMID: 32351800 PMCID: PMC7186895 DOI: 10.1002/aps3.11339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/03/2020] [Indexed: 05/27/2023]
Abstract
PREMISE In the ferns, cell size has been explored with spores, which are largely uniform within species, produced in abundance, and durable. However, spore size and shape have been variously defined, and the relationship of these traits to genome size has not been well established. Here, we explore the variation in fern spore size and shape by ploidy level and genome size. METHODS Measurements of spore dimensions for two study sets of ferns, Polystichum and Adiantum, both including diploid and tetraploid taxa, provided the basis for computing estimates of shape and size as defined here. These traits were compared between and within ploidy levels and regressed with genome size estimates from flow cytometry analysis. RESULTS All size traits were strongly correlated with genome size; the shape trait was weakly correlated. Tetraploids were larger than diploids as expected; the spores of some closely related diploid species were also significantly different in size. DISCUSSION Researchers with access to a student-grade compound microscope can develop a valid estimate of relative genome size for ferns. These estimates provide enough resolution to infer ploidy level and explore the relationship between genome size, habitat, and physiological constraints for species within ploidy level.
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Affiliation(s)
- David S. Barrington
- Pringle HerbariumUniversity of Vermont111 Jeffords HallBurlingtonVermont05405‐1737USA
| | - Nikisha R. Patel
- Ecology and Evolutionary BiologyUniversity of Connecticut75 North Eagleville RoadStorrsConnecticut06269USA
| | - Morgan W. Southgate
- Pringle HerbariumUniversity of Vermont111 Jeffords HallBurlingtonVermont05405‐1737USA
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Kirov I, Odintsov S, Omarov M, Gvaramiya S, Merkulov P, Dudnikov M, Ermolaev A, Van Laere K, Soloviev A, Khrustaleva L. Functional Allium fistulosum Centromeres Comprise Arrays of a Long Satellite Repeat, Insertions of Retrotransposons and Chloroplast DNA. FRONTIERS IN PLANT SCIENCE 2020; 11:562001. [PMID: 33193489 PMCID: PMC7644871 DOI: 10.3389/fpls.2020.562001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/07/2020] [Indexed: 05/08/2023]
Abstract
The centromere is a unique part of the chromosome combining a conserved function with an extreme variability in its DNA sequence. Most of our knowledge about the functional centromere organization is obtained from species with small and medium genome/chromosome sizes while the progress in plants with big genomes and large chromosomes is lagging behind. Here, we studied the genomic organization of the functional centromere in Allium fistulosum and A. cepa, both species with a large genome (13 Gb and 16 Gb/1C, 2n = 2x = 16) and large-sized chromosomes. Using low-depth DNA sequencing for these two species and previously obtained CENH3 immunoprecipitation data we identified two long (1.2 Kb) and high-copy repeats, AfCen1K and AcCen1K. FISH experiments showed that AfCen1K is located in all centromeres of A. fistulosum chromosomes while no AcCen1K FISH signals were identified on A. cepa chromosomes. Our molecular cytogenetic and bioinformatics survey demonstrated that these repeats are partially similar but differ in chromosomal location, sequence structure and genomic organization. In addition, we could conclude that the repeats are transcribed and their RNAs are not polyadenylated. We also observed that these repeats are associated with insertions of retrotransposons and plastidic DNA and the landscape of A. cepa and A. fistulosum centromeric regions possess insertions of plastidic DNA. Finally, we carried out detailed comparative satellitome analysis of A. cepa and A. fistulosum genomes and identified a new chromosome- and A. cepa-specific tandem repeat, TR2CL137, located in the centromeric region. Our results shed light on the Allium centromere organization and provide unique data for future application in Allium genome annotation.
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Affiliation(s)
- Ilya Kirov
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- *Correspondence: Ilya Kirov,
| | - Sergey Odintsov
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Murad Omarov
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
- National Research University Higher School of Economics, Moscow, Russia
| | - Sofya Gvaramiya
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Pavel Merkulov
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Maxim Dudnikov
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Alexey Ermolaev
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Katrijn Van Laere
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Alexander Soloviev
- Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Ludmila Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Plant Cell Engineering Laboratory, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
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Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy10010021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lupinus mutabilis (tarwi) is a species of Andean origin with high protein and oil content and regarded as a potential crop in Europe. The success in the introduction of this crop depends in part on in depth knowledge of the intra-specific genetic variability of the collections, enabling the establishment of breeding and conservation programs. In this study, we used morphological traits, Inter-Simple Sequence Repeat markers and genome size to assess genetic and genomic diversity of 23 tarwi accessions under Mediterranean conditions. Phenotypic analyses and yield component studies point out accession LM268 as that achieving the highest seed production, producing large seeds and efficiently using primary branches as an important component of total yield, similar to the L. albus cultivars used as controls. By contrast, accession JKI-L295 presents high yield concentrated on the main stem, suggesting a semi-determinate development pattern. Genetic and genomic analyses revealed important levels of diversity, however not relatable to phenotypic diversity, reflecting the recent domestication of this crop. This is the first study of genome size diversity within L. mutabilis, revealing an average size of 2.05 pg/2C (2001 Mbp) with 9.2% variation (1897–2003 Mbp), prompting further studies for the exploitation of this diversity.
