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Farkas A, Gaál E, Ivanizs L, Blavet N, Said M, Holušová K, Szőke-Pázsi K, Spitkó T, Mikó P, Türkösi E, Kruppa K, Kovács P, Darkó É, Szakács É, Bartoš J, Doležel J, Molnár I. Chromosome genomics facilitates the marker development and selection of wheat-Aegilops biuncialis addition, substitution and translocation lines. Sci Rep 2023; 13:20499. [PMID: 37993509 PMCID: PMC10665447 DOI: 10.1038/s41598-023-47845-8] [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: 07/24/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
The annual goatgrass, Aegilops biuncialis is a rich source of genes with considerable agronomic value. This genetic potential can be exploited for wheat improvement through interspecific hybridization to increase stress resistance, grain quality and adaptability. However, the low throughput of cytogenetic selection hampers the development of alien introgressions. Using the sequence of flow-sorted chromosomes of diploid progenitors, the present study enabled the development of chromosome-specific markers. In total, 482 PCR markers were validated on wheat (Mv9kr1) and Ae. biuncialis (MvGB642) crossing partners, and 126 on wheat-Aegilops additions. Thirty-two markers specific for U- or M-chromosomes were used in combination with GISH and FISH for the screening of 44 Mv9kr1 × Ae. biuncialis BC3F3 genotypes. The predominance of chromosomes 4M and 5M, as well as the presence of chromosomal aberrations, may indicate that these chromosomes have a gametocidal effect. A new wheat-Ae. biuncialis disomic 4U addition, 4M(4D) and 5M(5D) substitutions, as well as several introgression lines were selected. Spike morphology and fertility indicated that the Aegilops 4M or 5M compensated well for the loss of 4D and 5D, respectively. The new cytogenetic stocks represent valuable genetic resources for the introgression of key genes alleles into wheat.
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Affiliation(s)
- András Farkas
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Eszter Gaál
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary.
| | - László Ivanizs
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Nicolas Blavet
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Mahmoud Said
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Kateřina Holušová
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Kitti Szőke-Pázsi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Tamás Spitkó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Péter Mikó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Edina Türkösi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Klaudia Kruppa
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Péter Kovács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Éva Darkó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Éva Szakács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Jan Bartoš
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - István Molnár
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
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Sheeja TE, Kumar IPV, Giridhari A, Minoo D, Rajesh MK, Babu KN. Amplified Fragment Length Polymorphism: Applications and Recent Developments. Methods Mol Biol 2021; 2222:187-218. [PMID: 33301096 DOI: 10.1007/978-1-0716-0997-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.
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Affiliation(s)
- Thotten Elampilay Sheeja
- Indian Institute of Spices Research, Kozhikode, Kerala, India.
- Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India.
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Ivanizs L, Monostori I, Farkas A, Megyeri M, Mikó P, Türkösi E, Gaál E, Lenykó-Thegze A, Szőke-Pázsi K, Szakács É, Darkó É, Kiss T, Kilian A, Molnár I. Unlocking the Genetic Diversity and Population Structure of a Wild Gene Source of Wheat, Aegilops biuncialis Vis., and Its Relationship With the Heading Time. FRONTIERS IN PLANT SCIENCE 2019; 10:1531. [PMID: 31824545 PMCID: PMC6882925 DOI: 10.3389/fpls.2019.01531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/01/2019] [Indexed: 06/02/2023]
Abstract
Understanding the genetic diversity of Aegilops biuncialis, a valuable source of agronomical useful genes, may significantly facilitate the introgression breeding of wheat. The genetic diversity and population structure of 86 Ae. biuncialis genotypes were investigated by 32700 DArT markers with the simultaneous application of three statistical methods- neighbor-joining clustering, Principal Coordinate Analysis, and the Bayesian approach to classification. The collection of Ae. biuncialis accessions was divided into five groups that correlated well with their eco-geographic habitat: A (North Africa), B (mainly from Balkans), C (Kosovo and Near East), D (Turkey, Crimea, and Peloponnese), and E (Azerbaijan and the Levant region). The diversity between the Ae. biuncialis accessions for a phenological trait (heading time), which is of decisive importance in the adaptation of plants to different eco-geographical environments, was studied over 3 years. A comparison of the intraspecific variation in the heading time trait by means of analysis of variance and principal component analysis revealed four phenotypic categories showing association with the genetic structure and geographic distribution, except for minor differences. The detailed exploration of genetic and phenologic divergence provides an insight into the adaptation capacity of Ae. biuncialis, identifying promising genotypes that could be utilized for wheat improvement.
