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Guttery DS, Zeeshan M, Holder AA, Tromer EC, Tewari R. Meiosis in Plasmodium: how does it work? Trends Parasitol 2023; 39:812-821. [PMID: 37541799 DOI: 10.1016/j.pt.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 08/06/2023]
Abstract
Meiosis is sexual cell division, a process in eukaryotes whereby haploid gametes are produced. Compared to canonical model eukaryotes, meiosis in apicomplexan parasites appears to diverge from the process with respect to the molecular mechanisms involved; the biology of Plasmodium meiosis, and its regulation by means of post-translational modification, are largely unexplored. Here, we discuss the impact of technological advances in cell biology, evolutionary bioinformatics, and genome-wide functional studies on our understanding of meiosis in the Apicomplexa. These parasites, including Plasmodium falciparum, Toxoplasma gondii, and Eimeria spp., have significant socioeconomic impact on human and animal health. Understanding this key stage during the parasite's life cycle may well reveal attractive targets for therapeutic intervention.
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Affiliation(s)
- David S Guttery
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK; Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, UK.
| | - Mohammad Zeeshan
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, London, UK
| | - Eelco C Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Rita Tewari
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK.
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2
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Chen YJ, Pandey S, Catto M, Leal-Bertioli S, Abney MR, Bag S, Hopkins M, Culbreath A, Srinivasan R. Evaluation of Wild Peanut Species and Their Allotetraploids for Resistance against Thrips and Thrips-Transmitted Tomato Spotted Wilt Orthotospovirus (TSWV). Pathogens 2023; 12:1102. [PMID: 37764910 PMCID: PMC10536083 DOI: 10.3390/pathogens12091102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) causes spotted wilt disease in peanut (Arachis hypogaea L.) and limits yield. Breeding programs have been developing TSWV-resistant cultivars, but availability of sources of resistance against TSWV in cultivated germplasm is extremely limited. Diploid wild Arachis species can serve as important sources of resistance, and despite ploidy barriers (cultivated peanut is tetraploid), their usage in breeding programs is now possible because of the knowledge and development of induced interspecific allotetraploid hybrids. This study screened 10 wild diploid Arachis and six induced allotetraploid genotypes via thrips-mediated TSWV transmission assays and thrips' feeding assays in the greenhouse. Three parameters were evaluated: percent TSWV infection, virus accumulation, and temporal severity of thrips feeding injury. Results indicated that the diploid A. stenosperma accession V10309 and its derivative-induced allotetraploid ValSten1 had the lowest TSWV infection incidences among the evaluated genotypes. Allotetraploid BatDur1 had the lowest thrips-inflicted damage at each week post thrips release, while diploid A. batizocoi accession K9484 and A. duranensis accession V14167 had reduced feeding damage one week post thrips release, and diploids A. valida accession GK30011 and A. batizocoi had reduced feeding damage three weeks post thrips releasethan the others. Overall, plausible TSWV resistance in diploid species and their allotetraploid hybrids was characterized by reduced percent TSWV infection, virus accumulation, and feeding severity. Furthermore, a few diploids and tetraploid hybrids displayed antibiosis against thrips. These results document evidence for resistance against TSWV and thrips in wild diploid Arachis species and peanut-compatible-induced allotetraploids.
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Affiliation(s)
- Yi-Ju Chen
- Department of Entomology, University of Georgia, Griffin, GA 30223, USA; (Y.-J.C.); (S.P.)
| | - Sudeep Pandey
- Department of Entomology, University of Georgia, Griffin, GA 30223, USA; (Y.-J.C.); (S.P.)
| | - Michael Catto
- Department of Entomology, University of Georgia, Athens, GA 30602, USA;
| | - Soraya Leal-Bertioli
- Department of Plant Pathology, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
| | - Mark R. Abney
- Department of Entomology, University of Georgia, Tifton, GA 31794, USA;
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.B.); (A.C.)
| | - Mark Hopkins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.B.); (A.C.)
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3
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Singh L, Wu Y, McCurdy JD, Stewart BR, Warburton ML, Baldwin BS, Dong H. Genetic diversity and population structure of bermudagrass ( Cynodon spp.) revealed by genotyping-by-sequencing. Front Plant Sci 2023; 14:1155721. [PMID: 37360708 PMCID: PMC10285298 DOI: 10.3389/fpls.2023.1155721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023]
Abstract
Bermudagrass (Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. To explore diversity in bermudagrass, a total of 206 Cynodon accessions consisting of 193 common bermudagrass (C. dactylon var. dactylon) and 13 African bermudagrass (C. transvaalensis) accessions of worldwide origin were assembled for genetic characterization. Genotyping-by-sequencing (GBS) was employed for genetic marker development. With a minor allele frequency of 0.05 and a minimum call rate of 0.5, a total of 37,496 raw single nucleotide polymorphisms (SNPs) were called de novo and were used in the genetic diversity characterization. Population structure analysis using ADMIXTURE revealed four subpopulations in this germplasm panel, which was consistent with principal component analysis (PCA) and phylogenetic analysis results. The first three principal components explained 15.6%, 10.1%, and 3.8% of the variance in the germplasm panel, respectively. The first subpopulation consisted of C. dactylon accessions from various continents; the second subpopulation was comprised mainly of C. transvaalensis accessions; the third subpopulation contained C. dactylon accessions primarily of African origin; and the fourth subpopulation represented C. dactylon accessions obtained from the Oklahoma State University bermudagrass breeding program. Genetic diversity parameters including Nei's genetic distance, inbreeding coefficient, and Fst statistic revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs.
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Affiliation(s)
- Lovepreet Singh
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Yanqi Wu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - James D. McCurdy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Barry R. Stewart
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Marilyn L. Warburton
- United States Department of Agriculture – Agricultural Research Service (USDA ARS) Western Regional Plant Introduction Station, Pullman, WA, United States
| | - Brian S. Baldwin
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Hongxu Dong
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, United States
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Arora D, Hernandez AG, Walden KKO, Fields CJ, Yan G. First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing. Int J Mol Sci 2023; 24:ijms24087311. [PMID: 37108472 PMCID: PMC10138993 DOI: 10.3390/ijms24087311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Root-lesion nematodes (genus Pratylenchus) belong to a diverse group of plant-parasitic nematodes (PPN) with a worldwide distribution. Despite being an economically important PPN group of more than 100 species, genome information related to Pratylenchus genus is scarcely available. Here, we report the draft genome assembly of Pratylenchus scribneri generated on the PacBio Sequel IIe System using the ultra-low DNA input HiFi sequencing workflow. The final assembly created using 500 nematodes consisted of 276 decontaminated contigs, with an average contig N50 of 1.72 Mb and an assembled draft genome size of 227.24 Mb consisting of 51,146 predicted protein sequences. The benchmarking universal single-copy ortholog (BUSCO) analysis with 3131 nematode BUSCO groups indicated that 65.4% of the BUSCOs were complete, whereas 24.0%, 41.4%, and 1.8% were single-copy, duplicated, and fragmented, respectively, and 32.8% were missing. The outputs from GenomeScope2 and Smudgeplots converged towards a diploid genome for P. scribneri. The data provided here will facilitate future studies on host plant-nematode interactions and crop protection at the molecular level.
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Affiliation(s)
- Deepika Arora
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58105, USA
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Kimberly K O Walden
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Christopher J Fields
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Guiping Yan
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58105, USA
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He N, Umer MJ, Yuan P, Wang W, Zhu H, Lu X, xing Y, Gong C, Batool R, Sun X, Liu W. Physiological, biochemical, and metabolic changes in diploid and triploid watermelon leaves during flooding. Front Plant Sci 2023; 14:1108795. [PMID: 36968389 PMCID: PMC10033695 DOI: 10.3389/fpls.2023.1108795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Flooding is a major stress factor impacting watermelon growth and production globally. Metabolites play a crucial role in coping with both biotic and abiotic stresses. METHODS In this study, diploid (2X) and triploid (3X) watermelons were investigated to determine their flooding tolerance mechanisms by examining physiological, biochemical, and metabolic changes at different stages. Metabolite quantification was done using UPLC-ESI-MS/MS and a total of 682 metabolites were detected. RESULTS The results showed that 2X watermelon leaves had lower chlorophyll content and fresh weights compared to 3X. The activities of antioxidants, such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), were higher in 3X than in 2X. 3X watermelon leaves showed lower O2 production rates, MDA, and hydrogen peroxide (H2O2) levels in response to flooding, while higher ethylene production was observed. 3X had higher levels of dehydrogenase activity (DHA) and ascorbic acid + dehydrogenase (AsA + DHA), but both 2X and 3X showed a significant decline in the AsA/DHA ratio at later stages of flooding. Among them, 4-guanidinobutyric acid (mws0567), an organic acid, may be a candidate metabolite responsible for flooding tolerance in watermelon and had higher expression levels in 3X watermelon, suggesting that triploid watermelon is more tolerant to flooding. CONCLUSION This study provides insights into the response of 2X and 3X watermelon to flooding and the physiological, biochemical, and metabolic changes involved. It will serve as a foundation for future in-depth molecular and genetic studies on flooding response in watermelon.
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Affiliation(s)
- Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Department of Horticulture, Hunan Agricultural University, Changsha, Hunan, China
| | - Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, Henan, China
| | - Pingli Yuan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Weiwei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Yan xing
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Chengsheng Gong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Raufa Batool
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaowu Sun
- Department of Horticulture, Hunan Agricultural University, Changsha, Hunan, China
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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Šemberová K, Svitok M, Marhold K, Suda J, Schmickl RE. Morphological and environmental differentiation as prezygotic reproductive barriers between parapatric and allopatric Campanula rotundifolia agg. cytotypes. Ann Bot 2023; 131:71-86. [PMID: 34559179 PMCID: PMC9904352 DOI: 10.1093/aob/mcab123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/21/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Reproductive isolation and local establishment are necessary for plant speciation. Polyploidy, the possession of more than two complete chromosome sets, creates a strong postzygotic reproductive barrier between diploid and tetraploid cytotypes. However, this barrier weakens between polyploids (e.g. tetraploids and hexaploids). Reproductive isolation may be enhanced by cytotype morphological and environmental differentiation. Moreover, morphological adaptations to local conditions contribute to plant establishment. However, the relative contributions of ploidy level and the environment to morphology have generally been neglected. Thus, the extent of morphological variation driven by ploidy level and the environment was modelled for diploid, tetraploid and hexaploid cytotypes of Campanula rotundifolia agg. Cytotype distribution was updated, and morphological and environmental differentiation was tested in the presence and absence of natural contact zones. METHODS Cytotype distribution was assessed from 231 localities in Central Europe, including 48 localities with known chromosome counts, using flow cytometry. Differentiation in environmental niche and morphology was tested for cytotype pairs using discriminant analyses. A structural equation model was used to explore the synergies between cytotype, environment and morphology. KEY RESULTS Tremendous discrepancies were revealed between the reported and detected cytotype distribution. Neither mixed-ploidy populations nor interploidy hybrids were detected in the contact zones. Diploids had the broadest environmental niche, while hexaploids had the smallest and specialized niche. Hexaploids and spatially isolated cytotype pairs differed morphologically, including allopatric tetraploids. While leaf and shoot morphology were influenced by environmental conditions and polyploidy, flower morphology depended exclusively on the cytotype. CONCLUSIONS Reproductive isolation mechanisms vary between cytotypes. While diploids and polyploids are isolated postzygotically, the environmental niche shift is essential between higher polyploids. The impact of polyploidy and the environment on plant morphology implies the adaptive potential of polyploids, while the exclusive relationship between flower morphology and cytotype highlights the role of polyploidy in reproductive isolation.
