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Deng P, Du X, Wang Y, Yang X, Cheng X, Huang C, Li T, Li T, Chen C, Zhao J, Wang C, Liu X, Tian Z, Ji W. GenoBaits®WheatplusEE: a targeted capture sequencing panel for quick and accurate identification of wheat-Thinopyrum derivatives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:36. [PMID: 38291310 DOI: 10.1007/s00122-023-04538-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE A total of 90,000 capture probes derived from wheat and Thinopyrum elongatum were integrated into one chip, which served as an economical genotype for explorating Thinopyrumspecies and their derivatives. Thinopyrum species play a crucial role as a source of new genetic variations for enhancing wheat traits, including resistance to both abiotic and biotic factors. Accurate identification of exogenous chromosome(s) or chromosome segments or genes is essential following the introduction of alien genetic material into wheat, but this task remains challenging. This study aimed to develop a high-resolution wheat-Thinopyrum elongatum array, named GenoBaits®WheatplusEE, to trace alien genetic information by genotyping using a target sequencing system. This GenoBaits®WheatplusEE array included 90,000 capture probes derived from two species and integrated into one chip, with 10,000 and 80,000 originating from wheat and Th. elongatum, respectively. The capture probes were strategically positioned in genes and evenly distributed across the genome, facilitating the development of a roadmap for identifying each alien gene. The array was applied to the high-throughput identification of the alien chromosomes or segments in Thinopyrum and distantly related species and their derivatives. Our results demonstrated that the GenoBaits®WheatplusEE array could be used for direct identification of the breakpoint of alien segments, determine copy number of alien chromosomes, and reveal variations in wheat chromosomes by a single round of target sequencing of the sample. Additionally, we could efficiently and cost-effectively genotype, supporting the exploration of subgenome composition, phylogenetic relationships, and polymorphisms in essential genes (e.g., Fhb7 gene) among Thinopyrum species and their derivatives. We hope that GenoBaits®WheatplusEE will become a widely adopted tool for exporting wild germplasm for wheat improvement in the future.
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Affiliation(s)
- Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Xiaoying Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaofang Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chenxi Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tingting Li
- College of Bioengineering, Yangling Vocational Technical College, Yangling, 712100, Shaanxi, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jixin Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zengrong Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Chen C, Han Y, Xiao H, Zou B, Wu D, Sha L, Yang C, Liu S, Cheng Y, Wang Y, Kang H, Fan X, Zhou Y, Zhang T, Zhang H. Chromosome-specific painting in Thinopyrum species using bulked oligonucleotides. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:177. [PMID: 37540294 DOI: 10.1007/s00122-023-04423-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023]
Abstract
Chromosome-specific painting probes were developed to identify the individual chromosomes from 1 to 7E in Thinopyrum species and detect alien genetic material of the E genome in a wheat background. The E genome of Thinopyrum is closely related to the ABD genome of wheat (Triticum aestivum L.) and harbors genes conferring beneficial traits to wheat, including high yield, disease resistance, and unique end-use quality. Species of Thinopyrum vary from diploid (2n = 2x = 14) to decaploid (2n = 10x = 70), and chromosome structural variation and differentiation have arisen during polyploidization. To investigate the variation and evolution of the E genome, we developed a complete set of E genome-specific painting probes for identification of the individual chromosomes 1E to 7E based on the genome sequences of Th. elongatum (Host) D. R. Dewey and wheat. By using these new probes in oligonucleotide-based chromosome painting, we showed that Th. bessarabicum (PI 531711, EbEb) has a close genetic relationship with diploid Th. elongatum (EeEe), with five chromosomes (1E, 2E, 3E, 6E, and 7E) maintaining complete synteny in the two species except for a reciprocal translocation between 4 and 5Eb. All 14 pairs of chromosomes of tetraploid Th. elongatum have maintained complete synteny with those of diploid Th. elongatum (Thy14), but the two sets of E genomes have diverged. This study also demonstrated that the E genome-specific painting probes are useful for rapid and effective detection of the alien genetic material of E genome in wheat-Thinopyrum derived lines.