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Affiliation(s)
- László Ivanizs
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - István Monostori
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Mária Megyeri
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Péter Mikó
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Edina Türkösi
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Eszter Gaál
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | | | - Kitti Szőke-Pázsi
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Éva Szakács
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Tibor Kiss
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Andrzej Kilian
- University of Canberra, Diversity Array Technologies, Canberra, ACT, Australia
| | - István Molnár
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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4
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Said M, Parada AC, Gaál E, Molnár I, Cabrera A, Doležel J, Vrána J. Uncovering homeologous relationships between tetraploid Agropyron cristatum and bread wheat genomes using COS markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2881-2898. [PMID: 31312850 PMCID: PMC6763527 DOI: 10.1007/s00122-019-03394-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Using COS markers, the study reveals homeologous relationships between tetraploid Agropyron cristatum and bread wheat to support alien introgression breeding of wheat. Crested wheatgrass (Agropyron cristatum L. Gaertn.) is a wild relative of wheat that possesses many genes that are potentially useful in wheat improvement. The species comprises a complex of diploid, tetraploid and hexaploid forms. In this study, wheat-A. cristatum chromosome, telosome and translocation lines were used to characterize syntenic relationships between tetraploid A. cristatum and bread wheat. Prior to mapping COS markers, the cytogenetic stock lines were characterized for fertility and by FISH and GISH for karyotype stability. Out of 328 COS markers selected for the study, 279 consistently amplified products in tetraploid A. cristatum, and, out of these, 139 were polymorphic between tetraploid crested wheatgrass and wheat. Sixty-nine markers were found to be suitable for the detection of tetraploid A. cristatum chromosomes 1P-6P in wheat, ranging from 6 to 17 markers per chromosome. BLASTn of the source ESTs resulted in significant hits for 67 markers on the wheat pseudomolecules. Generally, COS markers of the same homeologous group were detected on similar arms in both Agropyron and wheat. However, some intragenomic duplications and chromosome rearrangements were detected in tetraploid A. cristatum. These results provide new insights into the structure and evolution of the tetraploid A. cristatum genome and will facilitate the exploitation of the wild species for introgression breeding of bread wheat.
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Affiliation(s)
- Mahmoud Said
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Alejandro Copete Parada
- Genetics Department, ETSIAM, Agrifood Campus of International Excellence (ceiA3), University of Córdoba, 14071, Córdoba, Spain
| | - Eszter Gaál
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, 2462, Hungary
| | - István Molnár
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, 2462, Hungary
| | - Adoración Cabrera
- Genetics Department, ETSIAM, Agrifood Campus of International Excellence (ceiA3), University of Córdoba, 14071, Córdoba, Spain
| | - Jaroslav Doležel
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.
