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Hassan AH, Mokhtar MM, El Allali A. Transposable elements: multifunctional players in the plant genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1330127. [PMID: 38239225 PMCID: PMC10794571 DOI: 10.3389/fpls.2023.1330127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
Transposable elements (TEs) are indispensable components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. Their ability to mobilize within the genome leads to gene expression and DNA structure changes. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function and evolution. This review takes a comprehensive look at TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology.
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Affiliation(s)
- Asmaa H. Hassan
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Morad M. Mokhtar
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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2
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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] [MESH Headings] [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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Yan H, Haak DC, Li S, Huang L, Bombarely A. Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice. PLANT COMMUNICATIONS 2022; 3:100270. [PMID: 35576152 PMCID: PMC9251385 DOI: 10.1016/j.xplc.2021.100270] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 10/29/2021] [Accepted: 12/16/2021] [Indexed: 06/10/2023]
Abstract
Transposable elements (TEs) are a major force in the production of new alleles during domestication; nevertheless, their use in association studies has been limited because of their complexity. We have developed a TE genotyping pipeline (TEmarker) and applied it to whole-genome genome-wide association study (GWAS) data from 176 Oryza sativa subsp. japonica accessions to identify genetic elements associated with specific agronomic traits. TE markers recovered a large proportion (69%) of single-nucleotide polymorphism (SNP)-based GWAS peaks, and these TE peaks retained ca. 25% of the SNPs. The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium (LD) among SNP markers. A genome scan revealed positive selection on TEs associated with agronomic traits. We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs, including an allele of LOC_Os11g08410 associated with plant height and panicle length traits. Together, these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.
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Affiliation(s)
- Haidong Yan
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - David C Haak
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA 24061, USA
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA 24061, USA
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China
| | - Aureliano Bombarely
- Department of Bioscience, Universita degli Studi di Milano (UNIMI), 20133 Milano, Italy; Instituto de Biologıa Molecular y Celular de Plantas (IBMCP), UPV-CSIC, 46022 Valencia, Spain.
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Su Y, Huang Q, Wang Z, Wang T. High genetic and epigenetic variation of transposable elements: Potential drivers to rapid adaptive evolution for the noxious invasive weed Mikania micrantha. Ecol Evol 2021; 11:13501-13517. [PMID: 34646486 PMCID: PMC8495827 DOI: 10.1002/ece3.8075] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022] Open
Abstract
Why invasive species can rapidly adapt to novel environments is a puzzling question known as the genetic paradox of invasive species. This paradox is explainable in terms of transposable elements (TEs) activity, which are theorized to be powerful mutational forces to create genetic variation. Mikania micrantha, a noxious invasive weed, in this sense provides an excellent opportunity to test the explanation. The genetic and epigenetic variation of 21 invasive populations of M. micrantha in southern China have been examined by using transposon display (TD) and transposon methylation display (TMD) techniques to survey 12 TE superfamilies. Our results showed that M. micrantha populations maintained an almost equally high level of TE-based genetic and epigenetic variation and they have been differentiated into subpopulations genetically and epigenetically. A similar positive spatial genetic and epigenetic structure pattern was observed within 300 m. Six and seven TE superfamilies presented significant genetic and epigenetic isolation by distance (IBD) pattern. In total, 59 genetic and 86 epigenetic adaptive TE loci were identified. Of them, 51 genetic and 44 epigenetic loci were found to correlate with 25 environmental variables (including precipitation, temperature, vegetation coverage, and soil metals). Twenty-five transposon-inserted genes were sequenced and homology-based annotated, which are found to be involved in a variety of molecular and cellular functions. Our research consolidates the importance of TE-associated genetic and epigenetic variation in the rapid adaptation and invasion of M. micrantha.