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Affiliation(s)
| | - Marek Svitok
- Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, T. G. Masaryka, Zvolen, Slovakia
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Karol Marhold
- Faculty of Science, Department of Botany, Charles University, Benátská, Prague, Czech Republic
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta, Bratislava, Slovakia
| | | | - Roswitha E Schmickl
- Faculty of Science, Department of Botany, Charles University, Benátská, Prague, Czech Republic
- Czech Academy of Sciences, Institute of Botany, Department of Evolutionary Plant Biology, Zámek, Průhonice, Czech Republic
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Berdugo-Cely JA, Céron-Lasso MDS, Yockteng R. Phenotypic and molecular analyses in diploid and tetraploid genotypes of Solanum tuberosum L. reveal promising genotypes and candidate genes associated with phenolic compounds, ascorbic acid contents, and antioxidant activity. Front Plant Sci 2023; 13:1007104. [PMID: 36743552 PMCID: PMC9889998 DOI: 10.3389/fpls.2022.1007104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/08/2022] [Indexed: 06/18/2023]
Abstract
Potato tubers contain biochemical compounds with antioxidant properties that benefit human health. However, the genomic basis of the production of antioxidant compounds in potatoes has largely remained unexplored. Therefore, we report the first genome-wide association study (GWAS) based on 4488 single nucleotide polymorphism (SNP) markers and the phenotypic evaluation of Total Phenols Content (TPC), Ascorbic Acid Content (AAC), and Antioxidant Activity (AA) traits in 404 diverse potato genotypes (84 diploids and 320 tetraploids) conserved at the Colombian germplasm bank that administers AGROSAVIA. The concentration of antioxidant compounds correlated to the skin tuber color and ploidy level. Especially, purple-blackish tetraploid tubers had the highest TPC (2062.41 ± 547.37 mg GAE), while diploid pink-red tubers presented the highest AA (DDPH: 14967.1 ± 4687.79 μmol TE; FRAP: 2208.63 ± 797.35 mg AAE) and AAC (4.52 mg ± 0.68 AA). The index selection allowed us to choose 20 promising genotypes with the highest values for the antioxidant compounds. Genome Association mapping identified 58 SNP-Trait Associations (STAs) with single-locus models and 28 Quantitative Trait Nucleotide (QTNs) with multi-locus models associated with the evaluated traits. Among models, eight STAs/QTNs related to TPC, AAC, and AA were detected in common, flanking seven candidate genes, from which four were pleiotropic. The combination in one population of diploid and tetraploid genotypes enabled the identification of more genetic associations. However, the GWAS analysis implemented independently in populations detected some regions in common between diploids and tetraploids not detected in the mixed population. Candidate genes have molecular functions involved in phenolic compounds, ascorbic acid biosynthesis, and antioxidant responses concerning plant abiotic stress. All candidate genes identified in this study can be used for further expression analysis validation and future implementation in marker-assisted selection pre-breeding platforms targeting fortified materials. Our study further revealed the importance of potato germplasm conserved in national genebanks, such as AGROSAVIA's, as a valuable genetic resource to improve existing potato varieties.
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Affiliation(s)
- Jhon A. Berdugo-Cely
- Corporación Colombiana de Investigación Agropecuaria-AGROSAVIA, Centro de Investigación Turipaná, Km 13 vía Montería-Cereté, Montería, Córdoba, Colombia
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
| | - María del Socorro Céron-Lasso
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Km 13 vía Mosquera-Bogotá, Mosquera, Cundinamarca, Colombia
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, Paris, France
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Wang N, Wang S, Qi F, Wang Y, Lin Y, Zhou Y, Meng W, Zhang C, Wang Y, Ma J. Autotetraploidization Gives Rise to Differential Gene Expression in Response to Saline Stress in Rice. Plants (Basel) 2022; 11:3114. [PMID: 36432844 PMCID: PMC9698567 DOI: 10.3390/plants11223114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Plant polyploidization represents an effective means for plants to perpetuate their adaptive advantage in the face of environmental variation. Numerous studies have identified differential responsiveness to environmental cues between polyploids and their related diploids, and polyploids might better adapt to changing environments. However, the mechanism that underlies polyploidization contribution during abiotic stress remains hitherto obscure and needs more comprehensive assessment. In this study, we profile morphological and physiological characteristics, and genome-wide gene expression between an autotetraploid rice and its diploid donor plant following saline stress. The results show that the autotetraploid rice is more tolerant to saline stress than its diploid precursor. The physiological characteristics were rapidly responsive to saline stress in the first 24 h, during which the elevations in sodium ion, superoxide dismutase, peroxidase, and 1-aminocyclopropane-1-carboxylic acid were all significantly higher in the autotetraploid than in the diploid rice. Meanwhile, the genome-wide gene expression analysis revealed that the genes related to ionic transport, peroxidase activity, and phytohormone metabolism were differentially expressed in a significant manner between the autotetraploid and the diploid rice in response to saline stress. These findings support the hypothesis that diverse mechanisms exist between the autotetraploid rice and its diploid donor plant in response to saline stress, providing vital information for improving our understanding on the enhanced performance of polyploid plants in response to salt stress.
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Affiliation(s)
- Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Shiyan Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yingkai Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yujie Lin
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yiming Zhou
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Weilong Meng
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Chunying Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
| | - Yunpeng Wang
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jian Ma
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130117, China
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Samatadze TE, Yurkevich OY, Khazieva FM, Basalaeva IV, Konyaeva EA, Burova AE, Zoshchuk SA, Morozov AI, Amosova AV, Muravenko OV. Agro-Morphological and Cytogenetic Characterization of Colchicine-Induced Tetraploid Plants of Polemonium caeruleum L. (Polemoniaceae). Plants (Basel) 2022; 11:plants11192585. [PMID: 36235449 PMCID: PMC9570621 DOI: 10.3390/plants11192585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 06/12/2023]
Abstract
Polemonium caeruleum L. (Polemoniaceae) is a valuable medicinal herb with a wide spectrum of biological activities. Under natural conditions, the productivity of this species is rather low. In this study, colchicine-induced tetraploid plants (2n = 4x = 36) of P. caeruleum were obtained, and for the first time, their morphological and cytogenetic characterization was performed. In the tetraploid plants, raw material productivity and also the content of triterpene saponins were significantly higher than in the control diploids. The analysis of chromosome behavior at meiosis and FISH chromosome mapping of 45S and 5S rDNA generally demonstrated stability of both genomes in the tetraploid plants. Based on chromosome morphology and distribution patterns of the studied molecular cytogenetic markers, all chromosome pairs in karyotypes were identified, and chromosome karyograms and idiograms of P. caeruleum were constructed. The revealed specific microdiagnostic characteristics of P. caeruleum (strongly sinuous cells and anomocytic stomata of the leaf epidermis, and also glandular hairs along the veins) could be useful for raw material identification. In the obtained tetraploids, the predominance of large stomata on the lower leaf epidermis was determined. The studied tetraploids can be used in various breeding programs to obtain high-quality pharmaceutical raw materials of P. caeruleum.
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Affiliation(s)
- Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
| | - Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
| | - Firdaus M. Khazieva
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Irina V. Basalaeva
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Elena A. Konyaeva
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Alla E. Burova
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Svyatoslav A. Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
| | - Alexander I. Morozov
- All-Russian Institute of Medicinal and Aromatic Plants, 7 Green St., Moscow 117216, Russia
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia
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Wang N, Fan X, Lin Y, Li Z, Wang Y, Zhou Y, Meng W, Peng Z, Zhang C, Ma J. Alkaline Stress Induces Different Physiological, Hormonal and Gene Expression Responses in Diploid and Autotetraploid Rice. Int J Mol Sci 2022; 23:ijms23105561. [PMID: 35628377 PMCID: PMC9142035 DOI: 10.3390/ijms23105561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
Saline−alkaline stress is a critical abiotic stress that negatively affects plants’ growth and development. Considerably higher enhancements in plant tolerance to saline−alkaline stress have often been observed in polyploid plants compared to their diploid relatives, the underlying mechanism of which remains elusive. In this study, we explored the variations in morphological and physiological characteristics, phytohormones, and genome-wide gene expression between an autotetraploid rice and its diploid relative in response to alkaline stress. It was observed that the polyploidization in the autotetraploid rice imparted a higher level of alkaline tolerance than in its diploid relative. An eclectic array of physiological parameters commonly used for abiotic stress, such as proline, soluble sugars, and malondialdehyde, together with the activities of some selected antioxidant enzymes, was analyzed at five time points in the first 24 h following the alkaline stress treatment between the diploid and autotetraploid rice. Phytohormones, such as abscisic acid and indole-3-acetic acid were also comparatively evaluated between the two types of rice with different ploidy levels under alkaline stress. Transcriptomic analysis revealed that gene expression patterns were altered in accordance with the variations in the cellular levels of phytohormones between diploid and autotetraploid plants upon alkaline stress. In particular, the expression of genes related to peroxide and transcription factors was substantially upregulated in autotetraploid plants compared to diploid plants in response to the alkaline stress treatment. In essence, diploid and autotetraploid rice plants exhibited differential gene expression patterns in response to the alkaline stress, which may shed more light on the mechanism underpinning the ameliorated plant tolerance to alkaline stress following genome duplication.
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Affiliation(s)
- Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (N.W.); (Y.L.); (Z.L.); (Y.W.); (Y.Z.); (W.M.); (C.Z.)
| | - Xuhong Fan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, China;
| | - Yujie Lin
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (N.W.); (Y.L.); (Z.L.); (Y.W.); (Y.Z.); (W.M.); (C.Z.)
| | - Zhe Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (N.W.); (Y.L.); (Z.L.); (Y.W.); (Y.Z.); (W.M.); (C.Z.)
| | - Yingkai Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (N.W.); (Y.L.); (Z.L.); (Y.W.); (Y.Z.); (W.M.); (C.Z.)
| | - Yiming Zhou
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (N.W.); (Y.L.); (Z.L.); (Y.W.); (Y.Z.); (W.M.); (C.Z.)
| | - Weilong Meng
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (N.W.); (Y.L.); (Z.L.); (Y.W.); (Y.Z.); (W.M.); (C.Z.)
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun 130000, China;
| | - Chunying Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (N.W.); (Y.L.); (Z.L.); (Y.W.); (Y.Z.); (W.M.); (C.Z.)
| | - Jian Ma
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (N.W.); (Y.L.); (Z.L.); (Y.W.); (Y.Z.); (W.M.); (C.Z.)
- Correspondence: ; Tel.: +86-431-845332776
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11
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Kaseb MO, Umer MJ, Anees M, Zhu H, Zhao S, Lu X, He N, El-Remaly E, El-Eslamboly A, Yousef AF, Salama EAA, Alrefaei AF, Kalaji HM, Liu W. Transcriptome Profiling to Dissect the Role of Genome Duplication on Graft Compatibility Mechanisms in Watermelon. Biology (Basel) 2022; 11:575. [PMID: 35453774 PMCID: PMC9029962 DOI: 10.3390/biology11040575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Watermelon (Citrullus lanatus) is a popular crop worldwide. Compared to diploid seeded watermelon, triploid seedless watermelon cultivars are in great demand. Grafting in triploid and tetraploid watermelon produces few seedlings. To learn more about how genome duplication affects graft compatibility, we compared the transcriptomes of tetraploid and diploid watermelons grafted on squash rootstock using a splicing technique. WGCNA was used to compare the expression of differentially expressed genes (DEGs) between diploid and tetraploid watermelon grafted seedlings at 0, 3, and 15 days after grafting (DAG). Only four gene networks/modules correlated significantly with phenotypic characteristics. We found 11 genes implicated in hormone, AOX, and starch metabolism in these modules based on intramodular significance and RT-qPCR. Among these genes, two were linked with IAA (r2 = 0.81), one with ZR (r2 = 0.85) and one with POD (r2 = 0.74). In the MElightsteelblue1 module, Cla97C11G224830 gene was linked with CAT (r2 = 0.81). Two genes from the MEivory module, Cla97C07G139710 and Cla97C04G077300, were highly linked with SOD (r2 = 0.72). Cla97C01G023850 and Cla97C01G006680 from the MEdarkolivegreen module were associated with sugars and starch (r2 = 0.87). Tetraploid grafted seedlings had higher survival rates and hormone, AOX, sugar, and starch levels than diploids. We believe that compatibility is a complicated issue that requires further molecular research. We found that genome duplication dramatically altered gene expression in the grafted plants' IAA and ZR signal transduction pathways and AOX biosynthesis pathways, regulating hormone levels and improving plant survival.
