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Arvas YE, Kocaçalışkan İ, Ordu E, Erişen S. Comparative retrotransposon analysis of mutant and non-mutant rice varieties grown at different salt concentrations. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2043777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Yunus Emre Arvas
- Department of Molecular Biology and Genetics, Graduate School of Natural and Applied Sciences, Yıldız Technical University, Istanbul, Turkey
| | - İsmail Kocaçalışkan
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yıldız Technical University, Istanbul, Turkey
| | - Emel Ordu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yıldız Technical University, Istanbul, Turkey
| | - Semiha Erişen
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yıldız Technical University, Istanbul, Turkey
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Minaei S, Mohammadi SA, Sabouri A, Dadras AR. High genetic diversity in Aegilops tauschii Coss. accessions from North Iran as revealed by IRAP and REMAP markers. J Genet Eng Biotechnol 2022; 20:86. [PMID: 35696009 PMCID: PMC9192835 DOI: 10.1186/s43141-022-00363-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Aegilops tauschii Coss. as a donor of wheat D genome has an important role in wheat breeding programs. Genetic and phylogeographic diversity of 79 Ae. tauschii accessions collected from north and northwest of Iran were analyzed based on retroelement insertional polymorphisms using inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers. RESULTS In total, 306 and 151 polymorphic bands were amplified in IRAP and REMAP analyses, respectively. As a result, a high level of polymorphism was observed among the studied accessions as revealed by an average of 25.5 bands per primer/primer combination and mean PIC value of 0.47 in IRAP and an average of 25.16 bands per primer combination and mean PIC value of 0.47 in REMAP. Genetic relationships of the accessions were analyzed using distance- and model-based cluster analyses. CONCLUSION The result showed that genetic distance did not seem to be related to geographic distribution, and the accessions could be divided into three groups, which was further supported by principal coordinate analysis. These results on genetic diversity and population structure of Ae. tauschii in Iran should provide important knowledge on genetic resources and their applications in wheat breeding programs.
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Affiliation(s)
- Sona Minaei
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Seyyed Abolghasem Mohammadi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran. .,Center of Excellence in Cereal Molecular Breeding, University of Tabriz, Tabriz, Iran. .,Department of Life Sciences, Center for Cell Pathology, Khazar University, Baku, AZ1096, Azerbaijan.
| | - Atefeh Sabouri
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Ahmad Reza Dadras
- Department of Crop and Horticultural Research, Zanjan Agricultural and Natural Resource Research and Education, AREEO, Zanjan, Iran
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Biswas MK, Darbar JN, Borrell JS, Bagchi M, Biswas D, Nuraga GW, Demissew S, Wilkin P, Schwarzacher T, Heslop-Harrison JS. The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development. Sci Rep 2020; 10:15312. [PMID: 32943659 PMCID: PMC7498607 DOI: 10.1038/s41598-020-71984-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/24/2020] [Indexed: 12/25/2022] Open
Abstract
Ensete ventricosum (Musaceae, enset) is an Ethiopian food security crop. To realize the potential of enset for rural livelihoods, further knowledge of enset diversity, genetics and genomics is required to support breeding programs and conservation. This study was conducted to explore the enset genome to develop molecular markers, genomics resources, and characterize enset landraces while giving insight into the organization of the genome. We identified 233 microsatellites (simple sequence repeats, SSRs) per Mbp in the enset genome, representing 0.28% of the genome. Mono- and di-nucleotide repeats motifs were found in a higher proportion than other classes of SSR-motifs. In total, 154,586 non-redundant enset microsatellite markers (EMM) were identified and 40 selected for primer development. Marker validation by PCR and low-cost agarose gel electrophoresis revealed that 92.5% were polymorphic, showing a high PIC (Polymorphism Information Content; 0.87) and expected heterozygosity (He = 0.79-0.82). In silico analysis of genomes of closely related species showed 46.86% of the markers were transferable among enset species and 1.90% were transferable to Musa. The SSRs are robust (with basic PCR methods and agarose gel electrophoresis), informative, and applicable in measuring enset diversity, genotyping, selection and potentially breeding. Enset SSRs are available in a web-based database at https://enset-project.org/EnMom@base.html (or https://enset.aau.edu.et/index.html , downloadable from Figshare).