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Affiliation(s)
- Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen UniversityShenzhenChina
| | - Qiqi Huang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Ting Wang
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Hasan N, Choudhary S, Naaz N, Sharma N, Laskar RA. Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes. J Genet Eng Biotechnol 2021; 19:128. [PMID: 34448979 PMCID: PMC8397809 DOI: 10.1186/s43141-021-00231-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/17/2021] [Indexed: 11/28/2022]
Abstract
Background DNA markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). The enormous number of quantitative trait loci (QTLs) mapping read for different plant species have given a plenitude of molecular marker-gene associations. Main body of the abstract In this review, we have discussed the positive aspects of molecular marker-assisted selection and its precise applications in plant breeding programmes. Molecular marker-assisted selection has considerably shortened the time for new crop varieties to be brought to the market. To explore the information about DNA markers, many reviews have been published in the last few decades; all these reviews were intended by plant breeders to obtain information on molecular genetics. In this review, we intended to be a synopsis of recent developments of DNA markers and their application in plant breeding programmes and devoted to early breeders with little or no knowledge about the DNA markers. The progress made in molecular plant breeding, plant genetics, genomics selection, and editing of genome contributed to the comprehensive understanding of DNA markers and provides several proofs on the genetic diversity available in crop plants and greatly complemented plant breeding devices. Short conclusion MAS has revolutionized the process of plant breeding with acceleration and accuracy, which is continuously empowering plant breeders around the world.
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Affiliation(s)
- Nazarul Hasan
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India.
| | - Sana Choudhary
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Neha Naaz
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Nidhi Sharma
- Cytogenetic and Plant Breeding Lab, Department of Botany, Aligarh Muslim University, Aligarh, U.P, 202002, India
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Detecting Genetic Mobility Using a Transposon-Based Marker System in Gamma-Ray Irradiated Soybean Mutants. PLANTS 2021; 10:plants10020373. [PMID: 33671964 PMCID: PMC7919005 DOI: 10.3390/plants10020373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
Transposable elements (TEs)—major components of eukaryotic genomes—have the ability to change location within a genome. Because of their mobility, TEs are important for genome diversification and evolution. Here, a simple rapid method, using the consensus terminal inverted repeat sequences of PONG, miniature inverted-repeat transposable element (MITE)-Tourist (M-t) and MITE-Stowaway (M-s) as target region amplification polymorphism (TE-TRAP) markers, was employed to investigate the mobility of TEs in a gamma-irradiated soybean mutant pool. Among the different TE-TRAP primer combinations, the average polymorphism level and polymorphism information content value were 57.98% and 0.14, respectively. Only the PONG sequence separated the mutant population into three major groups. The inter-mutant population variance, determined using the PONG marker (3.151 and 29%) was greater than that of the M-t (2.209 and 20%) and M-s (2.766 and 18%) markers, whereas the reverse was true for the intra-mutant population variations, with M-t and M-s values, being 15.151 (82%) and 8.895 (80%), respectively, compared with the PONG marker (7.646 and 71%). Thus, the MITE markers revealed more dynamic and active mobility levels than the PONG marker in gamma-ray irradiated soybean mutant lines. The TE-TRAP technique associated with sensitive MITEs is useful for investigating genetic diversity and TE mobilization, providing tools for mutant selection in soybean mutation breeding.
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Park D, Choi IY, Kim NS. Detection of mPing mobilization in transgenic rice plants. Genes Genomics 2019; 42:47-54. [PMID: 31721104 DOI: 10.1007/s13258-019-00877-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/18/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Various kinds of transposable elements (TEs) constitute high proportions of eukaryotic genomes. Although most of these TEs are not actively mobile, genome stress can induce mobilization of dormant TEs. Transgenic plants undergo tissue culture and subsequent whole-plant regeneration, which can cause genomic stress and in turn induce mobilization of inactive TEs. OBJECTIVES To investigate the activation of transposable elements on the genome wide of the GM plant. METHODS Transposon activities were analyzed in three transgenic rice plants carrying the insect resistance gene Cry1Ac and an herbicide resistance gene by the transposon display technique. These three transgenic plants were derived from a leading Korean rice variety, Illmi. RESULTS We detected seven mobile activities in the mPing element, which is a MITE family transposon. The identity of the novel fragments in the gel display was confirmed by checking TAA target site duplication via sequence analysis. The genomic integration sites were all on different chromosomes, and the integrations were specific to either one or two T1 transgenic lines, except for one common integration on chromosome 4. One integration was in the 5'-UTR of the Glycerol-3-phosphate acyltransferase 8 gene, two integrations were in introns of expressed genes, and the other four integrations were in intergenic regions. CONCLUSION Thus, novel mobilization of dormant TEs occurs in transgenic plants, which must be considered in the generation of genetically modified crops (GM crops).
