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Zong W, Zhao R, Wang X, Zhou C, Wang J, Chen C, Niu N, Zheng Y, Chen L, Liu X, Hou X, Zhao F, Wang L, Wang L, Song C, Zhang L. Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. DNA Res 2024; 31:dsae008. [PMID: 38447059 PMCID: PMC11090087 DOI: 10.1093/dnares/dsae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
Transposable elements (TEs) mobility is capable of generating a large number of structural variants (SVs), which can have considerable potential as molecular markers for genetic analysis and molecular breeding in livestock. Our results showed that the pig genome contains mainly TE-SVs generated by short interspersed nuclear elements (51,873/76.49%), followed by long interspersed nuclear elements (11,131/16.41%), and more than 84% of the common TE-SVs (Minor allele frequency, MAF > 0.10) were validated to be polymorphic. Subsequently, we utilized the identified TE-SVs to gain insights into the population structure, resulting in clear differentiation among the three pig groups and facilitating the identification of relationships within Chinese local pig breeds. In addition, we investigated the frequencies of TEs in the gene coding regions of different pig groups and annotated the respective TE types, related genes, and functional pathways. Through genome-wide comparisons of Large White pigs and Chinese local pigs utilizing the Beijing Black pigs, we identified TE-mediated SVs associated with quantitative trait loci and observed that they were mainly involved in carcass traits and meat quality traits. Lastly, we present the first documented evidence of TE transduction in the pig genome.
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Affiliation(s)
- Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Chenyu Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinbu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Li Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xin Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xinhua Hou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fuping Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ligang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lixian Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Arvas YE, Marakli S, Kaya Y, Kalendar R. The power of retrotransposons in high-throughput genotyping and sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1174339. [PMID: 37180380 PMCID: PMC10167742 DOI: 10.3389/fpls.2023.1174339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023]
Abstract
The use of molecular markers has become an essential part of molecular genetics through their application in numerous fields, which includes identification of genes associated with targeted traits, operation of backcrossing programs, modern plant breeding, genetic characterization, and marker-assisted selection. Transposable elements are a core component of all eukaryotic genomes, making them suitable as molecular markers. Most of the large plant genomes consist primarily of transposable elements; variations in their abundance contribute to most of the variation in genome size. Retrotransposons are widely present throughout plant genomes, and replicative transposition enables them to insert into the genome without removing the original elements. Various applications of molecular markers have been developed that exploit the fact that these genetic elements are present everywhere and their ability to stably integrate into dispersed chromosomal localities that are polymorphic within a species. The ongoing development of molecular marker technologies is directly related to the deployment of high-throughput genotype sequencing platforms, and this research is of considerable significance. In this review, the practical application to molecular markers, which is a use of technology of interspersed repeats in the plant genome were examined using genomic sources from the past to the present. Prospects and possibilities are also presented.
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Affiliation(s)
- Yunus Emre Arvas
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, Trabzon, Türkiye
| | - Sevgi Marakli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Türkiye
| | - Yılmaz Kaya
- Agricultural Biotechnology Department, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Türkiye
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Ruslan Kalendar
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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Mohamed M, Sabot F, Varoqui M, Mugat B, Audouin K, Pélisson A, Fiston-Lavier AS, Chambeyron S. TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches. Genome Biol 2023; 24:63. [PMID: 37013657 PMCID: PMC10069131 DOI: 10.1186/s13059-023-02911-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
Transposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software that combines assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements (TEs). Using high- or low-quality genome assemblies, TrEMOLO can detect most TE insertions and deletions and estimate their allele frequency in populations. Benchmarking with simulated data revealed that TrEMOLO outperforms other state-of-the-art computational tools. TE detection and frequency estimation by TrEMOLO were validated using simulated and experimental datasets. Therefore, TrEMOLO is a comprehensive and suitable tool to accurately study TE dynamics. TrEMOLO is available under GNU GPL3.0 at https://github.com/DrosophilaGenomeEvolution/TrEMOLO .
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Affiliation(s)
- Mourdas Mohamed
- Institute of Human Genetics, UMR9002, CNRS and Université de Montpellier, Montpellier, France
| | - François Sabot
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
- IFB - Southgreen Bioversity, CIRAD, INRAE, IRD, Montpellier, France
| | - Marion Varoqui
- Institute of Human Genetics, UMR9002, CNRS and Université de Montpellier, Montpellier, France
| | - Bruno Mugat
- Institute of Human Genetics, UMR9002, CNRS and Université de Montpellier, Montpellier, France
| | | | - Alain Pélisson
- Institute of Human Genetics, UMR9002, CNRS and Université de Montpellier, Montpellier, France
| | - Anna-Sophie Fiston-Lavier
- ISEM, Université Montpellier, CNRS, IRD, CIRAD, EPHE, Montpellier, France.
- Institut Universitaire de France (IUF), Paris, France.
| | - Séverine Chambeyron
- Institute of Human Genetics, UMR9002, CNRS and Université de Montpellier, Montpellier, France.
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Androsiuk P, Milarska SE, Dulska J, Kellmann-Sopyła W, Szablińska-Piernik J, Lahuta LB. The comparison of polymorphism among Avena species revealed by retrotransposon-based DNA markers and soluble carbohydrates in seeds. J Appl Genet 2023; 64:247-264. [PMID: 36719514 PMCID: PMC10076396 DOI: 10.1007/s13353-023-00748-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/01/2023]
Abstract
Here, we compared the polymorphism among 13 Avena species revealed by the iPBS markers and soluble carbohydrate profiles in seeds. The application of seven iPBS markers generated 83 bands, out of which 20.5% were polymorphic. No species-specific bands were scored. Shannon's information index (I) and expected heterozygosity (He) revealed low genetic diversity, with the highest values observed for A. nuda (I = 0.099; He = 0.068). UPGMA clustering of studied Avena accessions and PCoA results showed that the polyploidy level is the main grouping criterion. High-resolution gas chromatography revealed that the studied Avena accessions share the same composition of soluble carbohydrates, but significant differences in the content of total (5.30-22.38 mg g-1 of dry weight) and particular sugars among studied samples were observed. Sucrose appeared as the most abundant sugar (mean 61.52% of total soluble carbohydrates), followed by raffinose family oligosaccharides (31.23%), myo-inositol and its galactosides (6.16%), and monosaccharides (1.09%). The pattern of interspecific variation in soluble carbohydrates, showed by PCA, was convergent to that revealed by iPBS markers. Thus, both methods appeared as a source of valuable data useful in the characterization of Avena resources or in the discussion on the evolution of this genus.
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Affiliation(s)
- Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Sylwia Eryka Milarska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Justyna Dulska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Wioleta Kellmann-Sopyła
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Joanna Szablińska-Piernik
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Lesław Bernard Lahuta
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Papolu PK, Ramakrishnan M, Mullasseri S, Kalendar R, Wei Q, Zou L, Ahmad Z, Vinod KK, Yang P, Zhou M. Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1064847. [PMID: 36570931 PMCID: PMC9780303 DOI: 10.3389/fpls.2022.1064847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/21/2022] [Indexed: 05/28/2023]
Abstract
Long terminal repeat retrotransposons (LTR retrotransposons) are the most abundant group of mobile genetic elements in eukaryotic genomes and are essential in organizing genomic architecture and phenotypic variations. The diverse families of retrotransposons are related to retroviruses. As retrotransposable elements are dispersed and ubiquitous, their "copy-out and paste-in" life cycle of replicative transposition leads to new genome insertions without the excision of the original element. The overall structure of retrotransposons and the domains responsible for the various phases of their replication is highly conserved in all eukaryotes. The two major superfamilies of LTR retrotransposons, Ty1/Copia and Ty3/Gypsy, are distinguished and dispersed across the chromosomes of higher plants. Members of these superfamilies can increase in copy number and are often activated by various biotic and abiotic stresses due to retrotransposition bursts. LTR retrotransposons are important drivers of species diversity and exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution. Additionally, LTR retrotransposons influence the gene expression patterns of adjacent genes by modulating potential small interfering RNA (siRNA) and RNA-directed DNA methylation (RdDM) pathways. Furthermore, comparative and evolutionary analysis of the most important crop genome sequences and advanced technologies have elucidated the epigenetics and structural and functional modifications driven by LTR retrotransposon during speciation. However, mechanistic insights into LTR retrotransposons remain obscure in plant development due to a lack of advancement in high throughput technologies. In this review, we focus on the key role of LTR retrotransposons response in plants during heat stress, the role of centromeric LTR retrotransposons, and the role of LTR retrotransposon markers in genome expression and evolution.