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Tang Q, Xu Y, Deng C, Cheng C, Dai Z, Yang Z, Liu C, Su J. A Full-Length Reference Floral Transcriptome of Boehmeria tricuspis Provides Insights into Apomeiosis and Polyploidy. Int J Genomics 2019; 2019:4025747. [PMID: 31950027 PMCID: PMC6948294 DOI: 10.1155/2019/4025747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/21/2019] [Indexed: 01/27/2023] Open
Abstract
Boehmeria tricuspis (Hance) Makino constitutes a hardy herbaceous or shrubby perennial native to East Asia that includes different ploidy levels and reproductive modes (diplosporous to sexual). Although several apomeiosis-associated genes have been described, the genetic control and molecular mechanisms underlying apomeiosis remain poorly understood. Moreover, the basis of the correlation between polyploidy and apomixis has not yet been clarified. We utilized long-read sequencing to produce a full-length reference floral transcriptome of B. tricuspis. Based on the generated database, gene expression of the female flowers of different ploidy levels and reproductive mode cytotypes was compared. Overall, 1,387 genes related to apomeiosis, 217 genes related to ploidy, and 9 genes associated with both apomixis and ploidy were identified. Gene Ontology analyses of this set of transcripts indicated reproductive genes, especially those related to "cell differentiation" and "cell cycle process," as significant factors regulating apomeiosis. Furthermore, our results suggested that different expressions of stress response genes might be important in the preparation for apomeiosis transition. In addition, our observations indicated that the expression of apomeiosis may not depend on polyploidy but rather on deregulation of the sexual pathway in B. tricuspis.
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Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205 Hunan, China
- Key Laboratory of Biology and Processing of Bast Fiber, Ministry of Agriculture and Rural Affairs, Changsha, 410205 Hunan, China
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Maughan PJ, Lee R, Walstead R, Vickerstaff RJ, Fogarty MC, Brouwer CR, Reid RR, Jay JJ, Bekele WA, Jackson EW, Tinker NA, Langdon T, Schlueter JA, Jellen EN. Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biol 2019; 17:92. [PMID: 31757219 PMCID: PMC6874827 DOI: 10.1186/s12915-019-0712-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat's adaptive and food quality characteristics. RESULTS The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species-including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species. CONCLUSIONS The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.
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Affiliation(s)
- Peter J Maughan
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA.
| | - Rebekah Lee
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Rachel Walstead
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | - Melissa C Fogarty
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Cory R Brouwer
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Robert R Reid
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jeremy J Jay
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | | | | | - Tim Langdon
- IBERS, Aberystwyth University, Aberystwyth, Wales, UK
| | | | - Eric N Jellen
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
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Tanzi AS, Eagleton GE, Ho WK, Wong QN, Mayes S, Massawe F. Winged bean (Psophocarpus tetragonolobus (L.) DC.) for food and nutritional security: synthesis of past research and future direction. PLANTA 2019; 250:911-931. [PMID: 30911885 DOI: 10.1007/s00425-019-03141-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Winged bean is popularly known as "One Species Supermarket" for its nutrient-dense green pods, immature seeds, tubers, leaves, and mature seeds. This underutilised crop has potential beneficial traits related to its biological nitrogen-fixation to support low-input farming. Drawing from past knowledge, and based on current technologies, we propose a roadmap for research and development of winged bean for sustainable food systems. Reliance on a handful of "major" crops has led to decreased diversity in crop species, agricultural systems and human diets. To reverse this trend, we need to encourage the greater use of minor, "orphan", underutilised species. These could contribute to an increase in crop diversity within agricultural systems, to improve human diets, and to support more sustainable and resilient food production systems. Among these underutilised species, winged bean (Psophocarpus tetragonolobus) has long been proposed as a crop for expanded use particularly in the humid tropics. It is an herbaceous perennial legume of equatorial environments and has been identified as a rich source of protein, with most parts of the plant being edible when appropriately prepared. However, to date, limited progress in structured improvement programmes has restricted the expansion of winged bean beyond its traditional confines. In this paper, we discuss the reasons for this and recommend approaches for better use of its genetic resources and related Psophocarpus species in developing improved varieties. We review studies on the growth, phenology, nodulation and nitrogen-fixation activity, breeding programmes, and molecular analyses. We then discuss prospects for the crop based on the greater understanding that these studies have provided and considering modern plant-breeding technologies and approaches. We propose a more targeted and structured research approach to fulfil the potential of winged bean to contribute to food security.