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Affiliation(s)
- Doori Park
- Department of Agriculture and Life Industry, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea
| | - Ik-Young Choi
- Department of Molecular Bioscience, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea.
| | - Nam-Soo Kim
- Department of Agriculture and Life Industry, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 24341, Republic of Korea.
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Orozco-Arias S, Isaza G, Guyot R. Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning. Int J Mol Sci 2019; 20:E3837. [PMID: 31390781 PMCID: PMC6696364 DOI: 10.3390/ijms20153837] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 01/26/2023] Open
Abstract
Transposable elements (TEs) are genomic units able to move within the genome of virtually all organisms. Due to their natural repetitive numbers and their high structural diversity, the identification and classification of TEs remain a challenge in sequenced genomes. Although TEs were initially regarded as "junk DNA", it has been demonstrated that they play key roles in chromosome structures, gene expression, and regulation, as well as adaptation and evolution. A highly reliable annotation of these elements is, therefore, crucial to better understand genome functions and their evolution. To date, much bioinformatics software has been developed to address TE detection and classification processes, but many problematic aspects remain, such as the reliability, precision, and speed of the analyses. Machine learning and deep learning are algorithms that can make automatic predictions and decisions in a wide variety of scientific applications. They have been tested in bioinformatics and, more specifically for TEs, classification with encouraging results. In this review, we will discuss important aspects of TEs, such as their structure, importance in the evolution and architecture of the host, and their current classifications and nomenclatures. We will also address current methods and their limitations in identifying and classifying TEs.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales 170001, Colombia
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Gustavo Isaza
- Department of Systems and Informatics, Universidad de Caldas, Manizales 170001, Colombia
| | - Romain Guyot
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales 170001, Colombia.
- Institut de Recherche pour le Développement, CIRAD, University Montpellier, 34000 Montpellier, France.
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Lee SI, Nguyen TX, Kim JH, Kim NS. Cytological variations and long terminal repeat (LTR) retrotransposon diversities among diploids and B-chromosome aneuploids in Lilium amabile Palibin. Genes Genomics 2019; 41:941-950. [PMID: 31054075 DOI: 10.1007/s13258-019-00825-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/22/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND B chromosomes are supernumerary chromosomes found in numerous plant species, including in the genus Lilium. Lilium amabile, an endemic Korean Lilium species, carries B chromosomes which are highly variable in terms of numbers and shape among the accessions collected throughout the Korea. Class 1 retrotransposons are highly abundant in the genome of Lilium species, but their biological functions are still obscure. Lilium species were known to hold high diversities derived from retrotransposons. OBJECTIVE In this study, genetic diversities among the L. amabile accessions were analyzed to better understand relationships between genetic variations and cytological diversities. METHODS Chromosomes were prepared from 95 L. amabile accessions for cytological identification. Genetic variations were analyzed by inter-retrotransposon amplified polymorphism (IRAP), and genetic differentiation was evaluated via Tajima's D neutrality and FST analyses. Population structure and phylogenetic analyses were also carried out. RESULTS The L. amabile accessions were classified into 11 cytotypes by the chromosome constitutions. Genetic diversity measured by IRAP analysis revealed high genetic diversity among the accessions. In the joint analysis of cytological variation with genetical variation, IRAP diversity was not related to the cytological diversities of diploid and aneuploids among L. amabile accessions, and genetic differentiation was not obvious. Moreover, the geographical distribution of L. amabile was not related to either IRAP diversity or cytological diversity. CONCLUSION The B chromosome-carrying aneuploids occurred randomly among diploids throughout Korea, and IRAP diversification predated L. amabile dispersion in Korea without genetic differentiation.