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Affiliation(s)
- Mohamed Omar Kaseb
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
- Cross Pollenated Plants Department, Horticulture Research Institute, Agriculture Research Center, Giza 12119, Egypt; (E.E.-R.); (A.E.-E.)
| | - Muhammad Jawad Umer
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Muhammad Anees
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Hongju Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
| | - Eman El-Remaly
- Cross Pollenated Plants Department, Horticulture Research Institute, Agriculture Research Center, Giza 12119, Egypt; (E.E.-R.); (A.E.-E.)
| | - Ahmed El-Eslamboly
- Cross Pollenated Plants Department, Horticulture Research Institute, Agriculture Research Center, Giza 12119, Egypt; (E.E.-R.); (A.E.-E.)
| | - Ahmed F. Yousef
- Department of Horticulture, College of Agriculture, Al-Azhar University (Branch Assiut), Assiut 71524, Egypt;
| | - Ehab A. A. Salama
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt;
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 1145, Saudi Arabia;
| | - Hazem M. Kalaji
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences SGGW, 02-787 Warsaw, Poland;
- Institute of Technology and Life Sciences–National Research Institute (ITP), 05-090 Raszyn, Poland
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Henan Joint International Research Laboratory of Fruits and Cucurbits Biological Science in South Asia, Zhengzhou 450009, China; (M.O.K.); (M.J.U.); (M.A.); (H.Z.); (S.Z.); (X.L.); (N.H.)
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12
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Abstract
DNA repair is a well-covered topic as alteration of genetic integrity underlies many pathological conditions and important transgenerational consequences. Surprisingly, the ploidy status is rarely considered although the presence of homologous chromosomes dramatically impacts the repair capacities of cells. This is especially important for the haploid gametes as they must transfer genetic information to the offspring. An understanding of the different mechanisms monitoring genetic integrity in this context is, therefore, essential as differences in repair pathways exist that differentiate the gamete’s role in transgenerational inheritance. Hence, the oocyte must have the most reliable repair capacity while sperm, produced in large numbers and from many differentiation steps, are expected to carry de novo variations. This review describes the main DNA repair pathways with a special emphasis on ploidy. Differences between Saccharomyces cerevisiae and Schizosaccharomyces pombe are especially useful to this aim as they can maintain a diploid and haploid life cycle respectively.
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13
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Abstract
Loss of heterozygosity is a common mode of adaptation in asexual diploid populations. Because mitotic recombination frequently extends the full length of a chromosome arm, the selective benefit of loss of heterozygosity may be constrained by linked heterozygous mutations. In a previous laboratory evolution experiment with diploid yeast, we frequently observed homozygous mutations in the WHI2 gene on the right arm of Chromosome XV. However, when heterozygous mutations arose in the STE4 gene, another common target on Chromosome XV, loss of heterozygosity at WHI2 was not observed. Here, we show that mutations at WHI2 are partially dominant and that mutations at STE4 are overdominant. We test whether beneficial heterozygous mutations at these two loci interfere with one another by measuring loss of heterozygosity at WHI2 over 1,000 generations for ∼300 populations that differed initially only at STE4 and WHI2. We show that the presence of an overdominant mutation in STE4 reduces, but does not eliminate, loss of heterozygosity at WHI2. By sequencing 40 evolved clones, we show that populations with linked overdominant and partially dominant mutations show less parallelism at the gene level, more varied evolutionary outcomes, and increased rates of aneuploidy. Our results show that the degree of dominance and the phasing of heterozygous beneficial mutations can constrain loss of heterozygosity along a chromosome arm, and that conflicts between partially dominant and overdominant mutations can affect evolutionary outcomes.
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Affiliation(s)
- Kaitlin J Fisher
- Department of Biological Sciences, Lehigh University, USA.,Laboratory of Genetics, University of Wisconsin-Madison, USA
| | | | - Gregory I Lang
- Department of Biological Sciences, Lehigh University, USA
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14
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Han C, Kwon H, Park G, Jang M, Lee HJ, Seo S, Kwon M, Jeon W, Lee H, Lee H, Ahn J. Enhanced mating-type switching and sexual hybridization in heterothallic yeast Yarrowia lipolytica. FEMS Yeast Res 2021; 20:5762678. [PMID: 32105315 DOI: 10.1093/femsyr/foaa011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 02/26/2020] [Indexed: 12/12/2022] Open
Abstract
Yarrowia lipolytica is a non-conventional, heterothallic, oleaginous yeast with wide range of industrial applications. Increasing ploidy can improve advantageous traits for industrial applications including genetic stability, stress resistance, and productivity, but the construction of knockout mutant strains from polyploid cells requires significant effort due to the increased copy numbers of target genes. The goal of this study was to evaluate the effectiveness of a mating-type switching strategy by single-step transformation without a genetic manipulation vestige, and to optimize the conventional method for increasing ploidy (mating) in Y. lipolytica. In this study, mating-type genes in haploid Y. lipolytica cells were scarlessly converted into the opposite type genes by site-specific homologous recombination, and the resulting MATB-type cells were mated at low temperature (22°C) with addition of sodium citrate with each MATA-type haploid cell to yield a MATA/MATB-type diploid strain with genetic information from both parental strains. The results of this study can be used to increase ploidy and for whole genome engineering of a yeast strain with unparalleled versatility for industrial application.
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Affiliation(s)
- Changpyo Han
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea.,Interdisciplinary Program for Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Heeun Kwon
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea
| | - Gyuyeon Park
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea.,KRIBB School of Biotechnology, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Minjeong Jang
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea
| | - Hye-Jeong Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea
| | - Sunghwa Seo
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea
| | - Mincheol Kwon
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Biomolecular Science, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea
| | - Wooyoung Jeon
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea
| | - Heeseok Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea.,KRIBB School of Biotechnology, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Hongweon Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea.,KRIBB School of Biotechnology, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116, Republic of Korea.,KRIBB School of Biotechnology, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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15
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Bull L. On the Emergence of Intersexual Selection: Arbitrary Trait Preference Improves Female-Male Coevolution. Artif Life 2021; 27:15-25. [PMID: 34529754 DOI: 10.1162/artl_a_00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sexual selection is a fundamental aspect of evolution for all eukaryotic organisms with mating types. This article suggests intersexual selection is best viewed as a mechanism with which to compensate for the unavoidable dynamics of coevolution between sexes that emerge with isogamy. Using the NKCS model it is shown by varying fitness landscape size, ruggedness, and connectedness, how a purely arbitrary trait preference sexual selection mechanism proves beneficial with high dependence between the sexes. This is found to be the case whether one or both sexes exploit such intersexual selection.
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Affiliation(s)
- Larry Bull
- University of the West of England, Department of Computer Science & Creative Technologies.
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16
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Park CH, Park YE, Yeo HJ, Yoon JS, Park SY, Kim JK, Park SU. Comparative Analysis of Secondary Metabolites and Metabolic Profiling between Diploid and Tetraploid Morus alba L. J Agric Food Chem 2021; 69:1300-1307. [PMID: 33494603 DOI: 10.1021/acs.jafc.0c06863] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We profiled and quantified primary (amine, organic acids, tricarboxylic acid cycle intermediates, amino acids, and carbohydrates) and secondary metabolites (triterpenoids, phenolic acids, carotenoids, flavonoids, and anthocyanins) in the edible parts (leaves and fruits) of the diploid and tetraploid cultivar Morus alba L. 'Cheongil.' Through comprehensive metabolic profiling, the tetraploid mulberry cultivar was able to produce diverse metabolites supported by higher accumulation patterns of primary and secondary metabolites in their edible parts. In particular, the edible parts of the tetraploid showed higher accumulation patterns of most metabolites (amino acids, carbohydrates, carotenoids, and anthocyanins) than the diploid, which was supported by the results of principal component analyses (PCAs) showing a clear separation between the diploid and tetraploid groups. Additionally, this metabolome study comprehensively described the correlation between primary and secondary metabolites in the edible parts of diploid and tetraploid mulberry cultivars and provided information useful for plant breeding strategies to improve metabolite biosynthesis using polyploidy.
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Affiliation(s)
- Chang Ha Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Ye Eun Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Hyeon Ji Yeo
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Jeong Su Yoon
- Division of Life Sciences and Bio-Resource and Environmental Center, College of Life Sciences and Bioengineering, Incheon National University, Yeonsu-gu, Incheon 22012, Republic of Korea
| | - Soo-Yun Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Jae Kwang Kim
- Division of Life Sciences and Bio-Resource and Environmental Center, College of Life Sciences and Bioengineering, Incheon National University, Yeonsu-gu, Incheon 22012, Republic of Korea
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- Department of Smart Agriculture Systems, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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17
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Schoenrock KM, McHugh TA, Krueger-Hadfield SA. Revisiting the 'bank of microscopic forms' in macroalgal-dominated ecosystems. J Phycol 2021; 57:14-29. [PMID: 33135166 DOI: 10.1111/jpy.13092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
Theoretical ecological models, such as succession and facilitation, were defined in terrestrial habitats, and subsequently applied to marine and freshwater habitats in intertidal and then subtidal realms. One such model is the soil seed bank, defined as all viable seeds (or fruits) found near the soil surface that facilitate community restoration/recovery. "Banks of microscopic forms" have been hypothesized in aquatic habitats and recent work from aquaculture has highlighted dormancy in algal life cycle stages. To reinvigorate the discussions about these algal banks, we discuss differences in life cycles, dispersal, and summarize research on banks of macroalgal stages in aquatic ecosystems that may be easier to explore with modern advances in molecular technology. With focus on seminal work in global kelp forest ecosystems, we present a pilot study in northern California as proof of concept that Nereocystis luetkeana and Alaria marginata stages can be detected within kelp forests in the biofilm of rocks and bedrock using targeted primers long after zoospore release. Considering the increased interest in algae as an economic resource, [blue] carbon sink, and as ecosystem engineers, the potential for "banking" macroalgal forms could be a mechanism of resilience and recovery in aquatic populations that have complex life cycles and environmental cues for reproduction. Molecular barcoding is becoming an important tool for identifying banks of macroalgal forms in marine communities. Understanding banks of macroalgal stages, especially in deforested habitats with intense disturbance and grazer pressure, will allow researchers and marine resource managers to facilitate this natural process in recovery of the aquatic system.
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Affiliation(s)
- Kathryn M Schoenrock
- Department of Zoology, Ryan Institute, National University of Ireland, Galway, University Rd., Galway, H91 TK33, Ireland
| | - Tristin Anoush McHugh
- Long Marine Laboratory, Reef Check Foundation, 115 McAllister Road, Santa Cruz, California, 95060, USA
| | - Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, Campbell Hall, Room 464, Birmingham, Alabama, 35294, USA
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18
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Krueger-Hadfield SA, Flanagan BA, Godfroy O, Hill-Spanik KM, Nice CC, Murren CJ, Strand AE, Sotka EE. Using RAD-seq to develop sex-linked markers in a haplodiplontic alga. J Phycol 2021; 57:279-294. [PMID: 33098662 DOI: 10.1111/jpy.13088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
For many taxa, including isomorphic haplodiplontic macroalgae, determining sex and ploidy is challenging, thereby limiting the scope of some population demographic and genetic studies. Here, we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to identify sex-linked molecular markers in the widespread red alga Agarophyton vermiculophyllum. In the ddRAD-seq library, we included 10 female gametophytes, 10 male gametophytes, and 16 tetrasporophytes from one native and one non-native site (N = 40 gametophytes and N = 32 tetrasporophytes total). We identified seven putatively female-linked and 19 putatively male-linked sequences. Four female- and eight male-linked markers amplified in all three life cycle stages. Using one female- and one male-linked marker that were sex-specific, we developed a duplex PCR and tested the efficacy of this assay on a subset of thalli sampled at two sites in the non-native range. We confirmed ploidy based on the visual observation of reproductive structures and previous microsatellite genotyping at 10 polymorphic loci. For 32 vegetative thalli, we were able to assign sex and confirm ploidy in these previously genotyped thalli. These markers will be integral to ongoing studies of A. vermiculophyllum invasion. We discuss the utility of RAD-seq over other approaches previously used, such as RAPDs (random amplified polymorphic DNA), for future work designing sex-linked markers in other haplodiplontic macroalgae for which genomes are lacking.