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Affiliation(s)
- Pradeep K. Papolu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi, Kerala, India
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Long−Hai Zou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | | | - Ping Yang
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
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6
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Chen C, D'Alessandro E, Murani E, Zheng Y, Giosa D, Yang N, Wang X, Gao B, Li K, Wimmers K, Song C. SINE jumping contributes to large-scale polymorphisms in the pig genomes. Mob DNA 2021; 12:17. [PMID: 34183049 PMCID: PMC8240389 DOI: 10.1186/s13100-021-00246-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene activity and even on phenotypes. However, SINE RIP profiles in livestock remain largely unknown, and not be revealed in pigs. RESULTS Our data revealed that SINEA1 displayed the most polymorphic insertions (22.5 % intragenic and 26.5 % intergenic), followed by SINEA2 (10.5 % intragenic and 9 % intergenic) and SINEA3 (12.5 % intragenic and 5.0 % intergenic). We developed a genome-wide SINE RIP mining protocol and obtained a large number of SINE RIPs (36,284), with over 80 % accuracy and an even distribution in chromosomes (14.5/Mb), and 74.34 % of SINE RIPs generated by SINEA1 element. Over 65 % of pig SINE RIPs overlap with genes, most of them (> 95 %) are in introns. Overall, about one forth (23.09 %) of the total genes contain SINE RIPs. Significant biases of SINE RIPs in the transcripts of protein coding genes were observed. Nearly half of the RIPs are common in these pig breeds. Sixteen SINE RIPs were applied for population genetic analysis in 23 pig breeds, the phylogeny tree and cluster analysis were generally consistent with the geographical distributions of native pig breeds in China. CONCLUSIONS Our analysis revealed that SINEA1-3 elements, particularly SINEA1, are high polymorphic across different pig breeds, and generate large-scale structural variations in the pig genomes. And over 35,000 SINE RIP markers were obtained. These data indicate that young SINE elements play important roles in creating new genetic variations and shaping the evolution of pig genome, and also provide strong evidences to support the great potential of SINE RIPs as genetic markers, which can be used for population genetic analysis and quantitative trait locus (QTL) mapping in pig.
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Affiliation(s)
- Cai Chen
- College of Animal Science & Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Enrico D'Alessandro
- Department of Veterinary Science, University of Messina, 98168, Messina, Italy
| | - Eduard Murani
- Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Yao Zheng
- College of Animal Science & Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Domenico Giosa
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98125, Messina, Italy
| | - Naisu Yang
- College of Animal Science & Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Kui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China.
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Abstract
Retrotransposons are ubiquitous, generally dispersed components of eukaryotic genomes. These properties, together with their "copy and paste" lifecycle that generates insertional polymorphism without need for excision, makes them widely useful as a molecular-genetic tags. Various tagging systems have been developed that exploit the sequence conservation of retrotransposon components, such as those found in their long terminal repeats (LTRs). To detect polymorphisms for retrotransposon insertions, marker systems generally rely on PCR amplification between the termini and some component of flanking genomic DNA. As complements to various "wet lab" protocols for retrotransposon tagging, in silico bioinformatics approaches are useful for predicting likely outcomes from unsequenced accessions on the basis of reference genomes. In this chapter, we describe protocols for in silico retrotransposon-based fingerprinting techniques using the FastPCR software as an integrated tools environment for in silico PCR primer design and analysis.
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Genetic Diversity and Population Structures in Chinese Miniature Pigs Revealed by SINE Retrotransposon Insertion Polymorphisms, a New Type of Genetic Markers. Animals (Basel) 2021; 11:ani11041136. [PMID: 33921134 PMCID: PMC8071531 DOI: 10.3390/ani11041136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Our previous studies suggested that the short interspersed nuclear element (SINE) retrotransposon insertion polymorphisms (RIPs), as a new type of molecular marker developed very recently, are ideal molecular markers and have the potential to be used for population genetic analysis and molecular breeding in pigs and possibly it can be extended to other livestock animals as well. However, no report is available for the application of SINE RIPs in population genetic analysis in livestock, including pigs. Here, we evaluated 30 SINE RIPs in several indigenous Chinese miniature pig breeds, including three subpopulations of Bama pigs (BM-cov, BM-clo, and BM-inb). BM-cov is a subpopulation conserved in the national conservation farm, and BM-clo is a closed population maintained over 30 years with only 2 boars and 14 sows imported from its original area, while BM-inb herd is an 18 generation continuous inbreeding line based on the BM-clo population. To our knowledge, it is the first time to report the genetic diversity, breed differentiation, and population structures for these populations by using SINE RIPs, and which suggests the feasibility of SINE RIPs in pig genetic analysis. Abstract RIPs have been developed as effective genetic markers and popularly applied for genetic analysis in plants, but few reports are available for domestic animals. Here, we established 30 new molecular markers based on the SINE RIPs, and applied them for population genetic analysis in seven Chinese miniature pigs. The data revealed that the closed herd (BM-clo), inbreeding herd (BM-inb) of Bama miniature pigs were distinctly different from the BM-cov herds in the conservation farm, and other miniature pigs (Wuzhishan, Congjiang Xiang, Tibetan, and Mingguang small ear). These later five miniature pig breeds can further be classified into two clades based on a phylogenetic tree: one included BM-cov and Wuzhishan, the other included Congjiang Xiang, Tibetan, and Mingguang small ear, which was well-supported by structure analysis. The polymorphic information contents estimated by using SINE RIPs are lower than the predictions based on microsatellites. Overall, the genetic distances and breed-relationships between these populations revealed by 30 SINE RIPs generally agree with their evolutions and geographic distributions. We demonstrated the potential of SINE RIPs as new genetic markers for genetic monitoring and population structure analysis in pigs, which can even be extended to other livestock animals.
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Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks. Genes (Basel) 2020; 11:genes11101216. [PMID: 33081418 PMCID: PMC7602945 DOI: 10.3390/genes11101216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.