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Affiliation(s)
- Sung-Il Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Truong Xuan Nguyen
- Institute of Agro-Biology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Jong-Hwa Kim
- Department of Horticulture, Kangwon National University, Chuncheon, 200-701, Korea.
| | - Nam-Soo Kim
- Department of Molecular Biosciences, Kangwon National University, Chuncheon, 24341, Korea. .,Institute of Bioscience and Biomedical Sciences, Kangwon National University, Chuncheon, 24341, Korea.
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Ty3/Gypsy retrotransposons in the Pacific abalone Haliotis discus hannai: characterization and use for species identification in the genus Haliotis. Genes Genomics 2018; 40:177-187. [PMID: 29892921 DOI: 10.1007/s13258-017-0619-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 10/05/2017] [Indexed: 01/08/2023]
Abstract
Transposable elements are highly abundant elements that are present in all eukaryotic species. Here, we present a molecular description of abalone retrotransposon (Abret) elements. The genome of Haliotis discus hannai contains 130 Abret elements which were all Ty3/Gypsy retrotransposons. The Ty1/Copia elements were absent in the H. discus hannai genome. Most of the elements were not complete due to sequence truncation or coding region decay. However, three elements Abret-296, Abret-935, and Abret-3259 had most of the canonical features of LTR (long terminal repeat)-retrotransposons. There were several reading frame shifts in Abret-935 and Abret-3259 elements. Surprisingly, phylogenetic analysis indicated that all of the elements belonged to the Osvaldo lineage. The sequence divergence between LTRs revealed that the Abret elements were mostly active within 2 million years ago. Abret elements were used as molecular markers in SSAP analyses, which allowed clear distinction of different species in the genus Haliotis. The polymorphic markers were converted into SCAR markers for use in species identification by simple PCR in the Haliotis genus.
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Retrotransposons in Betula nana, and interspecific relationships in the Betuloideae, based on inter-retrotransposon amplified polymorphism (IRAP) markers. Genes Genomics 2018; 40:511-519. [PMID: 29892962 DOI: 10.1007/s13258-018-0655-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 01/09/2018] [Indexed: 01/13/2023]
Abstract
The Betulaceae family comprises two subfamilies, Betuloideae and Corylaceae. The subfamily Betuloideae contains two genera, Alnus Mill. and Betula L. Twenty putative long terminal repeat (LTR) retrotransposons were mined from 171 scaffolds containing 5,208,995 bp of dwarf birch (Betula nana) genome sequences. Five retrotransposons were finally selected after filtering the retrotransposon canonical features and nucleotide similarities between left and right LTR sequences. Of the five retroelements, three elements were found to be Ty1/Copia retrotransposons; identity of the other two elements could not be ascertained due to sequence undetermined 'N' bases in the sequence database. Inter-retrotranposon amplified polymorphism (IRAP) analysis, based on the LTR sequences of the mined LTR-retrotransposons, produced 179 discernible IRAP bands among the Alnus and Betula genera. Sequence analysis revealed no size homoplasy among the homologous IRAP bands. Phylogenetic and principle coordinate analysis, based on the band sharing among the taxa, showed the species in two different genera were clearly separated. The subgenera in each genus of Alnus and Betula were also distinguishable from the IRAP profiles. In the genus Betula, the species in subgenus Betula showed mixed clustering between species. This is incongruent with the phylogeographical distribution of the species.