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Affiliation(s)
- Alberto Stefano Tanzi
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Graham Ewen Eagleton
- Department of Planning, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, 15011, Myanmar
| | - Wai Kuan Ho
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Quin Nee Wong
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | - Sean Mayes
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
- School of Biosciences, Faculty of Science, University of Nottingham Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Festo Massawe
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
- Crops for the Future, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia.
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Genetic Diversity and Population Structure of Bermudagrass [Cynodon dactylon (L.) Pers.] along Latitudinal Gradients and the Relationship with Polyploidy Level. DIVERSITY 2019. [DOI: 10.3390/d11080135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding the population genetic pattern and process of gene flow requires a detailed knowledge of how landscape characteristics structure populations. Although Cynodon dactylon (L.) Pers. (common bermudagrass) is widely distributed in the world, information on its genetic pattern and population structure along latitudinal gradients is limited. We tried to estimate the genetic diversity and genetic structure of C. dactylon along a latitudinal gradient across China. Genetic diversity among different ploidy levels was also compared in the study. The material used consisted of 296 C. dactylon individuals sampled from 16 geographic sites from 22°35′ N to 36°18′ N. Genetic diversity was estimated using 153 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. Higher within-population genetic diversity appeared at low-latitude, as well as having positive correlation with temperature and precipitation. The genetic diversity increased with the ploidy level of C. dactylon, suggesting polyploidy creates higher genetic diversity. No isolation by distance and notable admixture structure existed among populations along latitudes. Both seed dispersal (or vegetative organs) and extrinsic pollen played important roles for gene flow in shaping the spatial admixture population structure of C. dactylon along latitudes. In addition, populations were separated into three clusters according to ploidy levels. C. dactylon has many such biological characters of perennial growth, wind-pollination, polyploidy, low genetic differentiation among populations, sexual and asexual reproduction leading to higher genetic diversity, which gives it strong adaptability with its genetic patterns being very complex across all the sampled latitudes. The findings of this study are related to landscape population evolution, polyploidy speciation, preservation, and use of bermudagrass breeding.
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Ben Halima N. New insights into phospholipases in oat (Avena sativa) from bioinformatic analysis. Int J Biol Macromol 2019; 133:804-810. [DOI: 10.1016/j.ijbiomac.2019.04.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 11/29/2022]
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Xu Y, Sun FY, Ji C, Hu QW, Wang CY, Wu DX, Sun G. Nucleotide diversity patterns at the DREB1 transcriptional factor gene in the genome donor species of wheat (Triticum aestivum L). PLoS One 2019; 14:e0217081. [PMID: 31136598 PMCID: PMC6538315 DOI: 10.1371/journal.pone.0217081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/05/2019] [Indexed: 11/19/2022] Open
Abstract
Bread wheat (AABBDD) originated from the diploid progenitor Triticum urartu (AA), a relative of Aegilops speltoides (BB), and Ae. tauschii (DD). The DREB1 transcriptional factor plays key regulatory role in low-temperature tolerance. The modern breeding strategies resulted in serious decrease of the agricultural biodiversity, which led to a loss of elite genes underlying abiotic stress tolerance in crops. However, knowledge of this gene's natural diversity is largely unknown in the genome donor species of wheat. We characterized the dehydration response element binding protein 1 (DREB1) gene-diversity pattern in Ae. speltoides, Ae. tauschii, T. monococcum and T. urartu. The highest nucleotide diversity value was detected in Ae. speltoides, followed by Ae. tauschii and T. monococcum. The lowest nucleotide diversity value was observed in T. urartu. Nucleotide diversity and haplotype data might suggest no reduction of nucleotide diversity during T. monococcum domestication. Alignment of the 68 DREB1 sequences found a large-size (70 bp) insertion/deletion in the accession PI486264 of Ae. speltoides, which was different from the copy of sequences from other accessions of Ae. speltoides, suggesting a likely existence of two different ancestral Ae. speltoides forms. Implication of sequences variation of Ae. speltoides on origination of B genome in wheat was discussed.