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Affiliation(s)
- Chen Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - He Xiao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bingcan Zou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Cairong Yang
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, Sichuan, China
| | - Songqing Liu
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, Sichuan, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Kroupin PY, Ulyanov DS, Karlov GI, Divashuk MG. The launch of satellite: DNA repeats as a cytogenetic tool in discovering the chromosomal universe of wild Triticeae. Chromosoma 2023:10.1007/s00412-023-00789-4. [PMID: 36905415 DOI: 10.1007/s00412-023-00789-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/16/2022] [Accepted: 02/22/2023] [Indexed: 03/12/2023]
Abstract
Fluorescence in situ hybridization is a powerful tool that enables plant researchers to perform systematic, evolutionary, and population studies of wheat wild relatives as well as to characterize alien introgression into the wheat genome. This retrospective review reflects on progress made in the development of methods for creating new chromosomal markers since the launch of this cytogenetic satellite instrument to the present day. DNA probes based on satellite repeats have been widely used for chromosome analysis, especially for "classical" wheat probes (pSc119.2 and Afa family) and "universal" repeats (45S rDNA, 5S rDNA, and microsatellites). The rapid development of new-generation sequencing and bioinformatical tools, and the application of oligo- and multioligonucleotides has resulted in an explosion in the discovery of new genome- and chromosome-specific chromosome markers. Owing to modern technologies, new chromosomal markers are appearing at an unprecedented velocity. The present review describes the specifics of localization when employing commonly used vs. newly developed probes for chromosomes in J, E, V, St, Y, and P genomes and their diploid and polyploid carriers Agropyron, Dasypyrum, Thinopyrum, Pseudoroegneria, Elymus, Roegneria, and Kengyilia. Particular attention is paid to the specificity of probes, which determines their applicability for the detection of alien introgression to enhance the genetic diversity of wheat through wide hybridization. The information from the reviewed articles is summarized into the TRepeT database, which may be useful for studying the cytogenetics of Triticeae. The review describes the trends in the development of technology used in establishing chromosomal markers that can be used for prediction and foresight in the field of molecular biology and in methods of cytogenetic analysis.
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Affiliation(s)
- Pavel Yu Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia.
| | - Daniil S Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Gennady I Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
| | - Mikhail G Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550, Moscow, Russia
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Development and application of specific FISH probes for karyotyping Psathyrostachys huashanica chromosomes. BMC Genomics 2022; 23:309. [PMID: 35436853 PMCID: PMC9017042 DOI: 10.1186/s12864-022-08516-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/24/2022] [Indexed: 11/30/2022] Open
Abstract
Background Psathyrostachys huashanica Keng has long been used as a genetic resource for improving wheat cultivar because of its genes mediating the resistance to various diseases (stripe rust, leaf rust, take-all, and powdery mildew) as well as its desirable agronomic traits. However, a high-resolution fluorescence in situ hybridization (FISH) karyotype of P. huashanica remains unavailable. Results To develop chromosome-specific FISH markers for P. huashanica, repetitive sequences, including pSc119.2, pTa535, pTa713, pAs1, (AAC)5, (CTT)12, pSc200, pTa71A-2, and Oligo-44 were used for a FISH analysis. The results indicated that the combination of pSc200, pTa71A-2 and Oligo-44 probes can clearly identify all Ns genomic chromosomes in the two P. huashanica germplasms. The homoeologous relationships between individual P. huashanica chromosomes and common wheat chromosomes were clarified by FISH painting. Marker validation analyses revealed that the combination of pSc200, pTa71A-2, and Oligo-44 for a FISH analysis can distinguish the P. huashanica Ns-genome chromosomes from wheat chromosomes, as well as all chromosomes (except 4Ns) from the chromosomes of diploid wheat relatives carrying St, E, V, I, P and R genomes. Additionally, the probes were applicable for discriminating between the P. huashanica Ns-genome chromosomes in all homologous groups and the corresponding chromosomes in Psathyrostachys juncea and most Leymus species containing the Ns genome. Furthermore, six wheat–P. huashanica chromosome addition lines (i.e., 2Ns, 3Ns, 4Ns, 7Ns chromosomes and chromosomal segments) were characterized using the newly developed FISH markers. Thus, these probes can rapidly and precisely detect P. huashanica alien chromosomes in the wheat background. Conclusions The FISH karyotype established in this study lays a solid foundation for the efficient identification of P. huashanica chromosomes in wheat genetic improvement programs.
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Wu X, Hu X, Chen X, Zhang J, Ren C, Song L, Fang F, Dong N, Hu T, Ru Z. Sequencing and characterization of the complete mitochondrial genome of Thinopyrum obtusiflorum (DC.) Banfi, 2018 (Poaceae). Mitochondrial DNA B Resour 2022; 7:539-540. [PMID: 35356795 PMCID: PMC8959512 DOI: 10.1080/23802359.2022.2054378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
In this study, the mitochondrial genome of Thinopyrum obtusiflorum was sequenced, assembled, and annotated. The complete circular mitogenome of Th. obtusiflorum is 390,725 bp in length and the overall A + T content of mitogenome is 55.61%. It harbors 33 protein-coding genes (PCGs), 21 transfer RNA genes (tRNAs), six ribosomal RNA genes (rRNAs), and 20 simple sequence repeats (SSRs). Phylogenetic analysis indicates that Th. obtusiflorum is a sister to the clade including Aegilops speltoides, Triticum aestivum, and Triticum aestivum cultivar Chinese Yumai in the Triticeae.