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10
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Assessment of genetic diversity of cultivated and wild Iranian grape germplasm using retrotransposon-microsatellite amplified polymorphism (REMAP) markers and pomological traits. Mol Biol Rep 2020; 47:7593-7606. [PMID: 32949305 DOI: 10.1007/s11033-020-05827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Abstract
Understanding the genetic diversity and relationships between genotypes is an effective step in designing effective breeding programs. Insertional polymorphisms of retrotransposons were studied in 75 cultivated and wild grape genotypes using retrotransposon-microsatellite amplified polymorphism (REMAP) technique. In the morphological part of work, seven pomological traits with a high breeding interest were also analyzed in the cultivated genotypes. A total of 328 markers were produced by 42 primer pairs, out of which 313 markers (95.43%) were polymorphic. Number of markers ranged from 4 in loci Tvv1Fa-873, Vine1-811, Gret1Ra-855 and Tvv1Fa-890 to 12 in locus Vine1Ra-841 with an average value of 7.45. Similarity values based on Dice's coefficient among all 75 grapevine genotypes varied from 0.41 to 0.77. Classification of genotypes using unweighted pair-group method using complete-linkage clustering led to six distinct groups. Some wild and cultivated varieties placed in the same groups. It seems there are close relationship between wild and cultivated genotypes and maybe wild genotypes are ancestor of native grapevines. Grouping of grapevine genotypes based on molecular marker data was not in agreement with clustering by agro-morphological data indicating that the most of multiplied sequences are confined to the non-coding regions of transposon elements. Results showed a substantial level of genetic diversity at molecular and pomological level and the potential of this diversity for future grape breeding programs.
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Yepuri V, Jalali S, Kancharla N, Reddy VB, Arockiasamy S. Development of genome wide transposable elements based repeat junction markers in Jatropha (Jatropha curcas L.). Mol Biol Rep 2020; 47:5091-5099. [PMID: 32562173 DOI: 10.1007/s11033-020-05579-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/10/2020] [Indexed: 11/29/2022]
Abstract
Jatropha curcas is a potential biodiesel crop and a highly adaptable species to various agro-climatic conditions. In this study, we have utilized transposable elements' (TE) repeat junctions (RJs) which are an important constituent of the genome, used to form a genome-wide molecular marker platform owing to its use in genomic studies of plants. We screened our previously generated Jatropha hybrid genome assembly of size 265 Mbp using RJPrimers pipeline software and identified a total of 1274 TE junctions. For the predicted RJs, we designed 2868 polymerase chain reaction (PCR) based RJ markers (RJMs) flanking the junction regions. In addition to marker design, the identified RJs were utilized to detect 225,517 TEs across the genome. The different types of transposable repeat elements mainly were scattered into Retro, LTR, Copia and Gypsy categories. The efficacy of the designed markers was tested by utilizing a subset of RJMs selected randomly. We have validated 96 randomly selected RJ primers in a group of 32 J. curcas genotypes and more than 90% of the markers effectively intensified as amplicons. Of these, 10 primers were shown to be polymorphic in estimating genetic diversity among the 32 Jatropha lines. UPGMA cluster analysis revealed the formation of two clusters such as A and B exhibiting 85.5% and 87% similarity coefficient respectively. The various RJMs identified in this study could be utilized as a significant asset in Jatropha functional genomics including genome determination, mapping and marker-assisted selection.
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Affiliation(s)
- Vijay Yepuri
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - Saakshi Jalali
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - Nagesh Kancharla
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - V B Reddy
- AgriGenome Labs Private Limited, Hyderabad, 500078, India
| | - S Arockiasamy
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India.
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Hirata C, Waki T, Shimomura K, Wada T, Tanaka S, Ikegami H, Uchimura Y, Hirashima K, Nakazawa Y, Okada K, Namai K, Tahara M, Monden Y. DNA markers based on retrotransposon insertion polymorphisms can detect short DNA fragments for strawberry cultivar identification. BREEDING SCIENCE 2020; 70:231-240. [PMID: 32523405 PMCID: PMC7272250 DOI: 10.1270/jsbbs.19116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/03/2019] [Indexed: 06/11/2023]
Abstract
In this study, DNA markers were developed for discrimination of strawberry (Fragaria × ananassa L.) cultivars based on retrotransposon insertion polymorphisms. We performed a comprehensive genomic search to identify retrotransposon insertion sites and subsequently selected one retrotransposon family, designated CL3, which provided reliable discrimination among strawberry cultivars. Through analyses of 75 strawberry cultivars, we developed eight cultivar-specific markers based on CL3 retrotransposon insertion sites. Used in combination with 10 additional polymorphic markers, we differentiated 35 strawberry cultivars commonly cultivated in Japan. In addition, we demonstrated that the retrotransposon-based markers were effective for PCR detection of DNA extracted from processed food materials, whereas a SSR marker was ineffective. These results indicated that the retrotransposon-based markers are useful for cultivar discrimination for processed food products, such as jams, in which DNA may be fragmented or degraded.
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Affiliation(s)
- Chiharu Hirata
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka 818-8549, Japan
| | - Takamitsu Waki
- Tochigi Prefectural Agricultural Experiment Station, 1080 Kawarayacho, Utsunomiya, Tochigi 320-0002, Japan
| | - Katsumi Shimomura
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka 818-8549, Japan
| | - Takuya Wada
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka 818-8549, Japan
| | - Seiya Tanaka
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hidetoshi Ikegami
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka 818-8549, Japan
| | - Yousuke Uchimura
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka 818-8549, Japan
| | - Keita Hirashima
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka 818-8549, Japan
| | - Yoshiko Nakazawa
- Tochigi Prefectural Agricultural Experiment Station, 1080 Kawarayacho, Utsunomiya, Tochigi 320-0002, Japan
| | - Kaori Okada
- Tochigi Prefectural Agricultural Experiment Station, 1080 Kawarayacho, Utsunomiya, Tochigi 320-0002, Japan
| | - Kiyoshi Namai
- Tochigi Prefectural Agricultural Experiment Station, 1080 Kawarayacho, Utsunomiya, Tochigi 320-0002, Japan
| | - Makoto Tahara
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
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13
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High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis. Mol Biol Rep 2020; 47:1589-1603. [PMID: 31919750 DOI: 10.1007/s11033-020-05246-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/03/2020] [Indexed: 01/08/2023]
Abstract
Maize is one of the world's most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons (Huck, Tekay, Opie, Ji, and Grande) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was expected to display ecogeographical patterns of variation and local adaptation. The clustering method showed that the varieties were grouped into three clusters differing in ecogeographical origin. Each of these clusters comprised divergent hybrids with convergent characters. The clusters reflected the differences among maize hybrids and were in accordance with their pedigree. The IRAP technique is an efficient high-throughput genetic marker-generating method.
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Bhat RS, Shirasawa K, Monden Y, Yamashita H, Tahara M. Developing Transposable Element Marker System for Molecular Breeding. Methods Mol Biol 2020; 2107:233-251. [PMID: 31893450 DOI: 10.1007/978-1-0716-0235-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Transposable element (TE) marker system was developed considering the useful properties of the transposable elements such as their large number in the animal and plant genomes, high rate of insertion polymorphism, and ease of detection. Various methods have been employed for developing a large number of TE markers in several crop plants for genomics studies. Here we describe some of these methods including the recent whole genome search. We also review the application of TE markers in molecular breeding.
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Affiliation(s)
- R S Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, Karnataka, India.
| | - K Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Y Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - H Yamashita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - M Tahara
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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15
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Coutinho JP, Carvalho A, Martín A, Lima-Brito J. Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers. Mol Biol Rep 2018; 45:133-142. [PMID: 29349607 DOI: 10.1007/s11033-018-4146-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
Abstract
Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes. Here, iPBS primers designed by other authors were tested alone and combined. Some of them were discriminative, revealed polymorphism within and among taxa allowing the production of a total of 150 iPBS markers. In addition, several monomorphic iPBS markers were also amplified in each taxon. The UPGMA dendrogram based on the pooled iPBS data revealed 27% of genetic similarity among species. The individuals were clustered per genus and most of the oaks per infrageneric group corroborating the adopted taxonomy. Globally, the iPBS markers demonstrated suitability for DNA fingerprinting, determination of phylogenies and taxonomic discrimination in Fagaceae, and could constitute a useful and alternative tool for germplasm characterization, and for definition of conservation strategies and forestry management. Moreover, these markers would be useful for fingerprinting natural hybrids that share morphological similarities with their parents. Since iPBS markers could also enable insights about RTNs evolution, an eventual correlation among iPBS polymorphism, variability of RTN insertions and/or genome size in Fagaceae is discussed.