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Affiliation(s)
- Yi Xu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Fang-Yao Sun
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Chun Ji
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Quan-Wen Hu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Cheng-Yu Wang
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - De-Xiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Genlou Sun
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
- Biology Department, Saint Mary’s University, Halifax, NS, Canada
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Skuza L, Szućko I, Filip E, Strzała T. Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis. PLoS One 2019; 14:e0213023. [PMID: 30811487 PMCID: PMC6392296 DOI: 10.1371/journal.pone.0213023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/13/2019] [Indexed: 11/18/2022] Open
Abstract
The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale, representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions. There was no clear genetic structure between different species and subspecies, which may indicated the introgression between these taxa. The obtained data confirmed that S. vavilovii was very similar to S. cereale, which confirmed the assumption that they might share a common ancestor. The results also confirmed the divergence of S. sylvestre from other species and subspecies of rye. Areas that may be useful molecular markers in studies on closely related species of the genus Secale were also indicated.
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Affiliation(s)
- Lidia Skuza
- Department of Molecular Biology and Cytology, The Institute for Research on Biodiversity, Faculty of Biology, University of Szczecin, Szczecin, Poland
- The Centre for Molecular Biology and Biotechnology, Faculty of Biology, University of Szczecin, Szczecin, Poland
- * E-mail:
| | - Izabela Szućko
- Department of Molecular Biology and Cytology, The Institute for Research on Biodiversity, Faculty of Biology, University of Szczecin, Szczecin, Poland
- The Centre for Molecular Biology and Biotechnology, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Ewa Filip
- Department of Molecular Biology and Cytology, The Institute for Research on Biodiversity, Faculty of Biology, University of Szczecin, Szczecin, Poland
- The Centre for Molecular Biology and Biotechnology, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Tomasz Strzała
- Department of Genetics, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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Peška V, Mandáková T, Ihradská V, Fajkus J. Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum. Int J Mol Sci 2019; 20:E733. [PMID: 30744119 PMCID: PMC6387171 DOI: 10.3390/ijms20030733] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/31/2019] [Accepted: 02/02/2019] [Indexed: 02/07/2023] Open
Abstract
Knowledge of the fascinating world of DNA repeats is continuously being enriched by newly identified elements and their hypothetical or well-established biological relevance. Genomic approaches can be used for comparative studies of major repeats in any group of genomes, regardless of their size and complexity. Such studies are particularly fruitful in large genomes, and useful mainly in crop plants where they provide a rich source of molecular markers or information on indispensable genomic components (e.g., telomeres, centromeres, or ribosomal RNA genes). Surprisingly, in Allium species, a comprehensive comparative study of repeats is lacking. Here we provide such a study of two economically important species, Allium cepa (onion), and A. sativum (garlic), and their distantly related A. ursinum (wild garlic). We present an overview and classification of major repeats in these species and have paid specific attention to sequence conservation and copy numbers of major representatives in each type of repeat, including retrotransposons, rDNA, or newly identified satellite sequences. Prevailing repeats in all three studied species belonged to Ty3/gypsy elements, however they significantly diverged and we did not detect them in common clusters in comparative analysis. Actually, only a low number of clusters was shared by all three species. Such conserved repeats were for example 5S and 45S rDNA genes and surprisingly a specific and quite rare Ty1/copia lineage. Species-specific long satellites were found mainly in A. cepa and A. sativum. We also show in situ localization of selected repeats that could potentially be applicable as chromosomal markers, e.g., in interspecific breeding.
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Affiliation(s)
- Vratislav Peška
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
| | - Terezie Mandáková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
| | - Veronika Ihradská
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
| | - Jiří Fajkus
- Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
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37
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Bell KL, Burgess KS, Botsch JC, Dobbs EK, Read TD, Brosi BJ. Quantitative and qualitative assessment of pollen
DNA
metabarcoding using constructed species mixtures. Mol Ecol 2018; 28:431-455. [DOI: 10.1111/mec.14840] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/20/2018] [Accepted: 07/28/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Karen L. Bell
- Department of Environmental Sciences Emory University Atlanta Georgia
| | - Kevin S. Burgess
- Columbus State University Department of Biology Columbus Georgia
| | | | - Emily K. Dobbs
- Department of Environmental Sciences Emory University Atlanta Georgia
| | - Timothy D. Read
- Division of Infectious Diseases Department of Human Genetics School of Medicine Emory University Atlanta Georgia
| | - Berry J. Brosi
- Department of Environmental Sciences Emory University Atlanta Georgia
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Keller B, Wicker T, Krattinger SG. Advances in Wheat and Pathogen Genomics: Implications for Disease Control. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:67-87. [PMID: 30149791 DOI: 10.1146/annurev-phyto-080516-035419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The gene pool of wheat and its wild and domesticated relatives contains a plethora of resistance genes that can be exploited to make wheat more resilient to pathogens. Only a few of these genes have been isolated and studied at the molecular level. In recent years, we have seen a shift from classical breeding to genomics-assisted breeding, which makes use of the enormous advancements in DNA sequencing and high-throughput molecular marker technologies for wheat improvement. These genomic advancements have the potential to transform wheat breeding in the near future and to significantly increase the speed and precision at which new cultivars can be bred. This review highlights the genomic improvements that have been made in wheat and its pathogens over the past years and discusses their implications for disease-resistance breeding.