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Affiliation(s)
- Xiaojun Wu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Xigui Hu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Xiangdong Chen
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Jinlong Zhang
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Cuicui Ren
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Lintong Song
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Fang Fang
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Na Dong
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Tiezhu Hu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
| | - Zhengang Ru
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
- Henan Key Laboratory of Hybrid Wheat, Xinxiang, China
- Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, China
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Dai Y, Huang S, Sun G, Li H, Chen S, Gao Y, Chen J. Origins and chromosome differentiation of Thinopyrum elongatum revealed by PepC and Pgk1 genes and ND-FISH. Genome 2021; 64:901-913. [PMID: 33596125 DOI: 10.1139/gen-2019-0176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Thinopyrum elongatum is an important gene pool for wheat genetic improvement. However, the origins of the Thinopyrum genomes and the nature of the genus' intraspecific relationships are still controversial. In this study, we used single-copy nuclear genes and non-denaturing fluorescence in situ hybridization (ND-FISH) to characterize genome constitution and chromosome differentiation in Th. elongatum. According to phylogenetic analyses based on PepC and Pgk1 genes, there was an E genome with three versions (Ee, Eb, Ex) and St genomes in the polyploid Th. elongatum. The ND-FISH results of pSc119.2 and pAs1 revealed that the karyotypes of diploid Th. elongatum and Th. bessarabicum were different, and the chromosome differentiation occurred among accessions of the diploid Th. elongatum. In addition, the tetraploid Th. elongatum has two groups of ND-FISH karyotype, indicating that the tetraploid Th. elongatum might be a segmental allotetraploid. In summary, our results suggested that the diploid Th. elongatum, Th. Bessarabicum, and Pseudoroegneria were the donors of the Ee, Eb, and St genomes to the polyploid Th. elongatum, respectively.
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Affiliation(s)
- Yi Dai
- Joint International Research Laboratory of Agriculture and Agri-product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.,Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Shuai Huang
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS B3H 3C3, Canada
| | - Haifeng Li
- Yangzhou Polytechnic College, Yangzhou 225009, China
| | - Shiqiang Chen
- Institute of Agricultural Sciences, Lixia River Region, Yangzhou 225009, China
| | - Yong Gao
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Jianmin Chen
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
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Badaeva ED, Surzhikov SA, Agafonov AV. Molecular-cytogenetic analysis of diploid wheatgrass Thinopyrum bessarabicum (Savul. and Rayss) A. Löve. COMPARATIVE CYTOGENETICS 2019; 13:389-402. [PMID: 31844506 PMCID: PMC6904353 DOI: 10.3897/compcytogen.v13i4.36879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
Thinopyrum bessarabicum (T. Săvulescu & T. Rayss, 1923) A. Löve, 1980 is diploid (2n=2x=14, JJ or EbEb), perennial self-fertilizing rhizomatous maritime beach grass, which is phylogenetically close to another diploid wheatgrass species, Agropyron elongatum (N. Host, 1797) P. de Beauvois, 1812. The detailed karyotype of Th. bessarabicum was constructed based on FISH with six DNA probes representing 5S and 45S rRNA gene families and four tandem repeats. We found that the combination of pAesp_SAT86 (= pTa-713) probe with pSc119.2 or pAs1/ pTa-535 allows the precise identification of all J-genome chromosomes. Comparison of our data with the results of other authors showed that karyotypically Th. bessarabicum is distinct from A. elongatum. On the other hand, differences between the J-genome chromosomes of Th. bessarabicum and the chromosomes of hexaploid Th. intermedium (N. Host, 1797) M. Barkworth & D.R. Dewey, 1985 and decaploid Th. ponticum (J. Podpěra, 1902) Z.-W. Liu & R.-C. Wang, 1993 in the distribution of rDNA loci and hybridization patterns of pSc119.2 and pAs1 probes could be an indicative of (1) this diploid species was probably not involved in the origin of these polyploids or (2) it could has contributed the J-genome to Th. intermedium and Th. ponticum, but it was substantially modified over the course of speciation.