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Liu C, Gong W, Han R, Guo J, Li G, Li H, Song J, Liu A, Cao X, Zhai S, Cheng D, Li G, Zhao Z, Yang Z, Liu J, Reader SM. Characterization, identification and evaluation of a set of wheat-Aegilops comosa chromosome lines. Sci Rep 2019; 9:4773. [PMID: 30886203 PMCID: PMC6423130 DOI: 10.1038/s41598-019-41219-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/26/2019] [Indexed: 11/21/2022] Open
Abstract
This study characterized and evaluated a set of wheat-Aegilops comosa introgression lines, including six additions and one substitution. A total of 47 PLUG markers and a set of cytogenetic markers specific for Ae. comosa chromosomes were established after screening 526 PLUG primer pairs and performing FISH using oligonucleotides as probes. Marker analysis confirmed that these lines were wheat-Ae. comosa 2M–7M addition lines and a 6M(6A) substitution line. The molecular and cytogenetic markers developed herein could be used to trace Ae. comosa chromatin in wheat background. In order to evaluate the breeding value of the material, disease resistance tests and agronomical trait investigations were carried out on these alien chromosome introgression lines. Disease resistance tests showed that chromosomes 2M and 7M of Ae. comosa might harbor new stripe rust and powdery mildew resistance genes, respectively, therefore, they could be used as resistance sources for wheat breeding. Investigations into agronomical traits showed that all chromosomes 2M to 7M had detrimental effects on the agronomic performance of wheat, therefore, the selection of plants with relatively negative effects should be avoided when inducing wheat-A. comosa chromosome translocations using chromosome engineering procedures.
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Affiliation(s)
- Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.,Colloge of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Wenping Gong
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Jun Guo
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Haosheng Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Jianmin Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.,Colloge of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Aifeng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Xinyou Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.,Colloge of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Shengnan Zhai
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Dungong Cheng
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.,Colloge of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Zhendong Zhao
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Jianjun Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Yellow & Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
| | - Stephen M Reader
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK.
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Molnár I, Vrána J, Burešová V, Cápal P, Farkas A, Darkó É, Cseh A, Kubaláková M, Molnár-Láng M, Doležel J. Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp.) into chromosomes and exploring their synteny with wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:452-467. [PMID: 27402341 DOI: 10.1111/tpj.13266] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 05/09/2023]
Abstract
Goat grasses (Aegilops spp.) contributed to the evolution of bread wheat and are important sources of genes and alleles for modern wheat improvement. However, their use in alien introgression breeding is hindered by poor knowledge of their genome structure and a lack of molecular tools. The analysis of large and complex genomes may be simplified by dissecting them into single chromosomes via flow cytometric sorting. In some species this is not possible due to similarities in relative DNA content among chromosomes within a karyotype. This work describes the distribution of GAA and ACG microsatellite repeats on chromosomes of the U, M, S and C genomes of Aegilops, and the use of microsatellite probes to label the chromosomes in suspension by fluorescence in situ hybridization (FISHIS). Bivariate flow cytometric analysis of chromosome DAPI fluorescence and fluorescence of FITC-labelled microsatellites made it possible to discriminate all chromosomes and sort them with negligible contamination by other chromosomes. DNA of purified chromosomes was used as a template for polymerase chain reation (PCR) using Conserved Orthologous Set (COS) markers with known positions on wheat A, B and D genomes. Wheat-Aegilops macrosyntenic comparisons using COS markers revealed significant rearrangements in the U and C genomes, while the M and S genomes exhibited structure similar to wheat. Purified chromosome fractions provided an attractive resource to investigate the structure and evolution of the Aegilops genomes, and the COS markers assigned to Aegilops chromosomes will facilitate alien gene introgression into wheat.
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Affiliation(s)
- István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Veronika Burešová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - András Cseh
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
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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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Tiwari VK, Wang S, Sehgal S, Vrána J, Friebe B, Kubaláková M, Chhuneja P, Doležel J, Akhunov E, Kalia B, Sabir J, Gill BS. SNP Discovery for mapping alien introgressions in wheat. BMC Genomics 2014; 15:273. [PMID: 24716476 PMCID: PMC4051138 DOI: 10.1186/1471-2164-15-273] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/31/2014] [Indexed: 11/30/2022] Open
Abstract
Background Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). Results The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. Conclusion This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and monitoring of alien segments in crop breeding programs and further enable mapping and cloning novel genes from the wild relatives of crop plants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
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Molnár I, Šimková H, Leverington-Waite M, Goram R, Cseh A, Vrána J, Farkas A, Doležel J, Molnár-Láng M, Griffiths S. Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers. PLoS One 2013; 8:e70844. [PMID: 23940651 PMCID: PMC3733919 DOI: 10.1371/journal.pone.0070844] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/23/2013] [Indexed: 11/19/2022] Open
Abstract
Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS) markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.