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Affiliation(s)
- João Paulo Coutinho
- BioISI - Biosystems & Integrative Sciences Institute, University of Tras-os-Montes and Alto Douro (BioISI-UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Ana Carvalho
- BioISI - Biosystems & Integrative Sciences Institute, University of Tras-os-Montes and Alto Douro (BioISI-UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal
| | - Antonio Martín
- CSIC - Consejo Superior de Investigaciones Científicas, Alameda del Obispo, 4084, 14080, Córdoba, Spain
| | - José Lima-Brito
- BioISI - Biosystems & Integrative Sciences Institute, University of Tras-os-Montes and Alto Douro (BioISI-UTAD), Quinta de Prados, 5000-801, Vila Real, Portugal. .,Department of Genetics and Biotechnology, University of Tras-os-Montes and Alto Douro, 5001-801, Vila Real, Portugal.
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Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, Hatipoğlu R, Ahmad F, Alsaleh A, Labhane N, Özkan H, Chung G, Baloch FS. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1400401] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Muhammad Azhar Nadeem
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, School of Engineering, Chonnam National University, Yeosu, Korea
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, P. R. China
| | - Yıldız Doğan
- Department of Field Crops, Eastern Mediterranean Agricultural Research Institute, Agricultural Ministry, Adana, Turkey
| | - Gonul Comertpay
- Department of Field Crops, Eastern Mediterranean Agricultural Research Institute, Agricultural Ministry, Adana, Turkey
| | - Mehtap Yıldız
- Department of Agricultural Biotechnology, Faculty of Agriculture, Yuzuncu Yıl University, Van, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Fiaz Ahmad
- Botany Division, Institute of Pure and Applied Biology, Bahauddin Zakariya University, Punjab, Pakistan
| | - Ahmad Alsaleh
- Molecular Genetics Laboratory, Science and Technology Application and Research Center, Bozok University, Yozgat, Turkey
| | - Nitin Labhane
- Department of Botany, Bhavan's College, University of Mumbai, Mumbai, India
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, School of Engineering, Chonnam National University, Yeosu, Korea
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
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17
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Singh S, Nandha PS, Singh J. Transposon-based genetic diversity assessment in wild and cultivated barley. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species. Sci Rep 2017; 7:5966. [PMID: 28729554 PMCID: PMC5519738 DOI: 10.1038/s41598-017-06084-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 01/07/2023] Open
Abstract
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.
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19
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Rey-Baños R, Sáenz de Miera LE, García P, Pérez de la Vega M. Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.). PLoS One 2017; 12:e0176728. [PMID: 28448614 PMCID: PMC5407846 DOI: 10.1371/journal.pone.0176728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/14/2017] [Indexed: 12/02/2022] Open
Abstract
Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F7 inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type) none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry out further genetic analyses.
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Affiliation(s)
- Rita Rey-Baños
- Área de Genética, Dpto. de Biología Molecular, Universidad de León, León, Spain
| | - Luis E. Sáenz de Miera
- Área de Genética, Dpto. de Biología Molecular, Universidad de León, León, Spain
- * E-mail:
| | - Pedro García
- Área de Genética, Dpto. de Biología Molecular, Universidad de León, León, Spain
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20
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Useful parasites: the evolutionary biology and biotechnology applications of transposable elements. J Genet 2017; 95:1039-1052. [PMID: 27994207 DOI: 10.1007/s12041-016-0702-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Transposable elements usually comprise the most abundant nongenic fraction of eukaryotic genomes. Because of their capacity to selfreplicate and to induce a wide range of mutations, transposable elements have long been considered as 'parasitic' or 'selfish'. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. Numerous studies have provided evidences that mobile elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of their hosts. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. I will provide examples that transposable elements, although having signatures of 'selfish' DNA, play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These features, along with the transpositional and mutagenic capacity to produce a raw genetic diversity, make the genome mobile fraction, a key player in species adaptation and microevolution. The last but not least, transposable elements stand as informative DNA markers that may complement other conventional DNA markers. Altogether, transposable elements represent a promising, but still largely unexplored research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.
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21
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Darvishzadeh R. Population structure, linkage disequilibrium and association mapping for morphological traits in sunflower ( Helianthus annuusL.). BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2015.1136568] [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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22
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Cheng C, Tarutani Y, Miyao A, Ito T, Yamazaki M, Sakai H, Fukai E, Hirochika H. Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:1069-1081. [PMID: 26243209 DOI: 10.1111/tpj.12952] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/21/2015] [Indexed: 06/04/2023]
Abstract
Methylation patterns of plants are unique as, in addition to the methylation at CG dinucleotides that occurs in mammals, methylation also occurs at non-CG sites. Genes are methylated at CG sites, but transposable elements (TEs) are methylated at both CG and non-CG sites. The role of non-CG methylation in transcriptional silencing of TEs is being extensively studied at this time, but only very rare transpositions have been reported when non-CG methylation machineries have been compromised. To understand the role of non-CG methylation in TE suppression and in plant development, we characterized rice mutants with changes in the chromomethylase gene, OsCMT3a. oscmt3a mutants exhibited a dramatic decrease in CHG methylation, changes in the expression of some genes and TEs, and pleiotropic developmental abnormalities. Genome resequencing identified eight TE families mobilized in oscmt3a during normal propagation. These TEs included tissue culture-activated copia retrotransposons Tos17 and Tos19 (Lullaby), a pericentromeric clustered high-copy-number non-autonomous gypsy retrotransposon Dasheng, two copia retrotransposons Osr4 and Osr13, a hAT-tip100 transposon DaiZ, a MITE transposon mPing, and a LINE element LINE1-6_OS. We confirmed the transposition of these TEs by polymerase chain reaction (PCR) and/or Southern blot analysis, and showed that transposition was dependent on the oscmt3a mutation. These results demonstrated that OsCMT3a-mediated non-CG DNA methylation plays a critical role in development and in the suppression of a wide spectrum of TEs. These in planta mobile TEs are important for studying the interaction between TEs and the host genome, and for rice functional genomics.