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Affiliation(s)
- Ekaterina D. Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences. Gubkina str. 3, Moscow 117333, RussiaEngelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscowRussia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences. Vavilova str. 34, Moscow 117334, RussiaN.I. Vavilov Institute of General Genetics, Russian Academy of SciencesMoscowRussia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences. Vavilova str. 34, Moscow 117334, RussiaN.I. Vavilov Institute of General Genetics, Russian Academy of SciencesMoscowRussia
| | - Alexander V. Agafonov
- Central Siberian Botanical Garden, Russian Academy of Sciences, Siberian Branch, Zolotodolinskaya st., 101, Novosibirsk 630090, RussiaCentral Siberian Botanical Garden, Russian Academy of SciencesNovosibirskRussia
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Identification of COS markers specific for Thinopyrum elongatum chromosomes preliminary revealed high level of macrosyntenic relationship between the wheat and Th. elongatum genomes. PLoS One 2018; 13:e0208840. [PMID: 30540828 PMCID: PMC6291125 DOI: 10.1371/journal.pone.0208840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/25/2018] [Indexed: 11/19/2022] Open
Abstract
Thinopyrum elongatum (Host) D.R. Dewey has served as an important gene source for wheat breeding improvement for many years. The exact characterization of its chromosomes is important for the detailed analysis of prebreeding materials produced with this species. The major aim of this study was to identify and characterize new molecular markers to be used for the rapid analysis of E genome chromatin in wheat background. Sixty of the 169 conserved orthologous set (COS) markers tested on diverse wheat-Th. elongatum disomic/ditelosomic addition lines were assigned to various Th. elongatum chromosomes and will be used for marker-assisted selection. The macrosyntenic relationship between the wheat and Th. elongatum genomes was investigated using EST sequences. Several rearrangements were revealed in homoeologous chromosome groups 2, 5, 6 and 7, while chromosomes 1 and 4 were conserved. Molecular cytogenetic and marker analysis showed the presence of rearranged chromosome involved in 6ES and 2EL arms in the 6E disomic addition line. The selected chromosome arm-specific COS markers will make it possible to identify gene introgressions in breeding programmes and will also be useful in the development of new chromosome-specific markers, evolutionary analysis and gene mapping.
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Pernickova K, Linc G, Gaal E, Kopecky D, Samajova O, Lukaszewski AJ. Out-of-position telomeres in meiotic leptotene appear responsible for chiasmate pairing in an inversion heterozygote in wheat (Triticum aestivum L.). Chromosoma 2018; 128:31-39. [PMID: 30483879 DOI: 10.1007/s00412-018-0686-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 11/26/2022]
Abstract
Chromosome pairing in meiosis usually starts in the vicinity of the telomere attachment to the nuclear membrane and congregation of telomeres in the leptotene bouquet is believed responsible for bringing homologue pairs together. In a heterozygote for an inversion of a rye (Secale cereale L.) chromosome arm in wheat, a distal segment of the normal homologue is capable of chiasmate pairing with its counterpart in the inverted arm, located near the centromere. Using 3D imaging confocal microscopy, we observed that some telomeres failed to be incorporated into the bouquet and occupied various positions throughout the entire volume of the nucleus, including the centromere pole. Rye telomeres appeared ca. 21 times more likely to fail to be included in the telomere bouquet than wheat telomeres. The frequency of the out-of-bouquet rye telomere position in leptotene was virtually identical to the frequency of telomeres deviating from Rabl's orientation in the nuclei of somatic cells, and was similar to the frequency of synapsis of the normal and inverted chromosome arms, but lower than the MI pairing frequency of segments of these two arms normally positioned across the volume of the nucleus. Out-of-position placement of the rye telomeres may be responsible for reduced MI pairing of rye chromosomes in hybrids with wheat and their disproportionate contribution to aneuploidy, but appears responsible for initiating chiasmate pairing of distantly positioned segments of homology in an inversion heterozygote.
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Affiliation(s)
- Katerina Pernickova
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, Olomouc, Czech Republic
| | - Gabriella Linc
- Centre for Agricultural Research, Agricultural Institute, Hungarian Academy of Sciences, Martonvasar, 2462, Hungary
- National Food Chain Safety Office, Budaörsi Str. 141-145, Budapest, 1118, Hungary
| | - Eszter Gaal
- Centre for Agricultural Research, Agricultural Institute, Hungarian Academy of Sciences, Martonvasar, 2462, Hungary
- National Food Chain Safety Office, Budaörsi Str. 141-145, Budapest, 1118, Hungary
| | - David Kopecky
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, Olomouc, Czech Republic
| | - Olga Samajova
- Faculty of Science, Centre of the Region Hana for Biotechnological and Agricultural Research, Department of Cell Biology, Palacky University Olomouc, Slechtitelu 27, Olomouc, Czech Republic
| | - Adam J Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
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Li D, Li T, Wu Y, Zhang X, Zhu W, Wang Y, Zeng J, Xu L, Fan X, Sha L, Zhang H, Zhou Y, Kang H. FISH-Based Markers Enable Identification of Chromosomes Derived From Tetraploid Thinopyrum elongatum in Hybrid Lines. FRONTIERS IN PLANT SCIENCE 2018; 9:526. [PMID: 29765383 PMCID: PMC5938340 DOI: 10.3389/fpls.2018.00526] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/04/2018] [Indexed: 05/19/2023]
Abstract
Tetraploid Thinopyrum elongatum, which has superior abiotic stress tolerance characteristics, and exhibits resistance to stripe rust, powdery mildew, and Fusarium head blight, is a wild relative of wheat and a promising source of novel genes for wheat improvement. Currently, a high-resolution Fluorescence in situ hybridization (FISH) karyotype of tetraploid Th. elongatum is not available. To develop chromosome-specific FISH-based markers, the hexaploid Trititrigia 8801 and two accessions of tetraploid Th. elongatum were characterized by different repetitive sequences probes. We found that all E-genome chromosomes could be unambiguously identified using a combination of pSc119.2, pTa535, pTa71, and pTa713 repeats, and the E-genome chromosomes of the wild accessions and the partial amphiploid failed to exhibit any significant variation in the probe hybridization patterns. To verify the validation of these markers, the chromosome constitution of eight wheat- Th. elongatum hybrid derivatives were analyzed. We revealed that these probes could quickly detect wheat and tetraploid Th. elongatum chromosomes in hybrid lines. K16-712-1-2 was a 1E (1D) chromosome substitution line, K16-681-4 was a 2E disomic chromosome addition line, K16-562-3 was a 3E, 4E (3D, 4D) chromosome substitution line, K15-1033-8-2 contained one 4E, two 5E, and one 4ES⋅1DL Robertsonian translocation chromosome, and four other lines carried monosomic 4E, 5E, 6E, and 7E chromosome, respectively. Furthermore, the E-genome specific molecular markers analysis corresponded perfectly with the FISH results. The developed FISH markers will facilitate rapid identification of tetraploid Th. elongatum chromosomes in wheat improvement programs and allow appropriate alien chromosome transfer.