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Affiliation(s)
- Manosh Kumar Biswas
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - Jaypal N Darbar
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Mita Bagchi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| | - Gizachew Woldesenbet Nuraga
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, Surrey, UK
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK. .,South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China.
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Development and characterization of non-coding RNA based simple sequence repeat markers in Capsicum species. Genomics 2020; 112:1554-1564. [DOI: 10.1016/j.ygeno.2019.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 02/06/2023]
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5
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Badaeva ED, Fisenko AV, Surzhikov SA, Yankovskaya AA, Chikida NN, Zoshchuk SA, Belousova MK, Dragovich AY. Genetic Heterogeneity of a Diploid Grass Aegilops tauschii Revealed by Chromosome Banding Methods and Electrophoretic Analysis of the Seed Storage Proteins (Gliadins). RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419110024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Pavia I, Roque J, Rocha L, Ferreira H, Castro C, Carvalho A, Silva E, Brito C, Gonçalves A, Lima-Brito J, Correia C. Zinc priming and foliar application enhances photoprotection mechanisms in drought-stressed wheat plants during anthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 140:27-42. [PMID: 31078782 DOI: 10.1016/j.plaphy.2019.04.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/18/2019] [Accepted: 04/21/2019] [Indexed: 05/24/2023]
Abstract
Drought is one of most important limiting factors in wheat productivity worldwide. The need to increase drought tolerance during anthesis is of the utmost importance for high yield potentials and yield stability. Photosynthesis is one of the major physiological processes affected by drought. Damages in the photosynthetic apparatus may also arise due to non-regulated dissipation of excessive energy. Zinc (Zn) is an indispensable micronutrient for plants and is required for a wide range of physiological and biochemical processes. In this work we evaluated the stress mitigation effects of Zn seed priming alone and coupled with Zn foliar application in wheat plants submitted to severe drought during anthesis, followed by a recovery period. Under such severe drought stress, photosynthesis was constrained by both stomatal and non-stomatal limitation. Severe drought also induced an increase in non-regulated energy dissipation and hindered a full recovery of the plant's photosynthetic processes after rewatering. We also report possible activation of transposable elements due to drought stress and Zn application. Yield was severely decreased by drought and Zn treatments were unable to counteract this effect. Although unable to oppose the reduction of net photosynthesis, Zn treatments positively enhance photoprotection. At the end of drought period, Zn priming alone and coupled with Zn foliar application increased, respectively, over 2- and 3- fold the regulated dissipation of excess energy. Zn treatments lessened the non-regulated energy dissipation caused by drought, protected the plants against irreversible damages to the photosynthetic apparatus and enabled a better recovery of wheat plants after stress relief.
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Affiliation(s)
- Ivo Pavia
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - João Roque
- BioISI - UTAD, Biosystems & Integrative Sciences Institute - Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Luís Rocha
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Helena Ferreira
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Cláudia Castro
- BioISI - UTAD, Biosystems & Integrative Sciences Institute - Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Ana Carvalho
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal; Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal; BioISI - UTAD, Biosystems & Integrative Sciences Institute - Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Ermelinda Silva
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Cátia Brito
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Alexandre Gonçalves
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - José Lima-Brito
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal; Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal; BioISI - UTAD, Biosystems & Integrative Sciences Institute - Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Carlos Correia
- CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Universidade de Trás-os-Montes e Alto Douro, Quinta de Prados, 5000-801, Vila Real, Portugal.