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Affiliation(s)
- Chaoyang Cheng
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yoshiaki Tarutani
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Akio Miyao
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Tasuku Ito
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Muneo Yamazaki
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Hiroaki Sakai
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Eigo Fukai
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Hirohiko Hirochika
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
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23
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Identification, characterization and diversification of non-autonomous hAT transposons and unknown insertions in Brassica. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0324-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica. Mol Genet Genomics 2015; 290:2297-312. [DOI: 10.1007/s00438-015-1076-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/29/2015] [Indexed: 11/26/2022]
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25
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Garbus I, Romero JR, Valarik M, Vanžurová H, Karafiátová M, Cáccamo M, Doležel J, Tranquilli G, Helguera M, Echenique V. Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes. BMC Genomics 2015; 16:375. [PMID: 25962417 PMCID: PMC4440537 DOI: 10.1186/s12864-015-1579-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/24/2015] [Indexed: 12/04/2022] Open
Abstract
Background The number and complexity of repetitive elements varies between species, being in general most represented in those with larger genomes. Combining the flow-sorted chromosome arms approach to genome analysis with second generation DNA sequencing technologies provides a unique opportunity to study the repetitive portion of each chromosome, enabling comparisons among them. Additionally, different sequencing approaches may produce different depth of insight to repeatome content and structure. In this work we analyze and characterize the repetitive sequences of Triticum aestivum cv. Chinese Spring homeologous group 4 chromosome arms, obtained through Roche 454 and Illumina sequencing technologies, hereinafter marked by subscripts 454 and I, respectively. Repetitive sequences were identified with the RepeatMasker software using the interspersed repeat database mips-REdat_v9.0p. The input sequences consisted of our 4DS454 and 4DL454 scaffolds and 4ASI, 4ALI, 4BSI, 4BLI, 4DSI and 4DLI contigs, downloaded from the International Wheat Genome Sequencing Consortium (IWGSC). Results Repetitive sequences content varied from 55% to 63% for all chromosome arm assemblies except for 4DLI, in which the repeat content was 38%. Transposable elements, small RNA, satellites, simple repeats and low complexity sequences were analyzed. SSR frequency was found one per 24 to 27 kb for all chromosome assemblies except 4DLI, where it was three times higher. Dinucleotides and trinucleotides were the most abundant SSR repeat units. (GA)n/(TC)n was the most abundant SSR except for 4DLI where the most frequently identified SSR was (CCG/CGG)n. Retrotransposons followed by DNA transposons were the most highly represented sequence repeats, mainly composed of CACTA/En-Spm and Gypsy superfamilies, respectively. This whole chromosome sequence analysis allowed identification of three new LTR retrotransposon families belonging to the Copia superfamily, one belonging to the Gypsy superfamily and two TRIM retrotransposon families. Their physical distribution in wheat genome was analyzed by fluorescent in situ hybridization (FISH) and one of them, the Carmen retrotransposon, was found specific for centromeric regions of all wheat chromosomes. Conclusion The presented work is the first deep report of wheat repetitive sequences analyzed at the chromosome arm level, revealing the first insight into the repeatome of T. aestivum chromosomes of homeologous group 4. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1579-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ingrid Garbus
- CERZOS (CCT - CONICET Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Argentina.
| | - José R Romero
- CERZOS (CCT - CONICET Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Argentina.
| | - Miroslav Valarik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Hana Vanžurová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Mario Cáccamo
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Gabriela Tranquilli
- Instituto Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina.
| | - Marcelo Helguera
- Estación Experimental Agropecuaria Marcos Juárez, Instituto Nacional de Tecnología Agropecuaria (INTA), Marcos Juárez, Córdoba, Argentina.
| | - Viviana Echenique
- CERZOS (CCT - CONICET Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Argentina.
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Yadav CB, Bonthala VS, Muthamilarasan M, Pandey G, Khan Y, Prasad M. Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database. DNA Res 2014; 22:79-90. [PMID: 25428892 PMCID: PMC4379977 DOI: 10.1093/dnares/dsu039] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) are major components of plant genome and are reported to play significant roles in functional genome diversity and phenotypic variations. Several TEs are highly polymorphic for insert location in the genome and this facilitates development of TE-based markers for various genotyping purposes. Considering this, a genome-wide analysis was performed in the model plant foxtail millet. A total of 30,706 TEs were identified and classified as DNA transposons (24,386), full-length Copia type (1,038), partial or solo Copia type (10,118), full-length Gypsy type (1,570), partial or solo Gypsy type (23,293) and Long- and Short-Interspersed Nuclear Elements (3,659 and 53, respectively). Further, 20,278 TE-based markers were developed, namely Retrotransposon-Based Insertion Polymorphisms (4,801, ∼24%), Inter-Retrotransposon Amplified Polymorphisms (3,239, ∼16%), Repeat Junction Markers (4,451, ∼22%), Repeat Junction-Junction Markers (329, ∼2%), Insertion-Site-Based Polymorphisms (7,401, ∼36%) and Retrotransposon-Microsatellite Amplified Polymorphisms (57, 0.2%). A total of 134 Repeat Junction Markers were screened in 96 accessions of Setaria italica and 3 wild Setaria accessions of which 30 showed polymorphism. Moreover, an open access database for these developed resources was constructed (Foxtail millet Transposable Elements-based Marker Database; http://59.163.192.83/ltrdb/index.html). Taken together, this study would serve as a valuable resource for large-scale genotyping applications in foxtail millet and related grass species.
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Affiliation(s)
- Chandra Bhan Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Venkata Suresh Bonthala
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | | | - Garima Pandey
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Yusuf Khan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
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Alzohairy AM, Gyulai GB, Ramadan MF, Edris S, Sabir JSM, Jansen RK, Eissa HF, Bahieldin A. Retrotransposon-based molecular markers for assessment of genomic diversity. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:781-789. [PMID: 32481032 DOI: 10.1071/fp13351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/19/2014] [Indexed: 06/11/2023]
Abstract
Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in 'repeat seas' or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).
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Affiliation(s)
- Ahmed M Alzohairy
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - G Bor Gyulai
- Institute of Genetics and Biotechnology, St. István University, Gödöll?, H-2103, Hungary
| | - Mohamed F Ramadan
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Sherif Edris
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Jamal S M Sabir
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Robert K Jansen
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
| | - Hala F Eissa
- Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
| | - Ahmed Bahieldin
- King Abdulaziz University, Faculty of Science, Department of Biological Sciences, Genomics and Biotechnology Section, Jeddah 21589, Saudi Arabia
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Monden Y, Fujii N, Yamaguchi K, Ikeo K, Nakazawa Y, Waki T, Hirashima K, Uchimura Y, Tahara M. Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site. Genome 2014; 57:245-52. [PMID: 25072847 DOI: 10.1139/gen-2014-0031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5' LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria × ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a "unique" insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars.
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Affiliation(s)
- Yuki Monden
- a Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530, Japan
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29
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A rapid and enhanced DNA detection method for crop cultivar discrimination. J Biotechnol 2014; 185:57-62. [PMID: 24954682 DOI: 10.1016/j.jbiotec.2014.06.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/14/2014] [Accepted: 06/10/2014] [Indexed: 01/31/2023]
Abstract
In many crops species, the development of a rapid and precise cultivar discrimination system has been required for plant breeding and patent protection of plant cultivars and agricultural products. Here, we successfully evaluated strawberry cultivars via a novel method, namely, the single tag hybridization (STH) chromatographic printed array strip (PAS) using the PCR products of eight genomic regions. In a previous study, we showed that genotyping of eight genomic regions derived from FaRE1 retrotransposon insertion site enabled to discriminate 32 strawberry cultivars precisely, however, this method required agarose/acrylamide gel electrophoresis, thus has the difficulty for practical application. In contrast, novel DNA detection method in this study has some great advantages over standard DNA detection methods, including agarose/acrylamide gel electrophoresis, because it produces signals for DNA detection with dramatically higher sensitivity in a shorter time without any preparation or staining of a gel. Moreover, this method enables the visualization of multiplex signals simultaneously in a single reaction using several independent amplification products. We expect that this novel method will become a rapid and convenient cultivar screening assay for practical purposes, and will be widely applied to various situations, including laboratory research, and on-site inspection of plant cultivars and agricultural products.