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Affiliation(s)
- Daiyan Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Tinghui Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanli Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaohui Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Zhu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lili Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiqin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Joint International Research Laboratory of Crop Resources and Genetic Improvement, Sichuan Agricultural University, Chengdu, China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Joint International Research Laboratory of Crop Resources and Genetic Improvement, Sichuan Agricultural University, Chengdu, China
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11
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Liu L, Luo Q, Teng W, Li B, Li H, Li Y, Li Z, Zheng Q. Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology. PLANTA 2018; 247:1099-1108. [PMID: 29356894 DOI: 10.1007/s00425-018-2845-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/07/2018] [Indexed: 05/06/2023]
Abstract
Based on SLAF-seq, 67 Thinopyrum ponticum-specific markers and eight Th. ponticum-specific FISH probes were developed, and these markers and probes could be used for detection of alien chromatin in a wheat background. Decaploid Thinopyrum ponticum (2n = 10x = 70) is a valuable gene reservoir for wheat improvement. Identification of Th. ponticum introgression would facilitate its transfer into diverse wheat genetic backgrounds and its practical utilization in wheat improvement. Based on specific-locus-amplified fragment sequencing (SLAF-seq) technology, 67 new Th. ponticum-specific molecular markers and eight Th. ponticum-specific fluorescence in situ hybridization (FISH) probes have been developed from a tiny wheat-Th. ponticum translocation line. These newly developed molecular markers allowed the detection of Th. ponticum DNA in a variety of materials specifically and steadily at high throughput. According to the hybridization signal pattern, the eight Th. ponticum-specific probes could be divided into two groups. The first group including five dispersed repetitive sequence probes could identify Th. ponticum chromatin more sensitively and accurately than genomic in situ hybridization (GISH). Whereas the second group having three tandem repetitive sequence probes enabled the discrimination of Th. ponticum chromosomes together with another clone pAs1 in wheat-Th. ponticum partial amphiploid Xiaoyan 68.
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Affiliation(s)
- Liqin Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Qiaoling Luo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan Teng
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Bin Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Hongwei Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Yiwen Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Zhensheng Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China.
| | - Qi Zheng
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China.
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12
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Tang S, Tang Z, Qiu L, Yang Z, Li G, Lang T, Zhu W, Zhang J, Fu S. Developing New Oligo Probes to Distinguish Specific Chromosomal Segments and the A, B, D Genomes of Wheat ( Triticum aestivum L.) Using ND-FISH. FRONTIERS IN PLANT SCIENCE 2018; 9:1104. [PMID: 30093909 PMCID: PMC6070686 DOI: 10.3389/fpls.2018.01104] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/09/2018] [Indexed: 05/03/2023]
Abstract
Non-denaturing FISH (ND-FISH) technology has been widely used to study the chromosomes of Triticeae species because of its convenience. The oligo probes for ND-FISH analysis of wheat (Triticum aestivum L.) chromosomes are still limited. In this study, the whole genome shotgun assembly sequences (IWGSC WGA v0.4) and the first version of the reference sequences (IWGSC RefSeq v1.0) of Chinese Spring (T. aestivum L.) were used to find new tandem repeats. One hundred and twenty oligo probes were designed according to the new tandem repeats and used for ND-FISH analysis of chromosomes of wheat Chinese Spring. Twenty nine of the 120 oligo probes produce clear or strong signals on wheat chromosomes. Two of the 29 oligo probes can be used to conveniently distinguish wheat A-, B-, and D-genome chromosomes. Sixteen of the 29 oligo probes only produce clear or strong signals on the subtelomeric regions of 1AS, 5AS, 7AL, 4BS, 5BS, and 3DS arms, on the telomeric regions of 1AL, 5AL, 2BS, 3BL, 6DS, and 7DL arms, on the intercalary regions of 4AL and 2DL arms, and on the pericentromeric regions of 3DL and 6DS arms. Eleven of the 29 oligo probes generate distinct signal bands on several chromosomes and they are different from those previously reported. In addition, the short and long arms of 6D chromosome have been confirmed. The new oligo probes developed in this study are useful and convenient for distinguishing wheat chromosomes or specific segments of wheat chromosomes.