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Affiliation(s)
- Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia;
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Conson ARO, Taniguti CH, Amadeu RR, Andreotti IAA, de Souza LM, dos Santos LHB, Rosa JRBF, Mantello CC, da Silva CC, José Scaloppi Junior E, Ribeiro RV, Le Guen V, Garcia AAF, Gonçalves PDS, de Souza AP. High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1255. [PMID: 30197655 PMCID: PMC6117502 DOI: 10.3389/fpls.2018.01255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/08/2018] [Indexed: 06/02/2023]
Abstract
Rubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67 to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.
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Affiliation(s)
- André R. O. Conson
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Cristiane H. Taniguti
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rodrigo R. Amadeu
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Livia M. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - João R. B. F. Rosa
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
- FTS Sementes S.A., Research and Development Center, Ponta Grossa, Brazil
| | - Camila C. Mantello
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Carla C. da Silva
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - Rafael V. Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Vincent Le Guen
- French Agricultural Research Centre for International Development (CIRAD), UMR AGAP, Montpellier, France
| | - Antonio A. F. Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Anete P. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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Neupane S, Ma Q, Mathew FM, Varenhorst AJ, Andersen EJ, Nepal MP. Evolutionary Divergence of TNL Disease-Resistant Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris). Biochem Genet 2018; 56:397-422. [PMID: 29500532 DOI: 10.1007/s10528-018-9851-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 02/21/2018] [Indexed: 10/17/2022]
Abstract
Disease-resistant genes (R genes) encode proteins that are involved in protecting plants from their pathogens and pests. Availability of complete genome sequences from soybean and common bean allowed us to perform a genome-wide identification and analysis of the Toll interleukin-1 receptor-like nucleotide-binding site leucine-rich repeat (TNL) proteins. Hidden Markov model (HMM) profiling of all protein sequences resulted in the identification of 117 and 77 regular TNL genes in soybean and common bean, respectively. We also identified TNL gene homologs with unique domains, and signal peptides as well as nuclear localization signals. The TNL genes in soybean formed 28 clusters located on 10 of the 20 chromosomes, with the majority found on chromosome 3, 6 and 16. Similarly, the TNL genes in common bean formed 14 clusters located on five of the 11 chromosomes, with the majority found on chromosome 10. Phylogenetic analyses of the TNL genes from Arabidopsis, soybean and common bean revealed less divergence within legumes relative to the divergence between legumes and Arabidopsis. Syntenic blocks were found between chromosomes Pv10 and Gm03, Pv07 and Gm10, as well as Pv01 and Gm14. The gene expression data revealed basal level expression and tissue specificity, while analysis of available microRNA data showed 37 predicted microRNA families involved in targeting the identified TNL genes in soybean and common bean.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Qin Ma
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Febina M Mathew
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Adam J Varenhorst
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.