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Shen L, Luo G, Song Y, Song S, Li Y, Yang W, Li X, Sun J, Liu D, Zhang A. Low molecular weight glutenin subunit gene composition at Glu-D3 loci of Aegilops tauschii and common wheat and a further view of wheat evolution. THEORETICAL AND APPLIED GENETICS 2018; 131:2745-2763. [PMID: 30225644 DOI: 10.1007/s00122-018-3188-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023]
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8
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Yuzbasioglu G, Yilmaz S, Marakli S, Gozukirmizi N. Analysis ofHopi/Osr27andHouba/Tos5/Osr13retrotransposons in rice. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2015.1124026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Alsayied NF, Fernández JA, Schwarzacher T, Heslop-Harrison JS. Diversity and relationships of Crocus sativus and its relatives analysed by inter-retroelement amplified polymorphism (IRAP). ANNALS OF BOTANY 2015; 116:359-68. [PMID: 26138822 PMCID: PMC4549961 DOI: 10.1093/aob/mcv103] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 04/08/2015] [Accepted: 05/27/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Saffron (Crocus sativus) is a sterile triploid (2n = 3x = 24) cultivated species, of unknown origin from other diploid and polyploid species in the genus Crocus (Iridaceae). Species in the genus have high morphological diversity, with no clear phylogenetic patterns below the level of section Crocus series Crocus. Using DNA markers, this study aimed to examine the diversity and relationships within and between species of Crocus series Crocus. METHODS Eleven inter-retroelement amplified polymorphism (IRAP) primers were used in 63 different combinations with 35 single-plant accessions of C. sativus and related Crocus species in order to determine genetic variability and to conduct phylogenetic analysis. KEY RESULTS A total of 4521 distinct polymorphic bands from 100 bp to approx. 4 kb were amplified; no fragment specific to all accessions of a single species was amplified. The polymorphic information content (PIC) values varied from approx. 0·37 to approx. 0·05 (mean 0·17 ± 0·1) and the major allele frequency had a mean of 0·87. High levels of polymorphism were identified between accessions of the six species of Crocus series Crocus related to C. sativus, with further variation between the species. In contrast, no polymorphisms were seen among 17 C. sativus accessions obtained in the region from Kashmir through Iran to Spain. CONCLUSIONS In contrast to the intraspecific variability seen in other Crocus species, C. sativus has minimal genetic variation, and it is concluded that the triploid hybrid species has most probably arisen only once. The data show that saffron is an allotriploid species, with the IRAP analysis indicating that the most likely ancestors are C. cartwrightianus and C. pallasii subsp. pallasii (or close relatives). The results may facilitate resynthesizing saffron with improved characteristics, and show the need for conservation and collection of wild Crocus.
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Affiliation(s)
| | - José Antonio Fernández
- Laboratorio de Biotecnología, Instituto de Desarrollo Regional, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Trude Schwarzacher
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK and
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10
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Eslami Farouji A, Khodayari H, Saeidi H, Rahiminejad MR. Genetic diversity of diploid Triticum species in Iran assessed using inter-retroelement amplified polymorphisms (IRAP) markers. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Hardion L, Verlaque R, Saltonstall K, Leriche A, Vila B. Origin of the invasive Arundo donax (Poaceae): a trans-Asian expedition in herbaria. ANNALS OF BOTANY 2014; 114:455-62. [PMID: 25081517 PMCID: PMC4204670 DOI: 10.1093/aob/mcu143] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/02/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The hypothesis of an ancient introduction, i.e. archaeophyte origin, is one of the most challenging questions in phylogeography. Arundo donax (Poaceae) is currently considered to be one of the worst invasive species globally, but it has also been widely utilzed by man across Eurasia for millennia. Despite a lack of phylogenetic data, recent literature has often speculated on its introduction to the Mediterranean region. METHODS This study tests the hypothesis of its ancient introduction from Asia to the Mediterranean by using plastid DNA sequencing and morphometric analysis on 127 herbarium specimens collected across sub-tropical Eurasia. In addition, a bioclimatic species distribution model calibrated on 1221 Mediterranean localities was used to identify similar ecological niches in Asia. KEY RESULTS Despite analysis of several plastid DNA hypervariable sites and the identification of 13 haplotypes, A. donax was represented by a single haplotype from the Mediterranean to the Middle East. This haplotype is shared with invasive samples worldwide, and its nearest phylogenetic relatives are located in the Middle East. Morphometric data characterized this invasive clone by a robust morphotype distinguishable from all other Asian samples. The ecological niche modelling designated the southern Caspian Sea, southern Iran and the Indus Valley as the most suitable regions of origin in Asia for the invasive clone of A. donax. CONCLUSIONS Using an integrative approach, an ancient dispersion of this robust, polyploid and non-fruiting clone is hypothesized from the Middle East to the west, leading to its invasion throughout the Mediterranean Basin.