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Affiliation(s)
- Shuyao Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, China
| | - Zongxiang Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, China
| | - Ling Qiu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
| | - Zujun Yang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Guangrong Li
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Tao Lang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenqian Zhu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, China
| | - Jiehong Zhang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
| | - Shulan Fu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Shulan Fu,
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13
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Ruban AS, Badaeva ED. Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis. FRONTIERS IN PLANT SCIENCE 2018; 9:1756. [PMID: 30564254 PMCID: PMC6288319 DOI: 10.3389/fpls.2018.01756] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/12/2018] [Indexed: 05/20/2023]
Abstract
Five diploid Aegilops species of the Sitopsis section: Ae. speltoides, Ae. longissima, Ae. sharonensis, Ae. searsii, and Ae. bicornis, two tetraploid species Ae. peregrina (= Ae. variabilis) and Ae. kotschyi (Aegilops section) and hexaploid Ae. vavilovii (Vertebrata section) carry the S-genomes. The B- and G-genomes of polyploid wheat are also the derivatives of the S-genome. Evolution of the S-genome species was studied using Giemsa C-banding and fluorescence in situ hybridization (FISH) with DNA probes representing 5S (pTa794) and 18S-5.8S-26S (pTa71) rDNAs as well as nine tandem repeats: pSc119.2, pAesp_SAT86, Spelt-1, Spelt-52, pAs1, pTa-535, and pTa-s53. To correlate the C-banding and FISH patterns we used the microsatellites (CTT)10 and (GTT)9, which are major components of the C-banding positive heterochromatin in wheat. According to the results obtained, diploid species split into two groups corresponding to Emarginata and Truncata sub-sections, which differ in the C-banding patterns, distribution of rDNA and other repeats. The B- and G-genomes of polyploid wheat are most closely related to the S-genome of Ae. speltoides. The genomes of allopolyploid wheat have been evolved as a result of different species-specific chromosome translocations, sequence amplification, elimination and re-patterning of repetitive DNA sequences. These events occurred independently in different wheat species and in Ae. speltoides . The 5S rDNA locus of chromosome 1S was probably lost in ancient Ae. speltoides prior to formation of Timopheevii wheat, but after the emergence of ancient emmer. Evolution of Emarginata species was associated with an increase of C-banding and (CTT)10-positive heterochromatin, amplification of Spelt-52, re-pattering of the pAesp_SAT86, and a gradual decrease in the amount of the D-genome-specific repeats pAs1, pTa-535, and pTa-s53. The emergence of Ae. peregrina and Ae. kotschyi did not lead to significant changes of the S*-genomes. However, partial elimination of 45S rDNA repeats from 5S* and 6S* chromosomes and alterations of C-banding and FISH-patterns have been detected. Similarity of the Sv-genome of Ae. vavilovii with the Ss genome of diploid Ae. searsii confirmed the origin of this hexaploid. A model of the S-genome evolution is suggested.
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Affiliation(s)
- Alevtina S. Ruban
- Laboratory of Chromosome Structure and Function, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ekaterina D. Badaeva
- Laboratory of Genetic Basis of Plant Identification, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Molecular Karyology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Ekaterina D. Badaeva
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Dai Y, Duan Y, Chi D, Liu H, Huang S, Cao W, Gao Y, Fedak G, Chen J. Chromosome identification by new molecular markers and genomic in situ hybridization in the Triticum-Secale-Thinopyrum trigeneric hybrids. Genome 2017. [PMID: 28636827 DOI: 10.1139/gen-2017-0025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
It is very important to use chromosome-specific markers for identifying alien chromosomes in advanced generations of distant hybridization. The chromosome-specific markers of rye and Thinopyrum elongatum, as well as genomic in situ hybridization, were used to identify the alien chromosomes in eight lines that were derived from the crossing between Triticum trititrigia (AABBEE) and triticale (AABBRR). The results showed that four lines contained all rye chromosomes but no Th. elongatum chromosomes. The line RE36-1 contained all of the rye chromosomes except for chromosome 2R. The lines RE33-2 and RE62-1 contained all rye chromosomes and 1E and 5E translocated chromosome, respectively. The line RE24-4 contained 12 rye chromosomes plus a 7E chromosome or 12 rye chromosomes plus one R-E translocated chromosome. Chromosome identification in the above lines was consistent using chromosome-specific markers and genomic in situ hybridization. These chromosome-specific markers provide useful tools for detecting alien chromosomes in trigeneric hybrids, and these lines could be utilized as valuable germplasm in wheat improvement.