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Affiliation(s)
- Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, Alabama, 35294, USA
| | - Ben A Flanagan
- Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Olivier Godfroy
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Kristina M Hill-Spanik
- Department of Biology and Grice Marine Lab, College of Charleston, 205 Fort Johnson Road, Charleston, South Carolina, 29412, USA
| | - Chris C Nice
- Department of Biology, Population and Conservation Biology Program, Texas State University, San Marcos, Texas, 78666, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
| | - Allan E Strand
- Department of Biology and Grice Marine Lab, College of Charleston, 205 Fort Johnson Road, Charleston, South Carolina, 29412, USA
| | - Erik E Sotka
- Department of Biology and Grice Marine Lab, College of Charleston, 205 Fort Johnson Road, Charleston, South Carolina, 29412, USA
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19
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Zhang CC, Gao Z, Luo LN, Liang HH, Xiang ZX. [Comparative analysis of active components and transcriptome between autotetraploid and diploid of Dendrobium huoshanense]. Zhongguo Zhong Yao Za Zhi 2020; 45:5669-5676. [PMID: 33496106 DOI: 10.19540/j.cnki.cjcmm.20200816.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this study, the roots, stems and leaves of diploid and autotetraploid Dendrobium huoshanense were used as materials to compare their contents of polysaccharides and alkaloids, and the transcriptome sequencing analysis was carried out. The results showed that the contents of polysaccharides and alkaloids in the roots, stems and leaves of tetraploid were 7.6%, 34.5%, 17.2%, 0.01%, 0.024% and 0.035% higher than those of diploid D. huoshanense, respectively. The contents of active components in different tissues were significantly different. There were 3 687 differentially expressed genes in diploid and tetraploid D. huoshanense, of which 2 346 genes were up-regulated and 1 341 down regulated. Go functional analysis showed that these genes were mainly involved in growth and development, stress resistance and other related functions. KEGG pathway analysis showed that most of the differential genes were concentrated in the processes of carbon metabolism, signal transduction, carbohydrate metabolism, amino acid metabolism and energy metabolism. The differential expression of key genes involved in the metabolism of polysaccharides, terpenes and polyketones, amino acid metabolism, hormone synthesis and signal transduction in diploid and tetraploid plants may be the main reason for the high energy content, the increase of active components and the growth potential of tetraploid plants.
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Affiliation(s)
- Cheng-Cai Zhang
- College of Horticulture, Nanjing Agricultural University Nanjing 210095, China
| | - Zhen Gao
- College of Horticulture, Nanjing Agricultural University Nanjing 210095, China
| | - Li-Na Luo
- College of Horticulture, Nanjing Agricultural University Nanjing 210095, China
| | - Hui-Hui Liang
- College of Horticulture, Nanjing Agricultural University Nanjing 210095, China
| | - Zeng-Xu Xiang
- College of Horticulture, Nanjing Agricultural University Nanjing 210095, China
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20
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Abstract
The new multidrug-resistant pathogen Candida auris was first described in 2009 in Japan and has emerged in many countries worldwide. This human fungal pathogen has long been considered a haploid fungus. Here, we report the discovery of the diploid form and spontaneous ploidy shifts in clinical isolates of C. auris. Haploid and diploid cells of C. auris differ in several aspects including growth rates, virulence, and global gene expression profiles. For example, diploid cells exhibit a slower growth rate than haploid cells in in vitro culture media; however, they are more virulent than haploid cells in a mouse systemic infection model. Global transcriptional expression analysis demonstrates that both haploid and diploid cells express a set of ploidy-enriched genes, which are involved in the regulation of metabolism, cell wall maintenance, translation and DNA replication, and other important biological processes. Antifungal susceptibility testing shows that haploid and diploid cells exhibit similar responses when treated with a number of antifungals. Taken together, haploid and diploid cells may have different fitness responses to diverse niches, and ploidy changes could be an adaptive strategy of C. auris to environmental changes. Our findings shed new light on the biology and pathogenesis of this emerging fungal pathogen.
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Affiliation(s)
- Shuru Fan
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chao Li
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Bing
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Guanghua Huang
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Han Du
- Department of Infectious Diseases, Huashan Hospital and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Velidandla S, Manikya S, Gajjada N, Reddy S, Gogulamudi L, Mediconda S. Correlation Between Histological Grading and Ploidy Status in Oral Leukoplakia, Oral Submucous Fibrosis, and Oral Squamous Cell Carcinoma: A Flow Cytometric Analysis. J Pharm Bioallied Sci 2020; 12:S91-S98. [PMID: 33149437 PMCID: PMC7595451 DOI: 10.4103/jpbs.jpbs_33_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/24/2020] [Accepted: 03/13/2020] [Indexed: 11/05/2022] Open
Abstract
Background: Methods to analyze progression of carcinogenesis and stage of cancer are vital nowadays due to the high prevalence of these lesions. DNA ploidy analysis is one such important method in early diagnosis and improving prognosis. Aims and Objectives: The aim of this study was to correlate histopathological grading and DNA ploidy in oral leukoplakia, oral submucous fibrosis (OSMF), and oral squamous cell carcinoma (OSCC) cases. Materials and Methods: Our study included 80 subjects, grouped into 4 groups of 20 each of OSCC, leukoplakia, OSMF, and healthy individuals. Histopathological grading was carried out in study cases, DNA ploidy was estimated using flow cytometry, and both the findings were correlated. Results: Among the 20 cases of leukoplakia group, 6 cases showed aneuploidy and 14 showed diploidy. In the 20 cases of OSF group, 2 cases showed aneuploidy and 18 showed diploidy, and in the 20 cases of OSCC group, 10 showed aneuploidy and 10 showed diploidy. Most of the aneuploidy cases showed severe dysplasia. Conclusion: Analysis of DNA ploidy status can serve as a diagnostic tool for early detection of malignancies owing to the subjective nature of traditional histopathological grading.
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Affiliation(s)
- Surekha Velidandla
- Department of Oral and Maxillofacial Pathology, MNR Dental College and Hospital, Sangareddy, Telangana, India
| | - Sangameshwar Manikya
- Department of Oral and Maxillofacial Pathology, MNR Dental College and Hospital, Sangareddy, Telangana, India
| | - Nirosha Gajjada
- Department of Oral and Maxillofacial Pathology, MNR Dental College and Hospital, Sangareddy, Telangana, India
| | - Sridhar Reddy
- Department of Oral and Maxillofacial Pathology, MNR Dental College and Hospital, Sangareddy, Telangana, India
| | - Lavanya Gogulamudi
- Department of Oral and Maxillofacial Pathology, MNR Dental College and Hospital, Sangareddy, Telangana, India
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Kaushik M, Rai S, Venkadesan S, Sinha SK, Mohan S, Mandal PK. Transcriptome Analysis Reveals Important Candidate Genes Related to Nutrient Reservoir, Carbohydrate Metabolism, and Defence Proteins during Grain Development of Hexaploid Bread Wheat and Its Diploid Progenitors. Genes (Basel) 2020; 11:E509. [PMID: 32380773 PMCID: PMC7290843 DOI: 10.3390/genes11050509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/25/2020] [Accepted: 04/29/2020] [Indexed: 12/21/2022] Open
Abstract
Wheat grain development after anthesis is an important biological process, in which major components of seeds are synthesised, and these components are further required for germination and seed vigour. We have made a comparative RNA-Seq analysis between hexaploid wheat and its individual diploid progenitors to know the major differentially expressed genes (DEGs) involved during grain development. Two libraries from each species were generated with an average of 55.63, 55.23, 68.13, and 103.81 million reads, resulting in 79.3K, 113.7K, 90.6K, and 121.3K numbers of transcripts in AA, BB, DD, and AABBDD genome species respectively. Number of expressed genes in hexaploid wheat was not proportional to its genome size, but marginally higher than that of its diploid progenitors. However, to capture all the transcripts in hexaploid wheat, sufficiently higher number of reads was required. Functional analysis of DEGs, in all the three comparisons, showed their predominance in three major classes of genes during grain development, i.e., nutrient reservoirs, carbohydrate metabolism, and defence proteins; some of them were subsequently validated through real time quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Further, developmental stage-specific gene expression showed most of the defence protein genes expressed during initial developmental stages in hexaploid contrary to the diploids at later stages. Genes related to carbohydrates anabolism expressed during early stages, whereas catabolism genes expressed at later stages in all the species. However, no trend was observed in case of different nutrient reservoirs gene expression. This data could be used to study the comparative gene expression among the three diploid species and homeologue-specific expression in hexaploid.
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Affiliation(s)
- Megha Kaushik
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
- Amity Institute of Biotechnology (AIB), Amity University, Sector 125, Noida, Uttar Pradesh 201313, India;
| | - Shubham Rai
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
| | - Sureshkumar Venkadesan
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
| | - Subodh Kumar Sinha
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
| | - Sumedha Mohan
- Amity Institute of Biotechnology (AIB), Amity University, Sector 125, Noida, Uttar Pradesh 201313, India;
| | - Pranab Kumar Mandal
- Indian Council of Agricultural Research -National Institute on Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi-110012, India; (M.K.); (S.R.); (S.V.); (S.K.S.)
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Skeffington AW, Grimm A, Schönefeld S, Petersen K, Scheffel A. An Efficient Method for the Plating of Haploid and Diploid Emiliania huxleyi on Solid Medium 1. J Phycol 2020; 56:238-242. [PMID: 31657459 DOI: 10.1111/jpy.12942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Emiliania huxleyi is a globally important coccolithophore and one of the most successful eukaryotic organisms in the modern oceans. Despite a large body of work on this organism, including the sequencing of its genome, the tools required for forward and reverse functional genetic studies are still undeveloped. Here we present an optimized method for the clonal isolation of E. huxleyi by plating on solid medium. We demonstrate the utility of this method for a variety of strains including haploid, calcifying-diploid, and noncalcifying diploid strains. We show that, in contrast to previous studies, no changes in cell ploidy status occur when the cells are plated. Our method will greatly aid attempts to elucidate the genetic basis of the remarkable physiology of E. huxleyi by forward and reverse genetic approaches.
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Affiliation(s)
- Alastair W Skeffington
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Annett Grimm
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Steffi Schönefeld
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476, Potsdam-Golm, Germany
| | - Kerstin Petersen
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476, Potsdam-Golm, Germany
| | - André Scheffel
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476, Potsdam-Golm, Germany
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24
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Zhang N, Bao Y, Xie Z, Huang X, Sun Y, Feng G, Zeng H, Ren J, Li Y, Xiong J, Chen W, Yan C, Tang M. Efficient Characterization of Tetraploid Watermelon. Plants (Basel) 2019; 8:E419. [PMID: 31623210 DOI: 10.3390/plants8100419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/23/2022]
Abstract
Watermelon (Citrullus lanatus (Thunb.) Matsum. &Nakai) is an economic crop, which is widely cultivated around the world. The ploidy study of watermelon has an important role in field breeding and production, therefore, timely and convenient ploidy detection is necessary to accelerate its application. Traditionally, the ploidy of watermelon was determined by a series of time-consuming, expensive, and less efficient methods. In this study, we developed a more efficient method to simplify and accelerate the polyploidy identification in watermelons. We first confirmed the ploidy of watermelon by traditional tetraploid morphological features and well-established flow cytometry (FCM). Then we developed a reliable real-time quantitative PCR (qPCR) technique by quantifying the highly conserved 5S rDNA sequence and its copy numbers. This technique requires less sample collection and has comparable accuracy to FCM, it accelerates the analysis process and provides a new method for the identification of polyploidy of watermelon.
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25
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Manzoor A, Ahmad T, Bashir MA, Hafiz IA, Silvestri C. Studies on Colchicine Induced Chromosome Doubling for Enhancement of Quality Traits in Ornamental Plants. Plants (Basel) 2019; 8:plants8070194. [PMID: 31261798 PMCID: PMC6681243 DOI: 10.3390/plants8070194] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022]
Abstract
Polyploidy has the utmost importance in horticulture for the development of new ornamental varieties with desirable morphological traits referring to plant size and vigor, leaf thickness, larger flowers with thicker petals, intense color of leaves and flowers, long lasting flowers, compactness, dwarfness and restored fertility. Polyploidy may occur naturally due to the formation of unreduced gametes or can be artificially induced by doubling the number of chromosomes in somatic cells. Usually, natural polyploid plants are unavailable, so polyploidy is induced synthetically with the help of mitotic inhibitors. Colchicine is a widely used mitotic inhibitor for the induction of polyploidy in plants during their cell division by inhibiting the chromosome segregation. Different plant organs like seeds, apical meristems, flower buds, and roots can be used to induce polyploidy through many application methods such as dipping/soaking, dropping or cotton wool. Flow cytometry and chromosome counting, with an observation of morphological and physiological traits are routine procedures for the determination of ploidy level in plants.