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Affiliation(s)
- István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Hana Šimková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | | | - Richard Goram
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - András Cseh
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Jan Vrána
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Simon Griffiths
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Wu J, Gu YQ, Hu Y, You FM, Dandekar AM, Leslie CA, Aradhya M, Dvorak J, Luo MC. Characterizing the walnut genome through analyses of BAC end sequences. PLANT MOLECULAR BIOLOGY 2012; 78:95-107. [PMID: 22101470 DOI: 10.1007/s11103-011-9849-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 10/29/2011] [Indexed: 05/31/2023]
Abstract
Persian walnut (Juglans regia L.) is an economically important tree for its nut crop and timber. To gain insight into the structure and evolution of the walnut genome, we constructed two bacterial artificial chromosome (BAC) libraries, containing a total of 129,024 clones, from in vitro-grown shoots of J. regia cv. Chandler using the HindIII and MboI cloning sites. A total of 48,218 high-quality BAC end sequences (BESs) were generated, with an accumulated sequence length of 31.2 Mb, representing approximately 5.1% of the walnut genome. Analysis of repeat DNA content in BESs revealed that approximately 15.42% of the genome consists of known repetitive DNA, while walnut-unique repetitive DNA identified in this study constitutes 13.5% of the genome. Among the walnut-unique repetitive DNA, Julia SINE and JrTRIM elements represent the first identified walnut short interspersed element (SINE) and terminal-repeat retrotransposon in miniature (TRIM) element, respectively; both types of elements are abundant in the genome. As in other species, these SINEs and TRIM elements could be exploited for developing repeat DNA-based molecular markers in walnut. Simple sequence repeats (SSR) from BESs were analyzed and found to be more abundant in BESs than in expressed sequence tags. The density of SSR in the walnut genome analyzed was also slightly higher than that in poplar and papaya. Sequence analysis of BESs indicated that approximately 11.5% of the walnut genome represents a coding sequence. This study is an initial characterization of the walnut genome and provides the largest genomic resource currently available; as such, it will be a valuable tool in studies aimed at genetically improving walnut.
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Affiliation(s)
- Jiajie Wu
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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11
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Dynamics of Vulmar/VulMITE group of transposable elements in Chenopodiaceae subfamily Betoideae. Genetica 2011; 139:1209-16. [PMID: 22170176 PMCID: PMC3247672 DOI: 10.1007/s10709-011-9622-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 12/05/2011] [Indexed: 12/15/2022]
Abstract
Transposable elements are important factors driving plant genome evolution. Upon their mobilization, novel insertion polymorphisms are being created. We investigated differences in copy number and insertion polymorphism of a group of Mariner-like transposable elements Vulmar and related VulMITE miniature inverted-repeat transposable elements (MITEs) in species representing subfamily Betoideae. Insertion sites of these elements were identified using a modified transposon display protocol, allowing amplification of longer fragments representing regions flanking insertion sites. Subsequently, a subset of TD fragments was converted into insertion site-based polymorphism (ISBP) markers. The investigated group of transposable elements was the most abundant in accessions representing the section Beta, showing intraspecific insertion polymorphisms likely resulting from their recent activity. In contrast, no unique insertions were observed for species of the genus Beta section Corollinae, while a set of section-specific insertions was observed in the genus Patellifolia, however, only two of them were polymorphic between P. procumbens and P. webbiana. We hypothesize that Vulmar and VulMITE elements were inactivated in the section Corollinae, while they remained active in the section Beta and the genus Patellifolia. The ISBP markers generally confirmed the insertion patterns observed with TD markers, including presence of distinct subsets of TE insertions specific to Beta and Patellifolia.