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Affiliation(s)
- Yi Dai
- a College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 88 Da Xue South Road, Yangzhou 225100, Jiangsu, China.,b Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Yamei Duan
- a College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 88 Da Xue South Road, Yangzhou 225100, Jiangsu, China
| | - Dawn Chi
- b Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Huiping Liu
- a College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 88 Da Xue South Road, Yangzhou 225100, Jiangsu, China.,b Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Shuai Huang
- a College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 88 Da Xue South Road, Yangzhou 225100, Jiangsu, China
| | - Wenguang Cao
- b Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Yong Gao
- a College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 88 Da Xue South Road, Yangzhou 225100, Jiangsu, China.,c Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - George Fedak
- b Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Jianmin Chen
- a College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, 88 Da Xue South Road, Yangzhou 225100, Jiangsu, China.,c Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, Jiangsu, China
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15
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Dai Y, Duan Y, Liu H, Chi D, Cao W, Xue A, Gao Y, Fedak G, Chen J. Molecular Cytogenetic Characterization of two Triticum-Secale-Thinopyrum Trigeneric Hybrids Exhibiting Superior Resistance to Fusarium Head Blight, Leaf Rust, and Stem Rust Race Ug99. FRONTIERS IN PLANT SCIENCE 2017; 8:797. [PMID: 28555151 PMCID: PMC5430057 DOI: 10.3389/fpls.2017.00797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/27/2017] [Indexed: 05/29/2023]
Abstract
Fusarium head blight (FHB), leaf rust, and stem rust are the most destructive fungal diseases in current world wheat production. The diploid wheatgrass, Thinopyrum elongatum (Host) Dewey (2n = 2x = 14, EE) is an excellent source of disease resistance genes. Two new Triticum-Secale-Thinopyrum trigeneric hybrids were derived from a cross between a hexaploid triticale (X Triticosecale Wittmack, 2n = 6x = 42, AABBRR) and a hexaploid Triticum trititrigia (2n = 6x = 42, AABBEE), were produced and analyzed using genomic in situ hybridization and molecular markers. The results indicated that line RE21 contained 14 A-chromosomes, 14 B-chromosomes, three pairs of R-chromosomes (4R, 6R, and 7R), and four pairs of E-chromosomes (1E, 2E, 3E, and 5E) for a total chromosome number of 2n = 42. Line RE62 contained 14 A-chromosomes, 14 B-chromosomes, six pairs of R-chromosomes, and one pair of translocation chromosomes between chromosome 5R and 5E, for a total chromosome number of 2n = 42. At the seedling and adult growth stages under greenhouse conditions, line RE21 showed high levels of resistance to FHB, leaf rust, and stem rust race Ug99, and line RE62 was highly resistant to leaf rust and stem rust race Ug99. These two lines (RE21 and RE62) display superior disease resistance characteristics and have the potential to be utilized as valuable germplasm sources for future wheat improvement.
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Affiliation(s)
- Yi Dai
- College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, OttawaON, Canada
| | - Yamei Duan
- College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
| | - Huiping Liu
- College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, OttawaON, Canada
| | - Dawn Chi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, OttawaON, Canada
| | - Wenguang Cao
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, OttawaON, Canada
| | - Allen Xue
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, OttawaON, Canada
| | - Yong Gao
- College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Jiangsu Key Laboratories of Crop Genetics and Physiology, Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, OttawaON, Canada
| | - Jianmin Chen
- College of Bioscience and Biotechnology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou UniversityYangzhou, China
- Jiangsu Key Laboratories of Crop Genetics and Physiology, Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
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16
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Linc G, Gaál E, Molnár I, Icsó D, Badaeva E, Molnár-Láng M. Molecular cytogenetic (FISH) and genome analysis of diploid wheatgrasses and their phylogenetic relationship. PLoS One 2017; 12:e0173623. [PMID: 28278169 PMCID: PMC5344461 DOI: 10.1371/journal.pone.0173623] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/23/2017] [Indexed: 11/22/2022] Open
Abstract
This paper reports detailed FISH-based karyotypes for three diploid wheatgrass species Agropyron cristatum (L.) Beauv., Thinopyrum bessarabicum (Savul.&Rayss) A. Löve, Pseudoroegneria spicata (Pursh) A. Löve, the supposed ancestors of hexaploid Thinopyrum intermedium (Host) Barkworth & D.R.Dewey, compiled using DNA repeats and comparative genome analysis based on COS markers. Fluorescence in situ hybridization (FISH) with repetitive DNA probes proved suitable for the identification of individual chromosomes in the diploid JJ, StSt and PP genomes. Of the seven microsatellite markers tested only the (GAA)n trinucleotide sequence was appropriate for use as a single chromosome marker for the P. spicata AS chromosome. Based on COS marker analysis, the phylogenetic relationship between diploid wheatgrasses and the hexaploid bread wheat genomes was established. These findings confirmed that the J and E genomes are in neighbouring clusters.