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Affiliation(s)
- Ayesha Manzoor
- Barani Agricultural Research Institute, Chakwal 48800, Pakistan.
| | - Touqeer Ahmad
- Department of Horticulture, PMAS Arid Agriculture University, Rawalpindi, Punjab 46000, Pakistan.
| | - Muhammad Ajmal Bashir
- Department of Horticulture, PMAS Arid Agriculture University, Rawalpindi, Punjab 46000, Pakistan.
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy.
| | - Ishfaq Ahmad Hafiz
- Department of Horticulture, PMAS Arid Agriculture University, Rawalpindi, Punjab 46000, Pakistan.
| | - Cristian Silvestri
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy.
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26
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Liu K, Meng W, Zheng L, Wang L, Zhou S. Cytogeography and chromosomal variation of the endemic East Asian herb Lycoris radiata. Ecol Evol 2019; 9:6849-6859. [PMID: 31380020 PMCID: PMC6662380 DOI: 10.1002/ece3.5252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 12/17/2018] [Accepted: 02/22/2019] [Indexed: 01/16/2023] Open
Abstract
Information on the spatial distribution of cytotypes and karyotype variation in plants is critical for studies of the origin and evolution of polyploid complexes. Here, the spatial distribution of cytological races and intraspecific variation in the karyotype of Lycoris radiata, an endemic species to East Asia, is investigated. Conventional karyotype analysis methods were used to determine ploidy level and karyotypical characteristics in 2,420 individuals from 114 populations of L. radiata nearly covering the whole distribution areas in China. Of 114 populations studied, 52 (45.61%), 58 (50.88%), and 4 (3.51%) are diploid, triploid, and mixoploid populations, respectively, with 1,224, 1,195, and 1 individuals being diploid, triploid, and tetraploid, respectively. The triploid possesses a much wider distribution range than the diploid, with the former almost occupying the entire range of this complex species in East Asia and the latter distributing in the middle and east regions of China. Triploids tend to occur at high altitudes, and the relationship between the ploidy and altitude is significantly positive but low (r 2 = 0.103, p < 0.01). About 98.6% of examined bulbs have a common karyotype consisting of 22 or 33 acrocentric (A) chromosomes. Some aberrant chromosomes which should be generated from A-type chromosome have been found including metacentrics (m), small metacentrics (m'), and B-type chromosome. The results can provide a fundamental cytogeographic data for further studies on the evolutionary origins and adaptive divergences of polyploids, especially the triploid, within L. radiata using molecular and/or ecological methods in the future.
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Affiliation(s)
- Kun Liu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological ResourcesCollege of Life SciencesAnhui Normal UniversityWuhuChina
| | - Weiqi Meng
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological ResourcesCollege of Life SciencesAnhui Normal UniversityWuhuChina
| | - Lu Zheng
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological ResourcesCollege of Life SciencesAnhui Normal UniversityWuhuChina
| | - Lida Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological ResourcesCollege of Life SciencesAnhui Normal UniversityWuhuChina
| | - Shoubiao Zhou
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological ResourcesCollege of Life SciencesAnhui Normal UniversityWuhuChina
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and RemediationCollege of Environmental Science and EngineeringAnhui Normal UniversityWuhuChina
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27
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Wilkinson PD, Delgado ER, Alencastro F, Leek MP, Roy N, Weirich MP, Stahl EC, Otero PA, Chen MI, Brown WK, Duncan AW. The Polyploid State Restricts Hepatocyte Proliferation and Liver Regeneration in Mice. Hepatology 2019; 69:1242-1258. [PMID: 30244478 PMCID: PMC6532408 DOI: 10.1002/hep.30286] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/16/2018] [Indexed: 12/12/2022]
Abstract
The liver contains a mixture of hepatocytes with diploid or polyploid (tetraploid, octaploid, etc.) nuclear content. Polyploid hepatocytes are commonly found in adult mammals, representing ~90% of the entire hepatic pool in rodents. The cellular and molecular mechanisms that regulate polyploidization have been well characterized; however, it is unclear whether diploid and polyploid hepatocytes function similarly in multiple contexts. Answering this question has been challenging because proliferating hepatocytes can increase or decrease ploidy, and animal models with healthy diploid-only livers have not been available. Mice lacking E2f7 and E2f8 in the liver (liver-specific E2f7/E2f8 knockout; LKO) were recently reported to have a polyploidization defect, but were otherwise healthy. Herein, livers from LKO mice were rigorously characterized, demonstrating a 20-fold increase in diploid hepatocytes and maintenance of the diploid state even after extensive proliferation. Livers from LKO mice maintained normal function, but became highly tumorigenic when challenged with tumor-promoting stimuli, suggesting that tumors in LKO mice were driven, at least in part, by diploid hepatocytes capable of rapid proliferation. Indeed, hepatocytes from LKO mice proliferate faster and out-compete control hepatocytes, especially in competitive repopulation studies. In addition, diploid or polyploid hepatocytes from wild-type (WT) mice were examined to eliminate potentially confounding effects associated with E2f7/E2f8 deficiency. WT diploid cells also showed a proliferative advantage, entering and progressing through the cell cycle faster than polyploid cells, both in vitro and during liver regeneration (LR). Diploid and polyploid hepatocytes responded similarly to hepatic mitogens, indicating that proliferation kinetics are unrelated to differential response to growth stimuli. Conclusion: Diploid hepatocytes proliferate faster than polyploids, suggesting that the polyploid state functions as a growth suppressor to restrict proliferation by the majority of hepatocytes.
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Affiliation(s)
- Patrick D. Wilkinson
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Evan R. Delgado
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Frances Alencastro
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Madeleine P. Leek
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Nairita Roy
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Matthew P. Weirich
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Elizabeth C. Stahl
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - P. Anthony Otero
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Maelee I. Chen
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Whitney K. Brown
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
| | - Andrew W. Duncan
- Department of Pathology, McGowan Institute for Regenerative Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, 450 Technology Drive, Suite 300, Pittsburgh, PA 15219
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Yang X, Liu J, Xu J, Duan S, Wang Q, Li G, Jin L. Transcriptome Profiling Reveals Effects of Drought Stress on Gene Expression in Diploid Potato Genotype P3-198. Int J Mol Sci 2019; 20:ijms20040852. [PMID: 30781424 PMCID: PMC6413097 DOI: 10.3390/ijms20040852] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/09/2019] [Accepted: 02/13/2019] [Indexed: 01/09/2023] Open
Abstract
Potato (Solanum tuberosum L.) is one of the three most important food crops worldwide; however, it is strongly affected by drought stress. The precise molecular mechanisms of drought stress response in potato are not very well understood. The diploid potato genotype P3-198 has been verified to be highly resistant to drought stress. Here, a time-course experiment was performed to identify drought resistance response genes in P3-198 under polyethylene glycol (PEG)-induced stress using RNA-sequencing. A total of 1665 differentially expressed genes (DEGs) were specifically identified, and based on gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the transcription factor activity, protein kinase activity, and the plant hormone signal transduction process were significantly enriched. Annotation revealed that these DEGs mainly encode transcription factors, protein kinases, and proteins related to redox regulation, carbohydrate metabolism, and osmotic adjustment. In particular, genes encoding abscisic acid (ABA)-dependent signaling molecules were significantly differentially expressed, which revealed the important roles of the ABA-dependent signaling pathway in the early response of P3-198 to drought stress. Quantitative real-time PCR experimental verification confirmed the differential expression of genes in the drought resistance signaling pathway. Our results provide valuable information for understanding potato drought-resistance mechanisms, and also enrich the gene resources available for drought-resistant potato breeding.
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Affiliation(s)
- Xiaohui Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable, Jinan 250100, China.
- National Vegetable Improvement Center Shandong Sub-Center/Huang-Huai-Hai Region Scientific Observation and Experimental Station of Vegetables, Ministry of Agriculture and Rural Affairs, Jinan 250100, China.
| | - Jie Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Jianfei Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Shaoguang Duan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Qianru Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Liping Jin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
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Zhang J, Snelders EE, Zwaan BJ, Schoustra SE, Kuijper EJ, Arendrup MC, Melchers WJG, Verweij PE, Debets AJM. Relevance of heterokaryosis for adaptation and azole-resistance development in Aspergillus fumigatus. Proc Biol Sci 2019; 286:20182886. [PMID: 30963936 PMCID: PMC6408600 DOI: 10.1098/rspb.2018.2886] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/21/2019] [Indexed: 12/27/2022] Open
Abstract
Aspergillus fumigatus causes a range of diseases in humans, some of which are characterized by fungal persistence. Aspergillus fumigatus, being a generalist saprotroph, may initially establish lung colonization due to its physiological versatility and subsequently adapt through genetic changes to the human lung environment and antifungal treatments. Human lung-adapted genotypes can arise by spontaneous mutation and/or recombination and subsequent selection of the fittest genotypes. Sexual and asexual spores are considered crucial contributors to the genetic diversity and adaptive potential of aspergilli by recombination and mutation supply, respectively. However, in certain Aspergillus diseases, such as cystic fibrosis and chronic pulmonary aspergillosis, A. fumigatus may not sporulate but persist as a network of fungal mycelium. During azole therapy, such mycelia may develop patient-acquired resistance and become heterokaryotic by mutations in one of the nuclei. We investigated the relevance of heterokaryosis for azole-resistance development in A. fumigatus. We found evidence for heterokaryosis of A. fumigatus in patients with chronic Aspergillus diseases. Mycelium from patient-tissue biopsies segregated different homokaryons, from which heterokaryons could be reconstructed. Whereas all variant homokaryons recovered from the same patient were capable of forming a heterokaryon, those from different patients were heterokaryon-incompatible. We furthermore compared heterokaryons and heterozygous diploids constructed from environmental isolates with different levels of azole resistance. When exposed to azole, the heterokaryons revealed remarkable shifts in their nuclear ratio, and the resistance level of heterokaryons exceeded that of the corresponding heterozygous diploids.
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Affiliation(s)
- Jianhua Zhang
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Eveline E. Snelders
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bas J. Zwaan
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sijmen E. Schoustra
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ed J. Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maiken C. Arendrup
- Unit of Mycology, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Willem J. G. Melchers
- Department of Medical Microbiology and Centre of Expertise in Mycology Radboudumc/CWZ, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology and Centre of Expertise in Mycology Radboudumc/CWZ, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Alfons J. M. Debets
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Qin Y, Zhang Y, Ma H, Wu X, Xiao S, Li J, Mo R, Yu Z. Comparison of the Biochemical Composition and Nutritional Quality Between Diploid and Triploid Hong Kong Oysters, Crassostrea hongkongensis. Front Physiol 2018; 9:1674. [PMID: 30534082 PMCID: PMC6275301 DOI: 10.3389/fphys.2018.01674] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/08/2018] [Indexed: 01/02/2023] Open
Abstract
This study is the first systematic comparison of the biochemical composition and nutritional quality between diploid and triploid Hong Kong oysters, Crassostrea hongkongensis. Results showed that in the reproductive season, the glycogen content in five tissues (gill, mantle, adductor muscle, labial palps and gonad) was significantly higher (P < 0.05) in triploids than in diploids, with odds ratios (ORs) of 96.26, 60.17, 72.59, 53.56, and 128.52%, respectively. In the non-reproductive phase, significant differences in glycogen content (P < 0.05) between diploid and triploid oysters existed only in gill and gonad. In both diploid and triploid Hong Kong oysters, quantitative real-time PCR analysis of the glycogen synthesis gene (ChGS) and glycogen phosphorylase gene (ChGP) showed that the gene expression patterns matched the pattern of variation in glycogen content. Moreover, in both the reproductive and the non-reproductive phases, triploid Hong Kong oysters had a well balance of essential amino acids and were thus a well source of high-quality protein. Surprisingly, in both phases, significantly higher (P < 0.05) percentages of four essential fatty acids (α-linolenic acid, linoleic acid, eicosapentaenoic acid, and docosahexaenoic acid) were observed in triploids than in diploids. Additionally, the ratio of n-3/n-6 polyunsaturated fatty acids (PUFAs) was much higher in triploids than that in diploids. Variations in Biochemical composition were consistent with the relative expression of the citrate synthase gene (ChCS) and the α-ketoglutarate dehydrogenase gene (ChKD), which are key enzyme genes of the tricarboxylic acid cycle. Overall, the triploid Hong Kong oyster has a better nutritional value and taste than the diploid in terms of glycogen content, protein quality and fatty acid content.