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A simple and efficient method to isolate LTR sequences of plant retrotransposon. BIOMED RESEARCH INTERNATIONAL 2014; 2014:658473. [PMID: 24883318 PMCID: PMC4032725 DOI: 10.1155/2014/658473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 03/22/2014] [Accepted: 04/09/2014] [Indexed: 11/17/2022]
Abstract
Retrotransposons (RTNs) have important roles in the formation of plant genome size, structure, and evolution. Ubiquitous distributions, abundant copy numbers, high heterogeneities, and insertional polymorphisms of RTNs have made them as excellent sources for molecular markers development. However, the wide application of RTNs-based molecular markers is restricted by the scarcity of the LTR (long terminal repeat) sequences information. A new, simple, and efficient method to isolate LTR sequences of RTNs was presented based on the degenerate RNase H nested primers and PPT (polypurine tract) primer of RTNs in tree peony. This method combined the characteristics and advantages of high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR), annealing control primer (ACP) system, and suppression PCR method. Nineteen LTR sequences were isolated using this new method in tree peony and the applicability of the LTR sequences based markers was validated by further SSAP analysis. The results showed that the new method is simple, of low-cost, and highly efficient, which is just conducted by three rounds of PCR and does not need any restriction enzymes and adapters, much less the hybridizations. This new method is rapid, economical, and cost- and time-saving, which could be easily used to isolate LTR sequences of RTNs.
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31
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Alavi-Kia S, Mohammadi S, Aharizad S, Moghaddam M. Analysis of Genetic Diversity and Phylogenetic Relationships inCrocus Genusof Iran Using Inter-Retrotransposon Amplified Polymorphism. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2008.10817555] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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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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34
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Almaraz-Abarca N, Delgado-Alvarado EA, Torres-Morán MI, Herrera-Corral J, Ávila-Reyes JA, Naranjo-Jiménez N, Uribe-Soto JN. Genetic Variability in Natural Populations of Agave durangensis(Agavaceae) Revealed by Morphological and Molecular Traits. SOUTHWEST NAT 2013. [DOI: 10.1894/0038-4909-58.3.314] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Santana MF, Batista AD, Ribeiro LE, de Araújo EF, de Queiroz MV. Terminal repeat retrotransposons as DNA markers in fungi. J Basic Microbiol 2013; 53:823-7. [PMID: 23440766 DOI: 10.1002/jobm.201200453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 09/12/2012] [Indexed: 11/10/2022]
Abstract
In this study, we demonstrate that ClIRAP primers designed using the transposable element RetroCl1 sequence from Colletotrichum lindemuthianum can be used to generate an efficient IRAP (inter-retrotransposon amplified polymorphism) molecular marker to study intra- and inter-species diversity in fungi. It has been previously demonstrated that primers generated from this TRIM-like element can be used in the Colletotrichum species. We now prove that the RetroCl1 sequence can also be used to analyze diversity in different fungi. IRAP profiles were successfully generated for 27 fungi species from 11 different orders, and intra-species genetic variability was detected in six species. The ClIRAP primers facilitate the use of the IRAP technique for a variety of fungi without prior knowledge of the genome.
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36
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Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R. Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics 2012. [PMID: 23161406 DOI: 10.1007/s10142‐012‐0300‐5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
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Affiliation(s)
- C Feuillet
- INRA-UBP UMR 1095 Genetics and Diversity of Cereals, Clermont-Ferrand, France.
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37
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Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R. Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics 2012; 12:573-83. [PMID: 23161406 PMCID: PMC3508266 DOI: 10.1007/s10142-012-0300-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 11/26/2022]
Abstract
The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
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Affiliation(s)
- C Feuillet
- INRA-UBP UMR 1095 Genetics and Diversity of Cereals, Clermont-Ferrand, France.
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38
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Li J, Zhao GH, Zhou DH, Sugiyama H, Nisbet AJ, Li XY, Zou FC, Li HL, Ai L, Zhu XQ. Retrotransposon-microsatellite amplified polymorphism, an electrophoretic approach for studying genetic variability among Schistosoma japonicum geographical isolates. Electrophoresis 2012; 33:2859-66. [PMID: 23019103 DOI: 10.1002/elps.201200110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the present study, retrotransposon-microsatellite amplified polymorphism (REMAP) was used to examine genetic variability among Schistosoma japonicum isolates from different endemic provinces in mainland China, using S. japonicum from Japan and the Philippines for comparison. Of the 50 primer combinations screened, eight produced highly reproducible REMAP fragments. Using these primers, 190 distinct DNA fragments were generated in total, of which 147 (77.37%) were polymorphic, indicating considerable genetic variation among the 43 S. japonicum isolates examined. The percentage of polymorphic bands (PPB) among S. japonicum isolates from mainland China, Japan, and the Philippines was 77.37%; PPB values of 18.42% and 53.68% were found among isolates from southwestern (SW) China and the lower Yangtze/Zhejiang province in eastern (E) China, respectively. Based on REMAP profiles, unweighted pair-group method with arithmetic averages (UPGMA) dendrogram analysis revealed that all of the S. japonicum samples grouped into three distinct clusters: parasites from mainland China, Japan, and the Philippines were clustered in each individual clade. Within the mainland China cluster, SW China isolates (from Sichuan and Yunnan provinces) grouped together, whereas worms from E China (Zhejiang, Anhui, Jiangxi, Jiangsu, Hunan, and Hubei provinces) grouped together. These results demonstrated that the REMAP marker system provides a reliable electrophoretic technique for studying genetic diversity and population structures of S. japonicum isolates from mainland China, and could be applied to other pathogens of human and animal health significance.
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Affiliation(s)
- Juan Li
- Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, People's Republic of China
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Jing R, Ambrose MA, Knox MR, Smykal P, Hybl M, Ramos Á, Caminero C, Burstin J, Duc G, van Soest LJM, Święcicki WK, Pereira MG, Vishnyakova M, Davenport GF, Flavell AJ, Ellis THN. Genetic diversity in European Pisum germplasm collections. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:367-80. [PMID: 22466957 PMCID: PMC3385700 DOI: 10.1007/s00122-012-1839-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/29/2012] [Indexed: 05/21/2023]
Abstract
The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European Genebanks has identified sources of novel genetic variation, and both reinforces and refines previous interpretations of the overall structure of genetic diversity in Pisum. Molecular marker analysis was based upon the presence/absence of polymorphism of retrotransposon insertions scored by a high-throughput microarray and SSAP approaches. We conclude that the diversity of Pisum constitutes a broad continuum, with graded differentiation into sub-populations which display various degrees of distinctness. The most distinct genetic groups correspond to the named taxa while the cultivars and landraces of Pisum sativum can be divided into two broad types, one of which is strongly enriched for modern cultivars. The addition of germplasm sets from six European Genebanks, chosen to represent high diversity, to a single collection previously studied with these markers resulted in modest additions to the overall diversity observed, suggesting that the great majority of the total genetic diversity collected for the Pisum genus has now been described. Two interesting sources of novel genetic variation have been identified. Finally, we have proposed reference sets of core accessions with a range of sample sizes to represent Pisum diversity for the future study and exploitation by researchers and breeders.