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Martinez MA, Baack EJ, Hovick SM, Whitney KD. A reassessment of the genome size-invasiveness relationship in reed canarygrass (Phalaris arundinacea). ANNALS OF BOTANY 2018; 121:1309-1318. [PMID: 29534147 PMCID: PMC6007324 DOI: 10.1093/aob/mcy028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 02/16/2018] [Indexed: 06/13/2023]
Abstract
Background and Aims Genome size is hypothesized to affect invasiveness in plants. Key evidence comes from a previous study of invasive eastern North American populations of the grass Phalaris arundinacea: invasive genotypes with smaller genomes had higher growth rates, and genome sizes were smaller in the invasive vs. native range. This study aimed to re-investigate those patterns by examining a broader range of North American populations and by employing the modern best-practice protocol for plant genome size estimation in addition to the previously used protocol. Methods Genome sizes were measured using both internal and pseudo-internal standardization protocols for 20 invasive and nine native range accessions of P. arundinacea. After a round of vegetative propagation to reduce maternal environmental effects, growth (stem elongation) rates of these accessions were measured in the greenhouse. Key Results Using the best-practice protocol, there was no evidence of a correlation between genome size and growth rates (P = 0.704), and no evidence for differences in genome sizes of invasive and native range accessions (P > 0.353). However, using the older genome size estimation protocol, both relationships were significant (reproducing the results of the previous study). Conclusions Genome size reduction has not driven increased invasiveness in a broad sample of North American P. arundinacea. Further, inappropriate genome size estimation techniques can create spurious correlations between genome size and plant traits such as growth rate. Valid estimation is vital to progress in understanding the potentially widespread effects of genome size on biological processes and patterns.
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Affiliation(s)
- Megan A Martinez
- Department of Biology, University of New Mexico, Albuquerque, NM USA
| | - Eric J Baack
- Department of Biology, Luther College, Decorah, IA USA
| | - Stephen M Hovick
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH USA
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM USA
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Buerstmayr M, Steiner B, Wagner C, Schwarz P, Brugger K, Barabaschi D, Volante A, Valè G, Cattivelli L, Buerstmayr H. High-resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTL Qfhs.ifa-5A. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1046-1056. [PMID: 29024288 PMCID: PMC5902775 DOI: 10.1111/pbi.12850] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/17/2017] [Accepted: 10/08/2017] [Indexed: 05/24/2023]
Abstract
The Qfhs.ifa-5A allele, contributing to enhanced Fusarium head blight resistance in wheat, resides in a low-recombinogenic region of chromosome 5A close to the centromere. A near-isogenic RIL population segregating for the Qfhs.ifa-5A resistance allele was developed and among 3650 lines as few as four recombined within the pericentromeric C-5AS1-0.40 bin, yielding only a single recombination point. Genetic mapping of the pericentromeric region using a recombination-dependent approach was thus not successful. To facilitate fine-mapping the physically large Qfhs.ifa-5A interval, two gamma-irradiated deletion panels were generated: (i) seeds of line NIL3 carrying the Qfhs.ifa-5A resistance allele in an otherwise susceptible background were irradiated and plants thereof were selfed to obtain deletions in homozygous state and (ii) a radiation hybrid panel was produced using irradiated pollen of the wheat line Chinese Spring (CS) for pollinating the CS-nullisomic5Atetrasomic5B. In total, 5157 radiation selfing and 276 radiation hybrid plants were screened for deletions on 5AS and plants containing deletions were analysed using 102 5AS-specific markers. Combining genotypic information of both panels yielded an 817-fold map improvement (cR/cM) for the centromeric bin and was 389-fold increased across the Qfhs.ifa-5A interval compared to the genetic map, with an average map resolution of 0.77 Mb/cR. We successfully proved that the RH mapping technique can effectively resolve marker order in low-recombining regions, including pericentromeric intervals, and simultaneously allow developing an in vivo panel of sister lines differing for induced deletions across the Qfhs.ifa-5A interval that can be used for phenotyping.
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Affiliation(s)
- Maria Buerstmayr
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Barbara Steiner
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Christian Wagner
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Petra Schwarz
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Klaus Brugger
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Delfina Barabaschi
- Council for Agricultural Research and Economics (CREA)Genomics Research CentreFiorenzuola d'ArdaItaly
| | - Andrea Volante
- Council for Agricultural Research and Economics (CREA)Research Centre for Cereal and Industrial CropsVercelliItaly
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CREA)Research Centre for Cereal and Industrial CropsVercelliItaly
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA)Genomics Research CentreFiorenzuola d'ArdaItaly
| | - Hermann Buerstmayr
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
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43
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Eltaher S, Sallam A, Belamkar V, Emara HA, Nower AA, Salem KFM, Poland J, Baenziger PS. Genetic Diversity and Population Structure of F 3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing. Front Genet 2018; 9:76. [PMID: 29593779 PMCID: PMC5857551 DOI: 10.3389/fgene.2018.00076] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/19/2018] [Indexed: 12/21/2022] Open
Abstract
The availability of information on the genetic diversity and population structure in wheat (Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F3:6) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon’s information index (I) = 0.494, diversity index (h) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity (I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.