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Gayathri M, Shirasawa K, Varshney RK, Pandey MK, Bhat RS. Development of AhMITE1 markers through genome-wide analysis in peanut (Arachis hypogaea L.). BMC Res Notes 2018; 11:10. [PMID: 29310707 PMCID: PMC5759262 DOI: 10.1186/s13104-017-3121-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/29/2017] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE In peanut, the DNA polymorphism is very low despite enormous phenotypic variations. This limits the use of genomics-assisted breeding to enhance peanut productivity. This study aimed to develop and validate new AhMITE1 and cleaved amplified polymorphic sequences (CAPS) markers. RESULTS In total, 2957 new AhMITE1 markers were developed in addition to identifying 465 already reported markers from the whole genome re-sequencing data (WGRS) of 33 diverse genotypes of peanut. The B sub-genome (1620) showed more number of markers than the A sub-genome (1337). Distribution also varied among the chromosomes of both the sub-genomes. Further, 52.6% of the markers were from genic regions; where 31.0% were from intronic regions and 5.2% were from exonic regions. Of the 343 randomly selected markers, 82.2% showed amplification validation, with up to 35.5% polymorphism. From the SNPs on the A03, B01, B02 and B03 chromosomes, 11,730 snip-SNPs (potential CAPS sites) were identified, and 500 CAPS markers were developed from chromosome A03. Of these markers, 30.0% showed validation and high polymorphism. This study demonstrated the potential of the WGRS data to develop AhMITE1 and CAPS markers, which showed high level of validation and polymorphism. These marker resources will be useful for various genetic studies and mapping in peanut.
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Affiliation(s)
- M. Gayathri
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005 India
| | - Kenta Shirasawa
- Department of Frontier Research, Kazusa DNA Research Institute, Chiba, 292-0818 Japan
| | - R. K. Varshney
- Center of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324 India
| | - M. K. Pandey
- Center of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324 India
| | - R. S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005 India
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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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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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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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Comparison of molecular genetic utilities of TD, AFLP, and MSAP among the accessions of japonica, indica, and Tongil of Oryza sativa L. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0426-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Roy NS, Kim NS. Genetic diversity analysis of maize lines using AFLP and TE-based molecular marker systems. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0461-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nguyen TX, Lee SI, Rai R, Kim NS, Kim JH. Ribosomal DNA locus variation and REMAP analysis of the diploid and triploid complexes of Lilium lancifolium. Genome 2016; 59:551-64. [PMID: 27458741 DOI: 10.1139/gen-2016-0011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Lilium lancifolium Thunb. (2n = 2x = 24) is a cytologically conspicuous species with both diploids and triploids in nature. Cytological and molecular genetic analyses were carried out in both diploids and triploids that were collected from 55 geographical locations in Korea, Japan, and China. While the 5S rRNA gene loci were located at duplicated loci on the long arm of chromosome 2, the 45S rRNA gene loci were present in chromosomes 1, 2, 4, 6, 7, and 11. While the loci on chromosomes 1 and 7 were constant, the loci on chromosomes 2, 4, 6, 7, and 11 were variable in some plants so that the L. lancifolium accessions were grouped into 7 cytotypes in diploids and 12 cytotypes in triploids. REMAP marker analysis revealed that the diploids were classified into seven clusters, and the triploids were classified into a large cluster. Geographic, cytological, and genetic differentiations were not related in both the diploid and triploid accessions of L. lancifolium. Thus, current genetic variations occurred prior to the geographic differentiation in both diploids and triploids, and the 45S rDNA cytotype variations occurred after geographic differentiation in the current habitats of L. lancifolium.
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Affiliation(s)
- Truong Xuan Nguyen
- a Oriental Bio-herb Research Institute, Kangwon National University, Chuncheon 200-701, Korea.,b Institute of Agro-Biology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Sung-Il Lee
- c Department of Molecular Biosciences, Kangwon National University, Chuncheon 200-701, Korea.,d Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea
| | - Rameshwar Rai
- e Department of Horticulture, Kangwon National University, Chuncheon 200-701, Korea
| | - Nam-Soo Kim
- c Department of Molecular Biosciences, Kangwon National University, Chuncheon 200-701, Korea.,d Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea
| | - Jong Hwa Kim
- a Oriental Bio-herb Research Institute, Kangwon National University, Chuncheon 200-701, Korea.,e Department of Horticulture, Kangwon National University, Chuncheon 200-701, Korea
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Lee SI, Nguyen XT, Kim JH, Kim NS. Genetic diversity and structure analyses on the natural populations of diploids and triploids of tiger lily, Lilium lancifolium Thunb., from Korea, China, and Japan. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0398-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Lee SI, Kim JH, Park KC, Kim NS. LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species. Genetica 2015; 143:343-52. [DOI: 10.1007/s10709-015-9833-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 03/16/2015] [Indexed: 01/05/2023]
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