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Affiliation(s)
- Laurent Hardion
- Institut Méditerranéen de Biodiversité et d'Ecologie, UMR CNRS IRD, Aix Marseille Université, 13331 Marseille, France
| | - Régine Verlaque
- Institut Méditerranéen de Biodiversité et d'Ecologie, UMR CNRS IRD, Aix Marseille Université, 13331 Marseille, France
| | | | - Agathe Leriche
- Institut Méditerranéen de Biodiversité et d'Ecologie, UMR CNRS IRD, Aix Marseille Université, 13331 Marseille, France
| | - Bruno Vila
- Institut Méditerranéen de Biodiversité et d'Ecologie, UMR CNRS IRD, Aix Marseille Université, 13331 Marseille, France
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Yilmaz S, Gozukirmizi N. Variation of Retrotransposon Movement in Callus Culture and Regenerated Shoots of Barley. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2013.0076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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13
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Kuhn BC, López-Ribera I, da Silva Machado MDFP, Vicient CM. Genetic diversity of maize germplasm assessed by retrotransposon-based markers. Electrophoresis 2014; 35:1921-7. [PMID: 24634146 DOI: 10.1002/elps.201400038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 02/28/2014] [Accepted: 03/07/2014] [Indexed: 12/19/2022]
Abstract
Maize is one of the most important crops and also a model for grass genome research. Transposable elements comprise over 78% of the maize genome and their ability to generate new copies makes them good potential markers. Interretrotransposon-amplified polymorphism (IRAP) and retrotransposon microsatellite amplified polymorphism (REMAP) protocols were used for the first time in maize to study the genetic variability between maize cultivars. Ten PCR primers were selected based on a systematic analysis of the sequence conservation in the extremities of different high copy number transposable elements, whereas one primer was chosen based on a microsatellite sequence. Of the 16 primer combinations tested, 14 produced polymorphic bands. These markers were used to identify genetic similarity among 20 maize cultivars selected by their different kernel oil content. Genetic similarity analysis was performed based on the polymorphic band profiles and dendrograms were developed by the unweighted pair-group method with arithmetic averages. Clustering technique revealed that samples were grouped into three clusters that differed in their kernel oil content and size, and in their relative embryo size. In the current investigation, there is evidence that IRAP/REMAP may be useful as markers in maize.
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Affiliation(s)
- Betty Cristiane Kuhn
- CAPES Scholarship, CAPES Foundation, Brasília, Brazil; Postgraduate Program in Genetics and Breeding, State University of Maringá, Maringá, PR, Brazil
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Genetic diversity and geographic distribution of variation of Hordeum murinum as revealed by retroelement insertional polymorphisms in Iran. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0340-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Nasri S, Abdollahi Mandoulakani B, Darvishzadeh R, Bernousi I. Retrotransposon insertional polymorphism in Iranian bread wheat cultivars and breeding lines revealed by IRAP and REMAP markers. Biochem Genet 2013; 51:927-43. [PMID: 23839088 DOI: 10.1007/s10528-013-9618-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 04/06/2013] [Indexed: 12/23/2022]
Abstract
Inter-retrotransposon amplified polymorphisms (IRAPs) and retrotransposon-microsatellite amplified polymorphisms (REMAPs) were used to detect retrotransposon integration events and genetic diversity in 101 Iranian bread wheat (Triticum aestivum L.) cultivars and breeding lines. The 9 IRAP primers amplified 128 loci, and 20 REMAP primers amplified 263 loci. Percentage of polymorphic loci, average expected heterozygosity, number of effective alleles, and Shannon's information index for the REMAP markers were slightly higher than those for the IRAP markers. The same estimated parameters calculated for native and nonnative retrotransposons were not considerably different. A Mantel test between IRAP and REMAP cophenetic matrices evidenced no significant correlation. Cluster analysis based on the Dice similarity coefficient and complete linkage algorithm using IRAP+REMAP loci identified five groups among the genotypes studied that could be applied as crossing parents in T. aestivum breeding programs.