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Affiliation(s)
- R. Jing
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA UK
- Present Address: Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, Haus 26, 14476 Potsdam-Golm, Germany
| | - M. A. Ambrose
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH UK
| | - M. R. Knox
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH UK
| | - P. Smykal
- Agritec Plant Research Ltd., Zemedelska 2520/16, 787 01 Sumperk, Czech Republic
- Department of Botany, Faculty of Sciences, Palacký University, Slechtitelu 11, 783 71 Olomouc, Czech Republic
| | - M. Hybl
- Agritec Plant Research Ltd., Zemedelska 2520/16, 787 01 Sumperk, Czech Republic
| | - Á. Ramos
- Centro para la calidad de los alimentos, INIA, Campus universitario, 42004 Soria, Spain
| | - C. Caminero
- Instituto Tecnológico Agrario, Consejería de Agricultura y Ganadería de la Junta de Castilla y León, Ctra Burgos, km 119, 47071 Valladolid, Spain
| | - J. Burstin
- Institut National de la Recherche Agronomique (INRA), UMR LEG, 17 rue de Sully-Building B1, Office 110, BP 86510, 21065 Dijon Cédex, France
| | - G. Duc
- Institut National de la Recherche Agronomique (INRA), UMR LEG, 17 rue de Sully-Building B1, Office 110, BP 86510, 21065 Dijon Cédex, France
| | - L. J. M. van Soest
- Centre for Genetic Resources, The Netherlands (CGN), P. O. Box 16, 6700 AA Wageningen, The Netherlands
| | - W. K. Święcicki
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479 Poznan, Poland
| | - M. G. Pereira
- Instituto Nacional de Investigação Agrária, Apartado 6, 7350-951 Elvas, Portugal
| | - M. Vishnyakova
- N.I. Vavilov Institute of Plant Industry (VIR), Bolshaya Morskaya Street 42-44, 190000 St. Petersburg, Russian Federation
| | - G. F. Davenport
- Crop Informatics, 211 Malecon Armenariz, Miraflores, Lima, Peru
| | - A. J. Flavell
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA UK
| | - T. H. N. Ellis
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH UK
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EB UK
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Palhares AC, Rodrigues-Morais TB, Van Sluys MA, Domingues DS, Maccheroni W, Jordão H, Souza AP, Marconi TG, Mollinari M, Gazaffi R, Garcia AAF, Vieira MLC. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet 2012; 13:51. [PMID: 22742069 PMCID: PMC3443450 DOI: 10.1186/1471-2156-13-51] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 06/13/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. RESULTS The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. CONCLUSIONS Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.
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Affiliation(s)
- Alessandra C Palhares
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Taislene B Rodrigues-Morais
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Douglas S Domingues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
- Present address: Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, 86047-902, Londrina, Brazil
| | - Walter Maccheroni
- CanaVialis/Monsanto Co, Condomínio Techno Park, 13069-380, Campinas, Brazil
- Present address: Companhia Vale do Rio Doce, 20020-900, Rio de Janeiro, Brazil
| | - Hamilton Jordão
- CanaVialis/Monsanto Co, Condomínio Techno Park, 13069-380, Campinas, Brazil
- Present address: Companhia Vale do Rio Doce, 20020-900, Rio de Janeiro, Brazil
| | - Anete P Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, Brazil
| | - Thiago G Marconi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, Brazil
| | - Marcelo Mollinari
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Rodrigo Gazaffi
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Antonio Augusto F Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
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Korir NK, Han J, Shangguan L, Wang C, Kayesh E, Zhang Y, Fang J. Plant variety and cultivar identification: advances and prospects. Crit Rev Biotechnol 2012; 33:111-25. [PMID: 22698516 DOI: 10.3109/07388551.2012.675314] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Plant variety and cultivar identification is one of the most important aspects in agricultural systems. The large number of varieties or landraces among crop plants has made it difficult to identify and characterize varieties solely on the basis of morphological characters because they are non stable and originate due to environmental and climatic conditions, and therefore phenotypic plasticity is an outcome of adaptation. To mitigate this, scientists have developed and employed molecular markers, statistical tests and software to identify and characterize the required plant cultivars or varieties for cultivation, breeding programs as well as for cultivar-right-protection. The establishment of genome and transcriptome sequencing projects for many crops has led to generation of a huge wealth of sequence information that could find much use in identification of plants and their varieties. We review the current status of plant variety and cultivar identification, where an attempt has been made to describe the different strategies available for plant identification. We have found that despite the availability of methods and suitable markers for a wide range of crops, there is dearth of simple ways of making both morphological descriptors and molecular markers easy, referable and practical to use although there are ongoing attempts at making this possible. Certain limitations present a number of challenges for the development and utilization of modern scientific methods in variety or cultivar identification in many important crops.
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Affiliation(s)
- Nicholas Kibet Korir
- College of Horticulture, Nanjing Agricultural University, Weigang, Nanjing, China
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Seibt KM, Wenke T, Wollrab C, Junghans H, Muders K, Dehmer KJ, Diekmann K, Schmidt T. Development and application of SINE-based markers for genotyping of potato varieties. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:185-196. [PMID: 22371142 DOI: 10.1007/s00122-012-1825-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 02/11/2012] [Indexed: 05/31/2023]
Abstract
Potato variety discrimination based on morphological traits is laborious and influenced by the environment, while currently applied molecular markers are either expensive or time-consuming in development or application. SINEs, short interspersed nuclear elements, are retrotransposons with a high copy number in plant genomes representing a potential source for new markers. We developed a marker system for potato genotyping, designated inter-SINE amplified polymorphism (ISAP). Based on nine potato SINE families recently characterized (Wenke et al. in Plant Cell 23:3117-3128, 2011), we designed species-specific SINE primers. From the resulting 153 primer combinations, highly informative primer sets were selected for potato variety analysis regarding number of bands, quality of the banding pattern, and the degree of polymorphism. Fragments representing ISAPs can be separated by conventional agarose gel electrophoresis; however, automation with a capillary sequencer is feasible. Two selected SINE families, SolS-IIIa and SolS-IV, were shown to be highly but differently amplified in Solanaceae, Solaneae tribe, including wild and cultivated potatoes, tomato, and eggplant. Fluorescent in situ hybridization demonstrated the genome-wide distribution of SolS-IIIa and SolS-IV along potato chromosomes, which is the basis for genotype discrimination and differentiation of somaclonal variants by ISAP markers.
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Affiliation(s)
- Kathrin M Seibt
- Institute of Botany, Dresden University of Technology, 01062, Dresden, Germany
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Yaakov B, Ceylan E, Domb K, Kashkush K. Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1365-73. [PMID: 22286503 DOI: 10.1007/s00122-012-1793-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 01/05/2012] [Indexed: 05/02/2023]
Abstract
Transposable elements (TEs) account for up to 80% of the wheat genome and are considered one of the main drivers of wheat genome evolution. However, the contribution of TEs to the divergence and evolution of wheat genomes is not fully understood. In this study, we have developed 55 miniature inverted-repeat transposable element (MITE) markers that are based on the presence/absence of an element, with over 60% of these 55 MITE insertions associated with wheat genes. We then applied these markers to assess genetic diversity among Triticum and Aegilops species, including diploid (AA, BB and DD genomes), tetraploid (BBAA genome) and hexaploid (BBAADD genome) species. While 18.2% of the MITE markers showed similar insertions in all species indicating that those are fossil insertions, 81.8% of the markers showed polymorphic insertions among species, subspecies, and accessions. Furthermore, a phylogenetic analysis based on MITE markers revealed that species were clustered based on genus, genome composition, and ploidy level, while 47.13% genetic divergence was observed between the two main clusters, diploids versus polyploids. In addition, we provide evidence for MITE dynamics in wild emmer populations. The use of MITEs as evolutionary markers might shed more light on the origin of the B-genome of polyploid wheat.
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Affiliation(s)
- Beery Yaakov
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
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Schulman AH, Flavell AJ, Paux E, Ellis THN. The application of LTR retrotransposons as molecular markers in plants. Methods Mol Biol 2012; 859:115-153. [PMID: 22367869 DOI: 10.1007/978-1-61779-603-6_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The key methods, SSAP, IRAP, REMAP, RBIP, and ISBP, all detect the sites at which the retrotransposon DNA, which is conserved between families of elements, is integrated into the genome. Marker systems exploiting these methods can be easily developed and inexpensively deployed in the absence of extensive genome sequence data. They offer access to the dynamic and polymorphic, nongenic portion of the genome and thereby complement methods, such as gene-derived SNPs, that target primarily the genic fraction.