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Affiliation(s)
- Shamseldeen Eltaher
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States.,Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat, Egypt
| | - Ahmed Sallam
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States.,Department of Genetics, Faculty of Agriculture, Assiut University, Assuit, Egypt
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Hamdy A Emara
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat, Egypt
| | - Ahmed A Nower
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat, Egypt
| | - Khaled F M Salem
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat, Egypt.,Department of Biology, College of Science and Humanitarian Studies, Shaqra University, Qwaieah, Saudi Arabia
| | - Jesse Poland
- Hard Winter Wheat Genetics Research Unit, Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Peter S Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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44
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Schmidt JP, Drake JM, Stephens P. Residence time, native range size, and genome size predict naturalization among angiosperms introduced to Australia. Ecol Evol 2017; 7:10289-10300. [PMID: 29238555 PMCID: PMC5723587 DOI: 10.1002/ece3.3505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/30/2017] [Accepted: 09/01/2017] [Indexed: 11/11/2022] Open
Abstract
Although critical to progress in understanding (i) if, and (ii) at what rate, introduced plants will naturalize and potentially become invasive, establishing causal links between traits and invasion success is complicated by data gaps, phylogenetic nonindependence of species, the inability to control for differences between species in residence time and propagule pressure, and covariance among traits. Here, we focus on statistical relationships between genomic factors, life history traits, native range size, and naturalization status of angiosperms introduced to Australia. In a series of analyses, we alternately investigate the role of phylogeny, incorporate introduction history, and use graphical models to explore the network of conditional probabilities linking traits and introduction history to naturalization status. Applying this ensemble of methods to the largest publicly available data set on plant introductions and their fates, we found that, overall, residence time and native range size best predicted probability of naturalization. Yet, importantly, probability of naturalization consistently increased as genome size decreased, even when the effects of shared ancestry and residence time in Australia were accounted for, and that this pattern was stronger in species without a history of cultivation, but present across annual-biennials, and herbaceous and woody perennials. Thus, despite introduction biases and indirect effects of traits via introduction history, across analyses, reduced genome size was nevertheless consistently associated with a tendency to naturalize.
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Affiliation(s)
| | - John M. Drake
- Odum School of EcologyUniversity of GeorgiaAthensGAUSA
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45
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Paternò A, Verginelli D, Bonini P, Misto M, Quarchioni C, Dainese E, Peddis S, Fusco C, Vinciguerra D, Marchesi U. In-House Validation and Comparison of Two Wheat (Triticum aestivum) Taxon-Specific Real-Time PCR Methods for GMO Quantification Supported by Droplet Digital PCR. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-1097-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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46
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Uauy C, Wulff BB, Dubcovsky J. Combining Traditional Mutagenesis with New High-Throughput Sequencing and Genome Editing to Reveal Hidden Variation in Polyploid Wheat. Annu Rev Genet 2017; 51:435-454. [DOI: 10.1146/annurev-genet-120116-024533] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Brande B.H. Wulff
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Jorge Dubcovsky
- Howard Hughes Medical Institute and Department of Plant Sciences, University of California, Davis, California 95616, USA
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47
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Swathy PS, Rupal G, Prabhu V, Mahato KK, Muthusamy A. In vitro culture responses, callus growth and organogenetic potential of brinjal ( Solanum melongena L.) to He-Ne laser irradiation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 174:333-341. [DOI: 10.1016/j.jphotobiol.2017.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 01/23/2023]
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48
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Hittalmani S, Mahesh HB, Shirke MD, Biradar H, Uday G, Aruna YR, Lohithaswa HC, Mohanrao A. Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties. BMC Genomics 2017; 18:465. [PMID: 28619070 PMCID: PMC5472924 DOI: 10.1186/s12864-017-3850-z] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/07/2017] [Indexed: 12/18/2022] Open
Abstract
Background Finger millet (Eleusine coracana (L.) Gaertn.) is an important staple food crop widely grown in Africa and South Asia. Among the millets, finger millet has high amount of calcium, methionine, tryptophan, fiber, and sulphur containing amino acids. In addition, it has C4 photosynthetic carbon assimilation mechanism, which helps to utilize water and nitrogen efficiently under hot and arid conditions without severely affecting yield. Therefore, development and utilization of genomic resources for genetic improvement of this crop is immensely useful. Results Experimental results from whole genome sequencing and assembling process of ML-365 finger millet cultivar yielded 1196 Mb covering approximately 82% of total estimated genome size. Genome analysis showed the presence of 85,243 genes and one half of the genome is repetitive in nature. The finger millet genome was found to have higher colinearity with foxtail millet and rice as compared to other Poaceae species. Mining of simple sequence repeats (SSRs) yielded abundance of SSRs within the finger millet genome. Functional annotation and mining of transcription factors revealed finger millet genome harbors large number of drought tolerance related genes. Transcriptome analysis of low moisture stress and non-stress samples revealed the identification of several drought-induced candidate genes, which could be used in drought tolerance breeding. Conclusions This genome sequencing effort will strengthen plant breeders for allele discovery, genetic mapping, and identification of candidate genes for agronomically important traits. Availability of genomic resources of finger millet will enhance the novel breeding possibilities to address potential challenges of finger millet improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3850-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shailaja Hittalmani
- Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India.