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12
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Molnár I, Kubaláková M, Šimková H, Cseh A, Molnár-Láng M, Doležel J. Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata. PLoS One 2011; 6:e27708. [PMID: 22132127 PMCID: PMC3223179 DOI: 10.1371/journal.pone.0027708] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 10/22/2011] [Indexed: 01/20/2023] Open
Abstract
This study evaluates the potential of flow cytometry for chromosome sorting in two wild diploid wheats Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata. Flow karyotypes obtained after the analysis of DAPI-stained chromosomes were characterized and content of chromosome peaks was determined. Peaks of chromosome 1U could be discriminated in flow karyotypes of Ae. umbellulata and Ae. biuncialis and the chromosome could be sorted with purities exceeding 95%. The remaining chromosomes formed composite peaks and could be sorted in groups of two to four. Twenty four wheat SSR markers were tested for their position on chromosomes of Ae. umbellulata and Ae. comosa using PCR on DNA amplified from flow-sorted chromosomes and genomic DNA of wheat-Ae. geniculata addition lines, respectively. Six SSR markers were located on particular Aegilops chromosomes using sorted chromosomes, thus confirming the usefulness of this approach for physical mapping. The SSR markers are suitable for marker assisted selection of wheat-Aegilops introgression lines. The results obtained in this work provide new opportunities for dissecting genomes of wild relatives of wheat with the aim to assist in alien gene transfer and discovery of novel genes for wheat improvement.
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Affiliation(s)
- István Molnár
- Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - András Cseh
- Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Márta Molnár-Láng
- Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
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13
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Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, Schulman AH. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity (Edinb) 2010; 106:520-30. [PMID: 20683483 DOI: 10.1038/hdy.2010.93] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants.
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Affiliation(s)
- R Kalendar
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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14
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Abstract
Retrotransposons can be used as markers because their integration creates new joints between genomic DNA and their conserved ends. To detect polymorphisms for retrotransposon insertion, marker systems generally rely on PCR amplification between these ends and some component of flanking genomic DNA. We have developed two methods, retrotransposon-microsatellite amplified polymorphism (REMAP) analysis and inter-retrotransposon amplified polymorphism (IRAP) analysis, that require neither restriction enzyme digestion nor ligation to generate the marker bands. The IRAP products are generated from two nearby retrotransposons using outward-facing primers. In REMAP, amplification between retrotransposons proximal to simple sequence repeats (microsatellites) produces the marker bands. Here, we describe protocols for the IRAP and REMAP techniques, including methods for PCR amplification with a single primer or with two primers and for agarose gel electrophoresis of the product using optimal electrophoresis buffers and conditions. This protocol can be completed in 1-2 d.
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Affiliation(s)
- Ruslan Kalendar
- MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 4, FIN-00014 Helsinki, Finland
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15
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Syed NH, Flavell AJ. Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions. Nat Protoc 2007; 1:2746-52. [PMID: 17406531 DOI: 10.1038/nprot.2006.407] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multiple copies of transposable elements, inserted at random around the host genome, can be used as molecular markers. Sequence-specific amplification polymorphisms (SSAPs) amplify the region between a PCR primer site near the end of an element and an adjacent restriction site in the flanking genomic DNA. Each amplified insertion is revealed as a band on a sequencing gel or capillary electrophoresis, and a genomic DNA sample produces a characteristic fingerprint of bands. Here, we explain the SSAP marker development method, which can be performed for any species, with recommendations for experimental parameters in several plant species. It takes about 1-2 weeks to complete the whole SSAP marker procedure.
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Affiliation(s)
- Naeem H Syed
- Plant Research Unit, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, UK
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