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Affiliation(s)
- Shilan Nasri
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
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Bonchev G, Parisod C. Transposable elements and microevolutionary changes in natural populations. Mol Ecol Resour 2013; 13:765-75. [DOI: 10.1111/1755-0998.12133] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/31/2013] [Accepted: 06/04/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Georgi Bonchev
- Laboratory of evolutionary botany Institute of biology University of Neuchâtel Rue Emile‐Argand 11 CH‐2000 Neuchâtel Switzerland
- Institute of plant physiology and genetics Bulgarian academy of sciences G. Bonchev Street, Bldg 24 Sofia 1113 Bulgaria
| | - Christian Parisod
- Laboratory of evolutionary botany Institute of biology University of Neuchâtel Rue Emile‐Argand 11 CH‐2000 Neuchâtel Switzerland
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Wang J, Luo MC, Chen Z, You FM, Wei Y, Zheng Y, Dvorak J. Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat. THE NEW PHYTOLOGIST 2013; 198:925-937. [PMID: 23374069 DOI: 10.1111/nph.12164] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/22/2012] [Indexed: 05/02/2023]
Abstract
Hexaploid wheat (Triticum aestivum, genomes AABBDD) originated by hybridization of tetraploid Triticum turgidum (genomes AABB) with Aegilops tauschii (genomes DD). Genetic relationships between A. tauschii and the wheat D genome are of central importance for the understanding of wheat origin and subsequent evolution. Genetic relationships among 477 A. tauschii and wheat accessions were studied with the A. tauschii 10K Infinium single nucleotide polymorphism (SNP) array. Aegilops tauschii consists of two lineages (designated 1 and 2) having little genetic contact. Each lineage consists of two closely related sublineages. A population within lineage 2 in the southwestern and southern Caspian appears to be the main source of the wheat D genome. Lineage 1 contributed as little as 0.8% of the wheat D genome. Triticum aestivum is subdivided into the western and Far Eastern populations. The Far Eastern population conserved the genetic make-up of the nascent T. aestivum more than the western population. In wheat, diversity is high in chromosomes 1D and 2D and it correlates in all wheat D-genome and A. tauschii chromosomes with recombination rates. Gene flow from A. tauschii was an important source of wheat genetic diversity and shaped its distribution along the D-genome chromosomes.
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Affiliation(s)
- Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Zhongxu Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Frank M You
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB R3T 2M9, Canada
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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Temel A, Gozukirmizi N. Analysis of retrotransposition and DNA methylation in barley callus culture. ACTA BIOLOGICA HUNGARICA 2013; 64:86-95. [PMID: 23567833 DOI: 10.1556/abiol.64.2013.1.8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mature barley (Hordeum vulgare cv. Zafer-160) embryos were cultured on callus induction medium (MS+ 4 mg l-1 Dicamba) for 30 days and embryogenic calli were transferred onto regeneration medium (MS+ 0.5 mg l-1 trans-zeatin riboside). Callus induction percentage was 67.2%; embryogenic callus induction percentage was 42.3% and their regeneration percentage was 63.8%. Retrotransposon movements and methylation alterations in 15-day-old, 30-day-old calli and 4-day-old barley seedling (control) were investigated with Inter-Retrotransposon Amplified Polymorphism (IRAP) and Methylation-Sensitive Restriction Fingerprinting (MSRF), respectively. IRAP patterns were quite monomorphic however MSRF indicated increase in cytosine methylation during callus formation. Changes in retroelement movements and methylation alterations were evaluated and discussed in the light of literature.