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Affiliation(s)
- Yanping Qin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuehuan Zhang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | - Haitao Ma
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | - Xiangwei Wu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shu Xiao
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | - Jun Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
| | - Riguan Mo
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ziniu Yu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China
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Cao Y, Jiang M, Xu F, Liu S, Meng F. The effects of elevated CO 2 (0.5%) on chloroplasts in the tetraploid black locust ( Robinia pseudoacacia L.). Ecol Evol 2017; 7:10546-10555. [PMID: 29299236 PMCID: PMC5743629 DOI: 10.1002/ece3.3545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 07/29/2017] [Accepted: 09/20/2017] [Indexed: 11/09/2022] Open
Abstract
Some ploidy plants demonstrate environmental stress tolerance. Tetraploid (4×) black locust (Robinia pseudoacacia L.) exhibits less chlorosis in response to high CO 2 than do the corresponding diploid (2×) plants of this species. We investigated the plant growth, anatomy, photosynthetic ability, chlorophyll (chl) fluorescence, and antioxidase activities in 2× and 4× black locusts cultivated under high CO 2 (0.5%). Elevated CO 2 (0.5%) induced a global decrease in the contents of total chl, chl a, and chl b in 2× leaves, while few changes were found in the chl content of 4× leaves. Analyses of the chl fluorescence intensity, maximum quantum yield of photosystem II (PSII) photochemistry (Fv/Fm), K-step (Vk), and J-step (VJ) revealed that 0.5% CO 2 had a negative effect on the photosynthetic capacity and growth of the 2× plants, especially the performance of PSII. In contrast, there was no significant effect of high CO 2 on the growth of the 4× plants. These analyses indicate that the decreased inhibition of the growth of 4× plants by high CO 2 (0.5%) may be attributed to an improved photosynthetic capacity, pigment content, and ultrastructure of the chloroplast compared to 2× plants.
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Affiliation(s)
- Yuan Cao
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Mingquan Jiang
- Jilin Province Product Quality Supervision and Inspection InstituteChangchunChina
| | - Fuling Xu
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Shuo Liu
- College of Life ScienceNortheast Forestry UniversityHarbinChina
| | - Fanjuan Meng
- College of Life ScienceNortheast Forestry UniversityHarbinChina
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Zhang XL, Zhang J, Guo YH, Sun P, Jia HX, Fan W, Lu MZ, Hu JJ. Comparative Proteomic Analysis of Mature Pollen in Triploid and Diploid Populus deltoides. Int J Mol Sci 2016; 17:ijms17091475. [PMID: 27598155 PMCID: PMC5037753 DOI: 10.3390/ijms17091475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/16/2016] [Accepted: 08/29/2016] [Indexed: 12/31/2022] Open
Abstract
Ploidy affects plant growth vigor and cell size, but the relative effects of pollen fertility and allergenicity between triploid and diploid have not been systematically examined. Here we performed comparative analyses of fertility, proteome, and abundances of putative allergenic proteins of pollen in triploid poplar ‘ZhongHuai1’ (‘ZH1’, triploid) and ‘ZhongHuai2’ (‘ZH2’, diploid) generated from the same parents. The mature pollen was sterile in triploid poplar ‘ZH1’. By applying two-dimensional gel electrophoresis (2-DE), a total of 72 differentially expressed protein spots (DEPs) were detected in triploid poplar pollen. Among them, 24 upregulated and 43 downregulated proteins were identified in triploid poplar pollen using matrix-assisted laser desorption/ionisation coupled with time of-flight tandem mass spectrometer analysis (MALDI-TOF/TOF MS/MS). The main functions of these DEPs were related with “S-adenosylmethionine metabolism”, “actin cytoskeleton organization”, or “translational elongation”. The infertility of triploid poplar pollen might be related to its abnormal cytoskeletal system. In addition, the abundances of previously identified 28 putative allergenic proteins were compared among three poplar varieties (‘ZH1’, ‘ZH2’, and ‘2KEN8‘). Most putative allergenic proteins were downregulated in triploid poplar pollen. This work provides an insight into understanding the protein regulation mechanism of pollen infertility and low allergenicity in triploid poplar, and gives a clue to improving poplar polyploidy breeding and decreasing the pollen allergenicity.
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Affiliation(s)
- Xiao-Ling Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Ying-Hua Guo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Pei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Hui-Xia Jia
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Wei Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
| | - Jian-Jun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
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Zhou H, Ma TY, Zhang R, Xu QZ, Shen F, Qin YJ, Xu W, Wang Y, Li YJ. Analysis of Different Ploidy and Parent-Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus. Int J Mol Sci 2016; 17:E1299. [PMID: 27556458 DOI: 10.3390/ijms17081299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/21/2016] [Accepted: 07/26/2016] [Indexed: 01/07/2023] Open
Abstract
In this study, we selected natural polyploidy loach (diploid, triploid and tetraploid) and hybrid F1 generation obverse cross (4 × 2) and inverse cross (2 × 4) by diploids and tetraploids as the research model. The MSAP (methylation-sensitive amplified polymorphism) reaction system was established by our laboratory to explore methylation levels and pattern diversification features at the whole genome level of the polyploidy loach. The results showed that the total methylation and full methylation rates decreased on increased ploidy individuals; moreover, the hemimethylation rate showed no consistent pattern. Compared with diploid loach, the methylation patterns of tetraploid sites changed 68.17%, and the methylation patterns of triploid sites changed 73.05%. The proportion of hypermethylation genes is significantly higher than the proportion of demethylation genes. The methylation level of reciprocal cross F1 generation is lower than the male diploid and higher than the female tetraploid. The hemimethylation and total methylation rate of the cross hybrid F1 generation is significantly higher than the orthogonal F1 generation (p < 0.01). After readjusting, the methylation pattern of genome DNA of reciprocal hybrids changed 69.59% and 72.83%, respectively.
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Sellis D, Kvitek DJ, Dunn B, Sherlock G, Petrov DA. Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae. Genetics 2016; 203:1401-13. [PMID: 27194750 DOI: 10.1534/genetics.115.185165] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/15/2016] [Indexed: 12/31/2022] Open
Abstract
Adaptation in diploids is predicted to proceed via mutations that are at least partially dominant in fitness. Recently, we argued that many adaptive mutations might also be commonly overdominant in fitness. Natural (directional) selection acting on overdominant mutations should drive them into the population but then, instead of bringing them to fixation, should maintain them as balanced polymorphisms via heterozygote advantage. If true, this would make adaptive evolution in sexual diploids differ drastically from that of haploids. The validity of this prediction has not yet been tested experimentally. Here, we performed four replicate evolutionary experiments with diploid yeast populations (Saccharomyces cerevisiae) growing in glucose-limited continuous cultures. We sequenced 24 evolved clones and identified initial adaptive mutations in all four chemostats. The first adaptive mutations in all four chemostats were three copy number variations, all of which proved to be overdominant in fitness. The fact that fitness overdominant mutations were always the first step in independent adaptive walks supports the prediction that heterozygote advantage can arise as a common outcome of directional selection in diploids and demonstrates that overdominance of de novo adaptive mutations in diploids is not rare.
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Roggero Luque JM, Moreno EMS, Kovalsky IE, Seijo JG, Solís Neffa VG. Evidence of the occurrence of structural chromosome changes at the initial diploid diversification of the autopolyploid Turnera sidoides L. (Passifloraceae) complex. Genome 2016; 59:127-36. [PMID: 26794024 DOI: 10.1139/gen-2015-0096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Turnera sidoides is an autopolyploid complex of obligate outcrossing perennial herbs. It includes five subspecies and five morphotypes in which diploid to octoploid cytotypes were found. Based on phenetic analyses of the complex and karyotype data of polyploid cytotypes, it has been hypothesized that morphological and chromosome differentiation of T. sidoides occurred at the diploid level. To test this hypothesis, we present the first detailed chromosome analysis of diploid populations of three subspecies and four morphotypes. CMA(+)/DAPI(-) bands were restricted to secondary constrictions (except in the andino morphotype) and varied in number and position among taxa. By contrast, DAPI staining was uniform in all the materials investigated. The number and position of 45S rDNA loci were coincident with the CMA(+)/DAPI(-) bands associated with secondary constrictions. Only one pair of 5S rDNA loci was detected in all the taxa (except in subsp. holosericea), but its position was variable. The identified chromosome markers varied among the three subspecies analyzed, but they were more conserved among the morphotypes of subsp. pinnatifida. Cluster analysis of these chromosome markers supports the current taxonomic arrangement of diploids and demonstrates that structural chromosome changes would have led or accompanied the initial differentiation of T. sidoides at the diploid level.
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Affiliation(s)
- Juan M Roggero Luque
- a Instituto de Botánica del Nordeste (UNNE-CONICET). CC 209. 3400, Corrientes, Argentina
| | - E M Sara Moreno
- a Instituto de Botánica del Nordeste (UNNE-CONICET). CC 209. 3400, Corrientes, Argentina
| | - I Evelin Kovalsky
- b Instituto de Botánica del Nordeste (UNNE-CONICET). CC 209. 3400, Corrientes, Argentina. Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE)
| | - J Guillermo Seijo
- b Instituto de Botánica del Nordeste (UNNE-CONICET). CC 209. 3400, Corrientes, Argentina. Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE)
| | - Viviana G Solís Neffa
- b Instituto de Botánica del Nordeste (UNNE-CONICET). CC 209. 3400, Corrientes, Argentina. Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE)
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Luo W, Liu C, Cao X, Huang S, Wang W, Wang Y. Transcriptome Profile Analysis of Ovarian Tissues from Diploid and Tetraploid Loaches Misgurnus anguillicaudatus. Int J Mol Sci 2015; 16:16017-33. [PMID: 26184186 DOI: 10.3390/ijms160716017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/25/2015] [Accepted: 07/08/2015] [Indexed: 01/31/2023] Open
Abstract
RNA sequencing and short-read assembly was utilized to produce a transcriptome of ovarian tissues from three-year-old diploid and tetraploid loaches (Misgurnus anguillicaudatus). A total of 28,369 unigenes were obtained, comprising 10,546 unigenes with length longer than 1000 bp. More than 73% of the unigenes were annotated through sequence comparison with databases. The RNA-seq data revealed that 2253 genes were differentially expressed between diploid and tetraploid loaches, including 1263 up-regulated and 990 down-regulated genes in tetraploid loach. Some differentially expressed genes, such as vitellogenin (Vtg), gonadotropin releasing hormone receptor type A (GnRHRA), steroidogenic acute regulatory protein (StAR), mitogen-activated protein kinase 14a (MAPK14a), ATP synthase subunit alpha (atp5a), and synaptonemal complex protein 1 (Scp1), were involved in regulation of cell proliferation, division, gene transcription, ovarian development and energy metabolism, suggesting that these genes were related to egg diameter of the loach. Results of transcriptome profiling here were validated using real time quantitative PCR in ten selected genes. The present study provided insights into the transcriptome profile of ovarian tissues from diploid and tetraploid loaches Misgurnus anguillicaudatus, which was made available to the research community for functional genomics, comparative genomics, polyploidy evolution and molecular breeding of this loach and other related species.
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Beesley NJ, Cwiklinski K, Williams DJ, Hodgkinson J. Fasciola hepatica from naturally infected sheep and cattle in Great Britain are diploid. Parasitology 2015; 142:1196-201. [PMID: 25990533 DOI: 10.1017/S0031182015000499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Diploid (2n = 2x = 20) and triploid (2n = 3x = 30) Fasciola hepatica have been reported in the UK, and in Asia diploid, triploid and mixoploid (2x/3x) Fasciola spp. exist but there is little information to indicate how common triploidy is, particularly in UK fluke. Here the ploidy of 565 adult F. hepatica from 66 naturally infected British sheep and 150 adult F. hepatica from 35 naturally infected British cattle was determined. All 715 of these parasites were diploid, based on observation of 10 bivalent chromosomes and sperm (n = 335) or, since triploids are aspermic, sperm alone (n = 380). This constitutes the first extensive analysis of the ploidy of F. hepatica field isolates from Great Britain and shows that most F. hepatica isolated from cattle and sheep are diploid and have the capacity to sexually reproduce. These data suggest that triploidy, and by extension parthenogenesis, is rare or non-existent in wild British F. hepatica populations. Given that F. hepatica is the only species of Fasciola present in Britain our results indicate that the parasite is predominantly diploid in areas where F. hepatica exists in isolation and suggests that triploidy may only originate in natural populations where co-infection of F. hepatica and its sister species Fasciola gigantica commonly occurs.