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Affiliation(s)
- Gabriella Linc
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
- * E-mail:
| | - Eszter Gaál
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - István Molnár
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Diana Icsó
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Ekaterina Badaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Márta Molnár-Láng
- Department of Plant Genetic Resources, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
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17
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Kruppa K, Molnár-Láng M. Simultaneous visualization of different genomes (J, JSt and St) in a Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid (Poaceae) and in its parental species by multicolour genomic in situ hybridization (mcGISH). COMPARATIVE CYTOGENETICS 2016; 10:283-93. [PMID: 27551349 PMCID: PMC4977803 DOI: 10.3897/compcytogen.v10i2.7305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/27/2016] [Indexed: 05/19/2023]
Abstract
Multicolour genomic in situ hybridization (mcGISH) using total genomic DNA probes from Thinopyrum bessarabicum (Săvulescu & Rayss, 1923) Á. Löve, 1984 (genome J(b) or E(b), 2n = 14), and Pseudoroegneria spicata (Pursh, 1814) Á. Löve, 1980 (genome St, 2n = 14) was used to characterize the mitotic metaphase chromosomes of a synthetic hybrid of Thinopyrum intermedium (Host, 1805) Barkworth & D.R. Dewey, 1985 and Thinopyrum ponticum (Podpěra, 1902) Z.-W. Liu et R.-C.Wang, 1993 named "Agropyron glael" and produced by N.V. Tsitsin in the former Soviet Union. The mcGISH pattern of this synthetic hybrid was compared to its parental wheatgrass species. Hexaploid Thinopyrum intermedium contained 19 J, 9 J(St) and 14 St chromosomes. The three analysed Thinopyrum ponticum accessions had different chromosome compositions: 43 J + 27 J(St) (PI531737), 40 J + 30 J(St) (VIR-44486) and 38 J + 32 J(St) (D-3494). The synthetic hybrid carried 18 J, 28 J(St) and 8 St chromosomes, including one pair of J-St translocation and/or decreased fluorescent intensity, resulting in unique hybridization patterns. Wheat line Mv9kr1 was crossed with the Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid in Hungary in order to transfer its advantageous agronomic traits (leaf rust and yellow rust resistance) into wheat. The chromosome composition of a wheat/A.glael F1 hybrid was 21 wheat + 28 wheatgrass (11 J + 14 J(St)+ 3 S). In the present study, mcGISH involving the simultaneous use of St and J genomic DNA as probes provided information about the type of Thinopyrum chromosomes in a Thinopyrum intermedium/Thinopyrum ponticum synthetic hybrid called A. glael.
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Affiliation(s)
- Klaudia Kruppa
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Department of Plant Genetic Resources, H-2462 Martonvásár, Brunszvik u. 2, Hungary
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Department of Plant Genetic Resources, H-2462 Martonvásár, Brunszvik u. 2, Hungary
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18
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Kruppa K, Türkösi E, Mayer M, Tóth V, Vida G, Szakács É, Molnár-Láng M. McGISH identification and phenotypic description of leaf rust and yellow rust resistant partial amphiploids originating from a wheat × Thinopyrum synthetic hybrid cross. J Appl Genet 2016; 57:427-437. [PMID: 26922334 PMCID: PMC5061834 DOI: 10.1007/s13353-016-0343-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/15/2016] [Indexed: 11/28/2022]
Abstract
A Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid wheatgrass is an excellent source of leaf and stem rust resistance produced by N.V.Tsitsin. Wheat line Mv9kr1 was crossed with this hybrid (Agropyron glael) in Hungary in order to transfer its advantageous agronomic traits into wheat. As the wheat parent was susceptible to leaf rust, the transfer of resistance was easily recognizable in the progenies. Three different partial amphiploid lines with leaf rust resistance were selected from the wheat/Thinopyrum hybrid derivatives by multicolour genomic in situ hybridization. Chromosome counting on the partial amphiploids revealed 58 chromosomes (18 wheatgrass) in line 194, 56 (14 wheatgrass) in line 195 and 54 (12 wheatgrass) in line 196. The wheat chromosomes present in these lines were identified and the wheatgrass chromosomes were characterized by fluorescence in situ hybridization using the repetitive DNA probes Afa-family, pSc119.2 and pTa71. The 3D wheat chromosome was missing from the lines. Molecular marker analysis showed the presence of the Lr24 leaf rust resistance gene in lines 195 and 196. The morphological traits were evaluated in the field during two consecutive seasons in two different locations.
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Affiliation(s)
- Klaudia Kruppa
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Edina Türkösi
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Marianna Mayer
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Viola Tóth
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Gyula Vida
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Éva Szakács
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary.
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Molecular cytogenetic characterisation of Salix viminalis L. using repetitive DNA sequences. J Appl Genet 2013; 54:265-9. [DOI: 10.1007/s13353-013-0153-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 10/26/2022]
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