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Affiliation(s)
- Aslihan Temel
- Department of Molecular Biology and Genetics, Istanbul University, Vezneciler, Istanbul, Turkey.
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Diversity of long terminal repeat retrotransposon genome distribution in natural populations of the wild diploid wheat Aegilops speltoides. Genetics 2011; 190:263-74. [PMID: 22042572 DOI: 10.1534/genetics.111.134643] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The environment can have a decisive influence on the structure of the genome, changing it in a certain direction. Therefore, the genomic distribution of environmentally sensitive transposable elements may vary measurably across a species area. In the present research, we aimed to detect and evaluate the level of LTR retrotransposon intraspecific variability in Aegilops speltoides (2n = 2x = 14), a wild cross-pollinated relative of cultivated wheat. The interretrotransposon amplified polymorphism (IRAP) protocol was applied to detect and evaluate the level of retrotransposon intraspecific variability in Ae. speltoides and closely related species. IRAP analysis revealed significant diversity in TE distribution. Various genotypes from the 13 explored populations significantly differ with respect to the patterns of the four explored LTR retrotransposons (WIS2, Wilma, Daniela, and Fatima). This diversity points to a constant ongoing process of LTR retrotransposon fraction restructuring in populations of Ae. speltoides throughout the species' range and within single populations in time. Maximum changes were recorded in genotypes from small stressed populations. Principal component analysis showed that the dynamics of the Fatima element significantly differ from those of WIS2, Wilma, and Daniela. In terms of relationships between Sitopsis species, IRAP analysis revealed a grouping with Ae. sharonensis and Ae. longissima forming a separate unit, Ae. speltoides appearing as a dispersed group, and Ae. bicornis being in an intermediate position. IRAP display data revealed dynamic changes in LTR retrotransposon fractions in the genome of Ae. speltoides. The process is permanent and population specific, ultimately leading to the separation of small stressed populations from the main group.
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Patel D, Power JB, Anthony P, Badakshi F, (Pat) Heslop-Harrison JS, Davey MR. Somatic hybrid plants of Nicotiana x sanderae (+) N. debneyi with fungal resistance to Peronospora tabacina. ANNALS OF BOTANY 2011; 108:809-19. [PMID: 21880657 PMCID: PMC3177675 DOI: 10.1093/aob/mcr197] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 06/16/2011] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS The genus Nicotiana includes diploid and tetraploid species, with complementary ecological, agronomic and commercial characteristics. The species are of economic value for tobacco, as ornamentals, and for secondary plant-product biosynthesis. They show substantial differences in disease resistance because of their range of secondary products. In the last decade, sexual hybridization and transgenic technologies have tended to eclipse protoplast fusion for gene transfer. Somatic hybridization was exploited in the present investigation to generate a new hybrid combination involving two sexually incompatible tetraploid species. The somatic hybrid plants were characterized using molecular, molecular cytogenetic and phenotypic approaches. METHODS Mesophyll protoplasts of the wild fungus-resistant species N. debneyi (2n = 4x = 48) were electrofused with those of the ornamental interspecific sexual hybrid N. × sanderae (2n = 2x = 18). From 1570 protoplast-derived cell colonies selected manually in five experiments, 580 tissues were sub-cultured to shoot regeneration medium. Regenerated plants were transferred to the glasshouse and screened for their morphology, chromosomal composition and disease resistance. KEY RESULTS Eighty-nine regenerated plants flowered; five were confirmed as somatic hybrids by their intermediate morphology compared with parental plants, cytological constitution and DNA-marker analysis. Somatic hybrid plants had chromosome complements of 60 or 62. Chromosomes were identified to parental genomes by genomic in situ hybridization and included all 18 chromosomes from N. × sanderae, and 42 or 44 chromosomes from N. debneyi. Four or six chromosomes of one ancestral genome of N. debneyi were eliminated during culture of electrofusion-treated protoplasts and plant regeneration. Both chloroplasts and mitochondria of the somatic hybrid plants were probably derived from N. debneyi. All somatic hybrid plants were fertile. In contrast to parental plants of N. × sanderae, the seed progeny of somatic hybrid plants were resistant to infection by Peronospora tabacina, a trait introgressed from the wild parent, N. debneyi. CONCLUSIONS Sexual incompatibility between N. × sanderae and N. debneyi was circumvented by somatic hybridization involving protoplast fusion. Asymmetrical nuclear hybridity was seen in the hybrids with loss of chromosomes, although importantly, somatic hybrids were fertile and stable. Expression of fungal resistance makes these somatic hybrids extremely valuable germplasm in future breeding programmes in ornamental tobacco.