| | - H B Mahesh
- Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India.
| | | | - Hanamareddy Biradar
- Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India
| | - Govindareddy Uday
- Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India
| | - Y R Aruna
- Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India
| | - H C Lohithaswa
- Department of Genetics and Plant Breeding, College of Agriculture, V. C. Farm, University of Agricultural Sciences, Mandya, 571405, India
| | - A Mohanrao
- Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India
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49
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Nadolska-Orczyk A, Rajchel IK, Orczyk W, Gasparis S. Major genes determining yield-related traits in wheat and barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1081-1098. [PMID: 28314933 PMCID: PMC5440550 DOI: 10.1007/s00122-017-2880-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 02/17/2017] [Indexed: 05/20/2023]
Abstract
Current development of advanced biotechnology tools allows us to characterize the role of key genes in plant productivity. The implementation of this knowledge in breeding strategies might accelerate the progress in obtaining high-yielding cultivars. The achievements of the Green Revolution were based on a specific plant ideotype, determined by a single gene involved in gibberellin signaling or metabolism. Compared with the 1950s, an enormous increase in our knowledge about the biological basis of plant productivity has opened new avenues for novel breeding strategies. The large and complex genomes of diploid barley and hexaploid wheat represent a great challenge, but they also offer a large reservoir of genes that can be targeted for breeding. We summarize examples of productivity-related genes/mutants in wheat and barley, identified or characterized by means of modern biology. The genes are classified functionally into several groups, including the following: (1) transcription factors, regulating spike development, which mainly affect grain number; (2) genes involved in metabolism or signaling of growth regulators-cytokinins, gibberellins, and brassinosteroids-which control plant architecture and in consequence stem hardiness and grain yield; (3) genes determining cell division and proliferation mainly impacting grain size; (4) floral regulators influencing inflorescence architecture and in consequence seed number; and (5) genes involved in carbohydrate metabolism having an impact on plant architecture and grain yield. The implementation of selected genes in breeding programs is discussed, considering specific genotypes, agronomic and climate conditions, and taking into account that many of the genes are members of multigene families.
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Affiliation(s)
- Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland.
| | - Izabela K Rajchel
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Wacław Orczyk
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Sebastian Gasparis
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
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50
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Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, Clissold L, Simmonds J, Ramirez-Gonzalez RH, Wang X, Borrill P, Fosker C, Ayling S, Phillips AL, Uauy C, Dubcovsky J. Uncovering hidden variation in polyploid wheat. Proc Natl Acad Sci U S A 2017; 114:E913-E921. [PMID: 28096351 PMCID: PMC5307431 DOI: 10.1073/pnas.1619268114] [Citation(s) in RCA: 324] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations. Here we exploited this property to sequence and catalog more than 10 million mutations in the protein-coding regions of 2,735 mutant lines of tetraploid and hexaploid wheat. We detected, on average, 2,705 and 5,351 mutations per tetraploid and hexaploid line, respectively, which resulted in 35-40 mutations per kb in each population. With these mutation densities, we identified an average of 23-24 missense and truncation alleles per gene, with at least one truncation or deleterious missense mutation in more than 90% of the captured wheat genes per population. This public collection of mutant seed stocks and sequence data enables rapid identification of mutations in the different copies of the wheat genes, which can be combined to uncover previously hidden variation. Polyploidy is a central phenomenon in plant evolution, and many crop species have undergone recent genome duplication events. Therefore, the general strategy and methods developed herein can benefit other polyploid crops.
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Affiliation(s)
- Ksenia V Krasileva
- Department of Plant Sciences, University of California, Davis, CA 95616
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Paul Bailey
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | - Francine Paraiso
- Department of Plant Sciences, University of California, Davis, CA 95616
| | - Leah Clissold
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | - Ricardo H Ramirez-Gonzalez
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
- John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Xiaodong Wang
- Department of Plant Sciences, University of California, Davis, CA 95616
| | | | | | - Sarah Ayling
- The Earlham Institute, Norwich NR4 7UG, United Kingdom
| | | | | | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616;
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
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