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Shcherban AB, Strygina KV, Salina EA. VRN-1 gene- associated prerequisites of spring growth habit in wild tetraploid wheat T. dicoccoides and the diploid A genome species. BMC Plant Biol 2015; 15:94. [PMID: 25888295 PMCID: PMC4383061 DOI: 10.1186/s12870-015-0473-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/16/2015] [Indexed: 05/13/2023]
Abstract
BACKGROUND In order to clarify the origin of spring growth habit in modern domesticated wheat, allelic variability of the VRN-1 gene was investigated in a wide set of accessions of the wild tetraploid species Triticum dicoccoides (BBAA), together with diploid species T. monococcum, T. boeoticum and T. urartu, presumable donors of the A genome to polyploid wheats. RESULTS No significant variation was found at the VRN-B1 locus of T. dicoccoides, whereas at VRN-A1 a number of previously described alleles were found with small deletions in the promoter (VRN-A1b, VRN-A1d) or a large deletion in the first (1st) intron (VRN-A1L). The diploid A genome species were characterized by their own set of VRN-1 alleles including previously described VRN-A1f and VRN-A1h alleles with deletions in the promoter region and the VRN-A1ins allele containing a 0.5 kb insertion in the 1st intron. Based on the CAPS screening data, alleles VRN-A1f and VRN-A1ins were species-specific for T. monococcum, while allele VRN-A1h was specific for T. boeoticum. Different indels were revealed in both the promoter and 1(st) intron of the recessive VRN-A1u allele providing specific identification of T. urartu, the proposed donor of the A genome to modern wheat. We found that alleles VRN-A1b and VRN-A1h, previously described as dominant, have either no or weak association with spring growth habit, while in some diploid accessions this habit was associated with the recessive VRN-A1 allele. CONCLUSIONS Spring growth habit in diploid wheats was only partially associated with indels in regulatory regions of the VRN-1 gene. An exception is T. monococcum where dominant mutations in both the promoter region and, especially, the 1st intron were selected during domestication resulting in a greater variety of spring forms. The wild tetraploid T. dicoccoides had a distinct set of VRN-A1 alleles compared to the diploids in this study, indicating an independent origin of spring tetraploid forms that likely occurred after combining of diploid genomes. These alleles were subsequently inherited by cultivated polyploid (tetraploid and hexaploid) descendants.
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Affiliation(s)
- Andrey B Shcherban
- Institute of Cytology and Genetics, Lavrentiev ave. 10, Novosibirsk, 630090, Russia.
| | - Kseniya V Strygina
- Institute of Cytology and Genetics, Lavrentiev ave. 10, Novosibirsk, 630090, Russia.
| | - Elena A Salina
- Institute of Cytology and Genetics, Lavrentiev ave. 10, Novosibirsk, 630090, Russia.
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Fraser TWK, Mayer I, Hansen T, Poppe TT, Skjaeraasen JE, Koppang EO, Fjelldal PG. Vaccination and triploidy increase relative heart weight in farmed Atlantic salmon, Salmo salar L. J Fish Dis 2015; 38:151-160. [PMID: 24422684 DOI: 10.1111/jfd.12216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/11/2013] [Accepted: 11/12/2013] [Indexed: 06/03/2023]
Abstract
Heart morphology is particularly plastic in teleosts and differs between farmed and wild Atlantic salmon. However, little is known about how different culture practices and sex affect heart morphology. This study investigated how vaccination, triploidy and sex affected heart size and heart morphology (ventricle shape, angle of the bulbus arteriosus) in farmed Atlantic salmon for 18 months following vaccination (from c. 50-3000 g body weight). In addition, hearts were examined histologically after 7 months in sea water. All fish sampled were sexually immature. Vaccinated fish had significantly heavier hearts relative to body weight and a more triangular ventricle than unvaccinated fish, suggesting a greater cardiac workload. Irrespective of time, triploids had significantly heavier hearts relative to body weight, a more acute angle of the bulbus arteriosus and less fat deposition in the epicardium than diploids. The ventricle was also more triangular in triploids than diploids at seawater transfer. Sex had transient effects on the angle of the bulbus arteriosus, but no effect on relative heart weight or ventricle shape. From a morphological perspective, the results indicate that vaccination and triploidy increase cardiac workload in farmed Atlantic salmon.
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Affiliation(s)
- T W K Fraser
- Department of Production Animal Clinical Sciences, Norwegian School of Veterinary Science, Oslo, Norway
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Gross K, Schiestl FP. Are tetraploids more successful? Floral signals, reproductive success and floral isolation in mixed-ploidy populations of a terrestrial orchid. Ann Bot 2015; 115:263-73. [PMID: 25652914 PMCID: PMC4551083 DOI: 10.1093/aob/mcu244] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/07/2014] [Accepted: 10/22/2014] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Polyploidization, the doubling of chromosome sets, is common in angiosperms and has a range of evolutionary consequences. Newly formed polyploid lineages are reproductively isolated from their diploid progenitors due to triploid sterility, but also prone to extinction because compatible mating partners are rare. Models have suggested that assortative mating and increased reproductive fitness play a key role in the successful establishment and persistence of polyploids. However, little is known about these factors in natural mixed-ploidy populations. This study investigated floral traits that can affect pollinator attraction and efficiency, as well as reproductive success in diploid and tetraploid Gymnadenia conopsea (Orchidaceae) plants in two natural, mixed-ploidy populations. METHODS Ploidy levels were determined using flow cytometry, and flowering phenology and herbivory were also assessed. Reproductive success was determined by counting fruits and viable seeds of marked plants. Pollinator-mediated floral isolation was measured using experimental arrays, with pollen flow tracked by means of staining pollinia with histological dye. KEY RESULTS Tetraploids had larger floral displays and different floral scent bouquets than diploids, but cytotypes differed only slightly in floral colour. Significant floral isolation was found between the two cytotypes. Flowering phenology of the two cytotypes greatly overlapped, and herbivory did not differ between cytotypes or was lower in tetraploids. In addition, tetraploids had higher reproductive success compared with diploids. CONCLUSIONS The results suggest that floral isolation and increased reproductive success of polyploids may help to explain their successful persistence in mixed-ploidy populations. These factors might even initiate transformation of populations from pure diploid to pure tetraploid.
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Affiliation(s)
- Karin Gross
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Florian P Schiestl
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
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Szövényi P, Devos N, Weston DJ, Yang X, Hock Z, Shaw JA, Shimizu KK, McDaniel SF, Wagner A. Efficient purging of deleterious mutations in plants with haploid selfing. Genome Biol Evol 2014; 6:1238-52. [PMID: 24879432 PMCID: PMC4041004 DOI: 10.1093/gbe/evu099] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In diploid organisms, selfing reduces the efficiency of selection in removing deleterious mutations from a population. This need not be the case for all organisms. Some plants, for example, undergo an extreme form of selfing known as intragametophytic selfing, which immediately exposes all recessive deleterious mutations in a parental genome to selective purging. Here, we ask how effectively deleterious mutations are removed from such plants. Specifically, we study the extent to which deleterious mutations accumulate in a predominantly selfing and a predominantly outcrossing pair of moss species, using genome-wide transcriptome data. We find that the selfing species purge significantly more nonsynonymous mutations, as well as a greater proportion of radical amino acid changes which alter physicochemical properties of amino acids. Moreover, their purging of deleterious mutation is especially strong in conserved regions of protein-coding genes. Our observations show that selfing need not impede but can even accelerate the removal of deleterious mutations, and do so on a genome-wide scale.
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Affiliation(s)
- Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandInstitute of Systematic Botany, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, SwitzerlandMTA-ELTE-MTM Ecology Research Group, ELTE, Biological Institute, Hungary
| | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Zsófia Hock
- Institute of Systematic Botany, University of Zurich, Switzerland
| | | | - Kentaro K Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | | | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, SwitzerlandBioinformatics Institute, Agency for Science, Technology and Research (A*STAR), SingaporeThe Santa Fe Institute, Santa Fe NM
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Larsen HAS, Austbø L, Nødtvedt A, Fraser TWK, Rimstad E, Fjelldal PG, Hansen T, Koppang EO. The effect of vaccination, ploidy and smolt production regime on pathological melanin depositions in muscle tissue of Atlantic salmon, Salmo salar L. J Fish Dis 2014; 37:327-340. [PMID: 23646928 DOI: 10.1111/jfd.12106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/20/2013] [Accepted: 02/26/2013] [Indexed: 06/02/2023]
Abstract
The presence of melanin in muscle fillets of farmed salmon represents a considerable quality problem for the salmon industry with major economic concerns. In this study, we have examined the presence of abnormal pigmentation in vaccinated versus unvaccinated Atlantic salmon, Salmo salar L., and evaluated possible differences between diploid and triploid fish. Furthermore, the impact of the smolt production regime at ambient (4.5 °C) versus elevated temperature (16 °C) was investigated. Pigmented muscle spots were analysed for the expression of genes involved in melanization (tyrosinase gene family) and immune-related response in addition to morphological investigations. The proportion of fish with intramuscular melanin deposits was not significantly different between vaccinated and unvaccinated fish, regardless of ploidy. However, an interaction between vaccination and smolt regime was shown, where smoltification at elevated temperature after vaccination increased the number of affected individuals compared with vaccination followed by simulated natural smoltification. Furthermore, there were overall more fish with melanin spots amongst the triploids compared with their diploid counterparts. Transcription of the tyrosinase gene family confirmed an onsite melanogenesis in all pigment spots. The histological examination and the expression of the immune-related genes revealed a chronic polyphasic myopathy that was not affected by vaccination, ploidy or smolt production regime.
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Affiliation(s)
- H A S Larsen
- Department of Basic Science and Aquatic Medicine, Section of Anatomy and Pathology, Norwegian School of Veterinary Science, Oslo, Norway
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Fraser TWK, Fleming MS, Poppe TT, Hansen T, Fjelldal PG. The effect of ploidy and incubation temperature on survival and the prevalence of aplasia of the septum transversum in Atlantic salmon, Salmo salar L. J Fish Dis 2014; 37:189-200. [PMID: 23488808 DOI: 10.1111/jfd.12091] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/08/2013] [Accepted: 01/08/2013] [Indexed: 06/01/2023]
Abstract
Heart deformities are a concern in aquaculture and are linked to egg incubation temperature. Diploid and triploid Atlantic salmon, Salmo salar L., were incubated at 6, 8 and 10 °C and analysed for aplasia of the septum transversum (n = 150 ploidy⁻¹ incubation temperature⁻¹). Heart morphology (size and shape) was assessed in fish incubated at 6 °C and in fish with and without aplasia of the septum transversum (n = 9 group⁻¹) incubated at 10 °C. Egg mortality was significantly higher in triploids than in diploids at all incubation temperatures, and increased egg incubation temperatures increased mortality in both ploidy. Triploids grew quicker than diploids after egg incubation at 10 °C, but not at 6 °C. Aplasia of the septum transversum occurred only in triploid fish after incubation at 6 °C and 8 °C (0.7% and 3.3%, respectively) and was significantly greater (P ≤ 0.05) in triploids after incubation at 10 °C compared with diploids (30% and 18%, respectively). Aplasia of the septum transversum significantly increased heart mass and resulted in a long flat ventricle compared with fish displaying a septum transversum. The results suggest triploid salmon should be incubated below 8 °C.