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Affiliation(s)
- Deval Patel
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - J. Brian Power
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Paul Anthony
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Farah Badakshi
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | | | - Michael R. Davey
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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Evrensel C, Yilmaz S, Temel A, Gozukirmizi N. Variations in BARE-1 insertion patterns in barley callus cultures. GENETICS AND MOLECULAR RESEARCH 2011; 10:980-7. [PMID: 21710447 DOI: 10.4238/vol10-2gmr965] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The stability of aging barley calli was investigated with the barley retroelement 1 (BARE-1) retrotransposon specific inter-retrotransposon amplified polymorphism (IRAP) technique. Mature embryos of barley (Hordeum vulgare cv. Zafer-160) were cultured on callus induction MS medium supplemented with 3 mg/L 2,4-D and maintained on the same medium for 60 days. Ten IRAP primers were used in 25 different combinations. The similarity index between 30-day-old and 45-day-old calli was 84%; however, the similarity index between mature embryos and 45-day-old calli was 75%. These culture conditions caused BARE-1 retrotransposon alterations to appear as different band profiles. This is the first report of the use of the IRAP technique in barley in an investigation of callus development.
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Affiliation(s)
- C Evrensel
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, Istanbul, Turkey
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Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, Schulman AH. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity (Edinb) 2010; 106:520-30. [PMID: 20683483 DOI: 10.1038/hdy.2010.93] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants.
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Affiliation(s)
- R Kalendar
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Tam SM, Lefebvre V, Palloix A, Sage-Palloix AM, Mhiri C, Grandbastien MA. LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:973-89. [PMID: 19618162 DOI: 10.1007/s00122-009-1102-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 06/25/2009] [Indexed: 05/03/2023]
Abstract
Plant genetic resources often constitute the foundation of successful breeding programs. Pepper (Capsicum annuum L.) is one of the most economically important and diversely utilized Solanaceous crop species worldwide, but less studied compared to tomato and potato. We developed and used molecular markers based on two copia-type retrotransposons, Tnt1 and T135, in a set of Capsicum species and wild relatives from diverse geographical origins. Results showed that Tnt1 and T135 insertion polymorphisms are very useful for studying genetic diversity and relationships within and among pepper species. Clusters of accessions correspond to cultivar types based on fruit shape, pungency, geographic origin and pedigree. Genetic diversity values, normally reflective of past transposition activity and population dynamics, showed positive correlation with the average number of insertions per accession. Similar evolutionary relationships are observed to that inferred by previous karyosystematics studies. These observations support the possibility that retrotransposons have contributed to genome inflation during Capsicum evolution.
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Affiliation(s)
- Sheh May Tam
- Laboratoire de Biologie Cellulaire, UR501, Institut Jean-Pierre Bourgin, INRA, 78026, Versailles Cedex, France
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Leitch IJ, Fay MF. Plant genome horizons: Michael Bennett's contribution to genome research. ANNALS OF BOTANY 2008; 101:737-746. [PMID: 18411257 PMCID: PMC2710207 DOI: 10.1093/aob/mcn045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- I J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.
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