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Affiliation(s)
- Alan H Schulman
- Plant Genomics, MTT Agrifood Research Finland, Jokioinen, Finland.
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Zou J, Fu D, Gong H, Qian W, Xia W, Pires JC, Li R, Long Y, Mason AS, Yang TJ, Lim YP, Park BS, Meng J. De novo genetic variation associated with retrotransposon activation, genomic rearrangements and trait variation in a recombinant inbred line population of Brassica napus derived from interspecific hybridization with Brassica rapa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:212-24. [PMID: 21689170 DOI: 10.1111/j.1365-313x.2011.04679.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Interspecific hybridization is a significant evolutionary force as well as a powerful method for crop breeding. Partial substitution of the AA subgenome in Brassica napus (A(n) A(n) C(n) C(n) ) with the Brassica rapa (A(r) A(r) ) genome by two rounds of interspecific hybridization resulted in a new introgressed type of B. napus (A(r) A(r) C(n) C(n) ). In this study, we construct a population of recombinant inbred lines of the new introgressed type of B. napus. Microsatellite, intron-based and retrotransposon markers were used to characterize this experimental population with genetic mapping, genetic map comparison and specific marker cloning analysis. Yield-related traits were also recorded for identification of quantitative trait loci (QTLs). A remarkable range of novel genomic alterations was observed in the population, including simple sequence repeat (SSR) mutations, chromosomal rearrangements and retrotransposon activations. Most of these changes occurred immediately after interspecific hybridization, in the early stages of genome stabilization and derivation of experimental lines. These novel genomic alterations affected yield-related traits in the introgressed B. napus to an even greater extent than the alleles alone that were introgressed from the A(r) subgenome of B. rapa, suggesting that genomic changes induced by interspecific hybridization are highly significant in both genome evolution and crop improvement.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Development of new molecular markers for the Colletotrichum genus using RetroCl1 sequences. World J Microbiol Biotechnol 2011; 28:1087-95. [PMID: 22805830 DOI: 10.1007/s11274-011-0909-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Accepted: 09/23/2011] [Indexed: 10/17/2022]
Abstract
A nonautonomous element of 624 bp, called RetroCl1 (Retroelement Colletotrichum lindemuthianum 1), was identified in the plant pathogenic fungus Colletotrichum lindemuthianum. RetroCl1 contains terminal direct repeats (223 bp) that are surrounded by CTAGT sequences. It has a short internal domain of 178 bp and shows characteristics of terminal-repeat retrotransposon in miniature (TRIM) family. We used RetroCl1 sequence to develop molecular markers for the Colletotrichum genus. IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) markers were used to analyze the genetic diversity of C. lindemuthianum. Fifty-four isolates belonging to different races were used. A total of 45 loci were amplified. The Nei index showed significant differences among the populations divided according to race, indicating that they are structured according to pathotype. No clear correlation between IRAP and REMAP markers with pathogenic characterization was found. C. lindemuthianum has high genetic diversity, and the analysis of molecular variance showed that 51% of variability is found among the populations of different races. The markers were also tested in different Colletotrichum species. In every case, multiple bands were amplified, indicating that these markers can be successfully used in different species belonging to the Colletotrichum genus.
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Paux E, Sourdille P, Mackay I, Feuillet C. Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 2011; 30:1071-88. [PMID: 21989506 DOI: 10.1016/j.biotechadv.2011.09.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 08/24/2011] [Accepted: 09/25/2011] [Indexed: 01/04/2023]
Abstract
In the past two decades, the wheat community has made remarkable progress in developing molecular resources for breeding. A wide variety of molecular tools has been established to accelerate genetic and physical mapping for facilitating the efficient identification of molecular markers linked to genes and QTL of agronomic interest. Already, wheat breeders are benefiting from a wide range of techniques to follow the introgression of the most favorable alleles in elite material and develop improved varieties. Breeders soon will be able to take advantage of new technological developments based on Next Generation Sequencing. In this paper, we review the molecular toolbox available to wheat scientists and breeders for performing fundamental genomic studies and breeding. Special emphasis is given on the production and detection of single nucleotide polymorphisms (SNPs) that should enable a step change in saturating the wheat genome for more efficient genetic studies and for the development of new selection methods. The perspectives offered by the access to an ordered full genome sequence for further marker development and enhanced precision breeding is also discussed. Finally, we discuss the advantages and limitations of marker-assisted selection for supporting wheat improvement.
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Affiliation(s)
- Etienne Paux
- INRA-UBP 1095, Genetics Diversity and Ecophysiology of Cereals, 234 Avenue du Brézet, Clermont-Ferrand, France
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Dubreuil-Tranchant C, Guyot R, Guellim A, Duret C, de la Mare M, Razafinarivo N, Poncet V, Hamon S, Hamon P, de Kochko A. Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2011; 2011:358412. [PMID: 21961075 PMCID: PMC3180848 DOI: 10.4061/2011/358412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/16/2011] [Indexed: 11/25/2022]
Abstract
Miniature Inverted-repeat Transposable Elements (MITEs) are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex) in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus.
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Abstract
There is increasing evidence that epigenetic marks such as DNA methylation contribute to phenotypic variation by regulating gene transcription, developmental plasticity, and interactions with the environment. However, relatively little is known about the relationship between the stability and distribution of DNA methylation within chromosomes and the ability to detect trait loci. Plant genomes have a distinct range of target sites and more extensive DNA methylation than animals. We analyzed the stability and distribution of epialleles within the complex genome of the oilseed crop plant Brassica napus. For methylation sensitive AFLP (MSAP) and retrotransposon (RT) epimarkers, we found a high degree of stability, with 90% of mapped markers retaining their allelic pattern in contrasting environments and developmental stages. Moreover, for two distinct parental lines 97% of epialleles were transmitted through five meioses and segregated in a mapping population. For the first time we have established the genetic position for 17 of the 19 centromeres within this amphidiploid species. Epiloci and genetic loci were distributed within distinct clusters, indicating differential detection of recombination events. This enabled us to identify additional significant QTL associated with seven important agronomic traits in the centromeric regions of five linkage groups.
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50
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Xu Z, Rafi S, Ramakrishna W. Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters. Genome 2011; 54:629-38. [DOI: 10.1139/g11-030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Retrotransposons are ubiquitous in higher plant genomes. The presence or absence of retrotransposons in whole genome and high throughput genomic sequence (HTGS) from cultivated and wild rice was investigated to understand the organization and evolution of retrotransposon insertions in promoter regions. Approximately half of the Oryza sativa subsp. japonica ‘Nipponbare’ promoters with retrotransposons conserved in Oryza sativa subsp. indica ‘93-11’ and four wild rice species showed higher sequence conservation in retrotransposon than nonretrotransposon regions. We further investigated, in detail, the evolutionary dynamics of five retrotransposons in the promoter regions of 95 rice genotypes. Our data suggest that four of five insertions (Rp2–Rp5) occurred in the ancestor of AA genome, while the other insertion (Rp1) predates the ancestral divergence of Oryza officinalis (CC genome). Four retrotransposons (Rp2–Rp5) were present in 52% (Rp2), 29% (Rp3), 53% (Rp4), and 43% (Rp5) of the rice genotypes with AA genome type, and the fifth retrotransposon (Rp1) was present in 95% of the rice genotypes with AA, BBCC, or CC genome types. Furthermore, most of these retrotransposons were found to evolve slower than flanking promoter regions, suggesting a role in promoter function for regulating downstream genes.
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Affiliation(s)
- Z. Xu
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - S. Rafi
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - W. Ramakrishna
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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