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Affiliation(s)
- T W K Fraser
- Department of Production Animal Clinical Sciences, Norwegian School of Veterinary Science, Oslo, Norway
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Christensen KI, Zarrei M, Kuzmina M, Talent N, Lin C, Dickinson TA. Crataegus ×ninae-celottiae and C. ×cogswellii (Rosaceae, Maleae), two spontaneously formed intersectional nothospecies. PhytoKeys 2014; 36:1-26. [PMID: 24843290 PMCID: PMC4023339 DOI: 10.3897/phytokeys.36.6784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/17/2014] [Indexed: 05/19/2023]
Abstract
Crataegus monogyna Jacq. is naturalized in North America, where it has hybridized with native diploid hawthorns at least twice. We provide names for the two nothospecies (as well as for the corresponding nothosections and nothoseries), referring to existing documentation in the literature for nothosp. nov. Crataegus ×ninae-celottiae K.I. Chr. & T.A. Dickinson (C. monogyna × C. punctata Jacq.). New data are provided to further document nothosp. nov. Crataegus ×cogswellii K.I. Chr. & T.A. Dickinson (C. monogyna × C. suksdorfii (Sarg.) Kruschke). In both cases, the striking differences in leaf shape between most New World hawthorns and Old World section Crataegus, and the intermediacy of the hybrids, account for the relative ease with which these hybrids can be recognized. Finally, new sequence data from ITS2 and chloroplast DNA barcoding loci confirm the genetic relationships between the two nothospecies and their respective parents.
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Affiliation(s)
- Knud Ib Christensen
- Assoc. Prof. M.Sc. Ph.D. Knud Ib Christensen (born 13 October 1955, deceased 16 January 2012), formerly at the Botanical Garden, Natural History Museum of Denmark, University of Copenhagen
| | - Mehdi Zarrei
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Rm. 139715, 686 Bay St., Toronto, Ontario, M5G 0A4
| | - Maria Kuzmina
- Department of Botany, MRC-166 National Museum of Natural History Smithsonian Institution Rm W106 Washington, DC 20013-7012 USA
| | - Nadia Talent
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario Canada M5S 2C6
| | - Charlotte Lin
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario Canada M5S 2C6
- School of Education, University of Stirling, Scotland UK FK9 4LA
| | - Timothy A. Dickinson
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario Canada M5S 2C6
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, Canada M5S 3B2
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Szövényi P, Ricca M, Hock Z, Shaw JA, Shimizu KK, Wagner A. Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss. Mol Biol Evol 2013; 30:1929-39. [PMID: 23686659 DOI: 10.1093/molbev/mst095] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The masking hypothesis predicts that selection is more efficient in haploids than in diploids, because dominant alleles can mask the deleterious effects of recessive alleles in diploids. However, gene expression breadth and noise can potentially counteract the effect of masking on the rate at which genes evolve. Land plants are ideal to ask whether masking, expression breadth, or expression noise dominate in their influence on the rate of molecular evolution, because they have a biphasic life cycle in which the duration and complexity of the haploid and diploid phase varies among organisms. Here, we generate and compile genome-wide gene expression, sequence divergence, and polymorphism data for Arabidopsis thaliana and for the moss Funaria hygrometrica to show that the evolutionary rates of haploid- and diploid-specific genes contradict the masking hypothesis. Haploid-specific genes do not evolve more slowly than diploid-specific genes in either organism. Our data suggest that gene expression breadth influence the evolutionary rate of phase-specific genes more strongly than masking. Our observations have implications for the role of haploid life stages in the purging of deleterious mutations, as well as for the evolution of ploidy.
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Affiliation(s)
- Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
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Yamashita KI, Nakazawa Y, Namai K, Amagai M, Tsukazaki H, Wako T, Kojima A. Modes of inheritance of two apomixis components, diplospory and parthenogenesis, in Chinese chive (Allium ramosum) revealed by analysis of the segregating population generated by back-crossing between amphimictic and apomictic diploids. Breed Sci 2012; 62:160-9. [PMID: 23136527 PMCID: PMC3405961 DOI: 10.1270/jsbbs.62.160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 03/25/2012] [Indexed: 05/07/2023]
Abstract
To investigate the mode of inheritance of apomixis in Chinese chive, the degrees of diplospory and parthenogenesis were evaluated in F(1) and BC(1) progenies derived from crosses between amphimictic and apomictic diploids (2n = 16, 2x). The F(1) population was generated by crossing three amphimictic diploids 94Mo13, 94Mo49 and 94Mo50 with an apomictic diploid KaD2 and comprised 110 diploids and 773 triploids. All the diploid F(1) plants examined were completely or highly eusporous and completely syngamic. All the triploid F(1) plants examined were highly diplosporous and highly parthenogenetic. KaD2 could not transmit its high level of apomixis via monoploid pollen grains. The BC(1) population, generated by crossing 94Mo49 with apomictic triploids found in the F(1) offspring, exhibited heteroploidy; it comprised haploid, diploid, triploid, tetraploid and various aneuploid individuals. In this generation, clear segregation was observed between diplospory and parthenogenesis. Analysis of the BC(1) population suggests that diplospory and parthenogenesis are each controlled by single dominant genes, D and P, respectively. However, all the BC(1) plants characterized as parthenogenetic were diplosporous. The absence of phenotypically eusporous parthenogenetic plants can be explained by assuming that the presence of diplospory gene is a prerequisite for the parthenogenesis gene expression in Chinese chive.
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Affiliation(s)
- Ken-ichiro Yamashita
- Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, 360 Kusawa, Tsu, Mie 514-2392, Japan
- Corresponding author (e-mail: )
| | - Yoshiko Nakazawa
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, 1080 Utsunomiya, Tochigi 320-0002, Japan
| | - Kiyoshi Namai
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, 1080 Utsunomiya, Tochigi 320-0002, Japan
| | - Masayuki Amagai
- Tochigi Prefectural Agricultural Experiment Station, Utsunomiya, 1080 Utsunomiya, Tochigi 320-0002, Japan
| | - Hikaru Tsukazaki
- Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, 360 Kusawa, Tsu, Mie 514-2392, Japan
| | - Tadayuki Wako
- Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, 360 Kusawa, Tsu, Mie 514-2392, Japan
| | - Akio Kojima
- Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, 360 Kusawa, Tsu, Mie 514-2392, Japan
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Singer TM, Moll C, Groß-Hardt R. When Double is not Twice as Much. Front Plant Sci 2011; 2:94. [PMID: 22645557 PMCID: PMC3355729 DOI: 10.3389/fpls.2011.00094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 11/22/2011] [Indexed: 06/01/2023]
Abstract
Gene and genome duplications provide a playground for various selective pressures and contribute significantly to genome complexity. It is assumed that the genomes of all major eukaryotic lineages possess duplicated regions that result from gene and genome duplication. There is evidence that the model plant Arabidopsis has been subjected to at least three whole-genome duplication events over the last 150-200 million years. As a result, many cellular processes are governed by redundantly acting gene families. Plants pass through two distinct life phases with a haploid gametophytic alternating with a diploid sporophytic generation. This ontogenetic difference in gene copy number has important implications for the outcome of deleterious mutations, which are masked by the second gene copy in diploid systems but expressed in a dominant fashion in haploid organisms. As a consequence, maintaining the activity of duplicated genes might be particularly advantageous during the haploid gametophytic generation. Here, we describe the distinctive features associated with the alteration of generations and discuss how activity profiles of duplicated genes might get modulated in a life phase dependent fashion.
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Affiliation(s)
- Theresa Maria Singer
- Cell and Developmental Genetics, Center for Plant Molecular Biology, University of TuebingenTuebingen, Germany
| | - Cordula Moll
- Cell and Developmental Genetics, Center for Plant Molecular Biology, University of TuebingenTuebingen, Germany
| | - Rita Groß-Hardt
- Cell and Developmental Genetics, Center for Plant Molecular Biology, University of TuebingenTuebingen, Germany
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Muchero W, Diop NN, Bhat PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA, Close TJ. A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proc Natl Acad Sci U S A 2009; 106:18159-64. [PMID: 19826088 PMCID: PMC2761239 DOI: 10.1073/pnas.0905886106] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2009] [Indexed: 11/18/2022] Open
Abstract
Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among "orphan crops" with limited genomic resources such as cowpea [Vigna unguiculata (L.) Walp.] (2n = 2x = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded approximately 10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean (Glycine max) and Medicago truncatula, revealed extensive macrosynteny encompassing 85 and 82%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with Arabidopsis revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes.
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Affiliation(s)
| | - Ndeye N. Diop
- Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Prasanna R. Bhat
- Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Raymond D. Fenton
- Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Steve Wanamaker
- Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Marti Pottorff
- Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Sarah Hearne
- The International Institute of Tropical Agriculture, Oyo Road, PMB 5320, Ibadan, Nigeria; and
| | - Ndiaga Cisse
- Senegalese Institute of Agricultural Research, Bambey, Senegal
| | - Christian Fatokun
- The International Institute of Tropical Agriculture, Oyo Road, PMB 5320, Ibadan, Nigeria; and
| | - Jeffrey D. Ehlers
- Botany and Plant Sciences, University of California, Riverside, CA 92521
| | | | - Timothy J. Close
- Botany and Plant Sciences, University of California, Riverside, CA 92521
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Abstract
Among the various abiotic stresses limiting the crop productivity, salinity stress is a major problem, which needs to be addressed and answered urgently. Since members of Brassicaceae are important contributor to total oilseed production, there is an immediate need being felt to raise Brassica plants which would be more suitable for saline and dry lands in years to come. One of the suggested way to develop salinity tolerant Brassica plants is to make use of the broad gene pool available within the family. Efforts of breeders have been successful in such endeavors to a large extent and several salinity tolerant Brassica genotypes have been developed within India and elsewhere. On the other hand, transgenic technology will undoubtedly continue to aid the search for the cellular mechanisms that confer tolerance, but the complexity of the trait is likely to mean that the road to engineer such tolerance into sensitive species will not be easy. However, with increasing number of reports available for suitable genetic transformation for various Brassica genotypes, there is a hope that salinity tolerance can be improved in this important crop plant. In this direction, the complete genome sequence of related wild plants such as Arabidopsis or crop plants such as rice can also serve as a platform for identification of "candidate genes". Recently, complete genome sequencing of the Brassica genomes has also been initiated with the view that availability of such useful information can pave way towards raising Brassica with improved tolerance towards these stresses. In the present paper, we discuss the success obtained so far; in raising brassica genotypes with improved salinity tolerance employing both plant breeding and/or genetic engineering tools.
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Affiliation(s)
- Ram Singh Purty
- />Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067 India
| | - Gautam Kumar
- />Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067 India
| | - Sneh L. Singla-Pareek
- />Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067 India
| | - Ashwani Pareek
- />Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067 India
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Thórsson AT, Pálsson S, Sigurgeirsson A, Anamthawat-Jónsson K. Morphological variation among Betula nana (diploid), B. pubescens (tetraploid) and their triploid hybrids in Iceland. Ann Bot 2007; 99:1183-93. [PMID: 17495985 PMCID: PMC3243578 DOI: 10.1093/aob/mcm060] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Introgressive hybridization between two co-existing Betula species in Iceland, diploid dwarf birch B. nana and tetraploid downy birch B. pubescens, has been well documented. The two species are highly variable morphologically, making taxonomic delineation difficult despite stable ploidy levels. Here an analysis is made of morphological variation within each ploidy group with an aim to establishing a reliable means to distinguish the species. METHODS Plant materials were collected from 14 woodlands in Iceland. The plants were identified based on 2n chromosome numbers. Morphological variation in species-specific characters within each ploidy group was analysed qualitatively and quantitatively. The morphological index was based on eight discrete characters, whereas the multivariate analysis was based on nine leaf variables. KEY RESULTS Of the 461 plants examined, 9.5 % were found to be triploid hybrids. The three ploidy groups were morphologically distinguishable but their variation overlapped. The diploid, triploid and tetraploid groups had average scores of 1.3, 4.1 and 8.3, respectively, in the morphology index scale from 0 (B. nana) to 13 (B. pubescens). A linear discriminant analysis also revealed significant separation among the three ploidy groups and the model assigned 96 % and 97 % of the B. nana and B. pubescens individuals correctly. The triploid hybrids were difficult to predict since only half of them could be assigned correctly. Leaf length was the most useful variable identifying triploid hybrids. Geographical patterns within the ploidy groups could partly be explained by differences in mean July temperature. CONCLUSIONS Hybridization between B. nana and B. pubescens is widespread in Iceland. The species can be distinguished from each other morphologically, and from the triploid hybrids. The overlapping morphological variation indicates bidirectional introgression between the two species via triploid hybrids. Iceland could be considered a birch hybrid zone, harbouring genetic variation which may be advantageous in subarctic regions.
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Affiliation(s)
- Ae Th Thórsson
- Institute of Biology, University of Iceland, Askja-Sturlugata 7, 101 Reykjavík, Iceland.
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